Starting phenix.real_space_refine on Sat Mar 16 07:16:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cet_7465/03_2024/6cet_7465.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cet_7465/03_2024/6cet_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_7465/03_2024/6cet_7465.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cet_7465/03_2024/6cet_7465.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cet_7465/03_2024/6cet_7465.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cet_7465/03_2024/6cet_7465.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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 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. 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.85, per 1000 atoms: 0.56 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: 5.71 Conformation dependent library (CDL) restraints added in 2.3 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: 1.64 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: 4.59 Time building geometry restraints manager: 6.16 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 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: 0.370 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: 2.500 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 39.800 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 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 % Allowed : 10.25 % Favored : 88.79 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP D1248 HIS 0.018 0.003 HIS D1389 PHE 0.029 0.004 PHE D 221 TYR 0.031 0.004 TYR M 519 ARG 0.014 0.002 ARG D 843 *********************** 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 : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 75 LYS cc_start: 0.6501 (tptt) cc_final: 0.5946 (mmpt) REVERT: M 39 THR cc_start: 0.6725 (p) cc_final: 0.6327 (t) REVERT: M 88 ILE cc_start: 0.7000 (pp) cc_final: 0.6706 (pt) REVERT: M 145 LEU cc_start: 0.8093 (tm) cc_final: 0.7873 (tt) REVERT: M 262 LEU cc_start: 0.6872 (mt) cc_final: 0.6538 (tp) REVERT: M 335 MET cc_start: 0.5596 (mtt) cc_final: 0.3746 (mmt) REVERT: M 526 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6047 (mt) REVERT: M 530 MET cc_start: 0.7633 (mpm) cc_final: 0.6749 (mpp) REVERT: D 86 TYR cc_start: 0.4393 (t80) cc_final: 0.2837 (m-80) REVERT: D 163 VAL cc_start: 0.8372 (t) cc_final: 0.7482 (m) REVERT: D 862 LYS cc_start: 0.8044 (mmpt) cc_final: 0.7327 (mmtm) REVERT: D 1234 MET cc_start: 0.4782 (tpt) cc_final: 0.4280 (tpp) REVERT: D 1401 MET cc_start: 0.7687 (mmm) cc_final: 0.7475 (mmm) REVERT: D 1435 LEU cc_start: 0.8133 (pt) cc_final: 0.7659 (pp) REVERT: D 1468 ARG cc_start: 0.6861 (mtt-85) cc_final: 0.6489 (tpt90) REVERT: D 1550 TYR cc_start: 0.7158 (m-10) cc_final: 0.6940 (m-80) outliers start: 15 outliers final: 5 residues processed: 283 average time/residue: 0.3040 time to fit residues: 119.1235 Evaluate side-chains 159 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 153 time to evaluate : 1.590 ------------------------------------------------------------------------------- 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: 0.9980 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: 6.9990 chunk 52 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 ** 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 797 GLN D 820 GLN D 981 GLN D1212 HIS D1217 HIS D1242 HIS ** D1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1470 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14336 Z= 0.246 Angle : 0.890 10.163 19437 Z= 0.464 Chirality : 0.050 0.238 2173 Planarity : 0.008 0.091 2492 Dihedral : 8.792 57.639 1876 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.89 % Favored : 82.11 % Rotamer: Outliers : 0.26 % Allowed : 6.98 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.30 % 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: -4.72 (0.17), residues: 1699 helix: -1.80 (0.20), residues: 539 sheet: -2.09 (0.28), residues: 279 loop : -4.57 (0.16), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D1390 