Starting phenix.real_space_refine (version: dev) on Tue Dec 13 05:34:13 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cet_7465/12_2022/6cet_7465.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cet_7465/12_2022/6cet_7465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cet_7465/12_2022/6cet_7465.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cet_7465/12_2022/6cet_7465.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cet_7465/12_2022/6cet_7465.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cet_7465/12_2022/6cet_7465.pdb" } resolution = 4.4 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= 0.001 sd= 0.009 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 "N ARG 6": "NH1" <-> "NH2" Residue "N ARG 78": "NH1" <-> "NH2" Residue "N ARG 144": "NH1" <-> "NH2" Residue "N ARG 204": "NH1" <-> "NH2" Residue "N ARG 221": "NH1" <-> "NH2" Residue "N ARG 279": "NH1" <-> "NH2" Residue "N ARG 324": "NH1" <-> "NH2" Residue "M PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 30": "NH1" <-> "NH2" Residue "M ARG 116": "NH1" <-> "NH2" Residue "M PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 131": "NH1" <-> "NH2" Residue "M ARG 148": "NH1" <-> "NH2" Residue "M TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 256": "NH1" <-> "NH2" Residue "M TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 401": "NH1" <-> "NH2" Residue "M ARG 422": "NH1" <-> "NH2" Residue "M ARG 424": "NH1" <-> "NH2" Residue "M ARG 433": "NH1" <-> "NH2" Residue "M ARG 515": "NH1" <-> "NH2" Residue "M PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 521": "NH1" <-> "NH2" Residue "M TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 548": "NH1" <-> "NH2" Residue "M PHE 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "D ARG 138": "NH1" <-> "NH2" Residue "D ARG 243": "NH1" <-> "NH2" Residue "D ARG 347": "NH1" <-> "NH2" Residue "D PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 422": "NH1" <-> "NH2" Residue "D ARG 763": "NH1" <-> "NH2" Residue "D TYR 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 843": "NH1" <-> "NH2" Residue "D ARG 974": "NH1" <-> "NH2" Residue "D PHE 986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 988": "NH1" <-> "NH2" Residue "D ARG 1087": "NH1" <-> "NH2" Residue "D ARG 1101": "NH1" <-> "NH2" Residue "D PHE 1294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1583": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 14012 Number of models: 1 Model: "" Number of chains: 3 Chain: "N" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2579 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 16, 'TRANS': 304} Chain breaks: 3 Chain: "M" Number of atoms: 4084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4084 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 34, 'TRANS': 484} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 7349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 7349 Classifications: {'peptide': 901} Link IDs: {'PTRANS': 44, 'TRANS': 856} Chain breaks: 10 Time building chain proxies: 7.77, per 1000 atoms: 0.55 Number of scatterers: 14012 At special positions: 0 Unit cell: (113.4, 122.85, 171.45, 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 79 16.00 O 2587 8.00 N 2371 7.00 C 8975 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.78 Conformation dependent library (CDL) restraints added in 2.0 seconds 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3338 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 16 sheets defined 34.8% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'N' and resid 39 through 47 Processing helix chain 'N' and resid 48 through 51 removed outlier: 4.049A pdb=" N GLN N 51 " --> pdb=" O PRO N 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 48 through 51' Processing helix chain 'N' and resid 98 through 117 Processing helix chain 'N' and resid 121 through 142 removed outlier: 3.877A pdb=" N LYS N 125 " --> pdb=" O MET N 121 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL N 129 " --> pdb=" O LYS N 125 " (cutoff:3.500A) Proline residue: N 130 - end of helix removed outlier: 4.193A pdb=" N ASN N 140 " --> pdb=" O LEU N 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 180 through 184 removed outlier: 3.849A pdb=" N ASP N 183 " --> pdb=" O ASP N 180 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE N 184 " --> pdb=" O LYS N 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 180 through 184' Processing helix chain 'N' and resid 190 through 197 Processing helix chain 'N' and resid 204 through 212 removed outlier: 3.762A pdb=" N SER N 210 " --> pdb=" O