Starting phenix.real_space_refine on Fri Aug 22 22:06:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uph_42448/08_2025/8uph_42448.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uph_42448/08_2025/8uph_42448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uph_42448/08_2025/8uph_42448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uph_42448/08_2025/8uph_42448.map" model { file = "/net/cci-nas-00/data/ceres_data/8uph_42448/08_2025/8uph_42448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uph_42448/08_2025/8uph_42448.cif" } resolution = 4.13 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= -0.000 sd= 0.007 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 19 5.16 5 C 5140 2.51 5 N 1473 2.21 5 O 1489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8121 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4101 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 501} Chain: "B" Number of atoms: 3934 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 516, 3924 Classifications: {'peptide': 516} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 480} Conformer: "B" Number of residues, atoms: 516, 3924 Classifications: {'peptide': 516} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 480} bond proxies already assigned to first conformer: 3997 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'BLA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'BLA': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS B 315 " occ=0.52 ... (18 atoms not shown) pdb=" NE2BHIS B 315 " occ=0.48 Time building chain proxies: 3.08, per 1000 atoms: 0.38 Number of scatterers: 8121 At special positions: 0 Unit cell: (81.024, 116.472, 163.736, 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 19 16.00 O 1489 8.00 N 1473 7.00 C 5140 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 425.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 11 sheets defined 45.6% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 removed outlier: 3.584A pdb=" N ARG A 15 " --> pdb=" O GLN A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 54 through 59 removed outlier: 3.909A pdb=" N LEU A 58 " --> pdb=" O PRO A 54 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 59 " --> pdb=" O PRO A 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 54 through 59' Processing helix chain 'A' and resid 62 through 67 removed outlier: 3.600A pdb=" N VAL A 66 " --> pdb=" O THR A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 74 removed outlier: 3.961A pdb=" N GLN A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 82 removed outlier: 3.580A pdb=" N LEU A 78 " --> pdb=" O GLN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 130 removed outlier: 4.099A pdb=" N THR A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 154 Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 194 through 202 Processing helix chain 'A' and resid 242 through 253 removed outlier: 3.603A pdb=" N MET A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 330 removed outlier: 3.888A pdb=" N VAL A 292 " --> pdb=" O ARG A 288 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR A 294 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Proline residue: A 322 - end of helix removed outlier: 3.637A pdb=" N GLY A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 340 Processing helix chain 'A' and resid 340 through 346 removed outlier: 3.716A pdb=" N VAL A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 340 through 346' Processing helix chain 'A' and resid 369 through 381 Processing helix chain 'A' and resid 399 through 403 removed outlier: 4.079A pdb=" N ALA A 403 " --> pdb=" O PRO A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 546 removed outlier: 3.900A pdb=" N LEU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) Proline residue: A 528 - end of helix removed outlier: 3.831A pdb=" N MET A 540 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU A 541 " --> pdb=" O GLY A 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 16 removed outlier: 3.536A pdb=" N GLU B 16 " --> pdb=" O GLN B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.897A pdb=" N LEU B 21 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY B 22 " --> pdb=" O HIS B 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 18 through 22' Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 62 through 66 removed outlier: 3.792A pdb=" N GLN B 65 " --> pdb=" O THR B 62 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B 66 " --> pdb=" O ALA B 