Starting phenix.real_space_refine on Fri Feb 6 08:19:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x83_38134/02_2026/8x83_38134_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x83_38134/02_2026/8x83_38134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x83_38134/02_2026/8x83_38134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x83_38134/02_2026/8x83_38134.map" model { file = "/net/cci-nas-00/data/ceres_data/8x83_38134/02_2026/8x83_38134_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x83_38134/02_2026/8x83_38134_neut_trim.cif" } resolution = 2.8 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= 0.006 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 S 72 5.16 5 Na 2 4.78 5 C 7820 2.51 5 N 2048 2.21 5 O 2116 1.98 5 H 12424 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24482 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 6107 Classifications: {'peptide': 380} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 373} Chain breaks: 1 Chain: "B" Number of atoms: 6107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 6107 Classifications: {'peptide': 380} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 373} Chain breaks: 1 Chain: "C" Number of atoms: 6107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 6107 Classifications: {'peptide': 380} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 373} Chain breaks: 1 Chain: "D" Number of atoms: 6107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 6107 Classifications: {'peptide': 380} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 373} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' NA': 2, 'FRU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.16, per 1000 atoms: 0.21 Number of scatterers: 24482 At special positions: 0 Unit cell: (110.67, 110.67, 106.02, 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) S 72 16.00 Na 2 11.00 O 2116 8.00 N 2048 7.00 C 7820 6.00 H 12424 1.00 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: 2.08 Conformation dependent library (CDL) restraints added in 801.2 milliseconds 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 85.3% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 7 through 17 Processing helix chain 'A' and resid 37 through 64 Processing helix chain 'A' and resid 73 through 100 Processing helix chain 'A' and resid 101 through 119 Processing helix chain 'A' and resid 120 through 123 removed outlier: 3.516A pdb=" N ASN A 123 " --> pdb=" O ASN A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 124 through 161 Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.722A pdb=" N VAL A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 215 removed outlier: 3.516A pdb=" N TYR A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 321 removed outlier: 6.329A pdb=" N ILE A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ALA A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 357 Proline residue: A 347 - end of helix Processing helix chain 'A' and resid 357 through 369 removed outlier: 3.740A pdb=" N ILE A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 387 removed outlier: 3.963A pdb=" N VAL A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 425 removed outlier: 4.312A pdb=" N LEU A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 17 Processing helix chain 'B' and resid 37 through 64 Processing helix chain 'B' and resid 73 through 100 Processing helix chain 'B' and resid 101 through 119 Processing helix chain 'B' and resid 120 through 123 removed outlier: 3.516A pdb=" N ASN B 123 " --> pdb=" O ASN B 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 124 through 161 Processing helix chain 'B' and resid 168 through 174 removed outlier: 3.722A pdb=" N VAL B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 215 removed outlier: 3.516A pdb=" N TYR B 179 " --> pdb=" O TYR B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 321 removed outlier: 6.329A pdb=" N ILE B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ALA B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 357 Proline residue: B 347 - end of helix Processing helix chain 'B' and resid 357 through 369 removed outlier: 3.740A pdb=" N ILE B 361 " --> pdb=" O LYS B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 387 removed outlier: 3.963A pdb=" N VAL B 387 " --> pdb=" O GLN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 425 removed outlier: 4.312A pdb=" N LEU B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 416 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 17 Processing helix chain 'C' and resid 37 through 64 Processing helix chain 