ILE N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 216 through 231 Processing helix chain 'N' and resid 254 through 264 removed outlier: 4.219A pdb=" N LYS N 258 " --> pdb=" O LEU N 254 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER N 259 " --> pdb=" O VAL N 255 " (cutoff:3.500A) Processing helix chain 'N' and resid 274 through 286 removed outlier: 3.749A pdb=" N PHE N 282 " --> pdb=" O LEU N 278 " (cutoff:3.500A) Processing helix chain 'N' and resid 351 through 359 Processing helix chain 'N' and resid 361 through 367 Processing helix chain 'M' and resid 64 through 75 removed outlier: 5.398A pdb=" N LEU M 73 " --> pdb=" O LEU M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 150 Processing helix chain 'M' and resid 160 through 173 Processing helix chain 'M' and resid 188 through 195 Processing helix chain 'M' and resid 203 through 213 Processing helix chain 'M' and resid 245 through 252 Processing helix chain 'M' and resid 256 through 269 removed outlier: 4.476A pdb=" N ALA M 260 " --> pdb=" O ARG M 256 " (cutoff:3.500A) Processing helix chain 'M' and resid 274 through 279 removed outlier: 3.888A pdb=" N SER M 279 " --> pdb=" O PRO M 275 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 307 Processing helix chain 'M' and resid 336 through 346 removed outlier: 4.093A pdb=" N ALA M 340 " --> pdb=" O LEU M 336 " (cutoff:3.500A) Processing helix chain 'M' and resid 347 through 359 removed outlier: 3.889A pdb=" N GLN M 351 " --> pdb=" O PRO M 347 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER M 353 " --> pdb=" O ALA M 349 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N HIS M 354 " --> pdb=" O GLU M 350 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN M 355 " --> pdb=" O GLN M 351 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE M 356 " --> pdb=" O PHE M 352 " (cutoff:3.500A) Proline residue: M 357 - end of helix Processing helix chain 'M' and resid 363 through 379 Proline residue: M 371 - end of helix Processing helix chain 'M' and resid 381 through 387 Processing helix chain 'M' and resid 391 through 402 removed outlier: 4.664A pdb=" N TRP M 396 " --> pdb=" O GLN M 392 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET M 397 " --> pdb=" O MET M 393 " (cutoff:3.500A) Processing helix chain 'M' and resid 476 through 486 Processing helix chain 'M' and resid 491 through 499 removed outlier: 3.948A pdb=" N ARG M 495 " --> pdb=" O SER M 491 " (cutoff:3.500A) Processing helix chain 'M' and resid 513 through 520 removed outlier: 4.630A pdb=" N LEU M 517 " --> pdb=" O PHE M 513 " (cutoff:3.500A) Processing helix chain 'M' and resid 523 through 532 Processing helix chain 'M' and resid 537 through 546 removed outlier: 3.791A pdb=" N LEU M 541 " --> pdb=" O ARG M 537 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE M 544 " --> pdb=" O LEU M 540 " (cutoff:3.500A) Processing helix chain 'M' and resid 547 through 550 Processing helix chain 'M' and resid 559 through 567 Processing helix chain 'D' and resid 71 through 76 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 190 through 211 Processing helix chain 'D' and resid 233 through 237 removed outlier: 4.337A pdb=" N GLU D 236 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE D 237 " --> pdb=" O PHE D 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 233 through 237' Processing helix chain 'D' and resid 268 through 280 removed outlier: 3.893A pdb=" N VAL D 272 " --> pdb=" O THR D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 287 removed outlier: 3.610A pdb=" N LEU D 284 " --> pdb=" O GLN D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 318 Processing helix chain 'D' and resid 346 through 358 removed outlier: 3.526A pdb=" N MET D 350 " --> pdb=" O ASP D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 744 through 749 Processing helix chain 'D' and resid 797 through 806 removed outlier: 4.241A pdb=" N GLU D 801 " --> pdb=" O GLN D 797 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG D 806 " --> pdb=" O PHE D 802 " (cutoff:3.500A) Processing helix chain 'D' and resid 975 through 989 removed outlier: 3.713A pdb=" N GLU D 979 " --> pdb=" O ALA D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 1087 through 1102 removed outlier: 4.049A pdb=" N PHE D1092 " --> pdb=" O LYS D1088 " (cutoff:3.500A) Proline residue: D1100 - end of helix Processing helix chain 'D' and resid 1179 through 1185 Processing helix chain 'D' and resid 1186 through 1189 removed outlier: 3.993A pdb=" N THR D1189 " --> pdb=" O HIS D1186 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1186 through 