Starting phenix.real_space_refine on Sun Jul 27 16:14:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cua_26997/07_2025/8cua_26997.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cua_26997/07_2025/8cua_26997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cua_26997/07_2025/8cua_26997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cua_26997/07_2025/8cua_26997.map" model { file = "/net/cci-nas-00/data/ceres_data/8cua_26997/07_2025/8cua_26997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cua_26997/07_2025/8cua_26997.cif" } resolution = 2.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.104 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: 6 Type Number sf(0) Gaussians Hg 3 10.96 5 K 3 8.98 5 S 63 5.16 5 C 6228 2.51 5 N 1512 2.21 5 O 1725 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9534 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3166 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 11, 'TRANS': 404} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' HG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1605 SG CYS A 269 23.791 36.895 25.246 1.00 69.82 S ATOM 2886 SG CYS A 441 25.221 34.804 25.594 1.00 76.78 S Restraints were copied for chains: C, B Time building chain proxies: 6.32, per 1000 atoms: 0.66 Number of scatterers: 9534 At special positions: 0 Unit cell: (106.5, 103.092, 78.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Hg 3 79.96 K 3 19.00 S 63 16.00 O 1725 8.00 N 1512 7.00 C 6228 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: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2310 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 3 sheets defined 86.1% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 removed outlier: 3.691A pdb=" N LEU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.831A pdb=" N ALA A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.558A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 81 removed outlier: 3.554A pdb=" N LEU A 70 " --> pdb=" O ILE A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 117 removed outlier: 3.629A pdb=" N ILE A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.519A pdb=" N LEU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 211 through 227 Processing helix chain 'A' and resid 229 through 232 removed outlier: 3.738A pdb=" N LYS A 232 " --> pdb=" O MET A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 233 through 270 removed outlier: 3.747A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.512A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.966A pdb=" N ARG A 280 " --> pdb=" O TRP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 299 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 312 through 319 Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 351 through 366 removed outlier: 3.675A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix removed outlier: 3.672A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 removed outlier: 3.624A pdb=" N LEU A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 405 removed outlier: 3.653A pdb=" N SER A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 427 removed outlier: 4.243A pdb=" N VAL A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 438 removed outlier: 4.001A pdb=" N ILE A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 3.926A pdb=" N ARG A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 477 removed outlier: 3.716A pdb=" N ASP A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 42 removed outlier: 3.691A pdb=" N LEU B 22 " --> pdb=" O ASN B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.832A pdb=" N ALA B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 66 removed outlier: 3.558A pdb=" N ILE B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 81 removed outlier: 3.554A pdb=" N LEU B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 117 removed outlier: 3.629A pdb=" N ILE B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.519A pdb=" N LEU B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 158 Processing helix chain 'B' and resid 211 through 227 Processing helix chain 'B' and resid 229 through 232 removed outlier: 3.738A pdb=" N LYS B 232 " --> pdb=" O MET B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'B' and resid 233 through 270 removed outlier: 3.749A pdb=" N TRP B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Proline residue: B 259 - end of helix removed outlier: 3.512A pdb=" N PHE B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 282 removed outlier: 3.967A pdb=" N ARG B 280 " --> pdb=" O TRP B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 299 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 312 through 319 Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 336 through 347 Processing helix chain 'B' and resid 351 through 366 removed outlier: 3.675A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Proline residue: B 