HIS 0.007 0.002 HIS D1470 PHE 0.028 0.002 PHE D 986 TYR 0.022 0.002 TYR N 267 ARG 0.007 0.001 ARG M 45 *********************** 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 214 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 210 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 19 LEU cc_start: 0.6401 (pp) cc_final: 0.6126 (pp) REVERT: N 71 ILE cc_start: 0.6627 (tt) cc_final: 0.6395 (tt) REVERT: N 75 LYS cc_start: 0.6775 (tptt) cc_final: 0.5728 (tppt) REVERT: N 360 MET cc_start: 0.6230 (mtm) cc_final: 0.5929 (mtm) REVERT: M 145 LEU cc_start: 0.7951 (tt) cc_final: 0.7618 (tp) REVERT: M 335 MET cc_start: 0.5905 (mtt) cc_final: 0.3417 (mmt) REVERT: D 86 TYR cc_start: 0.4388 (t80) cc_final: 0.3029 (m-80) REVERT: D 177 MET cc_start: 0.9049 (mpp) cc_final: 0.8816 (mpp) REVERT: D 862 LYS cc_start: 0.8058 (mmpt) cc_final: 0.7710 (mmpt) REVERT: D 869 MET cc_start: 0.5496 (tmm) cc_final: 0.5119 (tmm) REVERT: D 974 ARG cc_start: 0.5170 (pmt-80) cc_final: 0.4821 (ptp90) REVERT: D 1289 PHE cc_start: 0.7303 (p90) cc_final: 0.6801 (p90) REVERT: D 1401 MET cc_start: 0.7685 (mmm) cc_final: 0.7429 (mmm) REVERT: D 1435 LEU cc_start: 0.7899 (pt) cc_final: 0.7274 (pp) REVERT: D 1550 TYR cc_start: 0.7108 (m-10) cc_final: 0.6832 (m-80) outliers start: 4 outliers final: 1 residues processed: 213 average time/residue: 0.3017 time to fit residues: 91.3180 Evaluate side-chains 151 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 1.733 ------------------------------------------------------------------------------- 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: 6.9990 chunk 48 optimal weight: 0.0470 chunk 130 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 chunk 43 optimal weight: 0.1980 chunk 157 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- 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 205 HIS ** 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 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN D 823 ASN D 981 GLN D1375 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6185 moved from start: 0.2872 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= 0.199 Angle : 0.832 10.749 19437 Z= 0.426 Chirality : 0.048 0.227 2173 Planarity : 0.007 0.085 2492 Dihedral : 7.956 55.858 1876 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 16.77 % Favored : 83.17 % Rotamer: Outliers : 0.19 % Allowed : 6.66 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.25 % 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: -4.21 (0.18), residues: 1699 helix: -1.14 (0.21), residues: 531 sheet: -1.62 (0.31), residues: 255 loop : -4.42 (0.16), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP M 396 HIS 0.007 0.001 HIS D1186 PHE 0.027 0.002 PHE D 986 TYR 0.022 0.002 TYR M 519 ARG 0.008 0.001 ARG M 481 *********************** 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 225 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 222 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 335 MET cc_start: 0.6288 (mtt) cc_final: 0.3840 (mmt) REVERT: D 164 PHE cc_start: 0.7461 (m-80) cc_final: 0.7195 (m-10) REVERT: D 190 LEU cc_start: 0.8304 (tp) cc_final: 0.7743 (tp) REVERT: D 862 LYS cc_start: 0.7884 (mmpt) cc_final: 0.7498 (mmpt) REVERT: D 974 ARG cc_start: 0.5343 (pmt-80) cc_final: 0.4825 (ptp90) REVERT: D 1234 MET cc_start: 0.5181 (tpt) cc_final: 0.4798 (tpp) REVERT: D 1424 PHE cc_start: 0.7245 (m-10) cc_final: 0.6962 (m-80) REVERT: D 1435 LEU cc_start: 0.7675 (pt) cc_final: 0.7312 (pp) REVERT: D 1553 MET cc_start: 0.8021 (mmm) cc_final: 0.7806 (mmt) outliers start: 3 outliers final: 1 residues processed: 224 average time/residue: 0.2945 time to fit residues: 93.9002 Evaluate side-chains 154 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 1.747 ------------------------------------------------------------------------------- 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: 10.0000 chunk 118 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 105 optimal weight: 