1189' Processing helix chain 'D' and resid 1206 through 1217 removed outlier: 3.621A pdb=" N VAL D1210 " --> pdb=" O ILE D1206 " (cutoff:3.500A) Processing helix chain 'D' and resid 1222 through 1232 removed outlier: 3.675A pdb=" N MET D1226 " --> pdb=" O GLN D1222 " (cutoff:3.500A) Processing helix chain 'D' and resid 1303 through 1312 removed outlier: 3.593A pdb=" N GLU D1307 " --> pdb=" O LEU D1303 " (cutoff:3.500A) Proline residue: D1309 - end of helix Processing helix chain 'D' and resid 1394 through 1411 removed outlier: 4.069A pdb=" N LEU D1398 " --> pdb=" O THR D1394 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER D1411 " --> pdb=" O ARG D1407 " (cutoff:3.500A) Processing helix chain 'D' and resid 1464 through 1484 removed outlier: 3.614A pdb=" N ARG D1468 " --> pdb=" O THR D1464 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN D1484 " --> pdb=" O PHE D1480 " (cutoff:3.500A) Processing helix chain 'D' and resid 1566 through 1579 Processing helix chain 'D' and resid 1585 through 1596 Processing sheet with id=AA1, first strand: chain 'N' and resid 22 through 27 removed outlier: 4.521A pdb=" N LEU N 82 " --> pdb=" O PHE N 15 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL M 94 " --> pdb=" O PHE M 128 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE M 128 " --> pdb=" O VAL M 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 144 through 150 removed outlier: 6.630A pdb=" N ASN N 153 " --> pdb=" O ILE N 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 174 through 177 Processing sheet with id=AA4, first strand: chain 'M' and resid 47 through 48 Processing sheet with id=AA5, first strand: chain 'M' and resid 309 through 310 Processing sheet with id=AA6, first strand: chain 'M' and resid 312 through 316 Processing sheet with id=AA7, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AA8, first strand: chain 'D' and resid 131 through 134 Processing sheet with id=AA9, first strand: chain 'D' and resid 131 through 134 removed outlier: 4.172A pdb=" N LEU D 144 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU D 99 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL D 100 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ARG D 165 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU D 102 " --> pdb=" O ARG D 165 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 123 through 127 Processing sheet with id=AB2, first strand: chain 'D' and resid 238 through 241 removed outlier: 5.137A pdb=" N GLN D 260 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N VAL D 216 " --> pdb=" O GLN D 260 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLU D 262 " --> pdb=" O HIS D 214 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N HIS D 214 " --> pdb=" O GLU D 262 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N MET D 332 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N MET D 170 " --> pdb=" O MET D 332 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL D 334 " --> pdb=" O MET D 170 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TYR D 172 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE D 336 " --> pdb=" O TYR D 172 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE D 174 " --> pdb=" O ILE D 336 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N VAL D 364 " --> pdb=" O GLN D 331 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N SER D 333 " --> pdb=" O VAL D 364 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU D 366 " --> pdb=" O SER D 333 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL D 335 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN D 404 " --> pdb=" O GLY D 363 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 295 through 296 removed outlier: 6.816A pdb=" N HIS D 214 " --> pdb=" O GLU D 262 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLU D 262 " --> pdb=" O HIS D 214 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N VAL D 216 " --> pdb=" O GLN D 260 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLN D 260 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP D 253 " --> pdb=" O TYR D 836 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 342 through 345 Processing sheet with id=AB5, first strand: chain 'D' and resid 756 through 757 removed outlier: 7.082A pdb=" N THR D 873 " --> pdb=" O ARG D 995 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR D 771 " --> pdb=" O SER D 855 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N GLY D 857 " --> pdb=" O THR D 771 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY D 773 " --> pdb=" O GLY D 857 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 1352 through 1357 Processing sheet with id=AB7, first strand: chain 'D' and resid 1439 through 1441 removed outlier: 5.770A pdb=" N VAL D1509 " --> pdb=" O HIS D1504 " (cutoff:3.500A) 502 hydrogen bonds defined for protein. 