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 66' Processing helix chain 'B' and resid 74 through 82 Processing helix chain 'B' and resid 116 through 130 removed outlier: 4.009A pdb=" N THR B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA B 121 " --> pdb=" O MET B 117 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 154 removed outlier: 3.583A pdb=" N LEU B 141 " --> pdb=" O GLY B 137 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 142 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN B 143 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR B 148 " --> pdb=" O THR B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 194 through 204 removed outlier: 3.863A pdb=" N ARG B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 253 removed outlier: 3.723A pdb=" N LEU B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU B 247 " --> pdb=" O PRO B 243 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR B 248 " --> pdb=" O ILE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 327 removed outlier: 3.789A pdb=" N LEU B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA B 298 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU B 299 " --> pdb=" O GLN B 295 " (cutoff:3.500A) Proline residue: B 322 - end of helix Processing helix chain 'B' and resid 332 through 340 Processing helix chain 'B' and resid 344 through 348 removed outlier: 3.535A pdb=" N LEU B 347 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 380 removed outlier: 3.539A pdb=" N VAL B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU B 374 " --> pdb=" O MET B 370 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 375 " --> pdb=" O ASP B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 398 removed outlier: 4.596A pdb=" N LEU B 397 " --> pdb=" O ARG B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 403 removed outlier: 3.988A pdb=" N ALA B 402 " --> pdb=" O TYR B 398 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA B 403 " --> pdb=" O PRO B 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 398 through 403' Processing helix chain 'B' and resid 476 through 524 removed outlier: 3.549A pdb=" N ALA B 480 " --> pdb=" O ARG B 476 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLY B 491 " --> pdb=" O SER B 487 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 492 " --> pdb=" O ALA B 488 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU B 494 " --> pdb=" O ILE B 490 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 removed outlier: 3.658A pdb=" N VAL A 220 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 43 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU A 41 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ALA A 32 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL A 43 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU A 30 " --> pdb=" O VAL A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 188 removed outlier: 3.645A pdb=" N ARG A 207 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 362 through 365 removed outlier: 3.650A pdb=" N LEU A 425 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 412 " --> pdb=" O TRP A 426 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 391 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 433 through 438 removed outlier: 4.409A pdb=" N ARG A 433 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 467 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 435 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU A 465 " --> pdb=" O ILE A 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 446 through 447 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 33 removed outlier: 3.502A pdb=" N VAL B 29 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 105 " --> pdb=" O HIS B 98 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS B 98 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B 107 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 96 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 84 " --> pdb=" O ALA B 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 188 removed outlier: 5.786A pdb=" N VAL B 171 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG B 162 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA B 173 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG B 157 " --> pdb=" O HIS B 275 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TRP B 269 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LEU B 268 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS B 264 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY B 270 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 259 " --> pdb=" O ARG B 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 362 through 365 removed outlier: 3.757A pdb=" N GLY B 352 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 410 " --> pdb=" O ARG B 428 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 433 through 438 removed outlier: 3.848A pdb=" N ARG B 433 " --> pdb=" O VAL B 467 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 446 through 447 405 hydrogen bonds defined for protein. 