Starting phenix.real_space_refine (version: dev) on Mon Apr 4 21:17:40 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyo_26190/04_2022/7tyo_26190_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyo_26190/04_2022/7tyo_26190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyo_26190/04_2022/7tyo_26190.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyo_26190/04_2022/7tyo_26190.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyo_26190/04_2022/7tyo_26190_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyo_26190/04_2022/7tyo_26190_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.006 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 16": "OE1" <-> "OE2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "R GLU 204": "OE1" <-> "OE2" Residue "R ARG 258": "NH1" <-> "NH2" Residue "R ARG 321": "NH1" <-> "NH2" Residue "R ARG 362": "NH1" <-> "NH2" Residue "R GLU 397": "OE1" <-> "OE2" Residue "R ARG 404": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 9052 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1889 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "P" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 239 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1, 'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29, 'NH2_CTERM': 1} Chain: "R" Number of atoms: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2921 Unusual residues: {'Y01': 2, 'NAG': 1} Classifications: {'undetermined': 3, 'peptide': 359} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 14, 'TRANS': 344, None: 3} Not linked: pdbres="PHE R 409 " pdbres="NAG R 501 " Not linked: pdbres="NAG R 501 " pdbres="Y01 R 502 " Not linked: pdbres="Y01 R 502 " pdbres="Y01 R 503 " Chain breaks: 2 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 97 Time building chain proxies: 5.62, per 1000 atoms: 0.62 Number of scatterers: 9052 At special positions: 0 Unit cell: (116.086, 100.547, 140.766, 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 64 16.00 O 1646 8.00 N 1561 7.00 C 5781 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS P 1 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.04 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 Links applied NAG-ASN " NAG R 501 " - " ASN R 130 " Time building additional restraints: 3.63 Conformation dependent library (CDL) restraints added in 1.5 seconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 11 sheets defined 36.7% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.526A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.710A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.507A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 4 through 25 removed outlier: 4.068A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 30 through 43 removed outlier: 3.516A pdb=" N TYR G 40 " --> pdb=" O ASP G 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'P' and resid 8 through 19 removed outlier: 3.556A pdb=" N LYS P 18 " --> pdb=" O GLN P 14 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE P 19 " --> pdb=" O ASP P 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 59 Processing helix chain 'R' and resid 141 through 172 Processing helix chain 'R' and resid 174 through 176 No H-bonds generated for 'chain 'R' and resid 174 through 176' Processing helix chain 'R' and resid 179 through 204 removed outlier: 3.671A pdb=" N LEU R 183 " --> pdb=" O GLN R 179 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE R 199 " --> pdb=" O SER R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 214 Processing helix chain 'R' and resid 217 through 248 removed outlier: 3.666A pdb=" N MET R 237 " --> pdb=" O ASN R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 266 Processing helix chain 'R' and resid 269 through 283 Proline residue: R 273 - end of helix removed outlier: 3.773A pdb=" N ILE R 276 " --> pdb=" O PRO R 273 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA R 278 " --> pdb=" O THR R 275 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE R 279 " --> pdb=" O ILE R 276 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG R 281 " --> pdb=" O ALA R 278 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL R 283 " --> pdb=" O THR R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 290 No H-bonds generated for 'chain 'R' and resid 288 through 290' Processing helix chain 'R' and resid 297 through 328 removed outlier: 3.922A pdb=" N HIS R 302 " --> pdb=" O TYR R 299 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY R 303 " --> pdb=" O ILE R 300 " (cutoff:3.500A) Proline residue: R 304 - end of helix removed outlier: 3.710A pdb=" N LEU R 317 " --> pdb=" O PHE R 314 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE R 319 " --> pdb=" O LEU R 316 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL R 320 " --> pdb=" O LEU R 317 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU R 323 " --> pdb=" O VAL R 320 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL R 324 " --> pdb=" O ARG R 321 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS R 326 " --> pdb=" O LEU R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 334 through 352 removed outlier: 4.353A pdb=" N LEU R 339 " --> pdb=" O SER R 335 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL R 342 " --> pdb=" O TYR R 338 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS R 343 " --> pdb=" O LEU R 339 " (cutoff:3.500A) Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 358 removed outlier: 3.993A pdb=" N VAL R 358 " --> pdb=" O GLN