Starting phenix.real_space_refine on Thu Sep 18 04:24:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cet_7465/09_2025/6cet_7465.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cet_7465/09_2025/6cet_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/cci-nas-00/data/ceres_data/6cet_7465/09_2025/6cet_7465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cet_7465/09_2025/6cet_7465.map" model { file = "/net/cci-nas-00/data/ceres_data/6cet_7465/09_2025/6cet_7465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cet_7465/09_2025/6cet_7465.cif" } 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 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. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.55, per 1000 atoms: 0.18 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 - 3.00 Amino acid : True - 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: 0.75 Conformation dependent library (CDL) restraints added in 635.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.39 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: 2.14 Time building geometry restraints manager: 1.16 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: 0.00 - 3.10: 18600 3.10 - 6.19: 676 6.19 - 9.29: 128 9.29 - 12.39: 26 12.39 - 15.49: 7 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 3.040 nonbonded pdb=" OG1 THR D 224 " pdb=" OD2 ASP D 227 " model vdw 2.293 3.040 nonbonded pdb=" OH TYR D 775 " pdb=" O GLN D 797 " model vdw 2.300 3.040 nonbonded pdb=" OG1 THR M 120 " pdb=" OE2 GLU M 156 " model vdw 2.308 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 0.630 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: 0.170 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 11.660 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.090 ------------------------------------------------------------------------------- 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= 0.333 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.014 0.002 ARG D 843 TYR 0.031 0.004 TYR M 519 PHE 0.029 0.004 PHE D 221 TRP 0.043 0.004 TRP D1248 HIS 0.018 0.003 HIS D1389 Details of bonding type rmsd covalent geometry : bond 0.00697 (14336) covalent geometry : angle 1.42333 (19437) hydrogen bonds : bond 0.10953 ( 490) hydrogen bonds : angle 7.97151 ( 1428) *********************** 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 to be fit. rotamer outliers: 15 poor density : 270 time to evaluate : 0.470 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: 0.6700 (pt) REVERT: M 145 LEU cc_start: 0.8093 (tm) cc_final: 0.7873 (tt) 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: 0.6048 (mt) REVERT: M 530 MET cc_start: 0.7633 (mpm) cc_final: 0.6741 (mpp) REVERT: D 86 TYR cc_start: 0.4393 (t80) cc_final: 0.2836 (m-80) REVERT: D 163 VAL cc_start: 0.8372 (t) cc_final: 0.7479 (m) REVERT: D 862 LYS cc_start: 0.8044 (mmpt) cc_final: 0.7326 (mmtm) REVERT: D 1234 MET cc_start: 0.4782 (tpt) cc_final: 0.4281 (tpp) REVERT: D 1401 MET cc_start: 0.7687 (mmm) cc_final: 0.7477 (mmm) REVERT: D 1435 LEU cc_start: 0.8133 (pt) cc_final: 0.7652 (pp) REVERT: D 1468 ARG cc_start: 0.6861 (mtt-85) cc_final: 0.6486 (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: 0.1304 time to fit residues: 51.5969 Evaluate side-chains 161 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 155 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 153 ASN N 261 GLN ** M 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 174 GLN ** M 259 HIS ** 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 379 ASN M 399 GLN M 407 HIS D 45 ASN D 107 GLN D 298 ASN D 375 HIS 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.123210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.115554 restraints weight = 61297.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.116749 restraints weight = 44669.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.117436 restraints weight = 30796.