Starting phenix.real_space_refine on Tue May 7 21:49:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu6_29453/05_2024/8fu6_29453_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu6_29453/05_2024/8fu6_29453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu6_29453/05_2024/8fu6_29453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu6_29453/05_2024/8fu6_29453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu6_29453/05_2024/8fu6_29453_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu6_29453/05_2024/8fu6_29453_neut.pdb" } resolution = 2.9 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= -0.001 sd= 0.038 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 53 5.16 5 C 5608 2.51 5 N 1552 2.21 5 O 1621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 215": "OD1" <-> "OD2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N ASP 73": "OD1" <-> "OD2" Residue "N TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 9": "OD1" <-> "OD2" Residue "R TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 209": "OD1" <-> "OD2" Residue "R GLU 260": "OE1" <-> "OE2" Residue "R PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 299": "OD1" <-> "OD2" Residue "R PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 370": "OD1" <-> "OD2" Residue "R ASP 385": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 8834 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1773 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2597 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 240 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 2809 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2800 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 337} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 346, 2800 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 337} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2870 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN R 42 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN R 42 " occ=0.50 Time building chain proxies: 6.18, per 1000 atoms: 0.70 Number of scatterers: 8834 At special positions: 0 Unit cell: (84.348, 166.992, 101.388, 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 53 16.00 O 1621 8.00 N 1552 7.00 C 5608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 81 " - pdb=" SG CYS R 121 " distance=2.03 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: 3.05 Conformation dependent library (CDL) restraints added in 2.2 seconds 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 41.4% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 9 through 38 removed outlier: 4.178A pdb=" N ARG A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.752A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 239' Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.744A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.763A pdb=" N ASP A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.573A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.582A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.780A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.710A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.536A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.575A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 29 removed outlier: 3.516A pdb=" N SER P 16 " --> pdb=" O LYS P 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 43 removed outlier: 3.571A pdb=" N PHE R 31 " --> pdb=" O GLN R 27 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N CYS R 43 " --> pdb=" O TYR R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 166 removed outlier: 3.539A pdb=" N GLU R 133 " --> pdb=" O GLU R 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL R 134 " --> pdb=" O VAL R 130 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA R 135 " --> pdb=" O GLN R 131 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS R 136 " --> pdb=" O LYS R 132 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET R 137 " --> pdb=" O GLU R 133 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR R 138 " --> pdb=" O VAL R 134 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER R 150 " --> pdb=" O THR R 146 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU R 151 " --> pdb=" O VAL R 147 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER R 152 " --> pdb=" O GLY R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 197 Processing helix chain 'R' and resid 208 through 212 removed outlier: 3.667A pdb=" N VAL R 212 " --> pdb=" O ASP R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 255 removed outlier: 3.687A pdb=" N ARG R 225 " --> pdb=" O VAL R 221 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL R 226 " --> pdb=" O ALA R 222 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA R 227 " --> pdb=" O