Starting phenix.real_space_refine on Mon Apr 8 11:38:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cae_30328/04_2024/7cae_30328.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cae_30328/04_2024/7cae_30328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cae_30328/04_2024/7cae_30328.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cae_30328/04_2024/7cae_30328.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cae_30328/04_2024/7cae_30328.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cae_30328/04_2024/7cae_30328.pdb" } resolution = 3.44 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= 0.021 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 41 5.16 5 C 8565 2.51 5 N 2263 2.21 5 O 2496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 58": "OE1" <-> "OE2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ARG 151": "NH1" <-> "NH2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "C GLU 280": "OE1" <-> "OE2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C GLU 329": "OE1" <-> "OE2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "C GLU 369": "OE1" <-> "OE2" Residue "D GLU 3": "OE1" <-> "OE2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 151": "NH1" <-> "NH2" Residue "D ARG 183": "NH1" <-> "NH2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D GLU 369": "OE1" <-> "OE2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "E GLU 41": "OE1" <-> "OE2" Residue "E ARG 50": "NH1" <-> "NH2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E GLU 193": "OE1" <-> "OE2" Residue "E ARG 227": "NH1" <-> "NH2" Residue "E ARG 235": "NH1" <-> "NH2" Residue "E GLU 282": "OE1" <-> "OE2" Residue "E GLU 315": "OE1" <-> "OE2" Residue "E ARG 343": "NH1" <-> "NH2" Residue "E GLU 382": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13365 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2911 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2908 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2155 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 267} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2035 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 253} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3356 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 31, 'TRANS': 411} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 7.30, per 1000 atoms: 0.55 Number of scatterers: 13365 At special positions: 0 Unit cell: (79.54, 93.48, 170.56, 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 41 16.00 O 2496 8.00 N 2263 7.00 C 8565 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.40 Conformation dependent library (CDL) restraints added in 2.3 seconds 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3266 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 16 sheets defined 47.2% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'C' and resid 48 through 56 Processing helix chain 'C' and resid 96 through 108 Proline residue: C 104 - end of helix Processing helix chain 'C' and resid 111 through 126 Processing helix chain 'C' and resid 130 through 134 removed outlier: 3.997A pdb=" N ASP C 133 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.865A pdb=" N LEU C 139 " --> pdb=" O PRO C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 155 removed outlier: 4.773A pdb=" N ARG C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 169 removed outlier: 4.427A pdb=" N ASN C 168 " --> pdb=" O PRO C 165 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU C 169 " --> pdb=" O LEU C 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 165 through 169' Processing helix chain 'C' and resid 170 through 189 removed outlier: 4.368A pdb=" N VAL C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.654A pdb=" N ALA C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 266 through 275 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 299 through 303 Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'D' and resid 48 through 56 Processing helix chain 'D' and resid 76 through 80 removed outlier: 3.714A pdb=" N ARG D 80 " --> pdb=" O PRO D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 107 Proline residue: D 104 - end of helix Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.636A pdb=" N LEU D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 155 removed outlier: 4.514A pdb=" N ARG D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 189 removed outlier: 4.062A pdb=" N VAL D 175 " --> pdb=" O ALA D 171 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N GLN D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.587A pdb=" N ALA D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 