Starting phenix.real_space_refine on Mon Aug 5 11:22:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cae_30328/08_2024/7cae_30328.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cae_30328/08_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_30328/08_2024/7cae_30328.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cae_30328/08_2024/7cae_30328.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cae_30328/08_2024/7cae_30328.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cae_30328/08_2024/7cae_30328.cif" } 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 8.47, per 1000 atoms: 0.63 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: 5.66 Conformation dependent library (CDL) restraints added in 2.4 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: 1.51 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: 3.84 Time building geometry restraints manager: 6.04 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 3.120 nonbonded pdb=" OG1 THR E 221 " pdb=" OG1 THR E 451 " model vdw 2.247 3.040 nonbonded pdb=" O SER C 229 " pdb=" OG SER C 229 " model vdw 2.249 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 6.320 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 39.750 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.470 ------------------------------------------------------------------------------- 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 : 1.445 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: 0.2946 time to fit residues: 103.8684 Evaluate side-chains 178 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 173 time to evaluate : 1.459 ------------------------------------------------------------------------------- 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: 2.9990 chunk 73 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 70 optimal weight: 0.2980 chunk 137 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN D 168 ASN D 350 ASN A 201 GLN B 17 ASN B 72 ASN B 237 GLN E 52 ASN E 73 GLN E 137 GLN E 216 GLN E 256 ASN E 358 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13629 Z= 0.237 Angle : 0.694 8.762 18573 Z= 0.347 Chirality : 0.045 0.186 2201 Planarity : 0.005 0.054 2388 Dihedral : 5.753 70.863 1903 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.18 % Favored : 91.77 % Rotamer: Outliers : 2.66 % Allowed : 15.59 % Favored : 81.75 % 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: -4.23 (0.17), residues: 1749 helix: -1.65 (0.17), residues: 825 sheet: -3.71 (0.29), residues: 187 loop : -3.94 (0.18), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 136 HIS 0.003 0.001 HIS D 94 PHE 0.018 0.002 PHE B 232 TYR 0.015 0.001 TYR E 34 ARG 0.008 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 238 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 201 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 ASP cc_start: 0.6816 (p0) cc_final: 0.6579 (p0) REVERT: C 306 LEU cc_start: 0.6969 (mm) cc_final: 0.6619 (tt) REVERT: A 208 TRP cc_start: 0.7849 (t60) cc_final: 0.7642 (t-100) REVERT: B 52 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7920 (pt) REVERT: B 71 PHE cc_start: 0.7970 (t80) cc_final: 0.7474 (m-10) REVERT: B 220 GLN cc_start: 0.8135 (tp-100) cc_final: 0.7846 (tp40) REVERT: E 50 ARG cc_start: 0.7330 (ttp-110) cc_final: 0.7053 (ttp-110) REVERT: E 75 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8646 (mm) outliers start: 37 outliers final: 18 residues processed: 229 average time/residue: 0.2689 time to fit residues: 87.7355 Evaluate side-chains 200 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL 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 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 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 B residue 52 ILE 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 75 LEU Chi-restraints excluded: chain E residue 195 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 127 optimal weight: 0.0770 overall best weight: 1.5544 ------------------------------------------------------------------------------- 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** D 232 ASN A 201 GLN ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13629 Z= 0.277 Angle : 0.686 10.305 18573 Z= 0.340 Chirality : 0.045 0.200 2201 Planarity : 0.005 0.056 2388 Dihedral : 5.349 69.932 1895 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 3.52 % Allowed : 17.17 % Favored : 79.31 % 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: -1.25 (0.18), residues: 824 sheet: -3.35 (0.31), residues: 182 loop : -3.73 (0.18), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 136 HIS 0.005 0.001 HIS C 94 PHE 0.014 0.001 PHE B 232 TYR 0.017 0.001 TYR E 34 ARG 0.008 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 240 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 191 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 ASP cc_start: 0.6794 (p0) cc_final: 0.6539 (p0) REVERT: C 306 LEU cc_start: 0.6899 (mm) cc_final: 0.6604 (tt) REVERT: D 269 MET cc_start: 0.5911 (mmt) cc_final: 0.5643 (ttt) REVERT: B 52 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7867 (pt) REVERT: B 71 PHE cc_start: 0.7947 (t80) cc_final: 0.7434 (m-10) REVERT: B 220 GLN cc_start: 0.8199 (tp-100) cc_final: 0.7933 (tp40) REVERT: E 75 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8662 (mm) outliers start: 49 outliers final: 28 residues processed: 231 average time/residue: 0.2531 time to fit residues: 84.7736 Evaluate side-chains 204 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 174 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 222 THR 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 85 VAL Chi-restraints excluded: chain D residue 89 TYR 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 232 ASN Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 105 LEU 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 75 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 219 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 0.7980 chunk 119 optimal weight: 0.0030 chunk 82 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- 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 145 GLN D 219 GLN D 232 ASN A 201 GLN E 76 GLN ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13629 Z= 0.209 Angle : 0.641 10.187 18573 Z= 0.319 Chirality : 0.044 0.211 2201 Planarity : 0.005 0.055 2388 Dihedral : 5.123 66.468 1895 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.45 % Allowed : 19.32 % Favored : 77.23 % 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: -0.90 (0.18), residues: 821 sheet: -3.05 (0.34), residues: 180 loop : -3.50 (0.19), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 13 HIS 0.005 0.001 HIS C 268 PHE 0.012 0.001 PHE D 260 TYR 0.014 0.001 TYR E 34 ARG 0.008 0.000 ARG B 265 *********************** 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 241 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 193 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 ASP cc_start: 0.6710 (p0) cc_final: 0.6472 (p0) REVERT: D 268 HIS cc_start: 0.6013 (OUTLIER) cc_final: 0.5757 (p-80) REVERT: D 318 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8088 (pp) REVERT: B 52 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7870 (pt) REVERT: B 71 PHE cc_start: 0.7923 (t80) cc_final: 0.7428 (m-10) REVERT: B 220 GLN cc_start: 0.8120 (tp-100) cc_final: 0.7846 (tp40) REVERT: E 75 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8646 (mm) REVERT: E 310 PHE cc_start: 0.6517 (t80) cc_final: 0.6231 (t80) outliers start: 48 outliers final: 28 residues processed: 231 average time/residue: 0.2490 time to fit residues: 84.2247 Evaluate side-chains 214 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 182 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 85 VAL 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 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 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 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 75 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 440 ASP Chi-restraints excluded: chain E residue 448 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 144 optimal weight: 0.6980 chunk 116 optimal weight: 0.0170 chunk 0 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 151 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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** A 201 GLN ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13629 Z= 0.181 Angle : 0.637 11.142 18573 Z= 0.313 Chirality : 0.043 0.210 2201 Planarity : 0.005 0.054 2388 Dihedral : 4.883 63.238 1895 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.30 % Allowed : 20.69 % Favored : 76.01 % 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: -3.01 (0.19), residues: 1749 helix: -0.69 (0.19), residues: 822 sheet: -2.73 (0.36), residues: 178 loop : -3.35 (0.19), residues: 749 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 0.014 0.001 PHE B 54 TYR 0.012 0.001 TYR E 34 ARG 0.010 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 241 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 195 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 ASP cc_start: 0.6753 (p0) cc_final: 0.6469 (p0) REVERT: D 318 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7980 (pp) REVERT: A 168 ILE cc_start: 0.9224 (mm) cc_final: 0.8955 (mp) REVERT: B 52 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7687 (pt) REVERT: B 71 PHE cc_start: 0.7926 (t80) cc_final: 0.7401 (m-10) REVERT: B 220 GLN cc_start: 0.8055 (tp-100) cc_final: 0.7825 (tp40) REVERT: E 310 PHE cc_start: 0.6465 (t80) cc_final: 0.6190 (t80) outliers start: 46 outliers final: 29 residues processed: 229 average time/residue: 0.2519 time to fit residues: 84.6918 Evaluate side-chains 216 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 185 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain C residue 318 LEU 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 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 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 223 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 105 LEU 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 152 LEU Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 440 ASP Chi-restraints excluded: chain E residue 448 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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** A 201 GLN E 76 GLN ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 13629 Z= 0.300 Angle : 0.675 9.071 18573 Z= 0.332 Chirality : 0.045 0.225 2201 Planarity : 0.005 0.055 2388 Dihedral : 5.053 68.587 1895 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 