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.117692 restraints weight = 25178.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.117816 restraints weight = 22443.000| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14336 Z= 0.163 Angle : 0.894 10.795 19437 Z= 0.465 Chirality : 0.050 0.224 2173 Planarity : 0.008 0.090 2492 Dihedral : 8.729 58.111 1876 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 16.54 % Favored : 83.40 % Rotamer: Outliers : 0.26 % Allowed : 6.28 % Favored : 93.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.30 % Twisted General : 0.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.70 (0.17), residues: 1699 helix: -1.83 (0.20), residues: 535 sheet: -1.88 (0.29), residues: 268 loop : -4.57 (0.16), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 45 TYR 0.020 0.002 TYR N 267 PHE 0.028 0.002 PHE D 986 TRP 0.031 0.002 TRP D1390 HIS 0.006 0.002 HIS D1470 Details of bonding type rmsd covalent geometry : bond 0.00344 (14336) covalent geometry : angle 0.89409 (19437) hydrogen bonds : bond 0.05030 ( 490) hydrogen bonds : angle 6.58148 ( 1428) *********************** 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 226 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 222 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 147 LEU cc_start: 0.7677 (tp) cc_final: 0.7457 (tt) REVERT: N 217 LEU cc_start: 0.9013 (tp) cc_final: 0.8587 (pt) REVERT: N 319 MET cc_start: 0.3720 (mmt) cc_final: 0.3446 (mmt) REVERT: M 145 LEU cc_start: 0.8225 (tt) cc_final: 0.8006 (tp) REVERT: M 203 ASP cc_start: 0.5404 (t0) cc_final: 0.5009 (t0) REVERT: M 335 MET cc_start: 0.5444 (mtt) cc_final: 0.3206 (mmt) REVERT: M 337 SER cc_start: 0.8790 (t) cc_final: 0.8549 (p) REVERT: M 350 GLU cc_start: 0.8123 (mp0) cc_final: 0.7566 (pt0) REVERT: D 86 TYR cc_start: 0.4191 (t80) cc_final: 0.2872 (m-80) REVERT: D 177 MET cc_start: 0.8934 (mpp) cc_final: 0.8572 (mpp) REVERT: D 253 ASP cc_start: 0.7420 (p0) cc_final: 0.7158 (p0) REVERT: D 276 LYS cc_start: 0.8192 (mttt) cc_final: 0.7952 (mtmt) REVERT: D 862 LYS cc_start: 0.8271 (mmpt) cc_final: 0.7291 (mmtm) REVERT: D 1289 PHE cc_start: 0.7390 (p90) cc_final: 0.6888 (p90) REVERT: D 1401 MET cc_start: 0.7823 (mmm) cc_final: 0.7599 (mmm) REVERT: D 1435 LEU cc_start: 0.8173 (pt) cc_final: 0.7608 (pp) REVERT: D 1468 ARG cc_start: 0.6882 (mtt-85) cc_final: 0.6495 (tpt90) REVERT: D 1550 TYR cc_start: 0.7403 (m-10) cc_final: 0.6900 (m-80) outliers start: 4 outliers final: 1 residues processed: 225 average time/residue: 0.1329 time to fit residues: 42.3515 Evaluate side-chains 154 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 25 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 74 optimal weight: 0.0370 chunk 114 optimal weight: 2.9990 chunk 116 optimal weight: 0.0870 chunk 53 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 overall best weight: 1.9640 ------------------------------------------------------------------------------- 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 261 GLN M 96 HIS M 101 GLN ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 259 HIS ** M 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 407 HIS ** M 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN D 320 HIS D 820 GLN D 981 GLN D1375 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.121965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.114832 restraints weight = 62158.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.115671 restraints weight = 49529.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.115854 restraints weight = 35628.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.116296 restraints weight = 32916.