Starting phenix.real_space_refine (version: dev) on Mon Feb 20 02:25:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgz_10191/02_2023/6sgz_10191.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgz_10191/02_2023/6sgz_10191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgz_10191/02_2023/6sgz_10191.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgz_10191/02_2023/6sgz_10191.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgz_10191/02_2023/6sgz_10191.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgz_10191/02_2023/6sgz_10191.pdb" } resolution = 3.9 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= 0.004 sd= 0.119 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 Process input model Symmetric amino acids flipped Residue "E ASP 20": "OD1" <-> "OD2" Residue "E ARG 23": "NH1" <-> "NH2" Residue "E ARG 36": "NH1" <-> "NH2" Residue "E GLU 37": "OE1" <-> "OE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 66": "NH1" <-> "NH2" Residue "E ASP 80": "OD1" <-> "OD2" Residue "E ARG 107": "NH1" <-> "NH2" Residue "E ASP 114": "OD1" <-> "OD2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E ARG 124": "NH1" <-> "NH2" Residue "E ASP 238": "OD1" <-> "OD2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "E ARG 375": "NH1" <-> "NH2" Residue "E ARG 406": "NH1" <-> "NH2" Residue "E ASP 455": "OD1" <-> "OD2" Residue "E PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 36": "NH1" <-> "NH2" Residue "H ARG 44": "NH1" <-> "NH2" Residue "H ARG 107": "NH1" <-> "NH2" Residue "H ARG 312": "NH1" <-> "NH2" Residue "H ARG 325": "NH1" <-> "NH2" Residue "H ARG 406": "NH1" <-> "NH2" Residue "J ARG 10": "NH1" <-> "NH2" Residue "J GLU 25": "OE1" <-> "OE2" Residue "J ASP 113": "OD1" <-> "OD2" Residue "J GLU 127": "OE1" <-> "OE2" Residue "J GLU 132": "OE1" <-> "OE2" Residue "J ARG 143": "NH1" <-> "NH2" Residue "J ARG 148": "NH1" <-> "NH2" Residue "J ASP 154": "OD1" <-> "OD2" Residue "J ARG 159": "NH1" <-> "NH2" Residue "J ARG 162": "NH1" <-> "NH2" Residue "J ARG 191": "NH1" <-> "NH2" Residue "J ASP 202": "OD1" <-> "OD2" Residue "J ASP 208": "OD1" <-> "OD2" Residue "J TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 291": "OE1" <-> "OE2" Residue "J ASP 324": "OD1" <-> "OD2" Residue "J ARG 369": "NH1" <-> "NH2" Residue "D ARG 4": "NH1" <-> "NH2" Residue "D ARG 61": "NH1" <-> "NH2" Residue "D ARG 64": "NH1" <-> "NH2" Residue "D ARG 112": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 160": "NH1" <-> "NH2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D ASP 173": "OD1" <-> "OD2" Residue "D ARG 242": "NH1" <-> "NH2" Residue "D ARG 264": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 11177 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 3120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3120 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 24, 'TRANS': 410} Chain breaks: 2 Chain: "H" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3168 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 27, 'TRANS': 414} Chain breaks: 3 Chain: "I" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 461 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "J" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2603 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 26, 'TRANS': 301} Chain breaks: 4 Chain: "D" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1825 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 16, 'TRANS': 224} Chain breaks: 7 Time building chain proxies: 6.66, per 1000 atoms: 0.60 Number of scatterers: 11177 At special positions: 0 Unit cell: (132.938, 116.985, 101.033, 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 29 16.00 O 1980 8.00 N 1997 7.00 C 7171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.71 Conformation dependent library (CDL) restraints added in 1.7 seconds 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2804 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 6 sheets defined 58.9% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'E' and resid 34 through 47 removed outlier: 3.660A pdb=" N ILE E 38 " --> pdb=" O PRO E 34 " (cutoff:3.500A) Proline residue: E 40 - end of helix Processing helix chain 'E' and resid 82 through 87 removed outlier: 3.631A pdb=" N GLY E 87 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 119 Processing helix chain 'E' and resid 127 through 158 removed outlier: 3.748A pdb=" N HIS E 131 " --> pdb=" O TRP E 127 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE E 132 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ALA E 133 " --> pdb=" O PRO E 129 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG E 134 " --> pdb=" O THR E 130 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 181 removed outlier: 4.230A pdb=" N GLN E 164 " --> pdb=" O ASP E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'E' and resid 196 through 204 removed outlier: 3.522A pdb=" N ALA E 201 " --> pdb=" O LEU E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 233 removed outlier: 3.562A pdb=" N ALA E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 264 removed outlier: 3.656A pdb=" N PHE E 244 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU E 255 " --> pdb=" O GLY E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 285 removed