R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 368 through 381 Processing helix chain 'R' and resid 383 through 391 Processing helix chain 'R' and resid 396 through 408 removed outlier: 3.526A pdb=" N THR R 401 " --> pdb=" O GLU R 397 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG R 404 " --> pdb=" O THR R 400 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA R 407 " --> pdb=" O LYS R 403 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.245A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.993A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.699A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.642A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.826A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.503A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.578A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.551A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.061A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 75 through 77 removed outlier: 3.651A pdb=" N THR R 75 " --> pdb=" O TRP R 82 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TRP R 82 " --> pdb=" O THR R 75 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU R 80 " --> pdb=" O ASP R 77 " (cutoff:3.500A) 377 hydrogen bonds defined for protein. 1014 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: 3.02 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1454 1.32 - 1.44: 2621 1.44 - 1.57: 5100 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 9265 Sorted by residual: bond pdb=" N LYS A 280 " pdb=" CA LYS A 280 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.27e-02 6.20e+03 6.96e+00 bond pdb=" N THR A 285 " pdb=" CA THR A 285 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.22e-02 6.72e+03 5.00e+00 bond pdb=" N ASP A 284 " pdb=" CA ASP A 284 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.16e-02 7.43e+03 4.80e+00 bond pdb=" N LYS A 271 " pdb=" CA LYS A 271 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.23e-02 6.61e+03 4.23e+00 bond pdb=" C VAL R 206 " pdb=" N PRO R 207 " ideal model delta sigma weight residual 1.335 1.353 -0.018 9.40e-03 1.13e+04 3.79e+00 ... (remaining 9260 not shown) Histogram of bond angle deviations from ideal: 99.62 - 106.50: 232 106.50 - 113.38: 4992 113.38 - 120.26: 3361 120.26 - 127.14: 3884 127.14 - 134.02: 108 Bond angle restraints: 12577 Sorted by residual: angle pdb=" CA PRO P 32 " pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 112.00 105.03 6.97 1.40e+00 5.10e-01 2.48e+01 angle pdb=" CA ASP A 274 " pdb=" C ASP A 274 " pdb=" O ASP A 274 " ideal model delta sigma weight residual 120.82 117.05 3.77 1.05e+00 9.07e-01 1.29e+01 angle pdb=" N VAL R 357 " pdb=" CA VAL R 357 " pdb=" C VAL R 357 " ideal model delta sigma weight residual 112.96 109.57 3.39 1.00e+00 1.00e+00 1.15e+01 angle pdb=" C ILE R 248 " pdb=" N VAL R 249 " pdb=" CA VAL R 249 " ideal model delta sigma weight residual 122.97 120.20 2.77 9.80e-01 1.04e+00 7.99e+00 angle pdb=" N ALA A 226 " pdb=" CA ALA A 226 " pdb=" C ALA A 226 " ideal model delta sigma weight residual 109.39 113.75 -4.36 1.59e+00 3.96e-01 7.53e+00 ... (remaining 12572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5049 17.91 - 35.81: 316 35.81 - 53.72: 73 53.72 - 71.63: 14 71.63 - 89.53: 7 Dihedral angle restraints: 5459 sinusoidal: 2135 harmonic: 3324 Sorted by residual: dihedral pdb=" CB CYS P 1 " pdb=" SG CYS P 1 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual 93.00 50.74 42.26 1 1.00e+01 1.00e-02 2.49e+01 dihedral pdb=" CB CYS R 219 " pdb=" SG CYS R 219 " pdb=" SG CYS R 289 " pdb=" CB CYS R 289 " ideal model delta sinusoidal sigma weight residual 93.00 53.76 39.24 1 1.00e+01 1.00e-02 2.16e+01 dihedral pdb=" CB CYS R 55 " pdb=" SG CYS R 55 " pdb=" SG CYS R 81 " pdb=" CB CYS R 81 " ideal model delta sinusoidal sigma weight residual -86.00 -121.65 35.65 1 1.00e+01 1.00e-02 1.80e+01 ... (remaining 5456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1101 0.044 - 0.089: 232 0.089 - 0.133: 63 0.133 - 0.177: 4 0.177 - 0.222: 1 Chirality restraints: 1401 Sorted by residual: chirality pdb=" CBE Y01 R 503 " pdb=" CAP Y01 R 503 " pdb=" CBB Y01 R 503 " pdb=" CBI Y01 R 503 " both_signs ideal model delta sigma weight residual False 2.57 2.35 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA LYS A 280 " pdb=" N LYS A 280 " pdb=" C LYS A 280 " pdb=" CB LYS A 280 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA PRO P 32 " pdb=" N PRO P 32 " pdb=" C PRO P 32 " pdb=" CB PRO P 32 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.07e-01 ... (remaining 1398 not shown) Planarity restraints: 1595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA P 31 " -0.082 5.00e-02 4.00e+02 1.20e-01 2.32e+01 pdb=" N PRO P 32 " 0.208 5.00e-02 4.00e+02 pdb=" CA PRO P 32 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO P 32 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 138 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO R 139 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO R 139 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 139 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.023 5.00e-02 4.00e+02 3.55e-02 2.01e+00 pdb=" N PRO B 236 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.020 5.00e-02 4.00e+02 ... (remaining 1592 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 289 2.72 - 3.27: 9140 3.27 - 3.81: 14641 3.81 - 4.36: 19346 4.36 - 4.90: 31762 Nonbonded interactions: 75178 Sorted by model distance: nonbonded pdb=" OH TYR P 12 " pdb=" O ALA R 145 " model vdw 