266 through 274 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 335 through 343 Processing helix chain 'A' and resid 19 through 40 removed outlier: 3.686A pdb=" N LEU A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) Proline residue: A 30 - end of helix Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.736A pdb=" N VAL A 47 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TRP A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 84 through 89 Processing helix chain 'A' and resid 91 through 110 removed outlier: 3.702A pdb=" N ALA A 95 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 146 through 150 Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 162 through 190 removed outlier: 3.614A pdb=" N VAL A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) Proline residue: A 179 - end of helix removed outlier: 4.193A pdb=" N LEU A 183 " --> pdb=" O PRO A 179 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.978A pdb=" N LEU A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 228 through 234 removed outlier: 3.795A pdb=" N ALA A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 238 through 244 removed outlier: 3.964A pdb=" N ILE A 243 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU A 244 " --> pdb=" O ASN A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 264 removed outlier: 3.891A pdb=" N ASN A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 Processing helix chain 'A' and resid 274 through 291 removed outlier: 3.807A pdb=" N PHE A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 14 Processing helix chain 'B' and resid 15 through 26 removed outlier: 4.344A pdb=" N ILE B 21 " --> pdb=" O ASN B 17 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 24 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'B' and resid 67 through 93 removed outlier: 4.157A pdb=" N SER B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE B 83 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA B 91 " --> pdb=" O ILE B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 105 through 113 removed outlier: 4.231A pdb=" N LEU B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 removed outlier: 3.712A pdb=" N LEU B 121 " --> pdb=" O PRO B 117 " (cutoff:3.500A) removed outlier: 4.231A 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 140 Processing helix chain 'B' and resid 141 through 156 removed outlier: 3.604A pdb=" N TYR B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Proline residue: B 151 - end of helix Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.749A pdb=" N LYS B 170 " --> pdb=" O TRP B 166 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET B 174 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.550A pdb=" N ARG B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 removed outlier: 3.655A pdb=" N ALA B 191 " --> pdb=" O ILE B 187 " (cutoff:3.500A) Proline residue: B 193 - end of helix Processing helix chain 'B' and resid 197 through 207 removed outlier: 3.714A pdb=" N LEU B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 231 Processing helix chain 'B' and resid 242 through 273 Proline residue: B 255 - end of helix removed outlier: 3.848A pdb=" N ILE B 262 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 264 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ARG B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ARG B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 56 removed outlier: 4.255A pdb=" N ALA E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL E 47 " --> pdb=" O THR E 43 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA E 48 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY E 56 " --> pdb=" O ASN E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 83 Processing helix chain 'E' and resid 97 through 105 removed outlier: 3.989A pdb=" N GLY E 105 " --> pdb=" O PHE E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 132 Processing helix chain 'E' and resid 165 through 177 Processing helix chain 'E' and resid 192 through 207 removed outlier: 3.675A pdb=" N VAL E 196 " --> pdb=" O TYR E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 243 removed outlier: 3.674A pdb=" N ILE E 236 " --> pdb=" O LYS E 232 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA E 241 " --> pdb=" O ILE E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 253 removed outlier: 3.980A pdb=" N GLN E 252 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR E 253 " --> pdb=" O ILE E 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 249 through 253' Processing helix chain 'E' and resid 254 through 264 Processing helix chain 'E' and resid 275 through 284 