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.116355 restraints weight = 29981.773| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14336 Z= 0.167 Angle : 0.871 10.538 19437 Z= 0.453 Chirality : 0.049 0.225 2173 Planarity : 0.007 0.088 2492 Dihedral : 8.231 56.582 1876 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 17.83 % Favored : 82.11 % Rotamer: Outliers : 0.26 % Allowed : 7.11 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.30 (0.18), residues: 1699 helix: -1.30 (0.21), residues: 531 sheet: -1.64 (0.33), residues: 243 loop : -4.40 (0.16), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D1571 TYR 0.023 0.002 TYR M 345 PHE 0.026 0.002 PHE D 986 TRP 0.027 0.002 TRP D1548 HIS 0.007 0.001 HIS M 155 Details of bonding type rmsd covalent geometry : bond 0.00363 (14336) covalent geometry : angle 0.87063 (19437) hydrogen bonds : bond 0.04723 ( 490) hydrogen bonds : angle 6.19987 ( 1428) *********************** 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 to be fit. rotamer outliers: 4 poor density : 202 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 147 LEU cc_start: 0.7590 (tp) cc_final: 0.7216 (tt) REVERT: N 319 MET cc_start: 0.4381 (mmt) cc_final: 0.4033 (mmt) REVERT: M 101 GLN cc_start: 0.3629 (mp10) cc_final: 0.3263 (mp10) REVERT: M 121 MET cc_start: 0.2743 (mtt) cc_final: 0.2538 (mtt) REVERT: M 335 MET cc_start: 0.5681 (mtt) cc_final: 0.3601 (mmt) REVERT: M 350 GLU cc_start: 0.7963 (mp0) cc_final: 0.7542 (pt0) REVERT: M 420 GLU cc_start: 0.7437 (mp0) cc_final: 0.7101 (mp0) REVERT: M 518 HIS cc_start: 0.6851 (t-90) cc_final: 0.6641 (t-90) REVERT: D 86 TYR cc_start: 0.4206 (t80) cc_final: 0.2944 (m-80) REVERT: D 177 MET cc_start: 0.9189 (mpp) cc_final: 0.8419 (mmm) REVERT: D 253 ASP cc_start: 0.7461 (p0) cc_final: 0.7141 (p0) REVERT: D 276 LYS cc_start: 0.8233 (mttt) cc_final: 0.8019 (mtmm) REVERT: D 862 LYS cc_start: 0.8091 (mmpt) cc_final: 0.7583 (mmpt) REVERT: D 1185 LYS cc_start: 0.6197 (mttp) cc_final: 0.5712 (tptp) REVERT: D 1234 MET cc_start: 0.4934 (tpt) cc_final: 0.4689 (tpp) REVERT: D 1315 TRP cc_start: 0.6044 (m100) cc_final: 0.5100 (m100) REVERT: D 1401 MET cc_start: 0.7632 (mmm) cc_final: 0.7368 (mmm) REVERT: D 1435 LEU cc_start: 0.8326 (pt) cc_final: 0.7858 (pp) REVERT: D 1468 ARG cc_start: 0.6594 (mtt-85) cc_final: 0.6247 (tpt90) outliers start: 4 outliers final: 1 residues processed: 206 average time/residue: 0.1255 time to fit residues: 37.5854 Evaluate side-chains 147 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 77 optimal weight: 0.6980 chunk 166 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 76 optimal weight: 0.0980 chunk 135 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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** ** 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 407 HIS M 493 HIS ** M 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN D 823 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.123068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.116108 restraints weight = 61423.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.116841 restraints weight = 44889.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.118003 restraints weight = 32943.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.118185 restraints weight = 25239.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.118193 restraints weight = 20200.740| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.3272 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= 0.156 Angle : 0.845 11.679 19437 Z= 0.435 Chirality : 0.049 0.260 2173 Planarity : 0.007 0.083 2492 Dihedral : 7.904 57.593 1876 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.77 % Favored : 83.23 % Rotamer: Outliers : 0.06 % Allowed : 5.51 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.06 (0.18), residues: 1699 helix: -1.00 (0.22), residues: 533 sheet: -1.64 (0.32), residues: 252 loop : -4.30 (0.17), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 481 TYR 0.019 0.002 TYR M 345 PHE 0.040 0.002 PHE D 293 TRP 0.047 0.002 TRP M 396 HIS 0.006 0.001 HIS N 73 Details of bonding type rmsd covalent geometry : bond 0.00336 (14336) covalent geometry : angle 0.84527 (19437) hydrogen bonds : bond 0.04448 ( 490) hydrogen bonds : angle 6.03266 ( 