2.176 2.440 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.236 2.440 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.294 2.440 nonbonded pdb=" OH TYR R 149 " pdb=" O LEU R 202 " model vdw 2.294 2.440 nonbonded pdb=" O PRO R 270 " pdb=" OG1 THR R 274 " model vdw 2.306 2.440 ... (remaining 75173 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5781 2.51 5 N 1561 2.21 5 O 1646 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.620 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: 4.440 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.090 Process input model: 27.390 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 0.034 9265 Z= 0.129 Angle : 0.463 6.965 12577 Z= 0.287 Chirality : 0.039 0.222 1401 Planarity : 0.004 0.120 1594 Dihedral : 12.827 89.532 3290 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 1.37 % 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: -3.13 (0.21), residues: 1121 helix: -2.90 (0.16), residues: 427 sheet: -0.61 (0.31), residues: 239 loop : -1.84 (0.27), residues: 455 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 1.079 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 169 average time/residue: 1.3476 time to fit residues: 241.6475 Evaluate side-chains 119 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 1.073 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 1.1133 time to fit residues: 2.7129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 31 GLN A 294 GLN B 17 GLN B 36 ASN B 75 GLN G 24 ASN N 5 GLN N 13 GLN P 14 GLN R 135 ASN R 144 ASN R 179 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 9265 Z= 0.219 Angle : 0.568 10.485 12577 Z= 0.304 Chirality : 0.042 0.196 1401 Planarity : 0.005 0.060 1594 Dihedral : 4.656 51.228 1271 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 4.23 % 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: -1.13 (0.24), residues: 1121 helix: -0.27 (0.23), residues: 431 sheet: -0.38 (0.31), residues: 242 loop : -1.30 (0.29), residues: 448 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 119 time to evaluate : 1.180 Fit side-chains outliers start: 40 outliers final: 18 residues processed: 145 average time/residue: 1.2163 time to fit residues: 188.5236 Evaluate side-chains 128 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.054 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.5845 time to fit residues: 4.0790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 89 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 24 GLN R 135 ASN R 179 GLN R 405 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.089 9265 Z= 0.208 Angle : 0.538 11.881 12577 Z= 0.284 Chirality : 0.041 0.189 1401 Planarity : 0.004 0.056 1594 Dihedral : 4.693 54.181 1271 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 3.91 % 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: -0.44 (0.24), residues: 1121 helix: 0.61 (0.25), residues: 433 sheet: 0.04 (0.33), residues: 215 loop : -1.26 (0.27), residues: 473 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 117 time to evaluate : 1.059 Fit side-chains outliers start: 37 outliers final: 21 residues processed: 141 average time/residue: 1.1821 time to fit residues: 178.4062 Evaluate side-chains 131 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 17 residues processed: 4 average time/residue: 0.6231 time to fit residues: 4.2865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.082 9265 Z= 0.344 Angle : 0.665 8.964 12577 Z= 0.351 Chirality : 0.047 0.269 1401 Planarity : 0.005 0.067 1594 Dihedral : 5.413 50.921 1271 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 5.29 % 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: -0.57 (0.24), residues: 1121 helix: 0.44 (0.25), residues: 433 sheet: 0.05 (0.33), residues: 212 loop : -1.31 (0.27), residues: 476 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 108 time to evaluate : 1.171 Fit side-chains outliers start: 50 outliers final: 27 residues processed: 142 average time/residue: 1.2510 time to fit residues: 190.4522 Evaluate side-chains 134 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 21 residues processed: 6 average time/residue: 0.6307 time to fit residues: 5.7323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 30.0000 chunk 44 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.0000 chunk 0 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.120 9265 Z= 0.283 Angle : 0.596 12.251 12577 Z= 0.317 Chirality : 0.044 0.228 1401 Planarity : 0.005 0.120 1594 Dihedral : 5.281 54.730 1271 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 4.86 % 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: -0.34 (0.25), residues: 1121 helix: 0.68 (0.26), residues: 432 sheet: 0.12 (0.33), residues: 211 loop : -1.19 (0.27), residues: 478 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 110 time to evaluate : 1.108 Fit side-chains outliers start: 46 outliers final: 26 residues processed: 141 average time/residue: 1.1968 time to fit residues: 180.8567 Evaluate side-chains 130 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 1.072 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 20 residues processed: 6 average time/residue: 1.0092 time to fit residues: 7.9411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 0.0770 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 103 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN R 405 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.167 9265 Z= 0.212 Angle : 0.526 13.226 12577 Z= 0.279 Chirality : 0.040 0.183 1401 