1428 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: 5.07 Time building geometry restraints manager: 6.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4375 1.34 - 1.46: 2932 1.46 - 1.58: 6910 1.58 - 1.70: 1 1.70 - 1.82: 118 Bond restraints: 14336 Sorted by residual: bond pdb=" C VAL D 733 " pdb=" N PRO D 734 " ideal model delta sigma weight residual 1.337 1.393 -0.056 9.80e-03 1.04e+04 3.26e+01 bond pdb=" C LEU D 777 " pdb=" N LEU D 778 " ideal model delta sigma weight residual 1.329 1.393 -0.064 1.35e-02 5.49e+03 2.23e+01 bond pdb=" C LEU M 195 " pdb=" N PRO M 196 " ideal model delta sigma weight residual 1.334 1.406 -0.072 2.34e-02 1.83e+03 9.47e+00 bond pdb=" C PRO D 828 " pdb=" N PRO D 829 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.34e-02 1.83e+03 7.82e+00 bond pdb=" C HIS D1186 " pdb=" N PRO D1187 " ideal model delta sigma weight residual 1.334 1.395 -0.062 2.34e-02 1.83e+03 6.93e+00 ... (remaining 14331 not shown) Histogram of bond angle deviations from ideal: 97.99 - 105.21: 353 105.21 - 112.44: 6718 112.44 - 119.66: 5391 119.66 - 126.89: 6737 126.89 - 134.11: 238 Bond angle restraints: 19437 Sorted by residual: angle pdb=" C VAL D1393 " pdb=" N THR D1394 " pdb=" CA THR D1394 " ideal model delta sigma weight residual 121.31 130.53 -9.22 1.49e+00 4.50e-01 3.83e+01 angle pdb=" N SER M 476 " pdb=" CA SER M 476 " pdb=" C SER M 476 " ideal model delta sigma weight residual 109.81 121.63 -11.82 2.21e+00 2.05e-01 2.86e+01 angle pdb=" C LEU D 835 " pdb=" N TYR D 836 " pdb=" CA TYR D 836 " ideal model delta sigma weight residual 122.20 113.03 9.17 1.72e+00 3.38e-01 2.84e+01 angle pdb=" C PRO D 846 " pdb=" N GLU D 847 " pdb=" CA GLU D 847 " ideal model delta sigma weight residual 121.31 129.21 -7.90 1.49e+00 4.50e-01 2.81e+01 angle pdb=" N GLU D 847 " pdb=" CA GLU D 847 " pdb=" C GLU D 847 " ideal model delta sigma weight residual 110.35 117.59 -7.24 1.40e+00 5.10e-01 2.67e+01 ... (remaining 19432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 7625 15.63 - 31.27: 813 31.27 - 46.90: 175 46.90 - 62.53: 18 62.53 - 78.16: 10 Dihedral angle restraints: 8641 sinusoidal: 3519 harmonic: 5122 Sorted by residual: dihedral pdb=" CA VAL M 552 " pdb=" C VAL M 552 " pdb=" N VAL M 553 " pdb=" CA VAL M 553 " ideal model delta harmonic sigma weight residual -180.00 -118.23 -61.77 0 5.00e+00 4.00e-02 1.53e+02 dihedral pdb=" CA VAL D 258 " pdb=" C VAL D 258 " pdb=" N VAL D 259 " pdb=" CA VAL D 259 " ideal model delta harmonic sigma weight residual -180.00 -118.77 -61.23 0 5.00e+00 4.00e-02 1.50e+02 dihedral pdb=" CA LYS D 868 " pdb=" C LYS D 868 " pdb=" N MET D 869 " pdb=" CA MET D 869 " ideal model delta harmonic sigma weight residual 180.00 124.24 55.76 0 5.00e+00 4.00e-02 1.24e+02 ... (remaining 8638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1799 0.094 - 0.188: 332 0.188 - 0.282: 36 0.282 - 0.375: 5 0.375 - 0.469: 1 Chirality restraints: 2173 Sorted by residual: chirality pdb=" CB ILE D1240 " pdb=" CA ILE D1240 " pdb=" CG1 ILE D1240 " pdb=" CG2 ILE D1240 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.51e+00 chirality pdb=" CB VAL D 377 " pdb=" CA VAL D 377 " pdb=" CG1 VAL D 377 " pdb=" CG2 VAL D 377 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB THR D 420 " pdb=" CA THR D 420 " pdb=" OG1 THR D 420 " pdb=" CG2 THR D 420 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 2170 not shown) Planarity restraints: 2492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN M 379 " 0.072 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO M 380 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO M 380 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO M 380 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN M 506 " 0.069 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO M 507 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO M 507 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO M 507 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D1099 " -0.064 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO D1100 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO D1100 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO D1100 " -0.053 5.00e-02 4.00e+02 ... (remaining 2489 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2836 2.78 - 3.31: 13240 3.31 - 3.84: 22488 3.84 - 4.37: 24297 