1428) *********************** 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 204 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 147 LEU cc_start: 0.7702 (tp) cc_final: 0.7350 (tt) REVERT: N 208 LYS cc_start: 0.8529 (ptpp) cc_final: 0.8242 (ptpp) REVERT: M 335 MET cc_start: 0.5403 (mtt) cc_final: 0.3387 (mmt) REVERT: M 350 GLU cc_start: 0.7889 (mp0) cc_final: 0.7480 (pt0) REVERT: M 518 HIS cc_start: 0.7185 (t-90) cc_final: 0.6882 (t70) REVERT: D 86 TYR cc_start: 0.4505 (t80) cc_final: 0.3142 (m-80) REVERT: D 177 MET cc_start: 0.9203 (mpp) cc_final: 0.8519 (mmm) REVERT: D 253 ASP cc_start: 0.7383 (p0) cc_final: 0.7031 (p0) REVERT: D 397 TYR cc_start: 0.8129 (m-10) cc_final: 0.7698 (m-80) REVERT: D 862 LYS cc_start: 0.8133 (mmpt) cc_final: 0.7649 (mmpt) REVERT: D 1226 MET cc_start: 0.6759 (ptp) cc_final: 0.6487 (ptp) REVERT: D 1435 LEU cc_start: 0.8131 (pt) cc_final: 0.7763 (pp) REVERT: D 1501 GLN cc_start: 0.7721 (tm-30) cc_final: 0.7109 (tm-30) outliers start: 1 outliers final: 1 residues processed: 204 average time/residue: 0.1401 time to fit residues: 40.0276 Evaluate side-chains 153 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 171 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 371 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 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 GLN D 981 GLN ** D1493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.120531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.113380 restraints weight = 61288.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.114327 restraints weight = 44704.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.115501 restraints weight = 31184.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.115713 restraints weight = 24680.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.115784 restraints weight = 19031.782| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14336 Z= 0.189 Angle : 0.900 11.420 19437 Z= 0.465 Chirality : 0.050 0.208 2173 Planarity : 0.007 0.086 2492 Dihedral : 8.033 56.435 1876 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 18.60 % Favored : 81.34 % Rotamer: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.03 (0.18), residues: 1699 helix: -0.93 (0.22), residues: 535 sheet: -1.67 (0.32), residues: 249 loop : -4.30 (0.16), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 92 TYR 0.024 0.002 TYR D 226 PHE 0.037 0.002 PHE D 293 TRP 0.031 0.002 TRP D1248 HIS 0.015 0.002 HIS D1375 Details of bonding type rmsd covalent geometry : bond 0.00420 (14336) covalent geometry : angle 0.89956 (19437) hydrogen bonds : bond 0.04815 ( 490) hydrogen bonds : angle 6.12060 ( 1428) *********************** 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 191 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 89 CYS cc_start: 0.8331 (p) cc_final: 0.8089 (p) REVERT: N 208 LYS cc_start: 0.8566 (ptpp) cc_final: 0.8206 (ptpp) REVERT: N 285 TYR cc_start: 0.7942 (m-10) cc_final: 0.7727 (m-10) REVERT: M 335 MET cc_start: 0.5299 (mtt) cc_final: 0.3418 (mmt) REVERT: M 337 SER cc_start: 0.8544 (t) cc_final: 0.8292 (p) REVERT: D 43 HIS cc_start: 0.5284 (p90) cc_final: 0.4516 (t70) REVERT: D 86 TYR cc_start: 0.4204 (t80) cc_final: 0.2814 (m-80) REVERT: D 177 MET cc_start: 0.9186 (mpp) cc_final: 0.8980 (mpp) REVERT: D 253 ASP cc_start: 0.7522 (p0) cc_final: 0.7236 (p0) REVERT: D 1226 MET cc_start: 0.6784 (ptp) cc_final: 0.6556 (ptp) REVERT: D 1435 LEU cc_start: 0.8305 (pt) cc_final: 0.7656 (pp) REVERT: D 1550 TYR cc_start: 0.7000 (m-80) cc_final: 0.6653 (m-80) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1140 time to fit residues: 31.5470 Evaluate side-chains 149 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 26 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 103 optimal weight: 0.0870 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 261 GLN ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 311 GLN ** M 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN ** D1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.125080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.117872 restraints weight = 60822.