removed outlier: 3.644A pdb=" N SER E 279 " --> pdb=" O TYR E 275 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 304 removed outlier: 4.422A pdb=" N GLN E 301 " --> pdb=" O ASP E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 325 Processing helix chain 'E' and resid 359 through 371 Processing helix chain 'E' and resid 372 through 382 Processing helix chain 'E' and resid 389 through 394 removed outlier: 4.473A pdb=" N TYR E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP E 394 " --> pdb=" O THR E 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 389 through 394' Processing helix chain 'E' and resid 397 through 402 removed outlier: 4.421A pdb=" N LYS E 401 " --> pdb=" O ALA E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 413 Processing helix chain 'E' and resid 424 through 433 Processing helix chain 'E' and resid 442 through 459 removed outlier: 3.911A pdb=" N ALA E 447 " --> pdb=" O PRO E 443 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ASP E 448 " --> pdb=" O GLU E 444 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU E 449 " --> pdb=" O ARG E 445 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU E 452 " --> pdb=" O ASP E 448 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 9 removed outlier: 5.079A pdb=" N PHE C 27 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.589A pdb=" N ILE C 38 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY C 221 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN C 219 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU C 213 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.550A pdb=" N ALA C 83 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ASP C 163 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR C 191 " --> pdb=" O PHE C 160 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N MET C 162 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL C 193 " --> pdb=" O MET C 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 245 through 247 Processing sheet with id=AA5, first strand: chain 'C' and resid 291 through 293 Processing sheet with id=AA6, first strand: chain 'C' and resid 310 through 311 Processing sheet with id=AA7, first strand: chain 'C' and resid 315 through 317 Processing sheet with id=AA8, first strand: chain 'D' and resid 27 through 31 removed outlier: 5.337A pdb=" N PHE D 27 " --> pdb=" O ARG D 8 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 82 through 85 removed outlier: 6.249A pdb=" N ALA D 83 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N PHE D 160 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL D 195 " --> pdb=" O PHE D 160 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N MET D 162 " --> pdb=" O VAL D 195 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG D 208 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE D 38 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL D 211 " --> pdb=" O GLN D 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 245 through 247 Processing sheet with id=AB2, first strand: chain 'D' and resid 250 through 251 removed outlier: 3.549A pdb=" N GLY D 261 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 291 through 292 Processing sheet with id=AB4, first strand: chain 'D' and resid 310 through 311 Processing sheet with id=AB5, first strand: chain 'D' and resid 315 through 317 Processing sheet with id=AB6, first strand: chain 'E' and resid 64 through 65 removed outlier: 3.759A pdb=" N THR E 36 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N TYR E 35 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ASP E 94 " --> pdb=" O TYR E 35 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU E 349 " --> pdb=" O ILE E 145 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 269 through 272 removed outlier: 3.798A pdb=" N GLU E 270 " --> pdb=" O TRP E 153 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1440 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.48 Time building geometry restraints manager: 5.