0.1980 chunk 157 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 ** 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 ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 493 HIS ** M 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 GLN D 298 ASN D 981 GLN ** D1493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.3258 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= 0.270 Angle : 0.871 10.354 19437 Z= 0.451 Chirality : 0.050 0.241 2173 Planarity : 0.007 0.087 2492 Dihedral : 8.012 57.160 1876 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.25 % Favored : 81.75 % Rotamer: Outliers : 0.13 % Allowed : 7.05 % Favored : 92.83 % 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: -4.16 (0.18), residues: 1699 helix: -1.02 (0.21), residues: 534 sheet: -1.76 (0.30), residues: 270 loop : -4.43 (0.16), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 396 HIS 0.009 0.002 HIS M 155 PHE 0.042 0.002 PHE D 293 TYR 0.021 0.002 TYR M 345 ARG 0.005 0.001 ARG M 481 *********************** 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 194 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 192 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 319 MET cc_start: 0.4871 (mpp) cc_final: 0.4670 (mpp) REVERT: N 360 MET cc_start: 0.6145 (mtm) cc_final: 0.5853 (mtm) REVERT: M 335 MET cc_start: 0.5993 (mtt) cc_final: 0.3767 (mmt) REVERT: D 86 TYR cc_start: 0.4357 (t80) cc_final: 0.2925 (m-80) REVERT: D 862 LYS cc_start: 0.7862 (mmpt) cc_final: 0.7180 (mttp) REVERT: D 1226 MET cc_start: 0.6706 (ptp) cc_final: 0.6417 (ptp) REVERT: D 1315 TRP cc_start: 0.6021 (m100) cc_final: 0.5577 (m100) REVERT: D 1391 MET cc_start: 0.7331 (mpp) cc_final: 0.7022 (mpp) REVERT: D 1435 LEU cc_start: 0.7862 (pt) cc_final: 0.7453 (pp) REVERT: D 1553 MET cc_start: 0.7990 (mmm) cc_final: 0.7714 (mmt) outliers start: 2 outliers final: 1 residues processed: 194 average time/residue: 0.2827 time to fit residues: 78.4542 Evaluate side-chains 138 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.699 ------------------------------------------------------------------------------- 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: 0.0980 chunk 94 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 50 ASN ** 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 981 GLN ** D1493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14336 Z= 0.256 Angle : 0.870 11.309 19437 Z= 0.448 Chirality : 0.049 0.232 2173 Planarity : 0.007 0.083 2492 Dihedral : 7.948 56.667 1876 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.07 % Favored : 81.93 % Rotamer: Outliers : 0.13 % Allowed : 4.29 % Favored : 95.58 % 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: -4.00 (0.18), residues: 1699 helix: -0.84 (0.22), residues: 544 sheet: -1.81 (0.30), residues: 270 loop : -4.35 (0.17), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D1248 HIS 0.009 0.002 HIS D1406 PHE 0.043 0.002 PHE D1298 TYR 0.024 0.002 TYR D1550 ARG 0.014 0.001 ARG M 92 *********************** 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 197 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 195 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 360 MET cc_start: 0.6179 (mtm) cc_final: 0.5831 (mtm) REVERT: M 101 GLN cc_start: 0.3851 (mp10) cc_final: 0.3362 (mp10) REVERT: M 335 MET cc_start: 0.6079 (mtt) cc_final: 0.3915 (mmt) REVERT: D 86 TYR cc_start: 0.4666 (t80) cc_final: 0.3240 (m-80) REVERT: D 862 LYS cc_start: 0.7960 (mmpt) cc_final: 0.7564 (mmpt) REVERT: D 869 MET cc_start: 0.6533 (tmm) cc_final: 0.6058 (tmm) REVERT: D 1226 MET cc_start: 0.6712 (ptp) cc_final: 0.6483 (ptp) REVERT: D 1435 LEU cc_start: 0.7849 (pt) cc_final: 0.7398 (pp) REVERT: D 1550 TYR cc_start: 0.6948 (m-80) cc_final: 0.6610 (m-80) outliers start: 2 outliers final: 1 residues processed: 197 average time/residue: 0.2786 time to fit residues: 79.2732 Evaluate side-chains 145 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 1.409 ------------------------------------------------------------------------------- 