360 - end of helix removed outlier: 3.672A pdb=" N THR B 364 " --> pdb=" O PRO B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 385 removed outlier: 3.624A pdb=" N LEU B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 405 removed outlier: 3.653A pdb=" N SER B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 427 removed outlier: 4.244A pdb=" N VAL B 417 " --> pdb=" O GLN B 413 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 438 removed outlier: 4.002A pdb=" N ILE B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA B 438 " --> pdb=" O THR B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 466 removed outlier: 3.926A pdb=" N ARG B 445 " --> pdb=" O CYS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 477 removed outlier: 3.715A pdb=" N ASP B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 476 " --> pdb=" O GLN B 472 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER B 477 " --> pdb=" O MET B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 42 removed outlier: 3.691A pdb=" N LEU C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.832A pdb=" N ALA C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 66 removed outlier: 3.558A pdb=" N ILE C 66 " --> pdb=" O MET C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 81 removed outlier: 3.554A pdb=" N LEU C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 117 removed outlier: 3.629A pdb=" N ILE C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.519A pdb=" N LEU C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 211 through 227 Processing helix chain 'C' and resid 229 through 232 removed outlier: 3.738A pdb=" N LYS C 232 " --> pdb=" O MET C 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 229 through 232' Processing helix chain 'C' and resid 233 through 270 removed outlier: 3.747A pdb=" N TRP C 256 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 3.513A pdb=" N PHE C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 282 removed outlier: 3.966A pdb=" N ARG C 280 " --> pdb=" O TRP C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 299 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 312 through 319 Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 336 through 347 Processing helix chain 'C' and resid 351 through 366 removed outlier: 3.676A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Proline residue: C 360 - end of helix removed outlier: 3.671A pdb=" N THR C 364 " --> pdb=" O PRO C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 385 removed outlier: 3.624A pdb=" N LEU C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL C 376 " --> pdb=" O LEU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 405 removed outlier: 3.653A pdb=" N SER C 405 " --> pdb=" O ALA C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 427 removed outlier: 4.243A pdb=" N VAL C 417 " --> pdb=" O GLN C 413 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL C 420 " --> pdb=" O LEU C 416 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 432 through 438 removed outlier: 4.002A pdb=" N ILE C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA C 438 " --> pdb=" O THR C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 466 removed outlier: 3.926A pdb=" N ARG C 445 " --> pdb=" O CYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 477 removed outlier: 3.716A pdb=" N ASP C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 476 " --> pdb=" O GLN C 472 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER C 477 " --> pdb=" O MET C 473 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 167 Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 167 708 hydrogen bonds defined for protein. 2106 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2259 1.33 - 1.45: 1629 1.45 - 1.57: 5634 1.57 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 9639 Sorted by residual: bond pdb=" N ILE A 406 " pdb=" CA ILE A 406 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.87e+00 bond pdb=" N ILE C 406 " pdb=" CA ILE C 406 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.82e+00 bond pdb=" N ILE B 406 " pdb=" CA ILE B 406 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.80e+00 bond pdb=" N CYS C 441 " pdb=" CA CYS C 441 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.30e-02 5.92e+03 7.01e+00 bond pdb=" N CYS A 441 " pdb=" CA CYS A 441 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.30e-02 5.92e+03 6.99e+00 ... (remaining 9634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 12867 1.88 - 3.76: 168 3.76 - 5.63: 36 5.63 - 7.51: 3 7.51 - 9.39: 6 Bond angle restraints: 13080 Sorted by residual: angle pdb=" CB MET C 75 " pdb=" CG MET C 75 " pdb=" SD MET C 75 " ideal model delta sigma weight residual 112.70 103.31 9.39 3.00e+00 1.11e-01 9.79e+00 angle pdb=" CB MET B 75 " pdb=" CG MET B 75 " pdb=" SD MET B 75 " ideal model delta sigma weight residual 112.70 103.33 9.37 3.00e+00 1.11e-01 9.75e+00 angle