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2238 1.32 - 1.44: 3398 1.44 - 1.56: 7916 1.56 - 1.69: 0 1.69 - 1.81: 77 Bond restraints: 13629 Sorted by residual: bond pdb=" N PRO D 223 " pdb=" CA PRO D 223 " ideal model delta sigma weight residual 1.473 1.444 0.029 8.50e-03 1.38e+04 1.17e+01 bond pdb=" C PRO B 139 " pdb=" O PRO B 139 " ideal model delta sigma weight residual 1.235 1.192 0.043 1.30e-02 5.92e+03 1.08e+01 bond pdb=" N THR B 219 " pdb=" CA THR B 219 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.20e-02 6.94e+03 9.12e+00 bond pdb=" N SER E 25 " pdb=" CA SER E 25 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.86e+00 bond pdb=" N THR E 27 " pdb=" CA THR E 27 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.76e+00 ... (remaining 13624 not shown) Histogram of bond angle deviations from ideal: 80.16 - 91.43: 2 91.43 - 102.70: 77 102.70 - 113.97: 8258 113.97 - 125.24: 10019 125.24 - 136.52: 217 Bond angle restraints: 18573 Sorted by residual: angle pdb=" N ILE E 441 " pdb=" CA ILE E 441 " pdb=" C ILE E 441 " ideal model delta sigma weight residual 108.90 80.16 28.74 1.66e+00 3.63e-01 3.00e+02 angle pdb=" N VAL B 186 " pdb=" CA VAL B 186 " pdb=" C VAL B 186 " ideal model delta sigma weight residual 110.72 120.70 -9.98 1.01e+00 9.80e-01 9.76e+01 angle pdb=" N GLY D 221 " pdb=" CA GLY D 221 " pdb=" C GLY D 221 " ideal model delta sigma weight residual 113.18 136.52 -23.34 2.37e+00 1.78e-01 9.70e+01 angle pdb=" N ASP E 442 " pdb=" CA ASP E 442 " pdb=" CB ASP E 442 " ideal model delta sigma weight residual 111.03 96.25 14.78 1.76e+00 3.23e-01 7.05e+01 angle pdb=" N ASP E 442 " pdb=" CA ASP E 442 " pdb=" C ASP E 442 " ideal model delta sigma weight residual 108.74 90.66 18.08 2.22e+00 2.03e-01 6.64e+01 ... (remaining 18568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 7289 17.63 - 35.26: 750 35.26 - 52.90: 106 52.90 - 70.53: 16 70.53 - 88.16: 18 Dihedral angle restraints: 8179 sinusoidal: 3112 harmonic: 5067 Sorted by residual: dihedral pdb=" N ASP E 442 " pdb=" C ASP E 442 " pdb=" CA ASP E 442 " pdb=" CB ASP E 442 " ideal model delta harmonic sigma weight residual 122.80 96.94 25.86 0 2.50e+00 1.60e-01 1.07e+02 dihedral pdb=" N ILE E 441 " pdb=" C ILE E 441 " pdb=" CA ILE E 441 " pdb=" CB ILE E 441 " ideal model delta harmonic sigma weight residual 123.40 107.92 15.48 0 2.50e+00 1.60e-01 3.84e+01 dihedral pdb=" C ILE E 441 " pdb=" N ILE E 441 " pdb=" CA ILE E 441 " pdb=" CB ILE E 441 " ideal model delta harmonic sigma weight residual -122.00 -108.75 -13.25 0 2.50e+00 1.60e-01 2.81e+01 ... (remaining 8176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 2172 0.131 - 0.262: 24 0.262 - 0.393: 3 0.393 - 0.524: 0 0.524 - 0.655: 2 Chirality restraints: 2201 Sorted by residual: chirality pdb=" CA ASP E 442 " pdb=" N ASP E 442 " pdb=" C ASP E 442 " pdb=" CB ASP E 442 " both_signs ideal model delta sigma weight residual False 2.51 3.17 -0.66 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA ILE E 441 " pdb=" N ILE E 441 " pdb=" C ILE E 441 " pdb=" CB ILE E 441 " both_signs ideal model delta sigma weight residual False 2.43 3.01 -0.58 2.00e-01 2.50e+01 8.37e+00 chirality pdb=" CA LYS B 185 " pdb=" N LYS B 185 " pdb=" C LYS B 185 " pdb=" CB LYS B 185 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 2198 not shown) Planarity restraints: 2388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D 221 " -0.023 2.00e-02 2.50e+03 4.95e-02 2.45e+01 pdb=" C GLY D 221 " 0.085 2.00e-02 2.50e+03 pdb=" O GLY D 221 " -0.034 2.00e-02 2.50e+03 pdb=" N THR D 222 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 112 " 0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C GLU E 112 " -0.063 2.00e-02 2.50e+03 pdb=" O GLU E 112 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP E 113 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 53 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.20e+00 pdb=" C GLU E 53 " 0.052 2.00e-02 2.50e+03 pdb=" O GLU E 53 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN E 54 " -0.018 2.00e-02 2.50e+03 ... (remaining 2385 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 131 2.57 - 3.15: 11366 3.15 - 3.73: 19795 3.73 - 4.32: 26994 4.32 - 4.90: 46133 Nonbonded interactions: 104419 Sorted by model distance: nonbonded pdb=" N ILE E 441 " pdb=" O ILE E 441 " model vdw 1.985 2.496 nonbonded pdb=" O ALA C 342 " pdb=" O SER C 345 " model vdw 2.228 3.040 nonbonded pdb=" O ALA D 90 " pdb=" NH2 ARG D 151 " model vdw 2.240 2.520 nonbonded pdb=" OG1 THR E 221 " pdb=" OG1 THR E 451 " model vdw 2.247 2.440 nonbonded pdb=" O SER C 229 " pdb=" OG SER C 229 " model vdw 2.249 2.440 ... (remaining 104414 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 2 through 131 or (resid 132 through 133 and (name N or nam \ e CA or name C or name O or name CB )) or resid 134 or (resid 135 and (name N or \ name CA or name C or name O or name CB )) or resid 136 through 274 or (resid 27 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 276 through \ 391)) selection = (chain 'D' and (resid 2 through 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 through 360 or (resid 361 and (name N or na \ me CA or name C or name O or name CB )) or resid 362 through 383 or (resid 384 a \ nd (name N or name CA or name C or name O or name CB )) or resid 385 through 391 \ )) } 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: 2.830 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: 12.690 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 36.360 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 : 0.005 0.045 13629 Z= 0.318 Angle : 0.876 28.745 18573 Z= 0.501 Chirality : 0.053 0.655 2201 Planarity : 0.005 0.049 2388 Dihedral : 14.471 88.161 4913 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.06 % Favored : 89.71 % Rotamer: Outliers : 0.43 % Allowed : 10.27 % Favored : 89.30 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % 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: -5.42 (0.15), residues: 1749 helix: -2.73 (0.14), residues: 816 sheet: -4.09 (0.27), residues: 180 loop : -4.45 (0.16), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 136 HIS 0.003 0.001 HIS D 94 PHE 0.021 0.001 PHE B 232 TYR 0.016 0.001 TYR E 34 ARG 0.003 0.000 ARG C 287 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 247 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 127 ASP cc_start: 0.6833 (p0) cc_final: 0.6615 (p0) REVERT: D 143 GLN cc_start: 0.6644 (pt0) cc_final: 0.6396 (tt0) REVERT: D 227 TYR cc_start: 0.8250 (t80) cc_final: 0.7887 (t80) REVERT: A 208 TRP cc_start: 0.8055 (t60) cc_final: 0.7825 (t-100) REVERT: B 113 ILE cc_start: 0.8862 (pt) cc_final: 0.8643 (mt) outliers start: 6 outliers final: 5 residues processed: 253 average time/residue: 0.2945 time to fit residues: 103.4920 Evaluate side-chains 178 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 173 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 442 ASP Chi-restraints excluded: chain E residue 452 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 70 optimal weight: 20.0000 chunk 137 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 158 optimal weight: 20.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN ** C 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 ASN ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN A 240 ASN B 17 ASN B 72 ASN B 127 ASN B 237 GLN E 52 ASN E 73 GLN E 125 ASN E 137 GLN E 216 GLN E 256 ASN E 358 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13629 Z= 0.307 Angle : 0.710 7.808 18573 Z= 0.354 Chirality : 0.046 0.217 2201 Planarity : 0.005 0.056 2388 Dihedral : 5.946 73.000 1903 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 2.87 % Allowed : 16.88 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.40 (0.17), residues: 1749 helix: -1.79 (0.17), residues: 817 sheet: -3.74 (0.29), residues: 182 loop : -4.02 (0.17), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 136 HIS 0.004 0.001 HIS B 118 PHE 0.018 0.002 PHE B 232 TYR 0.020 0.002 TYR E 34 ARG 0.007 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 191 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 127 ASP cc_start: 0.6877 (p0) cc_final: 0.6638 (p0) REVERT: D 106 THR cc_start: 0.8401 (p) cc_final: 0.8165 (t) REVERT: A 208 TRP cc_start: 0.8029 (t60) cc_final: 0.7773 (t-100) REVERT: B 52 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7980 (pt) REVERT: B 113 ILE cc_start: 0.8876 (pt) cc_final: 0.8652 (mt) REVERT: E 50 ARG cc_start: 0.7418 (ttp-110) cc_final: 0.7018 (ttp-110) outliers start: 40 outliers final: 24 residues processed: 220 average time/residue: 0.2672 time to fit residues: 84.4786 Evaluate side-chains 193 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 168 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 45 CYS Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 253 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 132 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 157 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN C 197 HIS ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 HIS ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN E 411 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13629 Z= 0.217 Angle : 0.651 7.968 18573 Z= 0.322 Chirality : 0.044 0.242 2201 Planarity : 0.005 0.058 2388 Dihedral : 5.267 66.842 1895 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 3.66 % Allowed : 18.25 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.75 (0.18), residues: 1749 helix: -1.23 (0.18), residues: 817 sheet: -3.32 (0.31), residues: 188 loop : -3.74 (0.18), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 136 HIS 0.005 0.001 HIS C 94 PHE 0.013 0.001 PHE B 54 TYR 0.016 0.001 TYR E 34 ARG 0.009 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 200 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 ASP cc_start: 0.6851 (p0) cc_final: 0.6615 (p0) REVERT: A 208 TRP cc_start: 0.7931 (t60) cc_final: 0.7717 (t-100) REVERT: B 52 