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.118600 restraints weight = 42451.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.119106 restraints weight = 34119.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.120038 restraints weight = 25641.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.119983 restraints weight = 21160.346| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14336 Z= 0.143 Angle : 0.841 13.578 19437 Z= 0.426 Chirality : 0.048 0.270 2173 Planarity : 0.006 0.078 2492 Dihedral : 7.434 56.952 1876 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.95 % Favored : 85.05 % Rotamer: Outliers : 0.19 % Allowed : 3.72 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.81 (0.19), residues: 1699 helix: -0.64 (0.22), residues: 538 sheet: -1.61 (0.32), residues: 245 loop : -4.22 (0.17), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 92 TYR 0.017 0.001 TYR M 345 PHE 0.055 0.002 PHE D 293 TRP 0.023 0.002 TRP M 396 HIS 0.012 0.001 HIS D1375 Details of bonding type rmsd covalent geometry : bond 0.00301 (14336) covalent geometry : angle 0.84054 (19437) hydrogen bonds : bond 0.04084 ( 490) hydrogen bonds : angle 5.82397 ( 1428) *********************** 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 217 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 214 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 89 CYS cc_start: 0.8188 (p) cc_final: 0.7964 (p) REVERT: N 147 LEU cc_start: 0.7251 (tp) cc_final: 0.7013 (tt) REVERT: N 208 LYS cc_start: 0.8511 (ptpp) cc_final: 0.8229 (ptpp) REVERT: M 335 MET cc_start: 0.5223 (mtt) cc_final: 0.3290 (mmt) REVERT: M 350 GLU cc_start: 0.8183 (mp0) cc_final: 0.7492 (pt0) REVERT: M 512 MET cc_start: 0.4209 (tpt) cc_final: 0.3879 (tpt) REVERT: D 43 HIS cc_start: 0.5605 (p90) cc_final: 0.5031 (t-170) REVERT: D 86 TYR cc_start: 0.4549 (t80) cc_final: 0.3079 (m-80) REVERT: D 253 ASP cc_start: 0.7184 (p0) cc_final: 0.6890 (p0) REVERT: D 397 TYR cc_start: 0.7831 (m-10) cc_final: 0.7405 (m-80) REVERT: D 862 LYS cc_start: 0.7934 (mmpt) cc_final: 0.7143 (mmtm) REVERT: D 1226 MET cc_start: 0.6752 (ptp) cc_final: 0.6490 (ptp) REVERT: D 1550 TYR cc_start: 0.7051 (m-80) cc_final: 0.6731 (m-80) outliers start: 3 outliers final: 1 residues processed: 217 average time/residue: 0.1154 time to fit residues: 36.4200 Evaluate side-chains 156 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 70 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 117 optimal weight: 0.1980 chunk 5 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 315 HIS ** M 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.120109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.112663 restraints weight = 61473.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.113788 restraints weight = 41144.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.114581 restraints weight = 29512.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.114986 restraints weight = 22567.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.115386 restraints weight = 18815.237| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14336 Z= 0.198 Angle : 0.924 11.869 19437 Z= 0.474 Chirality : 0.051 0.254 2173 Planarity : 0.007 0.098 2492 Dihedral : 7.854 57.112 1876 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.72 % Favored : 81.28 % Rotamer: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.97 (0.19), residues: 1699 helix: -0.86 (0.22), residues: 535 sheet: -1.77 (0.30), residues: 276 loop : -4.28 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 481 TYR 0.023 0.002 TYR M 345 PHE 0.035 0.003 PHE D 293 TRP 0.037 0.002 TRP D1548 HIS 0.017 0.002 HIS D1375 Details of bonding type rmsd covalent geometry : bond 0.00445 (14336) covalent geometry : angle 0.92407 (19437) hydrogen bonds : bond 0.04876 ( 490) hydrogen bonds : angle 6.13043 ( 1428) *********************** 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 187 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 19 LEU cc_start: 0.6652 (pp) cc_final: 0.6284 (pp) REVERT: N 208 LYS cc_start: 0.8663 (ptpp) cc_final: 0.8373 (ptpp) REVERT: M 335 MET cc_start: 0.5093 (mtt) cc_final: 0.3253 (mmt) REVERT: M 350 GLU cc_start: 0.8090 (mp0) cc_final: 0.7393 (pt0) REVERT: D 43 HIS cc_start: 0.5199 (p90) cc_final: 0.4263 (t-170) REVERT: D 86 TYR cc_start: 0.4623 (t80) cc_final: 0.2656 (m-80) REVERT: D 177 MET cc_start: 0.9082 (mpp) cc_final: 0.8490 (mpp) REVERT: D 253 ASP cc_start: 0.7495 (p0) cc_final: 0.7208 (p0) REVERT: D 397 TYR cc_start: 0.8005 (m-10) cc_final: 0.7555 (m-80) REVERT: D 1226 MET cc_start: 0.6732 (ptp) cc_final: 0.6522 (ptp) REVERT: D 1435 LEU cc_start: 0.8234 (pt) cc_final: 0.7562 (pp) REVERT: D 1550 TYR cc_start: 0.7118 (m-80) cc_final: 0.6874 (m-80) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1218 time to fit residues: 33.6144 Evaluate side-chains 143 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 132 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 6 optimal weight: 0.0970 chunk 50 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 170 optimal weight: 0.6980 overall best weight: 1.5382 ------------------------------------------------------------------------------- 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 349 HIS ** N 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 399 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** D 298 ASN ** 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 = 0.4068 r_free = 0.4068 target = 0.122352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.114861 restraints weight = 60723.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.115983 restraints weight = 40222.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.116796 restraints weight = 28968.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.117391 restraints weight = 22014.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.117696 restraints weight = 17705.574| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14336 Z= 0.160 Angle : 0.876 14.389 19437 Z= 0.444 Chirality : 0.050 0.247 2173 Planarity : 0.007 0.093 2492 Dihedral : 7.590 56.925 1876 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.30 % Favored : 83.70 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.85 (0.19), residues: 1699 helix: -0.73 (0.22), residues: 537 sheet: -1.66 (0.32), residues: 250 loop : -4.20 (0.17), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D1407 TYR 0.021 0.002 TYR M 208 PHE 0.056 0.002 PHE D 293 TRP 0.060 0.002 TRP M 396 HIS 0.018 0.002 HIS D1504 Details of bonding type rmsd covalent geometry : bond 0.00350 (14336) covalent geometry : angle 0.87577 (19437) hydrogen bonds : bond 0.04511 ( 490) hydrogen bonds : angle 5.98281 ( 1428) *********************** 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 184 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: N 19 LEU cc_start: 0.6725 (pp) cc_final: 0.6384 (pp) REVERT: N 147 LEU cc_start: 0.7780 (tp) cc_final: 0.7429 (tt) REVERT: N 208 LYS cc_start: 0.8516 (ptpp) cc_final: 0.8264 (ptpp) REVERT: N 319 MET cc_start: 0.4968 (mpp) cc_final: 0.4709 (mpp) REVERT: M 335 MET cc_start: 0.5036 (mtt) cc_final: 0.3188 (mmt) REVERT: M 350 GLU cc_start: 0.8087 (mp0) cc_final: 0.7773 (mp0) REVERT: M 512 MET cc_start: 0.4144 (tpt) cc_final: 0.3852 (tpt) REVERT: M 530 MET cc_start: 0.7417 (mmt) cc_final: 0.6936 (mmm) REVERT: D 43 HIS cc_start: 0.5229 (p90) cc_final: 0.4586 (t70) REVERT: D 86 TYR cc_start: 0.4439 (t80) cc_final: 0.2589 (m-80) REVERT: D 177 MET cc_start: 0.9063 (mpp) cc_final: 0.8545 (mpp) REVERT: D 181 MET cc_start: 0.8489 (tpp) cc_final: 0.8092 (tpp) REVERT: D 190 LEU cc_start: 0.8453 (tp) cc_final: 0.8240 (tp) REVERT: D 397 TYR cc_start: 0.7886 (m-10) cc_final: 0.7494 (m-80) REVERT: D 862 LYS cc_start: 