GLY R 223 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL R 236 " --> pdb=" O GLN R 232 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR R 239 " --> pdb=" O ILE R 235 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS R 240 " --> pdb=" O VAL R 236 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TRP R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU R 242 " --> pdb=" O ASN R 238 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU R 243 " --> pdb=" O TYR R 239 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU R 253 " --> pdb=" O LEU R 249 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY R 254 " --> pdb=" O HIS R 250 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU R 255 " --> pdb=" O ASN R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 274 removed outlier: 3.781A pdb=" N ALA R 274 " --> pdb=" O ILE R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 289 removed outlier: 3.789A pdb=" N VAL R 280 " --> pdb=" O MET R 276 " (cutoff:3.500A) Proline residue: R 281 - end of helix Processing helix chain 'R' and resid 292 through 296 removed outlier: 4.225A pdb=" N THR R 296 " --> pdb=" O GLN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 305 Processing helix chain 'R' and resid 308 through 335 removed outlier: 3.588A pdb=" N ILE R 315 " --> pdb=" O VAL R 311 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE R 320 " --> pdb=" O LEU R 316 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE R 321 " --> pdb=" O ILE R 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 344 through 359 removed outlier: 4.149A pdb=" N THR R 351 " --> pdb=" O LEU R 347 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU R 352 " --> pdb=" O ALA R 348 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR R 353 " --> pdb=" O LYS R 349 " (cutoff:3.500A) Proline residue: R 356 - end of helix Processing helix chain 'R' and resid 360 through 365 removed outlier: 4.097A pdb=" N PHE R 365 " --> pdb=" O HIS R 361 " (cutoff:3.500A) Processing helix chain 'R' and resid 375 through 389 removed outlier: 3.705A pdb=" N SER R 379 " --> pdb=" O GLY R 375 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS R 381 " --> pdb=" O LEU R 377 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU R 386 " --> pdb=" O LEU R 382 " (cutoff:3.500A) Processing helix chain 'R' and resid 391 through 401 Processing helix chain 'R' and resid 404 through 421 removed outlier: 3.564A pdb=" N GLU R 410 " --> pdb=" O GLU R 406 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG R 412 " --> pdb=" O GLN R 408 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG R 413 " --> pdb=" O SER R 409 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG R 414 " --> pdb=" O GLU R 410 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP R 415 " --> pdb=" O LEU R 411 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214 removed outlier: 3.611A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 9.136A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.806A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.945A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.684A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.776A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.915A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.738A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.001A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.558A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.584A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA N 97 " --> pdb=" O ASN N 35 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR N 94 " --> pdb=" O THR N 122 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1095 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: 2.42 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2902 1.35 - 1.47: 2266 1.47 - 1.59: 3787 1.59 - 1.71: 0 1.71 - 1.83: 73 Bond restraints: 9028 Sorted by residual: bond pdb=" C ALA R 274 " pdb=" N PRO R 275 " ideal model delta sigma weight residual 1.335 1.355 -0.021 1.28e-02 6.10e+03 2.57e+00 bond pdb=" CA VAL A 224 " pdb=" CB VAL A 224 " ideal model delta sigma weight residual 1.528 1.543 -0.015 1.34e-02 5.57e+03 1.30e+00 bond pdb=" CA VAL R 280 " pdb=" C VAL R 280 " ideal model delta sigma weight residual 1.520 1.529 -0.009 8.80e-03 1.29e+04 1.13e+00 bond pdb=" C GLY N 9 " pdb=" O GLY N 9 " ideal model delta sigma weight residual 1.232 1.243 -0.011 1.03e-02 9.43e+03 1.11e+00 bond pdb=" C PHE B 235 " pdb=" N PRO B 236 " ideal model delta sigma weight residual 1.335 1.348 -0.013 1.36e-02 5.41e+03 9.18e-01 ... (remaining 9023 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.09: 188 107.09 - 113.84: 4944 113.84 - 120.59: 3581 120.59 - 127.34: 3412 127.34 - 134.09: 98 Bond angle restraints: 12223 Sorted by residual: angle