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7897 (pt) REVERT: B 71 PHE cc_start: 0.7972 (t80) cc_final: 0.7479 (m-10) REVERT: B 113 ILE cc_start: 0.8860 (pt) cc_final: 0.8652 (mt) REVERT: B 220 GLN cc_start: 0.8214 (tp-100) cc_final: 0.7793 (tp40) REVERT: E 50 ARG cc_start: 0.7262 (ttp-110) cc_final: 0.6877 (ttp-110) outliers start: 51 outliers final: 26 residues processed: 241 average time/residue: 0.2537 time to fit residues: 89.2710 Evaluate side-chains 204 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 177 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 45 CYS Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 253 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 9.9990 chunk 119 optimal weight: 0.0570 chunk 82 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 75 optimal weight: 0.0060 chunk 106 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.0116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13629 Z= 0.211 Angle : 0.628 7.677 18573 Z= 0.311 Chirality : 0.044 0.244 2201 Planarity : 0.004 0.056 2388 Dihedral : 5.060 64.449 1895 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 4.02 % Allowed : 19.54 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.31 (0.19), residues: 1749 helix: -0.87 (0.19), residues: 814 sheet: -2.77 (0.36), residues: 167 loop : -3.60 (0.18), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 13 HIS 0.004 0.001 HIS C 94 PHE 0.012 0.001 PHE A 113 TYR 0.016 0.001 TYR E 34 ARG 0.005 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 194 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 ASP cc_start: 0.6759 (p0) cc_final: 0.6544 (p0) REVERT: D 177 MET cc_start: 0.8656 (mmm) cc_final: 0.8412 (tpp) REVERT: D 269 MET cc_start: 0.5896 (mmt) cc_final: 0.5669 (ttt) REVERT: D 318 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8042 (pp) REVERT: B 52 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7879 (pt) REVERT: B 71 PHE cc_start: 0.7956 (t80) cc_final: 0.7433 (m-10) REVERT: B 220 GLN cc_start: 0.8184 (tp-100) cc_final: 0.7782 (tp40) REVERT: E 310 PHE cc_start: 0.6563 (t80) cc_final: 0.6246 (t80) outliers start: 56 outliers final: 32 residues processed: 235 average time/residue: 0.2516 time to fit residues: 86.7391 Evaluate side-chains 210 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 176 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 45 CYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 440 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 42 optimal weight: 0.0770 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 HIS ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN B 127 ASN E 150 GLN E 188 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13629 Z= 0.304 Angle : 0.668 8.275 18573 Z= 0.330 Chirality : 0.045 0.258 2201 Planarity : 0.005 0.056 2388 Dihedral : 5.166 67.012 1895 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.38 % Favored : 90.57 % Rotamer: Outliers : 4.60 % Allowed : 20.33 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.23 (0.19), residues: 1749 helix: -0.82 (0.19), residues: 821 sheet: -2.75 (0.37), residues: 173 loop : -3.55 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 13 HIS 0.004 0.001 HIS C 268 PHE 0.013 0.002 PHE D 36 TYR 0.019 0.001 TYR E 34 ARG 0.011 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 185 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 ASP cc_start: 0.6732 (p0) cc_final: 0.6531 (p0) REVERT: D 268 HIS cc_start: 0.6062 (OUTLIER) cc_final: 0.5735 (p90) REVERT: D 269 MET cc_start: 0.5837 (mmt) cc_final: 0.5602 (ttt) REVERT: D 318 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8089 (pp) REVERT: B 52 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7860 (pt) REVERT: B 71 PHE cc_start: 0.7967 (t80) cc_final: 0.7448 (m-10) REVERT: B 220 GLN cc_start: 0.8228 (tp-100) cc_final: 0.7836 (tp40) REVERT: E 310 PHE cc_start: 0.6487 (t80) cc_final: 0.6193 (t80) outliers start: 64 outliers final: 41 residues processed: 232 average time/residue: 0.2498 time to fit residues: 85.5136 Evaluate side-chains 226 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 182 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 45 CYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 89 TYR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 188 GLN Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 440 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 169 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN E 150 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13629 Z= 0.193 Angle : 0.621 7.817 18573 Z= 0.305 Chirality : 0.043 0.271 2201 Planarity : 0.004 0.054 2388 Dihedral : 4.889 62.794 