pdb=" CB MET A 75 " pdb=" CG MET A 75 " pdb=" SD MET A 75 " ideal model delta sigma weight residual 112.70 103.33 9.37 3.00e+00 1.11e-01 9.75e+00 angle pdb=" N MET C 258 " pdb=" CA MET C 258 " pdb=" C MET C 258 " ideal model delta sigma weight residual 109.81 116.17 -6.36 2.21e+00 2.05e-01 8.29e+00 angle pdb=" N MET A 258 " pdb=" CA MET A 258 " pdb=" C MET A 258 " ideal model delta sigma weight residual 109.81 116.16 -6.35 2.21e+00 2.05e-01 8.24e+00 ... (remaining 13075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 5029 15.67 - 31.34: 495 31.34 - 47.01: 164 47.01 - 62.69: 66 62.69 - 78.36: 9 Dihedral angle restraints: 5763 sinusoidal: 2184 harmonic: 3579 Sorted by residual: dihedral pdb=" CG ARG B 315 " pdb=" CD ARG B 315 " pdb=" NE ARG B 315 " pdb=" CZ ARG B 315 " ideal model delta sinusoidal sigma weight residual -90.00 -39.98 -50.02 2 1.50e+01 4.44e-03 1.25e+01 dihedral pdb=" CG ARG C 315 " pdb=" CD ARG C 315 " pdb=" NE ARG C 315 " pdb=" CZ ARG C 315 " ideal model delta sinusoidal sigma weight residual -90.00 -40.02 -49.98 2 1.50e+01 4.44e-03 1.25e+01 dihedral pdb=" CG ARG A 315 " pdb=" CD ARG A 315 " pdb=" NE ARG A 315 " pdb=" CZ ARG A 315 " ideal model delta sinusoidal sigma weight residual -90.00 -40.02 -49.98 2 1.50e+01 4.44e-03 1.25e+01 ... (remaining 5760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1105 0.031 - 0.063: 352 0.063 - 0.094: 148 0.094 - 0.125: 40 0.125 - 0.157: 14 Chirality restraints: 1659 Sorted by residual: chirality pdb=" CA LEU B 443 " pdb=" N LEU B 443 " pdb=" C LEU B 443 " pdb=" CB LEU B 443 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CA LEU A 443 " pdb=" N LEU A 443 " pdb=" C LEU A 443 " pdb=" CB LEU A 443 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA LEU C 443 " pdb=" N LEU C 443 " pdb=" C LEU C 443 " pdb=" CB LEU C 443 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 1656 not shown) Planarity restraints: 1593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 295 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" C ILE A 295 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE A 295 " 0.012 2.00e-02 2.50e+03 pdb=" N HIS A 296 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 295 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C ILE C 295 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE C 295 " -0.012 2.00e-02 2.50e+03 pdb=" N HIS C 296 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 295 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.23e+00 pdb=" C ILE B 295 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE B 295 " 0.012 2.00e-02 2.50e+03 pdb=" N HIS B 296 " 0.010 2.00e-02 2.50e+03 ... (remaining 1590 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.59: 57 2.59 - 3.23: 9248 3.23 - 3.87: 18958 3.87 - 4.50: 25091 4.50 - 5.14: 40074 Nonbonded interactions: 93428 Sorted by model distance: nonbonded pdb=" SG CYS B 441 " pdb="HG HG B 601 " model vdw 1.957 2.880 nonbonded pdb=" SG CYS C 441 " pdb="HG HG C 601 " model vdw 1.957 2.880 nonbonded pdb=" SG CYS A 441 " pdb="HG HG A 601 " model vdw 1.957 2.880 nonbonded pdb=" OD2 ASP A 368 " pdb=" O HOH A 701 " model vdw 2.226 3.040 nonbonded pdb=" OD2 ASP C 368 " pdb=" O HOH C 701 " model vdw 2.226 3.040 ... (remaining 93423 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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 individual isotropic 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: 10.130 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.680 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9639 Z= 0.226 Angle : 0.575 9.388 13080 Z= 0.345 Chirality : 0.039 0.157 1659 Planarity : 0.004 0.027 1593 Dihedral : 15.571 78.357 3453 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 21.61 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.24), residues: 1230 helix: 1.92 (0.17), residues: 963 sheet: 0.89 (0.66), residues: 48 loop : -1.20 (0.36), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 256 HIS 0.001 0.000 HIS C 41 PHE 0.007 0.001 PHE A 218 TYR 0.009 0.001 TYR B 285 ARG 0.003 0.000 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.12930 ( 708) hydrogen bonds : angle 5.13416 ( 2106) covalent geometry : bond 0.00336 ( 9639) covalent geometry : angle 0.57550 (13080) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.039 Fit side-chains REVERT: A 205 MET cc_start: 0.8426 (ptm) cc_final: 0.8177 (ptt) REVERT: A 385 ASN cc_start: 0.7509 (m-40) cc_final: 0.7298 (m110) REVERT: A 475 VAL cc_start: 0.7494 (p) cc_final: 0.7276 (m) REVERT: B 205 MET cc_start: 0.8250 (ptm) cc_final: 0.7960 (ptt) REVERT: B 315 ARG cc_start: 0.6984 (ttm-80) cc_final: 0.6409 (ttp80) REVERT: B 322 GLN cc_start: 0.7710 (mt0) cc_final: 0.7448 (tt0) REVERT: C 205 MET cc_start: 0.8319 (ptm) cc_final: 0.8055 (ptt) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 1.5309 time to fit residues: 221.6434 Evaluate side-chains 121 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 