pdb=" N VAL N 110 " pdb=" CA VAL N 110 " pdb=" C VAL N 110 " ideal model delta sigma weight residual 111.91 106.81 5.10 8.90e-01 1.26e+00 3.28e+01 angle pdb=" N VAL R 360 " pdb=" CA VAL R 360 " pdb=" C VAL R 360 " ideal model delta sigma weight residual 113.39 108.93 4.46 1.47e+00 4.63e-01 9.20e+00 angle pdb=" N PHE A 315 " pdb=" CA PHE A 315 " pdb=" C PHE A 315 " ideal model delta sigma weight residual 112.57 109.27 3.30 1.13e+00 7.83e-01 8.53e+00 angle pdb=" N TYR A 37 " pdb=" CA TYR A 37 " pdb=" C TYR A 37 " ideal model delta sigma weight residual 111.28 114.37 -3.09 1.09e+00 8.42e-01 8.02e+00 angle pdb=" CA VAL R 360 " pdb=" C VAL R 360 " pdb=" N HIS R 361 " ideal model delta sigma weight residual 118.55 116.14 2.41 8.60e-01 1.35e+00 7.87e+00 ... (remaining 12218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 4899 17.67 - 35.34: 368 35.34 - 53.02: 47 53.02 - 70.69: 7 70.69 - 88.36: 6 Dihedral angle restraints: 5327 sinusoidal: 2102 harmonic: 3225 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 1.91 -87.91 1 1.00e+01 1.00e-02 9.25e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 131.80 -38.80 1 1.00e+01 1.00e-02 2.12e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -160.07 -19.93 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 5324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 755 0.025 - 0.050: 346 0.050 - 0.076: 142 0.076 - 0.101: 61 0.101 - 0.126: 44 Chirality restraints: 1348 Sorted by residual: chirality pdb=" CA VAL N 110 " pdb=" N VAL N 110 " pdb=" C VAL N 110 " pdb=" CB VAL N 110 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA TYR R 145 " pdb=" N TYR R 145 " pdb=" C TYR R 145 " pdb=" CB TYR R 145 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 1345 not shown) Planarity restraints: 1562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS R 81 " 0.040 5.00e-02 4.00e+02 6.05e-02 5.87e+00 pdb=" N PRO R 82 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO R 82 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 82 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 274 " -0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO R 275 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO R 275 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO R 275 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 327 " 0.038 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO A 328 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 328 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 328 " 0.032 5.00e-02 4.00e+02 ... (remaining 1559 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 553 2.74 - 3.28: 8226 3.28 - 3.82: 13185 3.82 - 4.36: 15566 4.36 - 4.90: 28274 Nonbonded interactions: 65804 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.199 2.440 nonbonded pdb=" NH1 ARG A 38 " pdb=" O GLU R 260 " model vdw 2.254 2.520 nonbonded pdb=" O ARG B 22 " pdb=" NE2 GLN B 259 " model vdw 2.260 2.520 nonbonded pdb=" OG1 THR B 221 " pdb=" OE2 GLU G 22 " model vdw 2.286 2.440 nonbonded pdb=" NH2 ARG R 201 " pdb=" OE1 GLN R 293 " model vdw 2.298 2.520 ... (remaining 65799 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 1.830 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: 7.290 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.700 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 : 0.002 0.037 9028 Z= 0.162 Angle : 0.598 6.000 12223 Z= 0.367 Chirality : 0.040 0.126 1348 Planarity : 0.004 0.061 1562 Dihedral : 12.459 88.360 3232 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: 0.07 (0.25), residues: 1091 helix: 1.36 (0.26), residues: 425 sheet: 0.43 (0.35), residues: 218 loop : -1.48 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.009 0.001 HIS A 220 PHE 0.014 0.001 PHE N 108 TYR 0.014 0.001 TYR R 145 ARG 0.006 0.000 ARG R 201 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.969 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 1.2722 time to fit residues: 155.7996 Evaluate side-chains 91 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.0030 chunk 62 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 237 ASN R 131 GLN R 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9028 Z= 0.159 Angle : 0.527 7.330 12223 Z= 0.285 Chirality : 0.041 0.139 1348 Planarity : 0.004 0.055 1562 Dihedral : 4.054 19.457 1213 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.59 % Allowed : 6.56 % Favored : 91.85 % 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: 0.33 (0.25), residues: 1091 helix: 1.74 (0.26), residues: 429 sheet: 0.40 (0.34), residues: 220 loop : -1.44 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.009 0.001 HIS A 220 PHE 0.016 0.001 PHE N 108 TYR 0.029 0.001 TYR R 145 ARG 0.005 0.000 ARG R 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.985 Fit side-chains REVERT: B 152 