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: 6.9990 chunk 150 optimal weight: 4.9990 chunk 33 optimal weight: 0.0000 chunk 98 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- 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 207 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** ** M 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN D 805 GLN D 981 GLN ** D1493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6240 moved from start: 0.3936 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= 0.215 Angle : 0.838 12.309 19437 Z= 0.428 Chirality : 0.049 0.231 2173 Planarity : 0.007 0.081 2492 Dihedral : 7.576 56.548 1876 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.83 % Favored : 83.17 % Rotamer: Outliers : 0.06 % Allowed : 4.29 % Favored : 95.64 % 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: -3.84 (0.19), residues: 1699 helix: -0.65 (0.22), residues: 542 sheet: -1.67 (0.31), residues: 265 loop : -4.29 (0.17), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP M 396 HIS 0.009 0.001 HIS D1504 PHE 0.055 0.002 PHE D 293 TYR 0.031 0.002 TYR D1487 ARG 0.006 0.001 ARG M 92 *********************** 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 202 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 201 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 19 LEU cc_start: 0.6650 (pp) cc_final: 0.6292 (pp) REVERT: M 335 MET cc_start: 0.5627 (mtt) cc_final: 0.3609 (mmt) REVERT: M 530 MET cc_start: 0.7397 (mmt) cc_final: 0.7004 (mmm) REVERT: D 86 TYR cc_start: 0.4458 (t80) cc_final: 0.2960 (m-80) REVERT: D 177 MET cc_start: 0.9028 (mpp) cc_final: 0.8725 (mmm) REVERT: D 862 LYS cc_start: 0.7919 (mmpt) cc_final: 0.7552 (mmpt) REVERT: D 983 LEU cc_start: 0.8730 (mt) cc_final: 0.8501 (mt) REVERT: D 1226 MET cc_start: 0.6680 (ptp) cc_final: 0.6446 (ptp) outliers start: 1 outliers final: 0 residues processed: 202 average time/residue: 0.2646 time to fit residues: 77.9339 Evaluate side-chains 149 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.786 ------------------------------------------------------------------------------- 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: 0.0870 chunk 18 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 166 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 76 optimal weight: 0.0270 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 207 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 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 moved from start: 0.4332 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= 0.192 Angle : 0.837 13.722 19437 Z= 0.416 Chirality : 0.048 0.192 2173 Planarity : 0.006 0.078 2492 Dihedral : 7.160 57.630 1876 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.77 % Favored : 84.23 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % 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: -3.70 (0.19), residues: 1699 helix: -0.56 (0.22), residues: 543 sheet: -1.69 (0.30), residues: 264 loop : -4.15 (0.17), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP M 396 HIS 0.007 0.001 HIS D1504 PHE 0.034 0.002 PHE D 293 TYR 0.019 0.002 TYR M 345 ARG 0.005 0.001 ARG D1407 *********************** 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 211 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 19 LEU cc_start: 0.6660 (pp) cc_final: 0.6287 (pp) REVERT: M 335 MET cc_start: 0.5735 (mtt) cc_final: 0.3686 (mmt) REVERT: M 530 MET cc_start: 0.7356 (mmt) cc_final: 0.7032 (mmm) REVERT: D 86 TYR cc_start: 0.4536 (t80) cc_final: 0.2888 (m-80) REVERT: D 177 MET cc_start: 0.9086 (mpp) cc_final: 0.8779 (mmm) REVERT: D 862 LYS cc_start: 0.7862 (mmpt) cc_final: 0.7059 (mttp) REVERT: D 1226 MET cc_start: 0.6237 (ptp) cc_final: 0.5971 (ptp) REVERT: D 1550 TYR cc_start: 0.6957 (m-80) cc_final: 0.6689 (m-80) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.2631 time to fit residues: 81.7842 Evaluate side-chains 147 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.556 ------------------------------------------------------------------------------- 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: 0.0670 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 226 ASN ** M 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 174 GLN ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 399 GLN ** M 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN D 823 ASN D 981 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14336 Z= 0.197 Angle : 0.824 14.304 19437 Z= 0.413 Chirality : 0.048 0.239 2173 Planarity : 0.007 0.100 2492 Dihedral : 7.022 56.620 1876 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.07 % Favored : 83.93 % Rotamer: Outliers : 0.13 % Allowed : 2.31 % Favored : 97.57 % 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: -3.66 (0.19), residues: 1699 helix: -0.56 (0.22), residues: 545 sheet: -1.58 (0.31), residues: 251 loop : -4.12 (0.17), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP M 396 HIS 0.008 0.001 HIS D1504 PHE 0.056 0.002 PHE D 293 TYR 0.020 0.002 TYR M 345 ARG 0.007 0.000 ARG M 481 *********************** 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 204 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 19 LEU cc_start: 0.6645 (pp) cc_final: 0.6301 (pp) REVERT: M 335 MET cc_start: 0.5625 (mtt) cc_final: 0.3662 (mmt) REVERT: M 530 MET cc_start: 0.7564 (mmt) cc_final: 0.7347 (mmm) REVERT: D 177 MET cc_start: 0.9035 (mpp) cc_final: 0.8747 (mmm) REVERT: D 181 MET cc_start: 0.8539 (tpp) cc_final: 0.8161 (tpp) REVERT: D 862 LYS cc_start: 0.7868 (mmpt) cc_final: 0.7616 (mmpt) REVERT: D 1226 MET cc_start: 0.6334 (ptp) cc_final: 0.6120 (ptp) REVERT: D 1553 MET cc_start: 0.7232 (mmm) cc_final: 0.6361 (mmm) outliers start: 2 outliers final: 1 residues processed: 204 average time/residue: 0.2565 time to fit residues: 77.7234 Evaluate side-chains 144 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 1.821 ------------------------------------------------------------------------------- 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: 2.9990 chunk 145 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 chunk 146 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 102 optimal weight: 0.0170 overall best weight: 1.6024 ------------------------------------------------------------------------------- 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 207 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 184 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 moved from start: 0.4596 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= 0.229 Angle : 0.854 13.608 19437 Z= 0.431 Chirality : 0.049 0.233 2173 Planarity : 0.007 0.093 2492 Dihedral : 7.188 56.066 1876 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.60 % Favored : 82.40 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % 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: -0.65 (0.22), residues: 545 sheet: -1.65 (0.30), residues: 262 loop : -4.16 (0.17), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP M 396 HIS 0.008 0.001 HIS D1504 PHE 0.037 0.002 PHE D 293 TYR 0.022 0.002 TYR M 345 ARG 0.006 0.001 ARG M 481 *********************** 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 195 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 19 LEU cc_start: 0.6588 (pp) cc_final: 0.6274 (pp) REVERT: M 335 MET cc_start: 0.6077 (mtt) cc_final: 0.4012 (mmt) REVERT: M 512 MET cc_start: 0.3283 (tpt) cc_final: 0.3041 (tpt) REVERT: M 530 MET cc_start: 0.7365 (mmt) cc_final: 0.7129 (mmm) REVERT: M 544 PHE cc_start: 0.6939 (p90) cc_final: 0.6440 (p90) REVERT: D 177 MET cc_start: 0.9069 (mpp) cc_final: 0.8776 (mmm) REVERT: D 190 LEU cc_start: 0.8303 (tp) cc_final: 0.8089 (tp) REVERT: D 385 ARG cc_start: 0.6227 (ttp80) cc_final: 0.5127 (mmm-85) REVERT: D 862 LYS cc_start: 0.7864 (mmpt) cc_final: 0.7130 (mmtp) REVERT: D 1550 TYR cc_start: 0.6173 (m-10) cc_final: 0.5910 (m-80) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2625 time to fit residues: 76.0424 Evaluate