3.81 % Allowed : 21.12 % 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: -2.97 (0.19), residues: 1749 helix: -0.68 (0.19), residues: 824 sheet: -2.66 (0.36), residues: 180 loop : -3.33 (0.19), residues: 745 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 0.012 0.001 PHE D 326 TYR 0.018 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 234 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 181 time to evaluate : 1.509 Fit side-chains revert: symmetry clash REVERT: C 127 ASP cc_start: 0.6688 (p0) cc_final: 0.6441 (p0) REVERT: C 162 MET cc_start: 0.8268 (mtt) cc_final: 0.7952 (mtt) REVERT: D 318 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8078 (pp) REVERT: B 52 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7848 (pt) REVERT: B 71 PHE cc_start: 0.7963 (t80) cc_final: 0.7402 (m-10) REVERT: E 75 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8688 (mm) REVERT: E 310 PHE cc_start: 0.6507 (t80) cc_final: 0.6233 (t80) outliers start: 53 outliers final: 36 residues processed: 222 average time/residue: 0.2578 time to fit residues: 86.1522 Evaluate side-chains 213 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 174 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL 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 263 VAL Chi-restraints excluded: chain C residue 268 HIS 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 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 36 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 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 75 LEU 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 440 ASP Chi-restraints excluded: chain E residue 459 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 ASN A 201 GLN E 76 GLN ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13629 Z= 0.208 Angle : 0.638 8.787 18573 Z= 0.312 Chirality : 0.044 0.214 2201 Planarity : 0.005 0.054 2388 Dihedral : 4.850 66.357 1895 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.38 % Allowed : 22.05 % Favored : 74.57 % 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 (0.19), residues: 1749 helix: -0.49 (0.19), residues: 827 sheet: -2.49 (0.36), residues: 178 loop : -3.22 (0.20), residues: 744 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 0.011 0.001 PHE D 260 TYR 0.013 0.001 TYR E 34 ARG 0.012 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 232 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 185 time to evaluate : 1.581 Fit side-chains revert: symmetry clash REVERT: C 127 ASP cc_start: 0.6713 (p0) cc_final: 0.6477 (p0) REVERT: C 162 MET cc_start: 0.8256 (mtt) cc_final: 0.7906 (mtt) REVERT: D 269 MET cc_start: 0.5826 (mmt) cc_final: 0.5623 (ttt) REVERT: D 318 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8069 (pp) REVERT: A 168 ILE cc_start: 0.9221 (mm) cc_final: 0.8935 (mp) REVERT: B 52 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7690 (pt) REVERT: B 71 PHE cc_start: 0.7935 (t80) cc_final: 0.7379 (m-10) REVERT: E 75 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8643 (mm) REVERT: E 310 PHE cc_start: 0.6479 (t80) cc_final: 0.6189 (t80) outliers start: 47 outliers final: 36 residues processed: 222 average time/residue: 0.2483 time to fit residues: 81.4431 Evaluate side-chains 217 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 178 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL 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 258 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 268 HIS 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 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 D residue 349 THR Chi-restraints excluded: chain A residue 91 VAL 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 75 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 219 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: 0.8980 chunk 100 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 0.0010 chunk 83 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN A 201 GLN E 76 GLN ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2410 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= 0.185 Angle : 0.625 9.048 18573 Z= 0.306 Chirality : 0.043 0.225 2201 Planarity : 0.005 0.054 2388 Dihedral : 4.706 64.900 1895 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.95 % Allowed : 21.91 % Favored : 74.14 % 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: -2.51 (0.20), residues: 1749 helix: -0.30 (0.19), residues: 821 sheet: -2.43 (0.37), residues: 178 loop : -3.09 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 13 HIS 0.005 0.001 HIS C 268 PHE 0.012 0.001 PHE D 260 TYR 0.015 0.001 TYR A 138 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 242 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 187 time to evaluate : 1.584 Fit side-chains revert: symmetry clash REVERT: C 127 ASP cc_start: 0.6655 (p0) cc_final: 0.6427 (p0) REVERT: C 162 MET cc_start: 0.8233 (mtt) cc_final: 0.7850 (mtt) REVERT: D 318 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.7988 (pp) REVERT: A 56 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8255 (tt) REVERT: A 168 ILE cc_start: 0.9200 (mm) cc_final: 0.8951 (mp) REVERT: A 211 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7739 (tt) REVERT: B 52 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7651 (pt) REVERT: B 71 PHE cc_start: 0.7918 (t80) cc_final: 0.7364 (m-10) REVERT: B 184 ARG cc_start: 0.8465 (ttp80) cc_final: 0.8254 (ttm110) REVERT: E 75 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8584 (mm) outliers start: 55 outliers final: 38 residues processed: 230 average time/residue: 0.2505 time to fit residues: 84.8298 Evaluate side-chains 222 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 179 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 60 ILE 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 258 LEU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 268 HIS 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 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 D residue 349 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 211 LEU 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 E residue 75 LEU 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 440 ASP Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 459 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 7.9990 chunk 147 optimal weight: 7.9990 chunk 157 optimal weight: 0.0270 chunk 94 optimal weight: 0.5980 chunk 68 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 48 optimal weight: 20.0000 chunk 142 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 chunk 103 optimal weight: 0.0060 overall best weight: 0.4454 ------------------------------------------------------------------------------- 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** A 201 GLN E 76 GLN ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 0.048 13629 Z= 0.165 Angle : 0.621 10.911 18573 Z= 0.302 Chirality : 0.043 0.207 2201 Planarity : 0.005 0.058 2388 Dihedral : 4.541 62.908 1895 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.45 % Allowed : 22.56 % Favored : 73.99 % 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: -2.24 (0.20), residues: 1749 helix: -0.09 (0.19), residues: 822 sheet: -2.32 (0.37), residues: 178 loop : -2.92 (0.20), residues: 749 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 0.025 0.001 PHE E 328 TYR 0.010 0.001 TYR E 34 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 235 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 187 time to evaluate : 1.369 Fit side-chains revert: symmetry clash REVERT: C 127 ASP cc_start: 0.6694 (p0) cc_final: 0.6465 (p0) REVERT: D 38 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7949 (mt) REVERT: D 318 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7959 (pp) REVERT: A 56 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8202 (tt) REVERT: A 168 ILE cc_start: 0.9171 (mm) cc_final: 0.8934 (mp) REVERT: B 52 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7626 (pt) REVERT: B 71 PHE cc_start: 0.7908 (t80) cc_final: 0.7359 (m-10) REVERT: B 184 ARG cc_start: 0.8483 (ttp80) cc_final: 0.8273 (ttm110) REVERT: E 75 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8527 (mm) REVERT: E 448 ASP cc_start: 0.6748 (OUTLIER) cc_final: 0.6432 (t0) outliers start: 48 outliers final: 33 residues processed: 223 average time/residue: 0.2424 time to fit residues: 80.5485 Evaluate side-chains 212 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 173 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 60 ILE 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 258 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 89 TYR Chi-restraints excluded: chain D residue 143 GLN 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 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 E residue 75 LEU Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 440 ASP Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 459 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.5451 > 50: distance: 58 - 81: 5.248 distance: 68 - 93: 10.064 distance: 83 - 84: 3.357 distance: 83 - 86: 5.815 distance: 84 - 111: 5.789 distance: 86 - 87: 5.482 distance: 87 - 90: 3.473 distance: 88 - 89: 4.667 distance: 88 - 93: 10.211 distance: 89 - 116: 3.281 distance: 93 - 94: 3.008 distance: 94 - 95: 3.105 distance: 95 - 96: 4.765 distance: 95 - 102: 7.165 distance: 96 - 124: 26.754 distance: 98 - 99: 6.320 distance: 99 - 100: 3.944 distance: 99 - 101: 6.310 distance: 102 - 103: 5.140 distance: 103 - 104: 6.100 distance: 103 - 106: 3.946 distance: 104 - 105: 9.201 distance: 106 - 107: 9.103 distance: 107 - 108: 6.514 distance: 108 - 109: 3.426 distance: 109 - 110: 8.003 distance: 111 - 112: 7.886 distance: 112 - 113: 9.190 distance: 112 - 115: 6.058 distance: 113 - 114: 15.356 distance: 113 - 116: 8.476 distance: 116 - 117: 5.091 distance: 117 - 118: 19.180 distance: 117 - 120: 4.136 distance: 118 - 119: 29.013 distance: 118 - 124: 17.694 distance: 120 - 121: 23.465 distance: 120 - 122: 14.796 distance: 121 - 123: 17.818 distance: 124 - 125: 14.552 distance: 125 - 126: 17.826 distance: 125 - 128: 7.021 distance: 126 - 127: 27.950 distance: 126 - 132: 18.919 distance: 128 - 129: 7.376 distance: 129 - 130: 26.545 distance: 129 - 131: 15.994 distance: 132 - 133: 9.306 distance: 133 - 134: 36.618 distance: 134 - 135: 21.949 distance: 134 - 136: 15.679 distance: 136 - 137: 11.818 distance: 137 - 138: 3.410 distance: 137 - 140: 8.127 distance: 138 - 139: 9.126 distance: 138 - 145: 8.684 distance: 140 - 141: 3.607 distance: 141 - 142: 4.068 distance: 142 - 143: 5.535 distance: 143 - 144: 4.301