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8090 (tt) REVERT: N 3 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.7187 (tt0) REVERT: R 419 ARG cc_start: 0.6481 (ttp-170) cc_final: 0.6127 (tpp-160) outliers start: 15 outliers final: 7 residues processed: 103 average time/residue: 1.2278 time to fit residues: 135.3149 Evaluate side-chains 91 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 78 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 105 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9028 Z= 0.158 Angle : 0.503 6.586 12223 Z= 0.271 Chirality : 0.040 0.133 1348 Planarity : 0.004 0.051 1562 Dihedral : 4.080 20.186 1213 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.43 % Allowed : 8.36 % Favored : 89.21 % 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: 0.50 (0.25), residues: 1091 helix: 1.96 (0.26), residues: 424 sheet: 0.46 (0.34), residues: 223 loop : -1.39 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.007 0.001 HIS A 220 PHE 0.019 0.001 PHE R 289 TYR 0.027 0.001 TYR R 145 ARG 0.005 0.000 ARG R 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 1.024 Fit side-chains REVERT: A 317 ARG cc_start: 0.7221 (mtm-85) cc_final: 0.6976 (mtm-85) REVERT: B 152 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8080 (tt) REVERT: R 334 ARG cc_start: 0.6246 (OUTLIER) cc_final: 0.5180 (ttm170) REVERT: R 419 ARG cc_start: 0.6570 (ttp-170) cc_final: 0.6183 (tpp-160) outliers start: 23 outliers final: 9 residues processed: 107 average time/residue: 1.1659 time to fit residues: 134.1301 Evaluate side-chains 96 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 334 ARG Chi-restraints excluded: chain R residue 403 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/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-5322/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-5322/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-5322/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-5322/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-5322/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/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-5322/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-5322/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-5322/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: 60.554 > 50: distance: 56 - 114: 25.554 distance: 59 - 111: 6.361 distance: 72 - 95: 4.032 distance: 88 - 92: 11.591 distance: 92 - 93: 9.537 distance: 93 - 94: 9.368 distance: 93 - 96: 9.493 distance: 94 - 95: 11.567 distance: 96 - 97: 5.856 distance: 97 - 98: 4.922 distance: 98 - 99: 5.971 distance: 99 - 100: 7.578 distance: 100 - 101: 4.355 distance: 103 - 104: 5.809 distance: 104 - 105: 7.800 distance: 104 - 107: 9.677 distance: 105 - 106: 11.863 distance: 105 - 111: 13.093 distance: 106 - 180: 13.170 distance: 107 - 108: 17.166 distance: 108 - 109: 6.492 distance: 108 - 110: 11.242 distance: 111 - 112: 11.552 distance: 112 - 113: 19.612 distance: 112 - 115: 19.991 distance: 113 - 114: 14.865 distance: 113 - 122: 6.586 distance: 115 - 116: 14.667 distance: 116 - 117: 13.889 distance: 116 - 118: 3.413 distance: 117 - 119: 22.187 distance: 118 - 120: 11.993 distance: 119 - 121: 13.143 distance: 120 - 121: 7.227 distance: 122 - 123: 12.495 distance: 122 - 165: 29.520 distance: 123 - 124: 20.368 distance: 123 - 126: 38.294 distance: 124 - 125: 7.026 distance: 124 - 130: 8.064 distance: 126 - 127: 26.852 distance: 127 - 128: 29.376 distance: 127 - 129: 26.056 distance: 130 - 131: 32.050 distance: 131 - 132: 32.936 distance: 131 - 134: 19.374 distance: 132 - 133: 42.208 distance: 132 - 138: 27.962 distance: 134 - 135: 10.567 distance: 135 - 136: 38.135 distance: 135 - 137: 41.346 distance: 138 - 139: 15.516 distance: 139 - 140: 9.570 distance: 139 - 142: 24.936 distance: 140 - 141: 30.691 distance: 140 - 149: 34.887 distance: 142 - 143: 18.488 distance: 143 - 144: 19.133 distance: 144 - 145: 8.925 distance: 146 - 147: 6.453 distance: 149 - 150: 53.932 distance: 150 - 151: 28.853 distance: 150 - 153: 6.150 distance: 151 - 152: 21.888 distance: 151 - 154: 10.160 distance: 154 - 155: 15.299 distance: 155 - 156: 24.311 distance: 155 - 158: 34.955 distance: 156 - 157: 34.696 distance: 156 - 162: 11.994 distance: 158 - 159: 15.966 distance: 159 - 160: 36.278 distance: 159 - 161: 3.883 distance: 162 - 163: 16.746 distance: 163 - 164: 13.443 distance: 163 - 166: 5.260 distance: 164 - 165: 11.920 distance: 164 - 171: 5.781 distance: 166 - 167: 21.131 distance: 167 - 168: 29.625 distance: 168 - 169: 16.422 distance: 168 - 170: 23.574 distance: 171 - 172: 12.846 distance: 172 - 173: 12.822 distance: 172 - 175: 11.528 distance: 173 - 174: 13.839 distance: 173 - 180: 10.266 distance: 175 - 176: 21.283 distance: 176 - 177: 19.210 distance: 177 - 178: 12.193 distance: 177 - 179: 19.522