outlier: 4.157A pdb=" N CYS E 273 " --> pdb=" O ASP E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 293 removed outlier: 3.610A pdb=" N TRP E 293 " --> pdb=" O LEU E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 296 No H-bonds generated for 'chain 'E' and resid 294 through 296' Processing helix chain 'E' and resid 319 through 350 removed outlier: 3.715A pdb=" N ARG E 323 " --> pdb=" O ASP E 319 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA E 336 " --> pdb=" O THR E 332 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY E 342 " --> pdb=" O GLY E 338 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER E 346 " --> pdb=" O GLY E 342 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA E 348 " --> pdb=" O ALA E 344 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU E 349 " --> pdb=" O GLY E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 373 removed outlier: 3.819A pdb=" N TRP E 360 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL E 364 " --> pdb=" O TRP E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 378 removed outlier: 4.203A pdb=" N TRP E 377 " --> pdb=" O ARG E 373 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP E 378 " --> pdb=" O ALA E 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 373 through 378' Processing helix chain 'E' and resid 379 through 404 removed outlier: 4.833A pdb=" N SER E 390 " --> pdb=" O LEU E 386 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR E 391 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 430 Processing helix chain 'E' and resid 440 through 456 removed outlier: 4.309A pdb=" N ALA E 456 " --> pdb=" O THR E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 467 removed outlier: 4.313A pdb=" N VAL E 461 " --> pdb=" O SER E 457 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 37 removed outlier: 3.727A pdb=" N GLU H 37 " --> pdb=" O PRO H 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 34 through 37' Processing helix chain 'H' and resid 38 through 47 Processing helix chain 'H' and resid 82 through 87 Processing helix chain 'H' and resid 115 through 124 removed outlier: 3.533A pdb=" N PHE H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 159 removed outlier: 3.747A pdb=" N ARG H 134 " --> pdb=" O THR H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 179 removed outlier: 4.014A pdb=" N GLN H 164 " --> pdb=" O ASP H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 206 removed outlier: 3.652A pdb=" N LEU H 197 " --> pdb=" O ALA H 193 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL H 198 " --> pdb=" O VAL H 194 " (cutoff:3.500A) Proline residue: H 199 - end of helix Processing helix chain 'H' and resid 215 through 234 removed outlier: 3.609A pdb=" N GLY H 234 " --> pdb=" O ILE H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 264 removed outlier: 3.902A pdb=" N THR H 245 " --> pdb=" O ILE H 241 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA H 260 " --> pdb=" O LEU H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 285 removed outlier: 3.526A pdb=" N ILE H 271 " --> pdb=" O SER H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 294 removed outlier: 3.506A pdb=" N ALA H 294 " --> pdb=" O SER H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 345 Proline residue: H 321 - end of helix removed outlier: 4.093A pdb=" N ARG H 325 " --> pdb=" O PRO H 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 345 through 350 removed outlier: 3.932A pdb=" N VAL H 350 " --> pdb=" O SER H 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 373 removed outlier: 3.583A pdb=" N TRP H 360 " --> pdb=" O SER H 356 " (cutoff:3.500A) Processing helix chain 'H' and resid 374 through 376 No H-bonds generated for 'chain 'H' and resid 374 through 376' Processing helix chain 'H' and resid 379 through 404 removed outlier: 3.714A pdb=" N HIS H 389 " --> pdb=" O TRP H 385 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N SER H 390 " --> pdb=" O LEU H 386 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR H 391 " --> pdb=" O LEU H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 429 removed outlier: 3.702A pdb=" N TRP H 412 " --> pdb=" O GLN H 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 435 through 439 Processing helix chain 'H' and resid 440 through 467 removed outlier: 3.885A pdb=" N ASP H 455 " --> pdb=" O ALA H 451 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ILE H 459 " --> pdb=" O ASP H 455 " (cutoff:3.500A) Proline residue: H 460 - end of helix Processing helix chain 'H' and resid 468 through 471 Processing helix chain 'I' and resid 34 through 55 Processing helix chain 'I' and resid 62 through 90 Processing helix chain 'J' and resid 93 through 130 removed outlier: 3.546A pdb=" N VAL J 97 " --> pdb=" O ARG J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 139 removed outlier: 3.775A pdb=" N ALA J 137 " --> pdb=" O GLU J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 197 removed outlier: 4.025A pdb=" N LEU J 190 " --> pdb=" O ALA J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 212 No H-bonds generated for 'chain 'J' and resid 210 through 212' Processing helix chain 'J' and resid 220 through 237 removed outlier: 4.305A pdb=" N ALA J 226 " --> pdb=" O ASP J 