1135 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: 1.61 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1515 1.32 - 1.44: 1985 1.44 - 1.56: 4772 1.56 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 8304 Sorted by residual: bond pdb=" C1D BLA A 801 " pdb=" CHD BLA A 801 " ideal model delta sigma weight residual 1.440 1.339 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C1D BLA B 801 " pdb=" CHD BLA B 801 " ideal model delta sigma weight residual 1.440 1.339 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" C3C BLA A 801 " pdb=" CAC BLA A 801 " ideal model delta sigma weight residual 1.458 1.360 0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C3C BLA A 801 " pdb=" C4C BLA A 801 " ideal model delta sigma weight residual 1.471 1.375 0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C3C BLA B 801 " pdb=" C4C BLA B 801 " ideal model delta sigma weight residual 1.471 1.389 0.082 2.00e-02 2.50e+03 1.70e+01 ... (remaining 8299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 10987 1.90 - 3.79: 280 3.79 - 5.69: 34 5.69 - 7.58: 14 7.58 - 9.48: 4 Bond angle restraints: 11319 Sorted by residual: angle pdb=" CA ARG B 502 " pdb=" CB ARG B 502 " pdb=" CG ARG B 502 " ideal model delta sigma weight residual 114.10 123.58 -9.48 2.00e+00 2.50e-01 2.25e+01 angle pdb=" C GLU B 501 " pdb=" N ARG B 502 " pdb=" CA ARG B 502 " ideal model delta sigma weight residual 121.58 114.87 6.71 1.95e+00 2.63e-01 1.18e+01 angle pdb=" C1C BLA A 801 " pdb=" C2C BLA A 801 " pdb=" CMC BLA A 801 " ideal model delta sigma weight residual 121.37 130.29 -8.92 3.00e+00 1.11e-01 8.85e+00 angle pdb=" C GLY A 518 " pdb=" N HIS A 519 " pdb=" CA HIS A 519 " ideal model delta sigma weight residual 121.58 116.26 5.32 1.95e+00 2.63e-01 7.43e+00 angle pdb=" C GLN B 65 " pdb=" N VAL B 66 " pdb=" CA VAL B 66 " ideal model delta sigma weight residual 122.66 120.10 2.56 9.70e-01 1.06e+00 6.96e+00 ... (remaining 11314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 4525 17.42 - 34.85: 411 34.85 - 52.27: 73 52.27 - 69.69: 12 69.69 - 87.11: 11 Dihedral angle restraints: 5032 sinusoidal: 2014 harmonic: 3018 Sorted by residual: dihedral pdb=" CA ARG B 502 " pdb=" C ARG B 502 " pdb=" N LEU B 503 " pdb=" CA LEU B 503 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA LYS A 475 " pdb=" C LYS A 475 " pdb=" N ARG A 476 " pdb=" CA ARG A 476 " ideal model delta harmonic sigma weight residual -180.00 -155.41 -24.59 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA LEU B 489 " pdb=" C LEU B 489 " pdb=" N ILE B 490 " pdb=" CA ILE B 490 " ideal model delta harmonic sigma weight residual 180.00 159.01 20.99 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 5029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1032 0.050 - 0.100: 192 0.100 - 0.150: 43 0.150 - 0.200: 0 0.200 - 0.250: 1 Chirality restraints: 1268 Sorted by residual: chirality pdb=" CA ARG B 502 " pdb=" N ARG B 502 " pdb=" C ARG B 502 " pdb=" CB ARG B 502 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ASP B 265 " pdb=" N ASP B 265 " pdb=" C ASP B 265 " pdb=" CB ASP B 265 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CB ILE A 490 " pdb=" CA ILE A 490 " pdb=" CG1 ILE A 490 " pdb=" CG2 ILE A 490 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 1265 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C BLA A 801 " -0.127 2.00e-02 2.50e+03 4.54e-01 5.14e+03 pdb=" C1D BLA A 801 " 0.011 2.00e-02 2.50e+03 pdb=" C2C BLA A 801 " 0.163 2.00e-02 2.50e+03 pdb=" C3C BLA A 801 " -0.237 2.00e-02 2.50e+03 pdb=" C4C BLA A 801 " 0.119 2.00e-02 2.50e+03 pdb=" CAC BLA A 801 " -0.880 2.00e-02 2.50e+03 pdb=" CHD BLA A 801 " 0.602 2.00e-02 2.50e+03 pdb=" CMC BLA A 801 " 0.809 2.00e-02 2.50e+03 pdb=" NC BLA A 801 " -0.075 2.00e-02 2.50e+03 pdb=" OC BLA A 801 " -0.385 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BLA B 801 " -0.130 2.00e-02 2.50e+03 3.68e-01 3.39e+03 pdb=" C1D BLA B 801 " 0.123 2.00e-02 2.50e+03 