4.37 - 4.90: 39930 Nonbonded interactions: 102791 Sorted by model distance: nonbonded pdb=" O THR N 58 " pdb=" O LYS M 87 " model vdw 2.251 3.040 nonbonded pdb=" OH TYR M 318 " pdb=" OE2 GLU M 376 " model vdw 2.270 2.440 nonbonded pdb=" OG1 THR D 224 " pdb=" OD2 ASP D 227 " model vdw 2.293 2.440 nonbonded pdb=" OH TYR D 775 " pdb=" O GLN D 797 " model vdw 2.300 2.440 nonbonded pdb=" OG1 THR M 120 " pdb=" OE2 GLU M 156 " model vdw 2.308 2.440 ... (remaining 102786 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 79 5.16 5 C 8975 2.51 5 N 2371 2.21 5 O 2587 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=1.00 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: 0.400 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: 3.090 Check model and map are aligned: 0.210 Convert atoms to be neutral: 0.120 Process input model: 37.930 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 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 : 0.007 0.072 14336 Z= 0.465 Angle : 1.423 15.487 19437 Z= 0.759 Chirality : 0.073 0.469 2173 Planarity : 0.011 0.110 2492 Dihedral : 13.397 78.162 5303 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 19.66 % Favored : 80.11 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.45 % Twisted General : 0.92 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.52 (0.15), residues: 1699 helix: -3.04 (0.16), residues: 526 sheet: -2.03 (0.30), residues: 245 loop : -4.74 (0.15), residues: 928 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 270 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 283 average time/residue: 0.2985 time to fit residues: 118.3479 Evaluate side-chains 154 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 1.570 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1174 time to fit residues: 3.4197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.2980 chunk 131 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 26 GLN N 153 ASN ** M 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 315 HIS M 379 ASN M 399 GLN M 407 HIS D 45 ASN D 107 GLN D 298 ASN D 375 HIS D 797 GLN D 820 GLN D 981 GLN D1217 HIS D1242 HIS ** D1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1470 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 14336 Z= 0.216 Angle : 0.868 10.352 19437 Z= 0.449 Chirality : 0.049 0.226 2173 Planarity : 0.008 0.090 2492 Dihedral : 8.569 58.156 1876 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.95 % Favored : 83.05 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.30 % Twisted General : 0.37 % 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: -4.66 (0.17), residues: 1699 helix: -1.74 (0.20), residues: 541 sheet: -2.02 (0.28), residues: 279 loop : -4.56 (0.16), residues: 879 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 217 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 221 average time/residue: 0.2892 time to fit residues: 91.6173 Evaluate side-chains 156 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 1.736 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1262 time to fit residues: 2.7646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 0.0670 chunk 48 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 140 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 26 GLN N 205 HIS ** N 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 101 GLN ** M 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 259 HIS ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 407 HIS ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1375 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6144 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 14336 Z= 0.218 Angle : 0.846 10.679 19437 Z= 0.435 Chirality : 0.048 0.217 2173 Planarity : 0.007 0.087 2492 Dihedral : 8.048 56.714 1876 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 17.30 % Favored : 82.64 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.37 % 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: -4.24 (0.18), residues: 1699 helix: -1.11 (0.21), residues: 523 sheet: -1.78 (0.30), residues: 273 loop : -4.43 (0.16), residues: 903 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 204 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 206 average time/residue: 0.2682 time to fit residues: 81.2437 Evaluate side-chains 144 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 1.665 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1146 time to fit residues: 2.5493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 26 GLN ** N 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 407 HIS M 493 HIS D 176 GLN D 298 ASN D 823 ASN D1375 HIS ** D1493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 14336 Z= 0.341 Angle : 0.949 11.021 19437 Z= 0.496 Chirality : 0.052 0.259 2173 Planarity : 0.008 0.088 2492 Dihedral : 8.533 57.880 1876 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 22.