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 257 through 263 Processing helix chain 'J' and resid 285 through 294 Processing helix chain 'J' and resid 295 through 297 No H-bonds generated for 'chain 'J' and resid 295 through 297' Processing helix chain 'J' and resid 386 through 399 removed outlier: 4.080A pdb=" N ARG J 399 " --> pdb=" O ARG J 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 17 removed outlier: 3.571A pdb=" N LEU D 17 " --> pdb=" O VAL D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 38 Processing helix chain 'D' and resid 49 through 62 Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 89 through 95 Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.922A pdb=" N SER D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 163 Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'D' and resid 265 through 270 Processing sheet with id=AA1, first strand: chain 'E' and resid 67 through 71 removed outlier: 8.700A pdb=" N LEU E 94 " --> pdb=" O ARG E 11 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ALA E 13 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU E 96 " --> pdb=" O ALA E 13 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU E 15 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N ALA E 98 " --> pdb=" O LEU E 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 24 through 30 removed outlier: 8.577A pdb=" N LEU H 94 " --> pdb=" O ARG H 11 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA H 13 " --> pdb=" O LEU H 94 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LEU H 96 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU H 15 " --> pdb=" O LEU H 96 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N ALA H 98 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 23 through 24 removed outlier: 3.823A pdb=" N ILE J 24 " --> pdb=" O LYS J 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'J' and resid 157 through 165 removed outlier: 7.152A pdb=" N THR J 205 " --> pdb=" O ALA J 160 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG J 162 " --> pdb=" O ALA J 203 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ALA J 203 " --> pdb=" O ARG J 162 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASP J 164 " --> pdb=" O ARG J 201 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG J 201 " --> pdb=" O ASP J 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 244 through 249 removed outlier: 6.139A pdb=" N GLY J 245 " --> pdb=" O LEU J 315 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL J 317 " --> pdb=" O GLY J 245 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA J 247 " --> pdb=" O VAL J 317 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU J 314 " --> pdb=" O THR J 338 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE J 340 " --> pdb=" O LEU J 314 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL J 316 " --> pdb=" O ILE J 340 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ARG J 342 " --> pdb=" O VAL J 316 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU J 318 " --> pdb=" O ARG J 342 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LEU J 360 " --> pdb=" O ARG J 214 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR J 216 " --> pdb=" O LEU J 360 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL J 362 " --> pdb=" O THR J 216 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE J 218 " --> pdb=" O VAL J 362 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 167 through 168 removed outlier: 3.844A pdb=" N LYS D 106 " --> pdb=" O THR D 125 " (cutoff:3.500A) 654 hydrogen bonds defined for protein. 1920 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: 3.06 Time building geometry restraints manager: 5.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3727 1.34 - 1.46: 2139 1.46 - 1.58: 5473 1.58 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 11389 Sorted by residual: bond pdb=" CA ARG J 357 " pdb=" CB ARG J 357 " ideal model delta sigma weight residual 1.522 1.532 -0.010 8.90e-03 1.26e+04 1.26e+00 bond pdb=" CA VAL H 99 " pdb=" C VAL H 99 " ideal model delta sigma weight residual 1.526 1.535 -0.009 7.90e-03 1.60e+04 1.25e+00 bond pdb=" CB ASP E 378 " pdb=" CG ASP E 378 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.14e+00 bond pdb=" CB ASN E 354 " pdb=" CG ASN E 354 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.10e+00 bond pdb=" CA THR D 103 " pdb=" CB THR D 103 " ideal model delta sigma weight residual 1.527 1.544 -0.017 1.61e-02 3.86e+03 1.10e+00 ... (remaining 11384 not shown) Histogram of bond angle deviations from ideal: 99.05 - 106.07: 375 106.07 - 113.08: 6635 113.08 - 120.10: 3688 120.10 - 127.11: 4717 127.11 - 134.13: 183 Bond angle restraints: 15598 Sorted by residual: angle pdb=" N GLY J 256 " pdb=" CA GLY J 256 " pdb=" C GLY J 256 " ideal model delta sigma weight residual 115.42 111.22 4.20 1.27e+00 6.20e-01 1.09e+01 angle pdb=" CA TYR D 96 " pdb=" C TYR D 96 " pdb=" N LEU D 97 " ideal model delta sigma weight residual 118.27 123.38 -5.11 1.59e+00 3.96e-01 1.03e+01 angle pdb=" CA LEU D 278 " pdb=" CB LEU D 278 " pdb=" CG LEU D 278 " ideal model delta sigma weight residual 116.30 127.32 -11.02 3.50e+00 8.16e-02 9.91e+00 angle pdb=" N THR J 344 " pdb=" CA THR J 344 " pdb=" C THR J 344 " ideal model