pdb=" C2C BLA B 801 " 0.131 2.00e-02 2.50e+03 pdb=" C3C BLA B 801 " -0.183 2.00e-02 2.50e+03 pdb=" C4C BLA B 801 " 0.036 2.00e-02 2.50e+03 pdb=" CAC BLA B 801 " -0.663 2.00e-02 2.50e+03 pdb=" CHD BLA B 801 " 0.513 2.00e-02 2.50e+03 pdb=" CMC BLA B 801 " 0.663 2.00e-02 2.50e+03 pdb=" NC BLA B 801 " -0.310 2.00e-02 2.50e+03 pdb=" OC BLA B 801 " -0.179 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB BLA A 801 " -0.281 2.00e-02 2.50e+03 3.34e-01 2.79e+03 pdb=" OB BLA A 801 " -0.172 2.00e-02 2.50e+03 pdb=" C1B BLA A 801 " -0.168 2.00e-02 2.50e+03 pdb=" C2B BLA A 801 " -0.149 2.00e-02 2.50e+03 pdb=" C3B BLA A 801 " 0.167 2.00e-02 2.50e+03 pdb=" C4A BLA A 801 " 0.567 2.00e-02 2.50e+03 pdb=" C4B BLA A 801 " -0.103 2.00e-02 2.50e+03 pdb=" CAB BLA A 801 " 0.645 2.00e-02 2.50e+03 pdb=" CHB BLA A 801 " -0.090 2.00e-02 2.50e+03 pdb=" CMB BLA A 801 " -0.415 2.00e-02 2.50e+03 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1476 2.77 - 3.30: 8226 3.30 - 3.83: 13593 3.83 - 4.37: 14603 4.37 - 4.90: 24498 Nonbonded interactions: 62396 Sorted by model distance: nonbonded pdb=" O ARG A 127 " pdb=" OG SER A 130 " model vdw 2.236 3.040 nonbonded pdb=" O GLY A 330 " pdb=" NH1 ARG A 495 " model vdw 2.252 3.120 nonbonded pdb=" O GLU B 505 " pdb=" OG SER B 508 " model vdw 2.252 3.040 nonbonded pdb=" O ALA A 516 " pdb=" OG1 THR A 520 " model vdw 2.262 3.040 nonbonded pdb=" O PHE B 385 " pdb=" NH1 ARG B 415 " model vdw 2.274 3.120 ... (remaining 62391 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 314 or resid 316 through 524 or resid 801)) selection = (chain 'B' and (resid 9 through 314 or resid 316 through 801)) } 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=0.48 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.210 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:1.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 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 : 0.005 0.101 8306 Z= 0.258 Angle : 0.714 9.477 11319 Z= 0.352 Chirality : 0.040 0.250 1268 Planarity : 0.021 0.454 1488 Dihedral : 14.178 87.112 3084 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.29 % Favored : 97.62 % Rotamer: Outliers : 0.12 % Allowed : 0.37 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.18 (0.25), residues: 1053 helix: 0.39 (0.26), residues: 393 sheet: 0.35 (0.38), residues: 170 loop : -0.62 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 530 TYR 0.013 0.001 TYR B 27 PHE 0.020 0.001 PHE B 517 TRP 0.031 0.001 TRP B 72 HIS 0.015 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 8304) covalent geometry : angle 0.71437 (11319) hydrogen bonds : bond 0.21020 ( 405) hydrogen bonds : angle 8.53805 ( 1135) Misc. bond : bond 0.08193 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 345 LEU cc_start: 0.9388 (mt) cc_final: 0.9114 (mt) REVERT: A 362 LEU cc_start: 0.9222 (tp) cc_final: 0.8897 (tt) REVERT: B 252 MET cc_start: 0.9233 (tpp) cc_final: 0.8682 (tpp) REVERT: B 290 CYS cc_start: 0.9408 (m) cc_final: 0.9135 (m) outliers start: 1 outliers final: 1 residues processed: 64 average time/residue: 0.1069 time to fit residues: 9.3483 Evaluate side-chains 50 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.060026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.038415 restraints weight = 149155.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.040424 restraints weight = 49604.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.041803 restraints weight = 28314.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.042755 restraints weight = 20055.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.043299 restraints weight = 16009.325| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8306 Z= 0.131 Angle : 0.655 10.411 11319 Z= 0.323 Chirality : 0.040 0.155 1268 Planarity : 0.006 0.049 1488 Dihedral : 6.703 74.161 1215 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.25 % Allowed : 3.93 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.15 (0.25), residues: 1053 helix: 0.57 (0.26), residues: 394 sheet: 0.39 (0.37), residues: 180 loop : -0.80 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 150 TYR 0.012 0.001 TYR B 161 PHE 0.019 0.001 PHE B 517 TRP 0.025 0.001 TRP B 72 HIS 0.015 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8304) covalent geometry : angle 0.65513 (11319) hydrogen bonds : bond 0.05394 ( 405) hydrogen bonds : angle 6.43280 ( 1135) Misc. bond : bond 0.00035 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 78 LEU cc_start: 0.9790 (tp) cc_final: 0.9316 (pp) REVERT: A 159 MET cc_start: 0.8954 (mmm) cc_final: 0.8697 (mmm) REVERT: A 345 LEU cc_start: 0.9381 (mt) cc_final: 0.9069 (mt) REVERT: A 362 LEU cc_start: 0.9144 (tp) cc_final: 0.8781 (tt) REVERT: B 180 MET cc_start: 0.7828 (ptp) cc_final: 0.7617 (ptp) REVERT: B 290 CYS cc_start: 0.9430 (m) cc_final: 0.9155 (m) outliers start: 2 outliers final: 0 residues processed: 61 average time/residue: 0.1035 time to fit residues: 8.7537 Evaluate side-chains 45 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 43 optimal weight: 0.0010 chunk 53 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 0.1980 chunk 49 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.060104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.038928 restraints weight = 97235.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.040670 restraints weight = 42022.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.041871 restraints weight = 26199.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.042595 restraints weight = 19455.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.043142 restraints weight = 16257.165| |-----------------------------------------------------------------------------| r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8306 Z= 0.122 Angle : 0.625 9.214 11319 Z= 0.308 Chirality : 0.040 0.155 1268 Planarity : 0.005 0.049 1488 Dihedral : 6.461 74.246 1215 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.12 (0.25), residues: 1053 helix: 0.63 (0.26), residues: 387 sheet: 0.49 (0.38), residues: 180 loop : -0.82 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 530 TYR 0.010 0.001 TYR B 161 PHE 0.018 0.001 PHE B 517 TRP 0.014 0.001 TRP A 72 HIS 0.013 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8304) covalent geometry : angle 0.62478 (11319) hydrogen bonds : bond 0.05164 ( 405) hydrogen bonds : angle 6.09927 ( 1135) Misc. bond : bond 0.00099 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 LYS cc_start: 0.9417 (ptpp) cc_final: 0.9141 (ptpp) REVERT: A 345 LEU cc_start: 0.9405 (mt) cc_final: 0.9086 (mt) REVERT: A 362 LEU cc_start: 0.9131 (tp) cc_final: 0.8780 (tt) REVERT: A 370 MET cc_start: 0.9266 (pmm) cc_final: 0.9050 (pmm) REVERT: B 180 MET cc_start: 0.8040 (ptp) cc_final: 0.7502 (mpp) REVERT: B 186 MET cc_start: 0.8547 (mmm) cc_final: 0.8153 (mmm) REVERT: B 290 CYS cc_start: 0.9438 (m) cc_final: 0.9155 (m) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1124 time to fit residues: 8.8582 Evaluate side-chains 44 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 84 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.059842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.038249 restraints weight = 123169.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.040115 restraints weight = 47333.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.041398 restraints weight = 28257.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.042165 restraints weight = 20574.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.042647 restraints weight = 17020.687| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8306 Z= 0.126 Angle : 0.616 8.956 11319 Z= 0.303 Chirality : 0.040 0.160 1268 Planarity : 0.005 0.044 1488 Dihedral : 6.430 84.423 1215 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.15 (0.25), residues: 1053 helix: 0.70 (0.26), residues: 387 sheet: 0.20 (0.37), residues: 185 loop : -0.82 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 502 TYR 0.010 0.001 TYR B 161 PHE 0.018 0.001 PHE B 517 TRP 0.015 0.001 TRP A 72 HIS 0.013 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8304) covalent geometry : angle 0.61606 (11319) hydrogen bonds : bond 0.04951 ( 405) hydrogen bonds : angle 5.90456 ( 1135) Misc. bond : bond 0.00096 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 362 LEU cc_start: 0.9122 (tp) cc_final: 0.8765 (tt) REVERT: A 370 MET cc_start: 0.9287 (pmm) cc_final: 0.9061 (pmm) REVERT: B 180 MET cc_start: 0.8063 (ptp) cc_final: 0.7523 (mpp) REVERT: B 186 MET cc_start: 0.8667 (mmm) cc_final: 0.8249 (mmm) REVERT: B 290 CYS cc_start: 0.9452 (m) cc_final: 0.9177 (m) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1123 time to fit residues: 8.6904 Evaluate side-chains 45 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 100 optimal weight: 1.9990 chunk 65 optimal weight: 0.0970 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 97 optimal weight: 0.0770 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.060089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.038590 restraints weight = 115057.