7.9990 chunk 93 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN A 366 ASN A 413 GLN A 451 ASN B 252 GLN B 413 GLN B 451 ASN C 252 GLN C 413 GLN C 451 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.168073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.122342 restraints weight = 3227.404| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 0.90 r_work: 0.3324 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9639 Z= 0.194 Angle : 0.578 7.838 13080 Z= 0.306 Chirality : 0.040 0.153 1659 Planarity : 0.004 0.030 1593 Dihedral : 3.682 16.783 1308 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.92 % Allowed : 20.37 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.24), residues: 1230 helix: 1.54 (0.17), residues: 978 sheet: 1.00 (0.65), residues: 48 loop : -1.18 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 19 HIS 0.002 0.001 HIS A 296 PHE 0.012 0.002 PHE C 99 TYR 0.013 0.002 TYR C 285 ARG 0.007 0.001 ARG B 315 Details of bonding type rmsd hydrogen bonds : bond 0.07692 ( 708) hydrogen bonds : angle 4.33979 ( 2106) covalent geometry : bond 0.00438 ( 9639) covalent geometry : angle 0.57835 (13080) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7383 (mtp-110) REVERT: A 473 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7915 (mtp) REVERT: B 115 SER cc_start: 0.7710 (t) cc_final: 0.7209 (m) REVERT: B 205 MET cc_start: 0.8653 (ptm) cc_final: 0.8363 (ptm) REVERT: B 329 MET cc_start: 0.7796 (mmt) cc_final: 0.7530 (mmt) REVERT: B 385 ASN cc_start: 0.6867 (m-40) cc_final: 0.6666 (m110) outliers start: 20 outliers final: 7 residues processed: 147 average time/residue: 1.3816 time to fit residues: 217.0555 Evaluate side-chains 138 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 472 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 72 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN C 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.166760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119388 restraints weight = 2904.140| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 0.93 r_work: 0.3250 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9639 Z= 0.146 Angle : 0.505 7.278 13080 Z= 0.266 Chirality : 0.038 0.146 1659 Planarity : 0.004 0.032 1593 Dihedral : 3.550 15.607 1308 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.31 % Allowed : 20.46 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.24), residues: 1230 helix: 1.77 (0.17), residues: 978 sheet: 1.05 (0.64), residues: 48 loop : -0.88 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 19 HIS 0.001 0.000 HIS C 296 PHE 0.016 0.001 PHE B 99 TYR 0.011 0.001 TYR C 285 ARG 0.008 0.001 ARG C 315 Details of bonding type rmsd hydrogen bonds : bond 0.06317 ( 708) hydrogen bonds : angle 4.12433 ( 2106) covalent geometry : bond 0.00300 ( 9639) covalent geometry : angle 0.50535 (13080) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 1.114 Fit side-chains REVERT: A 39 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7128 (mtp-110) REVERT: A 241 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8426 (t0) REVERT: A 385 ASN cc_start: 0.6823 (m-40) cc_final: 0.6580 (m110) REVERT: A 471 GLU cc_start: 0.8079 (pt0) cc_final: 0.7861 (pt0) REVERT: A 473 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7843 (mtp) REVERT: B 115 SER cc_start: 0.7598 (t) cc_final: 0.7091 (m) REVERT: B 205 MET cc_start: 0.8581 (ptm) cc_final: 0.8288 (ptm) REVERT: B 329 MET cc_start: 0.7681 (mmt) cc_final: 0.7436 (mmt) REVERT: C 346 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7354 (mm-30) outliers start: 24 outliers final: 10 residues processed: 151 average time/residue: 1.2699 time to fit residues: 204.7350 Evaluate side-chains 144 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 472 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 69 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN B 385 ASN C 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.165357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.117847 restraints weight = 2828.973| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 0.91 r_work: 0.3231 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9639 Z= 0.164 Angle : 0.529 7.546 13080 Z= 0.279 Chirality : 0.038 0.148 1659 Planarity : 0.004 0.035 1593 Dihedral : 3.633 15.584 1308 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.46 % Allowed : 19.60 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.24), residues: 1230 helix: 1.66 (0.17), residues: 981 sheet: 1.00 (0.64), residues: 48 loop : -0.97 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 HIS 0.001 0.001 HIS C 296 PHE 0.016 0.002 PHE B 99 TYR 0.011 0.002 TYR A 285 ARG 0.008 0.001 ARG B 315 Details of bonding type rmsd hydrogen bonds : bond 0.06934 ( 708) hydrogen bonds : angle 4.15464 ( 2106) covalent geometry : bond 0.00355 ( 9639) covalent geometry : angle 0.52860 (13080) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 