1895 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.88 % Allowed : 21.91 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.91 (0.19), residues: 1749 helix: -0.57 (0.19), residues: 822 sheet: -2.61 (0.36), residues: 178 loop : -3.38 (0.19), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 13 HIS 0.004 0.001 HIS C 268 PHE 0.012 0.001 PHE D 260 TYR 0.013 0.001 TYR E 34 ARG 0.010 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 196 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 268 HIS cc_start: 0.5963 (OUTLIER) cc_final: 0.5736 (p-80) REVERT: D 318 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.7992 (pp) REVERT: A 168 ILE cc_start: 0.9231 (mm) cc_final: 0.8939 (mp) REVERT: B 52 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7840 (pt) REVERT: B 71 PHE cc_start: 0.7939 (t80) cc_final: 0.7408 (m-10) REVERT: B 220 GLN cc_start: 0.8124 (tp-100) cc_final: 0.7747 (tp40) REVERT: E 310 PHE cc_start: 0.6477 (t80) cc_final: 0.6174 (t80) outliers start: 54 outliers final: 36 residues processed: 237 average time/residue: 0.2538 time to fit residues: 88.3046 Evaluate side-chains 224 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 185 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 45 CYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 89 TYR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 440 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 142 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 105 optimal weight: 0.0870 chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13629 Z= 0.174 Angle : 0.607 7.229 18573 Z= 0.298 Chirality : 0.043 0.283 2201 Planarity : 0.004 0.054 2388 Dihedral : 4.708 60.799 1895 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.74 % Allowed : 22.99 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.73 (0.20), residues: 1749 helix: -0.42 (0.19), residues: 821 sheet: -2.50 (0.36), residues: 178 loop : -3.29 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 13 HIS 0.005 0.001 HIS C 268 PHE 0.013 0.001 PHE B 54 TYR 0.012 0.001 TYR E 34 ARG 0.011 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 194 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 318 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7972 (pp) REVERT: A 168 ILE cc_start: 0.9219 (mm) cc_final: 0.8947 (mp) REVERT: B 52 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7698 (pt) REVERT: B 71 PHE cc_start: 0.7941 (t80) cc_final: 0.7404 (m-10) REVERT: B 220 GLN cc_start: 0.8084 (tp-100) cc_final: 0.7720 (tp40) REVERT: E 310 PHE cc_start: 0.6437 (t80) cc_final: 0.6144 (t80) outliers start: 52 outliers final: 39 residues processed: 235 average time/residue: 0.2493 time to fit residues: 85.9560 Evaluate side-chains 220 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 179 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 45 CYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 89 TYR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 440 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.0270 chunk 100 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13629 Z= 0.250 Angle : 0.639 9.741 18573 Z= 0.313 Chirality : 0.044 0.292 2201 Planarity : 0.005 0.055 2388 Dihedral : 4.814 65.166 1895 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 4.38 % Allowed : 22.41 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.69 (0.20), residues: 1749 helix: -0.39 (0.19), residues: 818 sheet: -2.45 (0.37), residues: 178 loop : -3.26 (0.20), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 13 HIS 0.004 0.001 HIS C 268 PHE 0.011 0.001 PHE D 326 TYR 0.017 0.001 TYR E 34 ARG 0.013 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 188 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 208 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8122 (mtp-110) REVERT: D 318 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8010 (pp) REVERT: B 52 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7720 (pt) REVERT: B 71 PHE cc_start: 0.7979 (t80) cc_final: 0.7422 (m-10) REVERT: B 184 ARG cc_start: 0.8510 (ttp80) cc_final: 0.8307 (ttm110) REVERT: B 220 GLN cc_start: 0.8178 (tp-100) cc_final: 0.7822 (tp40) REVERT: E 310 PHE cc_start: 0.6482 (t80) cc_final: 0.6191 (t80) outliers start: 61 outliers final: 45 residues processed: 237 average time/residue: 0.2682 time to fit residues: 92.5459 Evaluate side-chains 225 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 177 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 45 CYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 208 ARG Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 89 TYR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 