delta sigma weight residual 114.04 110.15 3.89 1.24e+00 6.50e-01 9.84e+00 angle pdb=" CA GLY J 256 " pdb=" C GLY J 256 " pdb=" N ASP J 257 " ideal model delta sigma weight residual 118.52 114.71 3.81 1.22e+00 6.72e-01 9.77e+00 ... (remaining 15593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 6208 17.86 - 35.72: 497 35.72 - 53.58: 87 53.58 - 71.44: 16 71.44 - 89.30: 6 Dihedral angle restraints: 6814 sinusoidal: 2511 harmonic: 4303 Sorted by residual: dihedral pdb=" CA ALA J 323 " pdb=" C ALA J 323 " pdb=" N ASP J 324 " pdb=" CA ASP J 324 " ideal model delta harmonic sigma weight residual 180.00 151.08 28.92 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA LEU J 297 " pdb=" C LEU J 297 " pdb=" N ALA J 298 " pdb=" CA ALA J 298 " ideal model delta harmonic sigma weight residual 180.00 155.05 24.95 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA VAL E 99 " pdb=" C VAL E 99 " pdb=" N PRO E 100 " pdb=" CA PRO E 100 " ideal model delta harmonic sigma weight residual -180.00 -156.15 -23.85 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 6811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1248 0.032 - 0.065: 472 0.065 - 0.097: 152 0.097 - 0.129: 58 0.129 - 0.161: 11 Chirality restraints: 1941 Sorted by residual: chirality pdb=" CA TRP J 231 " pdb=" N TRP J 231 " pdb=" C TRP J 231 " pdb=" CB TRP J 231 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CA THR D 103 " pdb=" N THR D 103 " pdb=" C THR D 103 " pdb=" CB THR D 103 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CB THR D 103 " pdb=" CA THR D 103 " pdb=" OG1 THR D 103 " pdb=" CG2 THR D 103 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.76e-01 ... (remaining 1938 not shown) Planarity restraints: 1969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL J 165 " -0.041 5.00e-02 4.00e+02 6.22e-02 6.18e+00 pdb=" N PRO J 166 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO J 166 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO J 166 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 298 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO E 299 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 299 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 299 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 269 " 0.031 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO J 270 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO J 270 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO J 270 " 0.026 5.00e-02 4.00e+02 ... (remaining 1966 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1297 2.74 - 3.28: 12184 3.28 - 3.82: 18136 3.82 - 4.36: 20059 4.36 - 4.90: 33731 Nonbonded interactions: 85407 Sorted by model distance: nonbonded pdb=" O VAL H 347 " pdb=" OG SER H 351 " model vdw 2.203 2.440 nonbonded pdb=" O ALA J 233 " pdb=" OG1 THR J 237 " model vdw 2.222 2.440 nonbonded pdb=" O ASN J 348 " pdb=" NH1 ARG J 349 " model vdw 2.228 2.520 nonbonded pdb=" O TRP J 128 " pdb=" NH2 ARG J 144 " model vdw 2.234 2.520 nonbonded pdb=" OD2 ASP J 240 " pdb=" OG SER J 402 " model vdw 2.243 2.440 ... (remaining 85402 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'E' and (resid 8 through 16 or resid 21 through 47 or resid 65 through 21 \ 1 or resid 214 through 471)) selection = (chain 'H' and (resid 8 through 299 or resid 315 through 471)) } 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 29 5.16 5 C 7171 2.51 5 N 1997 2.21 5 O 1980 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=0.91 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.530 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: 16.050 Check model and map are aligned: 0.160 Process input model: 31.540 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.120 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 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 : 0.003 0.036 11389 Z= 0.233 Angle : 0.696 11.017 15598 Z= 0.390 Chirality : 0.041 0.161 1941 Planarity : 0.005 0.062 1969 Dihedral : 13.522 89.299 4010 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.32 % Favored : 89.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.18), residues: 1463 helix: -1.82 (0.15), residues: 797 sheet: -3.10 (0.35), residues: 134 loop : -4.05 (0.23), residues: 532 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2589 time to fit residues: 81.5917 Evaluate side-chains 163 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.388 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 8.9990 chunk 112 optimal weight: 0.2980 chunk 62 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 GLN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 216 ASN H 331 GLN I 67 GLN J 187 HIS ** J 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 GLN D 162 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 11389 Z= 0.303 Angle : 0.713 9.787 15598 Z= 0.355 Chirality : 0.042 0.179 1941 Planarity : 0.005 0.064 1969 Dihedral : 4.897 26.961 1614 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.46 % Favored : 89.47 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.21), residues: 1463 helix: -0.29 (0.17), residues: 808 sheet: -2.61 (0.37), residues: 135 loop : -3.62 (0.25), residues: 520 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 181 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 20 residues processed: 201 average time/residue: 0.2269 time to fit residues: 65.8522 Evaluate side-chains 182 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 1.426 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1014 time to fit residues: 5.5611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 0.0000 chunk 134 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 overall best weight: 2.