side-chains 146 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.803 ------------------------------------------------------------------------------- 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: 0.0980 chunk 77 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 172 optimal weight: 0.3980 chunk 158 optimal weight: 5.9990 chunk 137 optimal weight: 0.0980 chunk 14 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 226 ASN ** M 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 GLN ** 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** M 518 HIS D 298 ASN D1186 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6103 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14336 Z= 0.197 Angle : 0.837 13.946 19437 Z= 0.415 Chirality : 0.048 0.219 2173 Planarity : 0.007 0.089 2492 Dihedral : 6.909 56.252 1876 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.36 % Favored : 84.64 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -3.61 (0.19), residues: 1699 helix: -0.53 (0.23), residues: 544 sheet: -1.53 (0.30), residues: 262 loop : -4.11 (0.17), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D1548 HIS 0.006 0.001 HIS D1186 PHE 0.034 0.002 PHE D 293 TYR 0.021 0.001 TYR M 345 ARG 0.006 0.001 ARG D 974 ********************** 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 199 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 19 LEU cc_start: 0.6575 (pp) cc_final: 0.6272 (pp) REVERT: M 264 LEU cc_start: 0.5928 (pp) cc_final: 0.5233 (mm) REVERT: M 335 MET cc_start: 0.5338 (mtt) cc_final: 0.3678 (mmm) REVERT: M 530 MET cc_start: 0.7331 (mmt) cc_final: 0.7127 (mmm) REVERT: M 544 PHE cc_start: 0.7005 (p90) cc_final: 0.6531 (p90) REVERT: D 177 MET cc_start: 0.9019 (mpp) cc_final: 0.8684 (mmm) REVERT: D 385 ARG cc_start: 0.6590 (ttp80) cc_final: 0.5435 (mtt180) REVERT: D 862 LYS cc_start: 0.7893 (mmpt) cc_final: 0.7204 (mttp) REVERT: D 1226 MET cc_start: 0.6271 (ptp) cc_final: 0.6058 (ptp) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.2610 time to fit residues: 76.6032 Evaluate side-chains 151 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.655 ------------------------------------------------------------------------------- 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: 8.9990 chunk 42 optimal weight: 8.9990 chunk 126 optimal weight: 0.0020 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 141 optimal weight: 0.0770 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 overall best weight: 2.6152 ------------------------------------------------------------------------------- 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 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 349 HIS ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 96 HIS ** 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** ** M 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 518 HIS ** D 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.121461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.114176 restraints weight = 60484.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.115270 restraints weight = 42318.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.116050 restraints weight = 31088.202| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14336 Z= 0.284 Angle : 0.896 13.428 19437 Z= 0.458 Chirality : 0.050 0.224 2173 Planarity : 0.007 0.090 2492 Dihedral : 7.437 55.847 1876 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.19 % Favored : 80.81 % Rotamer: Outliers : 0.06 % Allowed : 0.70 % Favored : 99.23 % 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: -3.82 (0.19), residues: 1699 helix: -0.79 (0.22), residues: 545 sheet: -1.68 (0.29), residues: 288 loop : -4.22 (0.17), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP M 396 HIS 0.009 0.002 HIS D1504 PHE 0.048 0.003 PHE D 802 TYR 0.035 0.002 TYR D 226 ARG 0.007 0.001 ARG D 974 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2703.59 seconds wall clock time: 49 minutes 54.37 seconds (2994.37 seconds total)