1.092 Fit side-chains REVERT: A 39 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6846 (ttp-110) REVERT: A 241 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8439 (t0) REVERT: A 396 THR cc_start: 0.7527 (m) cc_final: 0.7319 (m) REVERT: A 471 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7782 (pt0) REVERT: A 473 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7804 (ttp) REVERT: B 115 SER cc_start: 0.7708 (t) cc_final: 0.7215 (m) REVERT: B 205 MET cc_start: 0.8570 (ptm) cc_final: 0.8289 (ptm) REVERT: B 329 MET cc_start: 0.7720 (mmt) cc_final: 0.7507 (mmt) REVERT: C 346 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7310 (mm-30) outliers start: 36 outliers final: 13 residues processed: 154 average time/residue: 1.2958 time to fit residues: 212.7843 Evaluate side-chains 143 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 472 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 69 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN C 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.164610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.118063 restraints weight = 2863.547| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 0.85 r_work: 0.3220 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9639 Z= 0.162 Angle : 0.525 7.507 13080 Z= 0.277 Chirality : 0.038 0.147 1659 Planarity : 0.004 0.038 1593 Dihedral : 3.637 15.525 1308 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.17 % Allowed : 18.92 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.24), residues: 1230 helix: 1.68 (0.17), residues: 981 sheet: 1.00 (0.65), residues: 48 loop : -0.95 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 HIS 0.001 0.001 HIS A 296 PHE 0.017 0.002 PHE B 99 TYR 0.011 0.002 TYR C 285 ARG 0.008 0.001 ARG C 315 Details of bonding type rmsd hydrogen bonds : bond 0.06808 ( 708) hydrogen bonds : angle 4.11142 ( 2106) covalent geometry : bond 0.00352 ( 9639) covalent geometry : angle 0.52501 (13080) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 1.038 Fit side-chains REVERT: A 39 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.6865 (ttp-110) REVERT: A 231 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7432 (mm-30) REVERT: A 241 ASN cc_start: 0.8926 (OUTLIER) cc_final: 0.8481 (t0) REVERT: A 396 THR cc_start: 0.7576 (m) cc_final: 0.7372 (m) REVERT: A 471 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7779 (pt0) REVERT: A 473 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7797 (ttp) REVERT: B 115 SER cc_start: 0.7736 (t) cc_final: 0.7253 (m) REVERT: B 205 MET cc_start: 0.8649 (ptm) cc_final: 0.8382 (ptm) REVERT: C 346 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7354 (mm-30) outliers start: 33 outliers final: 14 residues processed: 151 average time/residue: 1.2679 time to fit residues: 204.5603 Evaluate side-chains 142 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 472 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN C 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.166581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.119531 restraints weight = 2737.511| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 0.90 r_work: 0.3253 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9639 Z= 0.146 Angle : 0.506 7.309 13080 Z= 0.265 Chirality : 0.038 0.143 1659 Planarity : 0.004 0.039 1593 Dihedral : 3.580 15.420 1308 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.59 % Allowed : 19.79 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.24), residues: 1230 helix: 1.83 (0.17), residues: 978 sheet: 0.06 (0.69), residues: 54 loop : -0.66 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 19 HIS 0.001 0.001 HIS A 296 PHE 0.018 0.002 PHE B 99 TYR 0.011 0.001 TYR C 285 ARG 0.008 0.001 ARG B 315 Details of bonding type rmsd hydrogen bonds : bond 0.06268 ( 708) hydrogen bonds : angle 4.03301 ( 2106) covalent geometry : bond 0.00302 ( 9639) covalent geometry : angle 0.50561 (13080) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 1.143 Fit side-chains REVERT: A 39 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6809 (ttp-110) REVERT: A 241 ASN cc_start: 0.8849 (OUTLIER) cc_final: 0.8438 (t0) REVERT: A 396 THR cc_start: 0.7583 (m) cc_final: 0.7378 (m) REVERT: A 471 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7747 (pt0) REVERT: A 473 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7829 (mtp) REVERT: B 115 SER cc_start: 0.7632 (t) cc_final: 0.7142 (m) REVERT: B 205 MET cc_start: 0.8562 (ptm) cc_final: 0.8311 (ptm) REVERT: B 385 ASN cc_start: 0.6889 (m-40) cc_final: 0.6657 (m110) REVERT: C 346 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7295 (mm-30) outliers start: 27 outliers final: 14 residues processed: 148 average time/residue: 1.4291 time to fit residues: 226.4707 Evaluate side-chains 142 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 474 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 86 