Planarity : 0.003 0.045 1594 Dihedral : 4.835 59.279 1271 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer Outliers : 3.38 % 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: 0.14 (0.25), residues: 1121 helix: 1.16 (0.26), residues: 433 sheet: 0.33 (0.33), residues: 212 loop : -0.99 (0.28), residues: 476 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 112 time to evaluate : 1.102 Fit side-chains outliers start: 32 outliers final: 19 residues processed: 136 average time/residue: 1.1710 time to fit residues: 170.8314 Evaluate side-chains 123 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 0.0815 time to fit residues: 1.6376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 63 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.238 9265 Z= 0.279 Angle : 0.540 16.451 12577 Z= 0.294 Chirality : 0.040 0.183 1401 Planarity : 0.004 0.116 1594 Dihedral : 4.697 59.555 1271 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer Outliers : 3.38 % 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: 0.41 (0.25), residues: 1121 helix: 1.38 (0.26), residues: 432 sheet: 0.46 (0.34), residues: 212 loop : -0.83 (0.28), residues: 477 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 106 time to evaluate : 1.114 Fit side-chains outliers start: 32 outliers final: 22 residues processed: 126 average time/residue: 1.1502 time to fit residues: 155.5082 Evaluate side-chains 122 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 17 residues processed: 5 average time/residue: 1.2253 time to fit residues: 7.9481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 97 optimal weight: 0.0040 chunk 102 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 405 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.126 9265 Z= 0.211 Angle : 0.556 12.655 12577 Z= 0.295 Chirality : 0.041 0.188 1401 Planarity : 0.005 0.127 1594 Dihedral : 4.774 54.406 1271 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.25), residues: 1121 helix: 1.38 (0.26), residues: 433 sheet: 0.44 (0.34), residues: 215 loop : -0.85 (0.28), residues: 473 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 0.962 Fit side-chains outliers start: 25 outliers final: 19 residues processed: 125 average time/residue: 1.2332 time to fit residues: 165.0306 Evaluate side-chains 120 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 1.085 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 2 average time/residue: 0.9118 time to fit residues: 3.4646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 105 optimal weight: 0.4980 chunk 64 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.146 9265 Z= 0.236 Angle : 0.570 14.324 12577 Z= 0.307 Chirality : 0.042 0.190 1401 Planarity : 0.005 0.135 1594 Dihedral : 4.764 46.461 1271 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 2.96 % 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: 0.39 (0.25), residues: 1121 helix: 1.34 (0.26), residues: 433 sheet: 0.43 (0.33), residues: 215 loop : -0.82 (0.28), residues: 473 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 103 time to evaluate : 1.117 Fit side-chains outliers start: 28 outliers final: 19 residues processed: 125 average time/residue: 1.2893 time to fit residues: 172.5060 Evaluate side-chains 119 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 2.2434 time to fit residues: 3.7410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 405 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 1.015 9265 Z= 1.008 Angle : 0.844 40.941 12577 Z= 0.463 Chirality : 0.045 0.258 1401 Planarity : 0.006 0.145 1594 Dihedral : 4.949 32.576 1271 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.09 % 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: 0.10 (0.25), residues: 1121 helix: 1.06 (0.26), residues: 432 sheet: 0.34 (0.34), residues: 213 loop : -0.94 (0.28), residues: 476 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 1.102 Fit side-chains outliers start: 25 outliers final: 18 residues processed: 123 average time/residue: 1.2743 time to fit residues: 167.4391 Evaluate side-chains 119 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 1.161 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 1 average time/residue: 2.2107 time to fit residues: 3.8066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.163499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.125590 restraints weight = 10843.278| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.79 r_work: 0.3481 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 1.58 restraints_weight: 0.2500 r_work: 0.3446 rms_B_bonded: 1.70 restraints_weight: 0.1250 r_work: 0.3424 rms_B_bonded: 1.91 restraints_weight: 0.0625 r_work: 0.3399 rms_B_bonded: 2.23 restraints_weight: 0.0312 r_work: 0.3367 rms_B_bonded: 2.68 restraints_weight: 0.0156 r_work: 0.3328 rms_B_bonded: 3.31 restraints_weight: 0.0078 r_work: 0.3279 rms_B_bonded: 4.19 restraints_weight: 0.0039 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.660 9265 Z= 0.768 Angle : 0.761 29.023 12577 Z= 0.420 Chirality : 0.045 0.252 1401 Planarity : 0.006 0.146 1594 Dihedral : 4.949 33.250 1271 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.09 % 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: -0.03 (0.25), residues: 1121 helix: 0.94 (0.26), residues: 432 sheet: 0.21 (0.34), residues: 215 loop : -0.98 (0.28), residues: 474 =============================================================================== Job complete usr+sys time: 3227.01 seconds wall clock time: 58 minutes 4.91 seconds (3484.91 seconds total)