440 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 chunk 94 optimal weight: 0.3980 chunk 68 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 48 optimal weight: 0.0980 chunk 142 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 103 optimal weight: 0.1980 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13629 Z= 0.166 Angle : 0.626 13.485 18573 Z= 0.303 Chirality : 0.043 0.306 2201 Planarity : 0.004 0.058 2388 Dihedral : 4.605 61.310 1895 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.95 % Allowed : 23.42 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.47 (0.20), residues: 1749 helix: -0.21 (0.19), residues: 819 sheet: -2.33 (0.37), residues: 178 loop : -3.15 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 13 HIS 0.005 0.001 HIS C 268 PHE 0.014 0.001 PHE A 64 TYR 0.015 0.001 TYR A 138 ARG 0.014 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 190 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 318 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7948 (pp) REVERT: A 56 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8397 (tt) REVERT: A 115 LYS cc_start: 0.8409 (ttmt) cc_final: 0.8198 (mttt) REVERT: A 168 ILE cc_start: 0.9191 (mm) cc_final: 0.8928 (mp) REVERT: B 52 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7666 (pt) REVERT: B 71 PHE cc_start: 0.7936 (t80) cc_final: 0.7437 (m-10) REVERT: B 184 ARG cc_start: 0.8507 (ttp80) cc_final: 0.8306 (ttm110) REVERT: B 220 GLN cc_start: 0.8066 (tp-100) cc_final: 0.7496 (tp40) outliers start: 41 outliers final: 33 residues processed: 224 average time/residue: 0.2766 time to fit residues: 89.4820 Evaluate side-chains 219 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 183 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 45 CYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 89 TYR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 440 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 78 optimal weight: 0.1980 chunk 115 optimal weight: 0.4980 chunk 174 optimal weight: 0.2980 chunk 160 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13629 Z= 0.163 Angle : 0.625 12.191 18573 Z= 0.302 Chirality : 0.043 0.311 2201 Planarity : 0.004 0.059 2388 Dihedral : 4.449 59.793 1895 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.80 % Allowed : 23.85 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.29 (0.20), residues: 1749 helix: -0.11 (0.19), residues: 825 sheet: -2.26 (0.37), residues: 178 loop : -3.01 (0.20), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 13 HIS 0.005 0.001 HIS C 268 PHE 0.031 0.001 PHE E 328 TYR 0.016 0.001 TYR A 138 ARG 0.014 0.000 ARG B 265 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 188 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 115 ILE cc_start: 0.7632 (mm) cc_final: 0.7318 (mt) REVERT: D 318 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7930 (pp) REVERT: A 56 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8355 (tt) REVERT: A 168 ILE cc_start: 0.9164 (mm) cc_final: 0.8931 (mp) REVERT: B 52 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7607 (pt) REVERT: B 71 PHE cc_start: 0.7916 (t80) cc_final: 0.7354 (m-10) outliers start: 39 outliers final: 33 residues processed: 220 average time/residue: 0.2709 time to fit residues: 85.9592 Evaluate side-chains 223 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 187 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 45 CYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 89 TYR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 440 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 139 optimal weight: 0.0570 chunk 58 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 ASN A 60 HIS ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.169451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142998 restraints weight = 17132.088| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.66 r_work: 0.3530 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13629 Z= 0.179 Angle : 0.622 11.292 18573 Z= 0.301 Chirality : 0.043 0.306 2201 Planarity : 0.005 0.060 2388 Dihedral : 4.454 61.266 1895 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.23 % Allowed : 23.56 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.15 (0.20), residues: 1749 helix: 0.02 (0.19), residues: 819 sheet: -2.15 (0.37), residues: 180 loop : -2.95 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 13 HIS 0.004 0.001 HIS C 268 PHE 0.030 0.001 PHE E 328 TYR 0.013 0.001 TYR E 34 ARG 0.014 0.000 ARG B 265 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3135.77 seconds wall clock time: 60 minutes 11.36 seconds (3611.36 seconds total)