0.7946 (mmpt) cc_final: 0.7257 (mmtm) REVERT: D 1435 LEU cc_start: 0.8020 (pt) cc_final: 0.7408 (pp) REVERT: D 1550 TYR cc_start: 0.7197 (m-80) cc_final: 0.6686 (m-80) REVERT: D 1553 MET cc_start: 0.7852 (mmm) cc_final: 0.7646 (mmt) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1219 time to fit residues: 33.3892 Evaluate side-chains 148 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 8 optimal weight: 0.9980 chunk 131 optimal weight: 0.5980 chunk 71 optimal weight: 0.0870 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- 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 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 193 HIS ** M 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 981 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.124978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.117680 restraints weight = 60848.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.118778 restraints weight = 41136.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.119567 restraints weight = 29729.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.120122 restraints weight = 22866.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.120504 restraints weight = 18543.879| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14336 Z= 0.145 Angle : 0.856 13.957 19437 Z= 0.430 Chirality : 0.049 0.223 2173 Planarity : 0.007 0.086 2492 Dihedral : 7.169 56.847 1876 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.72 % Favored : 84.28 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.71 (0.19), residues: 1699 helix: -0.62 (0.23), residues: 541 sheet: -1.57 (0.32), residues: 246 loop : -4.12 (0.17), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 481 TYR 0.019 0.002 TYR M 345 PHE 0.048 0.002 PHE D 293 TRP 0.048 0.002 TRP M 396 HIS 0.014 0.001 HIS D1504 Details of bonding type rmsd covalent geometry : bond 0.00311 (14336) covalent geometry : angle 0.85570 (19437) hydrogen bonds : bond 0.04128 ( 490) hydrogen bonds : angle 5.87829 ( 1428) *********************** 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 to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: N 19 LEU cc_start: 0.6692 (pp) cc_final: 0.6378 (pp) REVERT: N 89 CYS cc_start: 0.8097 (p) cc_final: 0.7805 (p) REVERT: N 147 LEU cc_start: 0.7471 (tp) cc_final: 0.7127 (tt) REVERT: N 319 MET cc_start: 0.5067 (mpp) cc_final: 0.4762 (mpp) REVERT: M 335 MET cc_start: 0.5188 (mtt) cc_final: 0.3262 (mmt) REVERT: M 512 MET cc_start: 0.4044 (tpt) cc_final: 0.3754 (tpt) REVERT: M 530 MET cc_start: 0.7513 (mmt) cc_final: 0.7056 (mmm) REVERT: D 43 HIS cc_start: 0.5398 (p90) cc_final: 0.4735 (t-170) REVERT: D 177 MET cc_start: 0.8954 (mpp) cc_final: 0.8497 (mpp) REVERT: D 181 MET cc_start: 0.8492 (tpp) cc_final: 0.8054 (tpp) REVERT: D 190 LEU cc_start: 0.8407 (tp) cc_final: 0.8173 (tp) REVERT: D 397 TYR cc_start: 0.7904 (m-10) cc_final: 0.7548 (m-80) REVERT: D 862 LYS cc_start: 0.8052 (mmpt) cc_final: 0.7266 (mmtm) REVERT: D 1391 MET cc_start: 0.7392 (mpp) cc_final: 0.7013 (mpp) REVERT: D 1550 TYR cc_start: 0.7141 (m-80) cc_final: 0.6647 (m-80) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1199 time to fit residues: 35.9473 Evaluate side-chains 147 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 143 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 111 optimal weight: 0.4980 chunk 63 optimal weight: 9.9990 chunk 159 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 205 HIS ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 518 HIS D 298 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.125427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.118145 restraints weight = 60548.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.119225 restraints weight = 40814.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.120023 restraints weight = 29703.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.120558 restraints weight = 22836.