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN C 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.165899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118666 restraints weight = 2752.295| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 0.90 r_work: 0.3242 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9639 Z= 0.159 Angle : 0.529 7.445 13080 Z= 0.277 Chirality : 0.038 0.143 1659 Planarity : 0.004 0.042 1593 Dihedral : 3.621 15.488 1308 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.88 % Allowed : 19.88 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.24), residues: 1230 helix: 1.75 (0.17), residues: 981 sheet: 1.03 (0.64), residues: 48 loop : -0.97 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 19 HIS 0.001 0.001 HIS A 296 PHE 0.018 0.002 PHE B 99 TYR 0.010 0.002 TYR C 285 ARG 0.009 0.001 ARG C 315 Details of bonding type rmsd hydrogen bonds : bond 0.06665 ( 708) hydrogen bonds : angle 4.06530 ( 2106) covalent geometry : bond 0.00343 ( 9639) covalent geometry : angle 0.52890 (13080) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.954 Fit side-chains REVERT: A 39 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.6832 (ttp-110) REVERT: A 231 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7497 (mm-30) REVERT: A 241 ASN cc_start: 0.8869 (OUTLIER) cc_final: 0.8413 (t0) REVERT: A 471 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7726 (pt0) REVERT: A 473 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7792 (mtp) REVERT: B 115 SER cc_start: 0.7669 (t) cc_final: 0.7180 (m) REVERT: B 205 MET cc_start: 0.8556 (ptm) cc_final: 0.8278 (ptm) REVERT: B 346 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7013 (mt-10) REVERT: B 385 ASN cc_start: 0.6930 (m-40) cc_final: 0.6650 (m110) REVERT: C 272 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6967 (mt-10) REVERT: C 346 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7354 (mm-30) outliers start: 30 outliers final: 14 residues processed: 147 average time/residue: 1.3396 time to fit residues: 209.9055 Evaluate side-chains 145 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 474 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 109 optimal weight: 0.0470 chunk 6 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 103 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN C 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.168695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122228 restraints weight = 2737.363| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 0.90 r_work: 0.3294 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9639 Z= 0.125 Angle : 0.481 7.077 13080 Z= 0.250 Chirality : 0.037 0.136 1659 Planarity : 0.004 0.040 1593 Dihedral : 3.467 15.150 1308 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.59 % Allowed : 19.88 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.24), residues: 1230 helix: 2.05 (0.17), residues: 972 sheet: 0.07 (0.71), residues: 54 loop : -0.41 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 19 HIS 0.000 0.000 HIS C 296 PHE 0.018 0.001 PHE B 99 TYR 0.009 0.001 TYR B 285 ARG 0.009 0.001 ARG B 315 Details of bonding type rmsd hydrogen bonds : bond 0.05385 ( 708) hydrogen bonds : angle 3.89329 ( 2106) covalent geometry : bond 0.00241 ( 9639) covalent geometry : angle 0.48091 (13080) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 1.539 Fit side-chains REVERT: A 39 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.7088 (mtp-110) REVERT: A 231 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7316 (mm-30) REVERT: A 241 ASN cc_start: 0.8803 (OUTLIER) cc_final: 0.8473 (t0) REVERT: A 346 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7243 (mt-10) REVERT: A 396 THR cc_start: 0.7617 (m) cc_final: 0.7411 (m) REVERT: B 205 MET cc_start: 0.8516 (ptm) cc_final: 0.8270 (ptm) REVERT: B 346 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.6920 (mt-10) REVERT: B 385 ASN cc_start: 0.6889 (m-40) cc_final: 0.6594 (m110) REVERT: C 272 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6805 (mt-10) REVERT: C 346 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7289 (mm-30) outliers start: 27 outliers final: 8 residues processed: 150 average time/residue: 1.5356 time to fit residues: 246.2678 Evaluate side-chains 138 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 346 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 19 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN C 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.167134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.120264 restraints weight = 2699.700| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 0.89 r_work: 0.3263 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9639 Z= 0.142 Angle : 0.509 7.172 13080 Z= 0.264 Chirality : 0.038 0.140 1659 Planarity : 0.004 0.044 1593 Dihedral : 3.527 15.358 1308 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.83 % Allowed : 20.37 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.24), residues: 1230 helix: 1.99 (0.17), residues: 969 sheet: 0.05 (0.70), residues: 54 loop : -0.49 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 19 HIS 0.001 0.000 HIS A 296 PHE 0.019 0.001 PHE B 99 TYR 0.011 0.001 TYR A 285 ARG 0.009 0.001 ARG B 315 Details of bonding type rmsd hydrogen bonds : bond 0.06066 ( 708) hydrogen bonds : angle 3.95907 ( 2106) covalent geometry : bond 0.00294 ( 9639) covalent geometry : angle 0.50916 (13080) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.106 Fit side-chains REVERT: A 39 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.7090 (mtp-110) REVERT: A 231 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7467 (mm-30) REVERT: A 241 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8469 (t0) REVERT: A 396 THR cc_start: 0.7595 (m) cc_final: 0.7395 (m) REVERT: B 205 MET cc_start: 0.8512 (ptm) cc_final: 0.8265 (ptm) REVERT: B 346 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6977 (mt-10) REVERT: B 385 ASN cc_start: 0.6889 (m-40) cc_final: 0.6591 (m110) REVERT: B 396 THR cc_start: 0.7570 (m) cc_final: 0.7279 (t) REVERT: C 115 SER cc_start: 0.7640 (t) cc_final: 0.7036 (m) REVERT: C 272 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6846 (mt-10) REVERT: C 346 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7249 (mm-30) outliers start: 19 outliers final: 10 residues processed: 145 average time/residue: 1.2428 time to fit residues: 192.8280 Evaluate side-chains 143 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 346 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 39 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN C 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.167820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.120997 restraints weight = 2742.596| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 0.90 r_work: 0.3275 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9639 Z= 0.136 Angle : 0.502 7.112 13080 Z= 0.259 Chirality : 0.037 0.138 1659 Planarity : 0.004 0.043 1593 Dihedral : 3.496 15.290 1308 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.54 % Allowed : 20.46 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.24), residues: 1230 helix: 2.02 (0.17), residues: 972 sheet: 0.03 (0.71), residues: 54 loop : -0.43 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 19 HIS 0.001 0.000 HIS A 296 PHE 0.019 0.001 PHE B 99 TYR 0.010 0.001 TYR B 285 ARG 0.010 0.001 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.05793 ( 708) hydrogen bonds : angle 3.92249 ( 2106) covalent geometry : bond 0.00274 ( 9639) covalent geometry : angle 0.50168 (13080) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.045 Fit side-chains REVERT: A 39 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.7083 (mtp-110) REVERT: A 231 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7434 (mm-30) REVERT: A 241 ASN cc_start: 0.8821 (OUTLIER) cc_final: 0.8445 (t0) REVERT: A 396 THR cc_start: 0.7612 (m) cc_final: 0.7411 (m) REVERT: B 205 MET cc_start: 0.8504 (ptm) cc_final: 0.8241 (ptm) REVERT: B 346 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6922 (mt-10) REVERT: B 385 ASN cc_start: 0.6898 (m-40) cc_final: 0.6617 (m110) REVERT: C 115 SER cc_start: 0.7638 (t) cc_final: 0.7030 (m) REVERT: C 272 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6875 (mt-10) REVERT: C 346 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7239 (mm-30) outliers start: 16 outliers final: 10 residues processed: 139 average time/residue: 1.3409 time to fit residues: 198.9778 Evaluate side-chains 139 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 346 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 9 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN C 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.166163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.118835 restraints weight = 2722.897| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 0.89 r_work: 0.3245 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9639 Z= 0.159 Angle : 0.534 7.371 13080 Z= 0.277 Chirality : 0.038 0.142 1659 Planarity : 0.004 0.045 1593 Dihedral : 3.600 15.455 1308 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.63 % Allowed : 20.27 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.24), residues: 1230 helix: 1.87 (0.17), residues: 978 sheet: 1.02 (0.65), residues: 48 loop : -0.89 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 19 HIS 0.001 0.001 HIS C 296 PHE 0.019 0.002 PHE B 99 TYR 0.010 0.002 TYR A 285 ARG 0.010 0.001 ARG A 315 Details of bonding type rmsd hydrogen bonds : bond 0.06605 ( 708) hydrogen bonds : angle 4.03160 ( 2106) covalent geometry : bond 0.00344 ( 9639) covalent geometry : angle 0.53432 (13080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9260.30 seconds wall clock time: 164 minutes 50.10 seconds (9890.10 seconds total)