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.01 % Favored : 79.99 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.49 % 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: -4.33 (0.18), residues: 1699 helix: -1.23 (0.21), residues: 533 sheet: -1.86 (0.30), residues: 267 loop : -4.47 (0.16), residues: 899 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2776 time to fit residues: 71.8616 Evaluate side-chains 132 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.580 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 142 optimal weight: 0.0270 chunk 115 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 26 GLN ** N 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 261 GLN ** N 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 ASN ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6119 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 14336 Z= 0.200 Angle : 0.849 12.365 19437 Z= 0.429 Chirality : 0.048 0.220 2173 Planarity : 0.007 0.079 2492 Dihedral : 7.806 57.631 1876 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 16.13 % Favored : 83.81 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.37 % 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: -3.94 (0.18), residues: 1699 helix: -0.78 (0.22), residues: 536 sheet: -1.68 (0.31), residues: 264 loop : -4.31 (0.17), residues: 899 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 204 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 206 average time/residue: 0.2915 time to fit residues: 88.0555 Evaluate side-chains 144 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 1.770 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1233 time to fit residues: 2.6257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 77 optimal weight: 0.4980 chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 87 optimal weight: 0.2980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 26 GLN ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 155 HIS ** M 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 ASN ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 407 HIS ** M 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 GLN D 298 ASN ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 14336 Z= 0.197 Angle : 0.817 12.271 19437 Z= 0.414 Chirality : 0.048 0.220 2173 Planarity : 0.006 0.081 2492 Dihedral : 7.415 56.837 1876 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.83 % Favored : 83.17 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.31 % 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: -3.74 (0.19), residues: 1699 helix: -0.50 (0.23), residues: 523 sheet: -1.66 (0.31), residues: 250 loop : -4.15 (0.17), residues: 926 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.2469 time to fit residues: 72.3840 Evaluate side-chains 139 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.603 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 122 optimal weight: 0.0020 chunk 94 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 26 GLN ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 349 HIS ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 ASN ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 407 HIS D 176 GLN ** D1493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6218 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 14336 Z= 0.267 Angle : 0.888 11.417 19437 Z= 0.454 Chirality : 0.050 0.215 2173 Planarity : 0.007 0.082 2492 Dihedral : 7.706 56.494 1876 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.54 % Favored : 81.46 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.43 % 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: -3.87 (0.19), residues: 1699 helix: -0.65 (0.22), residues: 540 sheet: -1.78 (0.29), residues: 273 loop : -4.31 (0.17), residues: 886 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.2442 time to fit residues: 67.1410 Evaluate side-chains 135 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.577 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 0.0170 chunk 66 optimal weight: 0.1980 chunk 99 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 131 optimal weight: 0.4980 chunk 151 optimal weight: 9.9990 overall best weight: 1.1020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 26 GLN ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 ASN ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 GLN D 298 ASN ** D1493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6142 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 14336 Z= 0.208 Angle : 0.855 13.081 19437 Z= 0.431 Chirality : 0.049 0.243 2173 Planarity : 0.007 0.077 2492 Dihedral : 7.447 57.830 1876 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.83 % Favored : 83.17 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.31 % 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: -3.76 (0.19), residues: 1699 helix: -0.55 (0.23), residues: 526 sheet: -1.77 (0.30), residues: 262 loop : -4.16 (0.17), residues: 911 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 178 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 180 average time/residue: 0.2529 time to fit residues: 68.3577 Evaluate side-chains 136 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.698 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 0.5980 chunk 145 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 140 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 102 optimal weight: 0.0010 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 311 GLN M 407 HIS D 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6041 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 14336 Z= 0.198 Angle : 0.843 14.352 19437 Z= 0.419 Chirality : 0.048 0.212 2173 Planarity : 0.006 0.077 2492 Dihedral : 7.107 57.255 1876 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.01 % Favored : 82.99 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.37 % 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: -3.62 (0.19), residues: 1699 helix: -0.47 (0.23), residues: 536 sheet: -1.80 (0.29), residues: 267 loop : -4.05 (0.18), residues: 896 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.2630 time to fit residues: 78.8512 Evaluate side-chains 141 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.772 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 77 optimal weight: 0.0980 chunk 114 optimal weight: 0.9980 chunk 172 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 226 ASN ** N 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 ASN ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 311 GLN M 407 HIS D 43 HIS D 176 GLN D 298 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6055 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 14336 Z= 0.206 Angle : 0.851 13.649 19437 Z= 0.422 Chirality : 0.048 0.222 2173 Planarity : 0.007 0.106 2492 Dihedral : 7.009 56.958 1876 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.42 % Favored : 83.58 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.37 % 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: -3.68 (0.19), residues: 1699 helix: -0.63 (0.22), residues: 545 sheet: -1.67 (0.30), residues: 255 loop : -4.06 (0.18), residues: 899 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 195 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 196 average time/residue: 0.2556 time to fit residues: 75.0399 Evaluate side-chains 149 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.681 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 126 optimal weight: 0.4980 chunk 20 optimal weight: 0.3980 chunk 38 optimal weight: 0.3980 chunk 137 optimal weight: 9.9990 chunk 57 optimal weight: 0.2980 chunk 141 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 ASN ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 407 HIS D 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.125348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.118204 restraints weight = 60287.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.119102 restraints weight = 46437.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.119632 restraints weight = 33339.507| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6149 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.097 14336 Z= 0.206 Angle : 0.841 13.828 19437 Z= 0.417 Chirality : 0.048 0.218 2173 Planarity : 0.007 0.096 2492 Dihedral : 6.935 56.835 1876 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.66 % Favored : 83.34 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.31 % 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: -3.56 (0.19), residues: 1699 helix: -0.52 (0.22), residues: 542 sheet: -1.64 (0.30), residues: 259 loop : -3.98 (0.18), residues: 898 =============================================================================== Job complete usr+sys time: 2462.07 seconds wall clock time: 46 minutes 4.83 seconds (2764.83 seconds total)