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.121006 restraints weight = 18521.879| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.4793 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= 0.143 Angle : 0.849 13.101 19437 Z= 0.426 Chirality : 0.049 0.216 2173 Planarity : 0.007 0.081 2492 Dihedral : 7.043 56.025 1876 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.72 % Favored : 84.28 % 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 : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.63 (0.19), residues: 1699 helix: -0.59 (0.22), residues: 545 sheet: -1.54 (0.32), residues: 246 loop : -4.04 (0.18), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 481 TYR 0.020 0.001 TYR M 345 PHE 0.050 0.002 PHE D 293 TRP 0.036 0.002 TRP M 396 HIS 0.010 0.001 HIS N 363 Details of bonding type rmsd covalent geometry : bond 0.00307 (14336) covalent geometry : angle 0.84940 (19437) hydrogen bonds : bond 0.04130 ( 490) hydrogen bonds : angle 5.79423 ( 1428) ********************** 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 to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 89 CYS cc_start: 0.7986 (p) cc_final: 0.7705 (p) REVERT: N 147 LEU cc_start: 0.7309 (tp) cc_final: 0.7020 (tt) REVERT: M 335 MET cc_start: 0.5162 (mtt) cc_final: 0.3247 (mmt) REVERT: M 512 MET cc_start: 0.4075 (tpt) cc_final: 0.3866 (tpt) REVERT: M 530 MET cc_start: 0.7534 (mmt) cc_final: 0.7138 (mmm) REVERT: D 43 HIS cc_start: 0.5357 (p90) cc_final: 0.4940 (t-170) REVERT: D 152 MET cc_start: 0.8252 (mpp) cc_final: 0.7890 (mpp) REVERT: D 177 MET cc_start: 0.8964 (mpp) cc_final: 0.8707 (mpp) REVERT: D 181 MET cc_start: 0.8491 (tpp) cc_final: 0.8272 (tpp) REVERT: D 190 LEU cc_start: 0.8389 (tp) cc_final: 0.8145 (tp) REVERT: D 397 TYR cc_start: 0.7913 (m-10) cc_final: 0.7571 (m-80) REVERT: D 862 LYS cc_start: 0.8051 (mmpt) cc_final: 0.7308 (mmtm) REVERT: D 1234 MET cc_start: 0.5575 (tpt) cc_final: 0.4981 (tpp) REVERT: D 1550 TYR cc_start: 0.7097 (m-80) cc_final: 0.6701 (m-80) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1144 time to fit residues: 33.7014 Evaluate side-chains 147 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 127 optimal weight: 3.9990 chunk 143 optimal weight: 0.0030 chunk 19 optimal weight: 4.9990 chunk 160 optimal weight: 0.0270 chunk 65 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 overall best weight: 1.5852 ------------------------------------------------------------------------------- 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 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 518 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.123494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.117000 restraints weight = 61034.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.117590 restraints weight = 47751.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.117842 restraints weight = 40715.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.118666 restraints weight = 32138.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.118651 restraints weight = 26935.079| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14336 Z= 0.156 Angle : 0.860 11.729 19437 Z= 0.437 Chirality : 0.049 0.219 2173 Planarity : 0.007 0.088 2492 Dihedral : 7.120 56.073 1876 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.07 % Favored : 82.93 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.64 (0.19), residues: 1699 helix: -0.62 (0.22), residues: 546 sheet: -1.59 (0.32), residues: 248 loop : -4.02 (0.18), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 481 TYR 0.021 0.002 TYR M 345 PHE 0.049 0.002 PHE D 293 TRP 0.042 0.002 TRP M 396 HIS 0.008 0.002 HIS D1504 Details of bonding type rmsd covalent geometry : bond 0.00344 (14336) covalent geometry : angle 0.86018 (19437) hydrogen bonds : bond 0.04276 ( 490) hydrogen bonds : angle 5.82744 ( 1428) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1921.45 seconds wall clock time: 34 minutes 18.23 seconds (2058.23 seconds total)