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.040460 restraints weight = 45141.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.041732 restraints weight = 27317.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.042621 restraints weight = 19888.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.043121 restraints weight = 16188.048| |-----------------------------------------------------------------------------| r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8306 Z= 0.117 Angle : 0.617 8.964 11319 Z= 0.305 Chirality : 0.040 0.152 1268 Planarity : 0.005 0.044 1488 Dihedral : 6.335 85.588 1215 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.16 (0.25), residues: 1053 helix: 0.71 (0.26), residues: 385 sheet: 0.12 (0.37), residues: 185 loop : -0.80 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 495 TYR 0.011 0.001 TYR B 161 PHE 0.017 0.001 PHE B 517 TRP 0.034 0.001 TRP B 72 HIS 0.012 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8304) covalent geometry : angle 0.61686 (11319) hydrogen bonds : bond 0.04852 ( 405) hydrogen bonds : angle 5.82505 ( 1135) Misc. bond : bond 0.00076 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 345 LEU cc_start: 0.9452 (mt) cc_final: 0.9095 (mt) REVERT: A 362 LEU cc_start: 0.9137 (tp) cc_final: 0.8786 (tt) REVERT: A 370 MET cc_start: 0.9286 (pmm) cc_final: 0.9053 (pmm) REVERT: B 180 MET cc_start: 0.8091 (ptp) cc_final: 0.7598 (mpp) REVERT: B 186 MET cc_start: 0.8690 (mmm) cc_final: 0.8266 (mmm) REVERT: B 290 CYS cc_start: 0.9438 (m) cc_final: 0.9159 (m) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1237 time to fit residues: 10.0032 Evaluate side-chains 49 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 62 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.059522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.038531 restraints weight = 89509.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.040272 restraints weight = 40354.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.041413 restraints weight = 25571.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.042236 restraints weight = 19237.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.042667 restraints weight = 15935.912| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8306 Z= 0.133 Angle : 0.627 8.630 11319 Z= 0.309 Chirality : 0.040 0.150 1268 Planarity : 0.005 0.050 1488 Dihedral : 6.221 89.885 1215 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.23 (0.25), residues: 1053 helix: 0.67 (0.26), residues: 386 sheet: -0.00 (0.37), residues: 185 loop : -0.82 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 495 TYR 0.010 0.001 TYR B 161 PHE 0.012 0.001 PHE B 517 TRP 0.033 0.001 TRP B 72 HIS 0.012 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8304) covalent geometry : angle 0.62719 (11319) hydrogen bonds : bond 0.04914 ( 405) hydrogen bonds : angle 5.77470 ( 1135) Misc. bond : bond 0.00076 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 362 LEU cc_start: 0.9109 (tp) cc_final: 0.8753 (tt) REVERT: A 370 MET cc_start: 0.9294 (pmm) cc_final: 0.9049 (pmm) REVERT: B 180 MET cc_start: 0.8127 (ptp) cc_final: 0.7584 (mpp) REVERT: B 186 MET cc_start: 0.8801 (mmm) cc_final: 0.8368 (mmm) REVERT: B 290 CYS cc_start: 0.9473 (m) cc_final: 0.9187 (m) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1251 time to fit residues: 9.7200 Evaluate side-chains 45 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 66 optimal weight: 0.6980 chunk 96 optimal weight: 0.0570 chunk 33 optimal weight: 0.0370 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 22 optimal weight: 0.0370 chunk 65 optimal weight: 0.2980 chunk 86 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.2254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.061263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.039524 restraints weight = 146777.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.041564 restraints weight = 50238.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.042985 restraints weight = 28870.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.043930 restraints weight = 20302.