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 GLN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 408 GLN J 351 GLN ** J 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 11389 Z= 0.263 Angle : 0.682 9.556 15598 Z= 0.340 Chirality : 0.042 0.171 1941 Planarity : 0.005 0.061 1969 Dihedral : 4.824 26.766 1614 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.18 % Favored : 89.75 % Rotamer Outliers : 2.36 % 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: -1.69 (0.22), residues: 1463 helix: 0.42 (0.18), residues: 805 sheet: -2.19 (0.39), residues: 134 loop : -3.37 (0.25), residues: 524 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 180 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 11 residues processed: 198 average time/residue: 0.2218 time to fit residues: 63.1861 Evaluate side-chains 173 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 162 time to evaluate : 1.195 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0949 time to fit residues: 3.5039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 90 optimal weight: 0.4980 chunk 135 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 70 optimal weight: 0.0060 chunk 128 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 GLN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 371 GLN D 136 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11389 Z= 0.185 Angle : 0.667 10.957 15598 Z= 0.324 Chirality : 0.041 0.160 1941 Planarity : 0.005 0.054 1969 Dihedral : 4.559 23.393 1614 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.23 % Favored : 90.70 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.22), residues: 1463 helix: 0.83 (0.19), residues: 806 sheet: -1.83 (0.40), residues: 134 loop : -3.10 (0.26), residues: 523 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 198 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 11 residues processed: 214 average time/residue: 0.2163 time to fit residues: 67.5462 Evaluate side-chains 184 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 173 time to evaluate : 1.432 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1039 time to fit residues: 3.9127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 106 optimal weight: 0.4980 chunk 59 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 36 optimal weight: 0.6980 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 GLN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 ASN ** J 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 11389 Z= 0.282 Angle : 0.693 10.044 15598 Z= 0.342 Chirality : 0.042 0.170 1941 Planarity : 0.005 0.057 1969 Dihedral : 4.601 26.354 1614 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.53 % Favored : 89.41 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.23), residues: 1463 helix: 0.88 (0.19), residues: 805 sheet: -1.57 (0.42), residues: 134 loop : -3.03 (0.26), residues: 524 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 170 time to evaluate : 1.351 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 12 residues processed: 187 average time/residue: 0.2017 time to fit residues: 56.6546 Evaluate side-chains 171 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 159 time to evaluate : 1.409 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1046 time to fit residues: 4.1651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 GLN ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 331 GLN J 341 HIS D 136 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 11389 Z= 0.195 Angle : 0.668 9.884 15598 Z= 0.324 Chirality : 0.041 0.214 1941 Planarity : 0.004 0.053 1969 Dihedral : 4.426 24.359 1614 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.64 % Favored : 90.29 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.23), residues: 1463 helix: 1.03 (0.19), residues: 809 sheet: -1.30 (0.44), residues: 137 loop : -2.86 (0.27), residues: 517 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 188 time to evaluate : 1.349 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 6 residues processed: 204 average time/residue: 0.2033 time to fit residues: 63.2046 Evaluate side-chains 173 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 167 time to evaluate : 1.336 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1044 time to fit residues: 2.9888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 GLN E 216 ASN ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 331 GLN I 67 GLN D 131 ASN D 136 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 11389 Z= 0.217 Angle : 0.685 9.806 15598 Z= 0.331 Chirality : 0.042 0.199 1941 Planarity : 0.004 0.053 1969 Dihedral : 4.408 24.141 1614 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.71 % Favored : 90.23 % Rotamer Outliers : 1.48 % 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: -0.65 (0.23), residues: 