'C' and resid 73 through 100 Processing helix chain 'C' and resid 101 through 119 Processing helix chain 'C' and resid 120 through 123 removed outlier: 3.516A pdb=" N ASN C 123 " --> pdb=" O ASN C 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 124 through 161 Processing helix chain 'C' and resid 168 through 174 removed outlier: 3.722A pdb=" N VAL C 172 " --> pdb=" O THR C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 215 removed outlier: 3.516A pdb=" N TYR C 179 " --> pdb=" O TYR C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 321 removed outlier: 6.329A pdb=" N ILE C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ALA C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 357 Proline residue: C 347 - end of helix Processing helix chain 'C' and resid 357 through 369 removed outlier: 3.740A pdb=" N ILE C 361 " --> pdb=" O LYS C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 387 removed outlier: 3.963A pdb=" N VAL C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 425 removed outlier: 4.312A pdb=" N LEU C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR C 406 " --> pdb=" O ARG C 402 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU C 416 " --> pdb=" O ILE C 412 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL C 417 " --> pdb=" O ALA C 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 17 Processing helix chain 'D' and resid 37 through 64 Processing helix chain 'D' and resid 73 through 100 Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'D' and resid 120 through 123 removed outlier: 3.516A pdb=" N ASN D 123 " --> pdb=" O ASN D 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 120 through 123' Processing helix chain 'D' and resid 124 through 161 Processing helix chain 'D' and resid 168 through 174 removed outlier: 3.722A pdb=" N VAL D 172 " --> pdb=" O THR D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 215 removed outlier: 3.516A pdb=" N TYR D 179 " --> pdb=" O TYR D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 321 removed outlier: 6.329A pdb=" N ILE D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ALA D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 357 Proline residue: D 347 - end of helix Processing helix chain 'D' and resid 357 through 369 removed outlier: 3.740A pdb=" N ILE D 361 " --> pdb=" O LYS D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 387 removed outlier: 3.963A pdb=" N VAL D 387 " --> pdb=" O GLN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 425 removed outlier: 4.312A pdb=" N LEU D 405 " --> pdb=" O ASN D 401 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR D 406 " --> pdb=" O ARG D 402 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU D 416 " --> pdb=" O ILE D 412 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 392 through 393 removed outlier: 4.596A pdb=" N PHE A 392 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 26 Processing sheet with id=AA4, first strand: chain 'B' and resid 392 through 393 removed outlier: 4.596A pdb=" N PHE B 392 " --> pdb=" O VAL B 400 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26 Processing sheet with id=AA6, first strand: chain 'C' and resid 392 through 393 removed outlier: 4.596A pdb=" N PHE C 392 " --> pdb=" O VAL C 400 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 22 through 26 Processing sheet with id=AA8, first strand: chain 'D' and resid 392 through 393 removed outlier: 4.596A pdb=" N PHE D 392 " --> pdb=" O VAL D 400 " (cutoff:3.500A) 1056 hydrogen bonds defined for protein. 3168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.86 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 12392 1.02 - 1.22: 36 1.22 - 1.42: 4996 1.42 - 1.61: 7172 1.61 - 1.81: 112 Bond restraints: 24708 Sorted by residual: bond pdb=" C VAL D 417 " pdb=" N ALA D 418 " ideal model delta sigma weight residual 1.335 1.516 -0.181 1.31e-02 5.83e+03 1.91e+02 bond pdb=" C VAL A 417 " pdb=" N ALA A 418 " ideal model delta sigma weight residual 1.335 1.516 -0.181 1.31e-02 5.83e+03 1.91e+02 bond pdb=" C VAL B 417 " pdb=" N ALA B 418 " ideal model delta sigma weight residual 1.335 1.516 -0.181 1.31e-02 5.83e+03 1.91e+02 bond pdb=" C VAL C 417 " pdb=" N ALA C 418 " ideal model delta sigma weight residual 1.335 1.516 -0.181 1.31e-02 5.83e+03 1.91e+02 bond pdb=" NE ARG A 424 " pdb=" HE ARG A 424 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 24703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 43924 1.51 - 3.01: 584 3.01 - 4.52: 64 4.52 - 6.03: 32 6.03 - 7.53: 20 Bond angle restraints: 44624 Sorted by residual: angle pdb=" CA ALA A 418 " pdb=" C ALA A 418 " pdb=" N LEU A 419 " ideal model delta sigma weight residual 117.30 109.95 7.35 1.16e+00 7.43e-01 4.01e+01 angle pdb=" CA ALA B 418 " pdb=" C ALA B 418 " pdb=" N LEU B 419 " ideal model delta sigma weight residual 117.30 109.95 7.35 1.16e+00 7.43e-01 4.01e+01 angle pdb=" CA ALA D 418 " pdb=" C ALA D 418 " pdb=" N LEU D 419 " ideal model delta sigma weight residual 117.30 109.95 7.35 1.16e+00 7.43e-01 4.01e+01 angle pdb=" CA ALA C 418 " pdb=" C ALA C 418 " pdb=" N LEU C 419 " ideal model delta sigma weight residual 117.30 109.95 7.35 1.16e+00 7.43e-01 4.01e+01 angle pdb=" O VAL A 417 " pdb=" C VAL A 417 " pdb=" N ALA A 418 " ideal model delta sigma weight residual 121.87 116.25 5.62 9.70e-01 1.06e+00 3.36e+01 ... (remaining 44619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 10295 16.56 - 33.11: 917 33.11 - 49.67: 204 49.67 - 66.23: 132 66.23 - 82.79: 16 Dihedral angle restraints: 11564 sinusoidal: 6244 harmonic: 5320 Sorted by residual: dihedral pdb=" N ASN B 120 " pdb=" CA ASN B 120 " pdb=" CB ASN B 120 " pdb=" CG ASN B 120 " ideal model delta sinusoidal sigma weight residual -180.00 -121.21 -58.79 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N ASN A 120 " pdb=" CA ASN A 120 " pdb=" CB ASN A 120 " pdb=" CG ASN A 120 " ideal model delta sinusoidal sigma weight residual -180.00 -121.21 -58.79 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N ASN C 120 " pdb=" CA ASN C 120 " pdb=" CB ASN C 120 " pdb=" CG ASN C 120 " ideal model delta sinusoidal sigma weight residual -180.00 -121.21 -58.79 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 11561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1492 0.035 - 0.069: 388 0.069 - 0.104: 100 0.104 - 0.139: 16 0.139 - 0.173: 8 Chirality restraints: 2004 Sorted by residual: chirality pdb=" CA VAL D 417 " pdb=" N VAL D 417 " pdb=" C VAL D 417 " pdb=" CB VAL D 417 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CA VAL B 417 " pdb=" N VAL B 417 " pdb=" C VAL B 417 " pdb=" CB VAL B 417 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CA VAL C 417 " pdb=" N VAL C 417 " pdb=" C VAL C 417 " pdb=" CB VAL C 417 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.50e-01 ... (remaining 2001 not shown) Planarity restraints: 3520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN C 423 " 0.135 2.00e-02 2.50e+03 1.50e-01 3.35e+02 pdb=" CD GLN C 423 " -0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN C 423 " -0.129 2.00e-02 2.50e+03 pdb=" NE2 GLN C 423 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN C 423 " 0.225 2.00e-02 2.50e+03 pdb="HE22 GLN C 423 " -0.219 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 423 " 0.135 2.00e-02 2.50e+03 1.50e-01 3.35e+02 pdb=" CD GLN B 423 " -0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN B 423 " -0.129 2.00e-02 2.50e+03 pdb=" NE2 GLN B 423 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN B 423 " 0.225 2.00e-02 2.50e+03 pdb="HE22 GLN B 423 " -0.219 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 423 " 0.135 2.00e-02 2.50e+03 1.50e-01 3.35e+02 pdb=" CD GLN A 423 " -0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN A 423 " -0.129 2.00e-02 2.50e+03 pdb=" NE2 GLN A 423 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 423 " 0.225 2.00e-02 2.50e+03 pdb="HE22 GLN A 423 " -0.219 2.00e-02 2.50e+03 ... (remaining 3517 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1420 2.20 - 2.80: 51656 2.80 - 3.40: 71708 3.40 - 4.00: 92624 4.00 - 4.60: 146175 Nonbonded interactions: 363583 Sorted by model distance: nonbonded pdb=" OD1 ASN D 401 " pdb=" HG1 THR D 403 " model vdw 1.599 2.450 nonbonded pdb=" OD1 ASN C 401 " pdb=" HG1 THR C 403 " model vdw 1.599 2.450 nonbonded pdb=" OD1 ASN A 401 " pdb=" HG1 THR A 403 " model vdw 1.599 2.450 nonbonded pdb=" OD1 ASN B 401 " pdb=" HG1 THR B 403 " model vdw 1.599 2.450 nonbonded pdb="HH22 ARG A 31 " pdb=" OD1 ASP A 110 " model vdw 1.674 2.450 ... (remaining 363578 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 1 through 425) selection = (chain 'B' and resid 1 through 425) selection = (chain 'C' and resid 1 through 425) selection = (chain 'D' and resid 1 through 425) } 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: 1.350 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: 0.190 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 24.320 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 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 0.181 12284 Z= 0.319 Angle : 0.597 7.346 16668 Z= 0.375 Chirality : 0.034 0.173 2004 Planarity : 0.003 0.041 2032 Dihedral : 14.831 82.787 4452 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.22 % Allowed : 12.23 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.34 (0.21), residues: 1504 helix: 2.08 (0.14), residues: 1244 sheet: 0.86 (0.73), residues: 48 loop : -1.52 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 322 TYR 0.007 0.001 TYR C 312 PHE 0.010 0.001 PHE A 315 TRP 0.005 0.001 TRP D 154 HIS 0.002 0.000 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00510 (12284) covalent geometry : angle 0.59658 (16668) hydrogen bonds : bond 0.10124 ( 1056) hydrogen bonds : angle 4.81562 ( 3168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 ARG cc_start: 0.7525 (mmt180) cc_final: 0.7274 (mpp-170) REVERT: B 399 ARG cc_start: 0.7523 (mmt180) cc_final: 0.7273 (mpp-170) REVERT: C 399 ARG cc_start: 0.7524 (mmt180) cc_final: 0.7273 (mpp-170) REVERT: D 399 ARG cc_start: 0.7524 (mmt180) cc_final: 0.7274 (mpp-170) outliers start: 16 outliers final: 4 residues processed: 136 average time/residue: 1.6334 time to fit residues: 238.2537 Evaluate side-chains 124 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 113 ASN C 113 ASN D 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.140657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.111224 restraints weight = 36637.765| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.61 r_work: 0.3073 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12284 Z= 0.186 Angle : 0.480 4.288 16668 Z= 0.266 Chirality : 0.035 0.139 2004 Planarity : 0.003 0.035 2032 Dihedral : 4.828 55.731 1760 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.53 % Allowed : 11.01 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.77 (0.21), residues: 1504 helix: 2.39 (0.14), residues: 1252 sheet: 0.46 (0.81), residues: 48 loop : -1.58 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 205 TYR 0.009 0.002 TYR A 56 PHE 0.012 0.002 PHE B 11 TRP 0.007 0.001 TRP C 328 HIS 0.003 0.001 HIS D 337 Details of bonding type rmsd covalent geometry : bond 0.00405 (12284) covalent geometry : angle 0.48031 (16668) hydrogen bonds : bond 0.04569 ( 1056) hydrogen bonds : angle 3.96081 ( 3168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.7852 (ttt) cc_final: 0.7592 (ttp) REVERT: A 272 LYS cc_start: 0.7327 (tppt) cc_final: 0.6603 (tmmt) REVERT: A 354 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8142 (mm-30) REVERT: B 209 MET cc_start: 0.7863 (ttt) cc_final: 0.7602 (ttp) REVERT: B 272 LYS cc_start: 0.7319 (tppt) cc_final: 0.6592 (tmmt) REVERT: B 354 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8151 (mm-30) REVERT: B 424 ARG cc_start: 0.6367 (mpt90) cc_final: 0.5968 (mtp85) REVERT: C 209 MET cc_start: 0.7860 (ttt) cc_final: 0.7602 (ttp) REVERT: C 272 LYS cc_start: 0.7333 (tppt) cc_final: 0.6604 (tmmt) REVERT: C 354 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8150 (mm-30) REVERT: C 424 ARG cc_start: 0.6370 (mpt90) cc_final: 0.5973 (mtp85) REVERT: D 209 MET cc_start: 0.7848 (ttt) cc_final: 0.7589 (ttp) REVERT: D 272 LYS cc_start: 0.7324 (tppt) cc_final: 0.6596 (tmmt) REVERT: D 354 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8132 (mm-30) REVERT: D 424 ARG cc_start: 0.6365 (mpt90) cc_final: 0.5973 (mtp85) outliers start: 20 outliers final: 8 residues processed: 156 average time/residue: 1.3487 time to fit residues: 228.6228 Evaluate side-chains 144 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain D residue 391 ASP Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 74 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 113 ASN C 113 ASN D 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.139496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.108518 restraints weight = 36101.938| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.67 r_work: 0.3050 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12284 Z= 0.186 Angle : 0.465 4.447 16668 Z= 0.256 Chirality : 0.035 0.141 2004 Planarity : 0.003 0.036 2032 Dihedral : 4.919 57.186 1760 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.83 % Allowed : 10.09 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.84 (0.21), residues: 1504 helix: 2.42 (0.14), residues: 1256 sheet: 0.53 (0.82), residues: 48 loop : -1.49 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 340 TYR 0.009 0.001 TYR C 56 PHE 0.012 0.002 PHE C 11 TRP 0.007 0.001 TRP B 154 HIS 0.004 0.001 HIS D 337 Details of bonding type rmsd covalent geometry : bond 0.00408 (12284) covalent geometry : angle 0.46502 (16668) hydrogen bonds : bond 0.04576 ( 1056) hydrogen bonds : angle 3.89920 ( 3168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7927 (mt-10) REVERT: A 272 LYS cc_start: 0.7537 (tppt) cc_final: 0.6780 (tmmt) REVERT: A 424 ARG cc_start: 0.6299 (mpt90) cc_final: 0.5963 (ttt90) REVERT: B 33 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7942 (mt-10) REVERT: B 272 LYS cc_start: 0.7553 (tppt) cc_final: 0.6794 (tmmt) REVERT: B 424 ARG cc_start: 0.6307 (mpt90) cc_final: 0.6025 (ttt90) REVERT: C 33 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7921 (mt-10) REVERT: C 272 LYS cc_start: 0.7547 (tppt) cc_final: 0.6787 (tmmt) REVERT: C 424 ARG cc_start: 0.6295 (mpt90) cc_final: 0.6020 (ttt90) REVERT: D 33 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7928 (mt-10) REVERT: D 272 LYS cc_start: 0.7544 (tppt) cc_final: 0.6783 (tmmt) REVERT: D 424 ARG cc_start: 0.6308 (mpt90) cc_final: 0.6021 (ttt90) outliers start: 24 outliers final: 8 residues processed: 168 average time/residue: 1.3065 time to fit residues: 239.0716 Evaluate side-chains 152 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 31 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 113 ASN C 113 ASN D 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.139838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.108894 restraints weight = 36089.782| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.66 r_work: 0.3058 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12284 Z= 0.157 Angle : 0.433 4.096 16668 Z= 0.240 Chirality : 0.034 0.139 2004 Planarity : 0.003 0.036 2032 Dihedral : 4.875 58.519 1760 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.53 % Allowed : 11.31 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 3.05 (0.21), residues: 1504 helix: 2.55 (0.14), residues: 1256 sheet: 0.66 (0.79), residues: 48 loop : -1.32 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 399 TYR 0.006 0.001 TYR C 56 PHE 0.012 0.001 PHE D 11 TRP 0.006 0.001 TRP C 154 HIS 0.002 0.001 HIS D 337 Details of bonding type rmsd covalent geometry : bond 0.00336 (12284) covalent geometry : angle 0.43341 (16668) hydrogen bonds : bond 0.04320 ( 1056) hydrogen bonds : angle 3.80568 ( 3168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 LYS cc_start: 0.7581 (tppt) cc_final: 0.6831 (tmmt) REVERT: A 391 ASP cc_start: 0.6200 (OUTLIER) cc_final: 0.5910 (t0) REVERT: A 424 ARG cc_start: 0.6437 (mpt90) cc_final: 0.6181 (ttt90) REVERT: B 272 LYS cc_start: 0.7590 (tppt) cc_final: 0.6839 (tmmt) REVERT: B 391 ASP cc_start: 0.6205 (OUTLIER) cc_final: 0.5914 (t0) REVERT: B 424 ARG cc_start: 0.6401 (mpt90) cc_final: 0.6168 (ttt90) REVERT: C 272 LYS cc_start: 0.7592 (tppt) cc_final: 0.6841 (tmmt) REVERT: C 391 ASP cc_start: 0.6179 (OUTLIER) cc_final: 0.5883 (t0) REVERT: C 424 ARG cc_start: 0.6382 (mpt90) cc_final: 0.6157 (ttt90) REVERT: D 272 LYS cc_start: 0.7595 (tppt) cc_final: 0.6839 (tmmt) REVERT: D 391 ASP cc_start: 0.6199 (OUTLIER) cc_final: 0.5980 (t0) REVERT: D 424 ARG cc_start: 0.6399 (mpt90) cc_final: 0.6164 (ttt90) outliers start: 20 outliers final: 8 residues processed: 164 average time/residue: 1.2949 time to fit residues: 231.8542 Evaluate side-chains 164 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 113 ASN Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 391 ASP Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 124 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.137864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.107277 restraints weight = 36346.170| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.65 r_work: 0.3041 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12284 Z= 0.204 Angle : 0.474 4.266 16668 Z= 0.261 Chirality : 0.035 0.140 2004 Planarity : 0.003 0.036 2032 Dihedral : 5.089 59.327 1760 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.14 % Allowed : 11.31 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.85 (0.21), residues: 1504 helix: 2.42 (0.14), residues: 1256 sheet: 0.64 (0.80), residues: 48 loop : -1.41 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 31 TYR 0.008 0.001 TYR B 182 PHE 0.011 0.002 PHE A 11 TRP 0.008 0.002 TRP A 174 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd covalent geometry : bond 0.00453 (12284) covalent geometry : angle 0.47409 (16668) hydrogen bonds : bond 0.04607 ( 1056) hydrogen bonds : angle 3.88293 ( 3168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 LYS cc_start: 0.7632 (tppt) cc_final: 0.6883 (tmmt) REVERT: A 391 ASP cc_start: 0.6199 (OUTLIER) cc_final: 0.5970 (t0) REVERT: A 424 ARG cc_start: 0.6374 (mpt90) cc_final: 0.6110 (ttt90) REVERT: B 272 LYS cc_start: 0.7646 (tppt) cc_final: 0.6897 (tmmt) REVERT: B 391 ASP cc_start: 0.6197 (OUTLIER) cc_final: 0.5970 (t0) REVERT: B 424 ARG cc_start: 0.6361 (mpt90) cc_final: 0.6099 (ttt90) REVERT: C 117 ASN cc_start: 0.7737 (OUTLIER) cc_final: 0.7536 (m110) REVERT: C 272 LYS cc_start: 0.7660 (tppt) cc_final: 0.6910 (tmmt) REVERT: C 391 ASP cc_start: 0.6171 (OUTLIER) cc_final: 0.5940 (t0) REVERT: C 424 ARG cc_start: 0.6353 (mpt90) cc_final: 0.6099 (ttt90) REVERT: D 272 LYS cc_start: 0.7647 (tppt) cc_final: 0.6895 (tmmt) REVERT: D 391 ASP cc_start: 0.6250 (OUTLIER) cc_final: 0.5971 (t0) REVERT: D 424 ARG cc_start: 0.6361 (mpt90) cc_final: 0.6095 (ttt90) outliers start: 28 outliers final: 8 residues processed: 168 average time/residue: 1.3264 time to fit residues: 243.0543 Evaluate side-chains 169 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 391 ASP Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 134 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 105 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 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 383 GLN B 383 GLN C 383 GLN D 383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.139324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.108518 restraints weight = 36103.610| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.66 r_work: 0.3061 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12284 Z= 0.155 Angle : 0.433 4.133 16668 Z= 0.240 Chirality : 0.034 0.151 2004 Planarity : 0.003 0.035 2032 Dihedral : 4.942 59.993 1760 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.14 % Allowed : 11.62 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 3.08 (0.21), residues: 1504 helix: 2.56 (0.14), residues: 1256 sheet: 0.67 (0.78), residues: 48 loop : -1.24 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 399 TYR 0.007 0.001 TYR B 182 PHE 0.012 0.001 PHE D 11 TRP 0.009 0.001 TRP C 174 HIS 0.003 0.001 HIS D 337 Details of bonding type rmsd covalent geometry : bond 0.00330 (12284) covalent geometry : angle 0.43342 (16668) hydrogen bonds : bond 0.04288 ( 1056) hydrogen bonds : angle 3.77807 ( 3168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 VAL cc_start: 0.7755 (p) cc_final: 0.7495 (p) REVERT: A 272 LYS cc_start: 0.7677 (tppt) cc_final: 0.6937 (tmmt) REVERT: A 391 ASP cc_start: 0.6089 (OUTLIER) cc_final: 0.5831 (t0) REVERT: A 424 ARG cc_start: 0.6386 (mpt90) cc_final: 0.6151 (ttt90) REVERT: B 25 VAL cc_start: 0.7757 (p) cc_final: 0.7499 (p) REVERT: B 272 LYS cc_start: 0.7689 (tppt) cc_final: 0.6949 (tmmt) REVERT: B 391 ASP cc_start: 0.6095 (OUTLIER) cc_final: 0.5838 (t0) REVERT: B 424 ARG cc_start: 0.6371 (mpt90) cc_final: 0.6150 (ttt90) REVERT: C 25 VAL cc_start: 0.7763 (p) cc_final: 0.7504 (p) REVERT: C 117 ASN cc_start: 0.7902 (t0) cc_final: 0.7642 (m110) REVERT: C 272 LYS cc_start: 0.7701 (tppt) cc_final: 0.6968 (tmmt) REVERT: C 391 ASP cc_start: 0.6073 (OUTLIER) cc_final: 0.5813 (t0) REVERT: C 424 ARG cc_start: 0.6373 (mpt90) cc_final: 0.6158 (ttt90) REVERT: D 25 VAL cc_start: 0.7763 (p) cc_final: 0.7502 (p) REVERT: D 272 LYS cc_start: 0.7697 (tppt) cc_final: 0.6956 (tmmt) REVERT: D 391 ASP cc_start: 0.6144 (OUTLIER) cc_final: 0.5879 (t0) REVERT: D 424 ARG cc_start: 0.6383 (mpt90) cc_final: 0.6158 (ttt90) outliers start: 28 outliers final: 12 residues processed: 176 average time/residue: 1.2667 time to fit residues: 244.1252 Evaluate side-chains 166 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 391 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 107 optimal weight: 0.6980 chunk 145 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 148 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 383 GLN B 383 GLN C 113 ASN C 383 GLN D 113 ASN D 383 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.139518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.109811 restraints weight = 37477.007| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.63 r_work: 0.3059 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12284 Z= 0.126 Angle : 0.415 4.009 16668 Z= 0.228 Chirality : 0.033 0.135 2004 Planarity : 0.003 0.034 2032 Dihedral : 3.765 23.517 1752 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.83 % Allowed : 11.62 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 3.32 (0.21), residues: 1504 helix: 2.73 (0.14), residues: 1256 sheet: 0.61 (0.78), residues: 48 loop : -1.11 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 399 TYR 0.005 0.001 TYR A 182 PHE 0.011 0.001 PHE A 11 TRP 0.008 0.001 TRP C 174 HIS 0.003 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00260 (12284) covalent geometry : angle 0.41459 (16668) hydrogen bonds : bond 0.04073 ( 1056) hydrogen bonds : angle 3.65246 ( 3168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.7882 (ttt) cc_final: 0.7582 (ttm) REVERT: A 272 LYS cc_start: 0.7678 (tppt) cc_final: 0.6934 (tmmt) REVERT: A 424 ARG cc_start: 0.6328 (mpt90) cc_final: 0.6095 (ttt90) REVERT: B 209 MET cc_start: 0.7874 (ttt) cc_final: 0.7573 (ttm) REVERT: B 272 LYS cc_start: 0.7675 (tppt) cc_final: 0.6931 (tmmt) REVERT: B 424 ARG cc_start: 0.6338 (mpt90) cc_final: 0.6115 (ttt90) REVERT: C 117 ASN cc_start: 0.7742 (t0) cc_final: 0.7503 (m110) REVERT: C 209 MET cc_start: 0.7888 (ttt) cc_final: 0.7589 (ttm) REVERT: C 272 LYS cc_start: 0.7669 (tppt) cc_final: 0.6930 (tmmt) REVERT: C 424 ARG cc_start: 0.6351 (mpt90) cc_final: 0.6125 (ttt90) REVERT: D 209 MET cc_start: 0.7886 (ttt) cc_final: 0.7589 (ttm) REVERT: D 272 LYS cc_start: 0.7687 (tppt) cc_final: 0.6944 (tmmt) REVERT: D 424 ARG cc_start: 0.6338 (mpt90) cc_final: 0.6108 (ttt90) outliers start: 24 outliers final: 11 residues processed: 173 average time/residue: 1.5124 time to fit residues: 281.7992 Evaluate side-chains 153 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain C residue 113 ASN Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 189 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 131 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 113 ASN B 383 GLN C 383 GLN D 113 ASN D 383 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.138138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.108526 restraints weight = 37810.925| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.66 r_work: 0.3040 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12284 Z= 0.161 Angle : 0.442 4.199 16668 Z= 0.243 Chirality : 0.034 0.142 2004 Planarity : 0.003 0.035 2032 Dihedral : 3.907 25.791 1752 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.53 % Allowed : 11.09 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.20 (0.21), residues: 1504 helix: 2.64 (0.14), residues: 1256 sheet: 0.69 (0.78), residues: 48 loop : -1.19 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 205 TYR 0.007 0.001 TYR B 182 PHE 0.011 0.001 PHE A 11 TRP 0.010 0.001 TRP D 174 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd covalent geometry : bond 0.00348 (12284) covalent geometry : angle 0.44184 (16668) hydrogen bonds : bond 0.04269 ( 1056) hydrogen bonds : angle 3.69019 ( 3168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 VAL cc_start: 0.7640 (p) cc_final: 0.7384 (p) REVERT: A 209 MET cc_start: 0.7883 (ttt) cc_final: 0.7583 (ttm) REVERT: A 272 LYS cc_start: 0.7677 (tppt) cc_final: 0.6926 (tmmt) REVERT: A 424 ARG cc_start: 0.6313 (mpt90) cc_final: 0.6070 (ttt90) REVERT: B 25 VAL cc_start: 0.7635 (p) cc_final: 0.7380 (p) REVERT: B 209 MET cc_start: 0.7883 (ttt) cc_final: 0.7582 (ttm) REVERT: B 272 LYS cc_start: 0.7680 (tppt) cc_final: 0.6932 (tmmt) REVERT: B 424 ARG cc_start: 0.6315 (mpt90) cc_final: 0.6090 (ttt90) REVERT: C 25 VAL cc_start: 0.7644 (p) cc_final: 0.7387 (p) REVERT: C 117 ASN cc_start: 0.7904 (t0) cc_final: 0.7599 (m110) REVERT: C 209 MET cc_start: 0.7881 (ttt) cc_final: 0.7581 (ttm) REVERT: C 272 LYS cc_start: 0.7672 (tppt) cc_final: 0.6927 (tmmt) REVERT: C 424 ARG cc_start: 0.6339 (mpt90) cc_final: 0.6111 (ttt90) REVERT: D 25 VAL cc_start: 0.7627 (p) cc_final: 0.7372 (p) REVERT: D 209 MET cc_start: 0.7878 (ttt) cc_final: 0.7578 (ttm) REVERT: D 272 LYS cc_start: 0.7693 (tppt) cc_final: 0.6947 (tmmt) REVERT: D 424 ARG cc_start: 0.6324 (mpt90) cc_final: 0.6087 (ttt90) outliers start: 20 outliers final: 11 residues processed: 165 average time/residue: 1.3267 time to fit residues: 237.8957 Evaluate side-chains 153 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 280 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 12 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 383 GLN B 113 ASN B 383 GLN C 113 ASN C 383 GLN D 383 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.136593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.106141 restraints weight = 36525.432| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.65 r_work: 0.3015 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12284 Z= 0.227 Angle : 0.494 4.331 16668 Z= 0.274 Chirality : 0.036 0.144 2004 Planarity : 0.003 0.036 2032 Dihedral : 4.458 35.188 1752 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.30 % Allowed : 12.00 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.75 (0.21), residues: 1504 helix: 2.33 (0.14), residues: 1256 sheet: 0.76 (0.80), residues: 48 loop : -1.34 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 399 TYR 0.009 0.002 TYR B 182 PHE 0.011 0.002 PHE D 392 TRP 0.014 0.002 TRP A 174 HIS 0.003 0.001 HIS D 337 Details of bonding type rmsd covalent geometry : bond 0.00512 (12284) covalent geometry : angle 0.49435 (16668) hydrogen bonds : bond 0.04763 ( 1056) hydrogen bonds : angle 3.93952 ( 3168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 LYS cc_start: 0.7723 (tppt) cc_final: 0.7007 (tmmt) REVERT: A 424 ARG cc_start: 0.6355 (mpt90) cc_final: 0.6100 (ttt90) REVERT: B 272 LYS cc_start: 0.7704 (tppt) cc_final: 0.6989 (tmmt) REVERT: B 424 ARG cc_start: 0.6397 (mpt90) cc_final: 0.6119 (ttt90) REVERT: C 117 ASN cc_start: 0.8005 (t0) cc_final: 0.7690 (m110) REVERT: C 272 LYS cc_start: 0.7711 (tppt) cc_final: 0.7000 (tmmt) REVERT: C 424 ARG cc_start: 0.6385 (mpt90) cc_final: 0.6112 (ttt90) REVERT: D 272 LYS cc_start: 0.7724 (tppt) cc_final: 0.7010 (tmmt) REVERT: D 424 ARG cc_start: 0.6390 (mpt90) cc_final: 0.6104 (ttt90) outliers start: 17 outliers final: 12 residues processed: 160 average time/residue: 1.2399 time to fit residues: 217.1172 Evaluate side-chains 157 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 280 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 74 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 383 GLN B 383 GLN C 113 ASN C 383 GLN D 113 ASN D 383 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.139125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.108778 restraints weight = 36022.336| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.64 r_work: 0.3060 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12284 Z= 0.145 Angle : 0.434 4.119 16668 Z= 0.240 Chirality : 0.033 0.135 2004 Planarity : 0.003 0.035 2032 Dihedral : 3.993 27.821 1752 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.22 % Allowed : 12.23 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 3.11 (0.21), residues: 1504 helix: 2.57 (0.14), residues: 1256 sheet: 0.57 (0.77), residues: 48 loop : -1.10 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 399 TYR 0.006 0.001 TYR B 182 PHE 0.012 0.001 PHE A 11 TRP 0.009 0.001 TRP C 174 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd covalent geometry : bond 0.00310 (12284) covalent geometry : angle 0.43398 (16668) hydrogen bonds : bond 0.04234 ( 1056) hydrogen bonds : angle 3.75430 ( 3168) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 VAL cc_start: 0.7740 (p) cc_final: 0.7478 (p) REVERT: A 272 LYS cc_start: 0.7721 (tppt) cc_final: 0.7015 (tmmt) REVERT: A 424 ARG cc_start: 0.6333 (mpt90) cc_final: 0.6095 (ttt90) REVERT: B 25 VAL cc_start: 0.7749 (p) cc_final: 0.7494 (p) REVERT: B 272 LYS cc_start: 0.7720 (tppt) cc_final: 0.7018 (tmmt) REVERT: B 424 ARG cc_start: 0.6398 (mpt90) cc_final: 0.6131 (ttt90) REVERT: C 25 VAL cc_start: 0.7742 (p) cc_final: 0.7484 (p) REVERT: C 117 ASN cc_start: 0.7912 (t0) cc_final: 0.7638 (m110) REVERT: C 272 LYS cc_start: 0.7726 (tppt) cc_final: 0.7031 (tmmt) REVERT: C 424 ARG cc_start: 0.6387 (mpt90) cc_final: 0.6123 (ttt90) REVERT: D 25 VAL cc_start: 0.7744 (p) cc_final: 0.7481 (p) REVERT: D 272 LYS cc_start: 0.7727 (tppt) cc_final: 0.7025 (tmmt) REVERT: D 424 ARG cc_start: 0.6382 (mpt90) cc_final: 0.6109 (ttt90) outliers start: 16 outliers final: 12 residues processed: 165 average time/residue: 1.3604 time to fit residues: 242.2973 Evaluate side-chains 159 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain C residue 113 ASN Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 189 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 52 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 383 GLN B 383 GLN C 113 ASN C 383 GLN D 113 ASN D 383 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.139032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.109365 restraints weight = 36134.015| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.58 r_work: 0.3055 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.194 12284 Z= 0.280 Angle : 1.102 59.200 16668 Z= 0.677 Chirality : 0.063 1.395 2004 Planarity : 0.003 0.035 2032 Dihedral : 4.043 27.781 1752 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.22 % Allowed : 12.54 % Favored : 86.24 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 3.10 (0.21), residues: 1504 helix: 2.56 (0.14), residues: 1256 sheet: 0.56 (0.77), residues: 48 loop : -1.10 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 205 TYR 0.006 0.001 TYR A 182 PHE 0.012 0.001 PHE A 11 TRP 0.008 0.001 TRP C 174 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd covalent geometry : bond 0.00551 (12284) covalent geometry : angle 1.10237 (16668) hydrogen bonds : bond 0.04296 ( 1056) hydrogen bonds : angle 3.78205 ( 3168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8006.84 seconds wall clock time: 136 minutes 23.75 seconds (8183.75 seconds total)