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.044481 restraints weight = 16183.696| |-----------------------------------------------------------------------------| r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8306 Z= 0.108 Angle : 0.615 8.897 11319 Z= 0.299 Chirality : 0.040 0.149 1268 Planarity : 0.005 0.050 1488 Dihedral : 6.245 79.014 1215 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.13 (0.25), residues: 1053 helix: 0.72 (0.26), residues: 383 sheet: 0.07 (0.37), residues: 187 loop : -0.74 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 39 TYR 0.010 0.001 TYR B 161 PHE 0.014 0.001 PHE B 517 TRP 0.032 0.001 TRP B 72 HIS 0.011 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8304) covalent geometry : angle 0.61468 (11319) hydrogen bonds : bond 0.04527 ( 405) hydrogen bonds : angle 5.65668 ( 1135) Misc. bond : bond 0.00057 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 339 LYS cc_start: 0.9337 (ptpp) cc_final: 0.9079 (ptpp) REVERT: A 362 LEU cc_start: 0.9110 (tp) cc_final: 0.8752 (tt) REVERT: A 370 MET cc_start: 0.9278 (pmm) cc_final: 0.9045 (pmm) REVERT: B 180 MET cc_start: 0.8100 (ptp) cc_final: 0.7576 (mpp) REVERT: B 186 MET cc_start: 0.8798 (mmm) cc_final: 0.8343 (mmm) REVERT: B 252 MET cc_start: 0.9316 (tpp) cc_final: 0.8672 (tpp) REVERT: B 290 CYS cc_start: 0.9412 (m) cc_final: 0.9199 (m) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1080 time to fit residues: 9.8689 Evaluate side-chains 52 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 9 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 88 optimal weight: 0.5980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.057853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.036755 restraints weight = 109509.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.038446 restraints weight = 46100.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.039576 restraints weight = 28491.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.040342 restraints weight = 21232.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.040778 restraints weight = 17572.859| |-----------------------------------------------------------------------------| r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8306 Z= 0.204 Angle : 0.685 8.056 11319 Z= 0.340 Chirality : 0.041 0.189 1268 Planarity : 0.005 0.048 1488 Dihedral : 6.296 80.861 1215 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.34 (0.25), residues: 1053 helix: 0.67 (0.26), residues: 387 sheet: -0.26 (0.37), residues: 188 loop : -0.89 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 207 TYR 0.018 0.002 TYR B 27 PHE 0.014 0.002 PHE B 517 TRP 0.030 0.002 TRP B 72 HIS 0.012 0.002 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8304) covalent geometry : angle 0.68479 (11319) hydrogen bonds : bond 0.05282 ( 405) hydrogen bonds : angle 5.78714 ( 1135) Misc. bond : bond 0.00092 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 345 LEU cc_start: 0.9467 (mt) cc_final: 0.9246 (mt) REVERT: A 362 LEU cc_start: 0.9189 (tp) cc_final: 0.8838 (tt) REVERT: A 370 MET cc_start: 0.9316 (pmm) cc_final: 0.9077 (pmm) REVERT: B 180 MET cc_start: 0.8065 (ptp) cc_final: 0.7483 (mpp) REVERT: B 186 MET cc_start: 0.8912 (mmm) cc_final: 0.8308 (mmm) REVERT: B 290 CYS cc_start: 0.9662 (m) cc_final: 0.9369 (m) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1219 time to fit residues: 9.0148 Evaluate side-chains 45 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 84 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.057906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.039386 restraints weight = 162434.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.041226 restraints weight = 58088.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.041837 restraints weight = 27257.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.041663 restraints weight = 21564.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.042049 restraints weight = 20426.430| |-----------------------------------------------------------------------------| r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8306 Z= 0.172 Angle : 0.659 8.385 11319 Z= 0.328 Chirality : 0.041 0.161 1268 Planarity : 0.005 0.045 1488 Dihedral : 6.351 86.612 1215 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.40 (0.25), residues: 1053 helix: 0.64 (0.26), residues: 388 sheet: -0.35 (0.36), residues: 188 loop : -0.93 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 502 TYR 0.013 0.002 TYR B 27 PHE 0.014 0.001 PHE B 517 TRP 0.031 0.001 TRP B 72 HIS 0.011 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8304) covalent geometry : angle 0.65939 (11319) hydrogen bonds : bond 0.05132 ( 405) hydrogen bonds : angle 5.80006 ( 1135) Misc. bond : bond 0.00082 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 362 LEU cc_start: 0.9183 (tp) cc_final: 0.8828 (tt) REVERT: A 370 MET cc_start: 0.9229 (pmm) cc_final: 0.8993 (pmm) REVERT: B 180 MET cc_start: 0.8040 (ptp) cc_final: 0.7508 (mpp) REVERT: B 186 MET cc_start: 0.8959 (mmm) cc_final: 0.8281 (mmm) REVERT: B 290 CYS cc_start: 0.9659 (m) cc_final: 0.9375 (m) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1020 time to fit residues: 7.1932 Evaluate side-chains 43 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 40 optimal weight: 0.5980 chunk 21 optimal weight: 0.0870 chunk 46 optimal weight: 0.0770 chunk 18 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 33 optimal weight: 0.0970 overall best weight: 0.