1463 helix: 1.11 (0.19), residues: 806 sheet: -0.99 (0.46), residues: 128 loop : -2.81 (0.26), residues: 529 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 173 time to evaluate : 1.397 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 183 average time/residue: 0.1910 time to fit residues: 53.5140 Evaluate side-chains 179 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 169 time to evaluate : 1.276 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1014 time to fit residues: 3.7211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 0.0980 chunk 13 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 129 optimal weight: 0.0170 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 GLN E 216 ASN ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 331 GLN D 131 ASN D 136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 11389 Z= 0.186 Angle : 0.691 9.646 15598 Z= 0.332 Chirality : 0.041 0.193 1941 Planarity : 0.004 0.052 1969 Dihedral : 4.316 23.319 1614 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.43 % Favored : 90.50 % Rotamer Outliers : 0.87 % 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: -0.51 (0.23), residues: 1463 helix: 1.18 (0.19), residues: 808 sheet: -0.84 (0.48), residues: 128 loop : -2.73 (0.27), residues: 527 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 183 time to evaluate : 1.330 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 191 average time/residue: 0.1886 time to fit residues: 55.1842 Evaluate side-chains 175 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 171 time to evaluate : 1.347 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1132 time to fit residues: 2.6254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 80 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 120 optimal weight: 0.0170 chunk 125 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 overall best weight: 1.1024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 GLN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 331 GLN J 163 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 11389 Z= 0.205 Angle : 0.695 9.725 15598 Z= 0.335 Chirality : 0.042 0.227 1941 Planarity : 0.004 0.051 1969 Dihedral : 4.279 22.987 1614 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.23 % Favored : 90.70 % Rotamer Outliers : 0.70 % 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 (0.23), residues: 1463 helix: 1.22 (0.19), residues: 807 sheet: -0.74 (0.47), residues: 128 loop : -2.68 (0.27), residues: 528 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 176 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 180 average time/residue: 0.2030 time to fit residues: 55.4810 Evaluate side-chains 175 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 170 time to evaluate : 1.324 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1148 time to fit residues: 2.7412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 135 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 12 optimal weight: 0.0020 chunk 90 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 93 optimal weight: 0.0570 chunk 125 optimal weight: 8.9990 overall best weight: 0.4906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 331 GLN D 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 11389 Z= 0.192 Angle : 0.704 9.426 15598 Z= 0.337 Chirality : 0.042 0.204 1941 Planarity : 0.004 0.050 1969 Dihedral : 4.206 22.446 1614 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.30 % Favored : 90.64 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.23), residues: 1463 helix: 1.27 (0.19), residues: 804 sheet: -0.64 (0.48), residues: 128 loop : -2.66 (0.27), residues: 531 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 183 time to evaluate : 1.489 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 185 average time/residue: 0.2224 time to fit residues: 62.1821 Evaluate side-chains 174 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 172 time to evaluate : 1.352 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1055 time to fit residues: 2.1556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 120 optimal weight: 0.0040 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 GLN ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 331 GLN D 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.086063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.070967 restraints weight = 35732.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.073077 restraints weight = 17792.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.074489 restraints weight = 11156.473| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 11389 Z= 0.213 Angle : 0.704 9.424 15598 Z= 0.340 Chirality : 0.042 0.204 1941 Planarity : 0.005 0.050 1969 Dihedral : 4.197 21.898 1614 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.36 % Favored : 90.57 % Rotamer Outliers : 0.26 % 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 (0.23), residues: 1463 helix: 1.26 (0.19), residues: 808 sheet: -0.67 (0.48), residues: 125 loop : -2.57 (0.27), residues: 530 =============================================================================== Job complete usr+sys time: 2186.64 seconds wall clock time: 40 minutes 50.36 seconds (2450.36 seconds total)