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 390 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.060171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.039018 restraints weight = 119263.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.040816 restraints weight = 45795.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.042084 restraints weight = 27475.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.042945 restraints weight = 19988.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.043444 restraints weight = 16256.942| |-----------------------------------------------------------------------------| r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8306 Z= 0.112 Angle : 0.641 9.020 11319 Z= 0.313 Chirality : 0.041 0.175 1268 Planarity : 0.005 0.048 1488 Dihedral : 6.281 78.402 1215 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.17 (0.25), residues: 1053 helix: 0.77 (0.26), residues: 384 sheet: -0.16 (0.36), residues: 188 loop : -0.75 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 530 TYR 0.011 0.001 TYR A 93 PHE 0.015 0.001 PHE B 517 TRP 0.034 0.001 TRP B 72 HIS 0.011 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8304) covalent geometry : angle 0.64120 (11319) hydrogen bonds : bond 0.04647 ( 405) hydrogen bonds : angle 5.66851 ( 1135) Misc. bond : bond 0.00047 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.8791 (mmm) cc_final: 0.8414 (mmm) REVERT: A 284 TYR cc_start: 0.8554 (t80) cc_final: 0.8331 (t80) REVERT: A 345 LEU cc_start: 0.9479 (mt) cc_final: 0.9244 (mt) REVERT: A 362 LEU cc_start: 0.9116 (tp) cc_final: 0.8752 (tt) REVERT: A 370 MET cc_start: 0.9222 (pmm) cc_final: 0.8985 (pmm) REVERT: B 180 MET cc_start: 0.8124 (ptp) cc_final: 0.7632 (mpp) REVERT: B 186 MET cc_start: 0.8887 (mmm) cc_final: 0.8142 (mmm) REVERT: B 252 MET cc_start: 0.9354 (tpp) cc_final: 0.8731 (tpp) REVERT: B 290 CYS cc_start: 0.9617 (m) cc_final: 0.9319 (m) REVERT: B 489 LEU cc_start: 0.9549 (tt) cc_final: 0.9069 (mt) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0948 time to fit residues: 7.8363 Evaluate side-chains 47 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 103 optimal weight: 0.8980 chunk 65 optimal weight: 0.0040 chunk 63 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 43 optimal weight: 0.0570 chunk 18 optimal weight: 3.9990 chunk 89 optimal weight: 0.0570 chunk 66 optimal weight: 0.0270 overall best weight: 0.1886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 390 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.060647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.039661 restraints weight = 124054.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.041601 restraints weight = 47066.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.042916 restraints weight = 27732.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.043759 restraints weight = 19813.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.044281 restraints weight = 15914.013| |-----------------------------------------------------------------------------| r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8306 Z= 0.108 Angle : 0.623 8.690 11319 Z= 0.302 Chirality : 0.040 0.152 1268 Planarity : 0.005 0.049 1488 Dihedral : 6.161 75.790 1215 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.06 (0.25), residues: 1053 helix: 0.80 (0.26), residues: 385 sheet: 0.09 (0.37), residues: 187 loop : -0.72 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 139 TYR 0.011 0.001 TYR B 161 PHE 0.015 0.001 PHE B 517 TRP 0.026 0.001 TRP A 72 HIS 0.011 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8304) covalent geometry : angle 0.62254 (11319) hydrogen bonds : bond 0.04456 ( 405) hydrogen bonds : angle 5.52094 ( 1135) Misc. bond : bond 0.00046 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2237.80 seconds wall clock time: 39 minutes 4.89 seconds (2344.89 seconds total)