Starting phenix.real_space_refine on Sat Jul 4 23:27:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x83_38134/07_2026/8x83_38134_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x83_38134/07_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_38134/07_2026/8x83_38134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x83_38134/07_2026/8x83_38134.map" model { file = "/net/cci-nas-00/data/ceres_data/8x83_38134/07_2026/8x83_38134_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x83_38134/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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, 12 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'FRU': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 4.19, per 1000 atoms: 0.17 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: 2.04 Conformation dependent library (CDL) restraints added in 647.7 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: 0.48 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: 6.01 Time building geometry restraints manager: 2.68 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: 0.950 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: 0.110 Extract box with map and model: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 22.740 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:10.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 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/Z covalent geometry : bond 0.00510 / 0.32 (12284) covalent geometry : angle 0.59658 / 0.37 (16668) hydrogen bonds : bond 0.10124 / 7.06 ( 1056) hydrogen bonds : angle 4.81562 / 3.49 ( 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 : 0.525 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: 1.3555 time to fit residues: 199.2420 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 : 0.612 ------------------------------------------------------------------------------- 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... 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 = 0.140639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.111232 restraints weight = 36669.210| |-----------------------------------------------------------------------------| r_work (start): 0.3211 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: 0.7924 moved from start: 0.1462 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= 0.184 Angle : 0.478 4.268 16668 Z= 0.264 Chirality : 0.035 0.140 2004 Planarity : 0.003 0.035 2032 Dihedral : 4.834 55.997 1760 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.26 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: 2.75 (0.21), residues: 1504 helix: 2.38 (0.14), residues: 1252 sheet: 0.45 (0.81), residues: 48 loop : -1.58 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 201 TYR 0.009 0.002 TYR D 56 PHE 0.012 0.002 PHE B 11 TRP 0.007 0.001 TRP C 328 HIS 0.003 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (12284) covalent geometry : angle 0.47830 / 0.26 (16668) hydrogen bonds : bond 0.04576 / 3.09 ( 1056) hydrogen bonds : angle 3.95303 / 2.86 ( 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 : 0.659 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: 0.7853 (ttt) cc_final: 0.7593 (ttp) REVERT: A 272 LYS cc_start: 0.7328 (tppt) cc_final: 0.6603 (tmmt) REVERT: A 354 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8144 (mm-30) REVERT: A 424 ARG cc_start: 0.6361 (mpt90) cc_final: 0.5970 (mtp85) REVERT: B 209 MET cc_start: 0.7862 (ttt) cc_final: 0.7603 (ttp) REVERT: B 272 LYS cc_start: 0.7321 (tppt) cc_final: 0.6594 (tmmt) REVERT: B 354 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8148 (mm-30) REVERT: B 424 ARG cc_start: 0.6368 (mpt90) cc_final: 0.5975 (mtp85) REVERT: C 209 MET cc_start: 0.7858 (ttt) cc_final: 0.7600 (ttp) REVERT: C 272 LYS cc_start: 0.7335 (tppt) cc_final: 0.6606 (tmmt) REVERT: C 424 ARG cc_start: 0.6369 (mpt90) cc_final: 0.5979 (mtp85) REVERT: D 209 MET cc_start: 0.7849 (ttt) cc_final: 0.7588 (ttp) REVERT: D 272 LYS cc_start: 0.7324 (tppt) cc_final: 0.6598 (tmmt) REVERT: D 424 ARG cc_start: 0.6365 (mpt90) cc_final: 0.5974 (mtp85) outliers start: 20 outliers final: 8 residues processed: 156 average time/residue: 1.0623 time to fit residues: 182.2559 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 : 0.624 ------------------------------------------------------------------------------- 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: 0.7980 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: 1.9990 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: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3547 r_free = 0.3547 target = 0.138954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.107975 restraints weight = 36192.634| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.67 r_work: 0.3045 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12284 Z= 0.201 Angle : 0.478 4.623 16668 Z= 0.263 Chirality : 0.035 0.146 2004 Planarity : 0.003 0.037 2032 Dihedral : 4.993 57.365 1760 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: 2.75 (0.21), residues: 1504 helix: 2.36 (0.14), residues: 1256 sheet: 0.54 (0.83), residues: 48 loop : -1.53 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 340 TYR 0.010 0.002 TYR D 56 PHE 0.012 0.002 PHE D 11 TRP 0.008 0.002 TRP B 154 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (12284) covalent geometry : angle 0.47798 / 0.26 (16668) hydrogen bonds : bond 0.04687 / 3.17 ( 1056) hydrogen bonds : angle 3.94191 / 2.86 ( 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 : 0.669 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: 0.7550 (tppt) cc_final: 0.6797 (tmmt) REVERT: A 424 ARG cc_start: 0.6309 (mpt90) cc_final: 0.6028 (ttt90) REVERT: B 272 LYS cc_start: 0.7562 (tppt) cc_final: 0.6807 (tmmt) REVERT: B 424 ARG cc_start: 0.6323 (mpt90) cc_final: 0.6039 (ttt90) REVERT: C 272 LYS cc_start: 0.7558 (tppt) cc_final: 0.6802 (tmmt) REVERT: C 354 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8156 (mm-30) REVERT: C 424 ARG cc_start: 0.6309 (mpt90) cc_final: 0.6033 (ttt90) REVERT: D 272 LYS cc_start: 0.7553 (tppt) cc_final: 0.6794 (tmmt) REVERT: D 354 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8134 (mm-30) REVERT: D 424 ARG cc_start: 0.6327 (mpt90) cc_final: 0.6039 (ttt90) outliers start: 24 outliers final: 8 residues processed: 168 average time/residue: 1.0306 time to fit residues: 190.5712 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 : 0.547 ------------------------------------------------------------------------------- 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: 0.9980 chunk 96 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN B 27 ASN C 27 ASN D 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.143603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.114783 restraints weight = 36804.458| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.53 r_work: 0.3092 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12284 Z= 0.118 Angle : 0.410 3.952 16668 Z= 0.226 Chirality : 0.033 0.135 2004 Planarity : 0.003 0.034 2032 Dihedral : 4.701 58.199 1760 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.53 % Allowed : 10.70 % Favored : 87.77 % 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: 3.29 (0.21), residues: 1504 helix: 2.71 (0.14), residues: 1256 sheet: 0.51 (0.76), residues: 48 loop : -1.17 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 201 TYR 0.004 0.001 TYR D 96 PHE 0.012 0.001 PHE A 11 TRP 0.005 0.001 TRP B 154 HIS 0.002 0.001 HIS D 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 (12284) covalent geometry : angle 0.40976 / 0.23 (16668) hydrogen bonds : bond 0.04048 / 2.73 ( 1056) hydrogen bonds : angle 3.68786 / 2.67 ( 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 : 0.668 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: 0.7709 (p) cc_final: 0.7435 (p) REVERT: A 272 LYS cc_start: 0.7537 (tppt) cc_final: 0.6757 (tmmt) REVERT: A 391 ASP cc_start: 0.6164 (OUTLIER) cc_final: 0.5906 (t0) REVERT: A 424 ARG cc_start: 0.6242 (mpt90) cc_final: 0.6002 (ttt90) REVERT: B 25 VAL cc_start: 0.7694 (p) cc_final: 0.7439 (p) REVERT: B 272 LYS cc_start: 0.7543 (tppt) cc_final: 0.6763 (tmmt) REVERT: B 391 ASP cc_start: 0.6174 (OUTLIER) cc_final: 0.5913 (t0) REVERT: B 424 ARG cc_start: 0.6250 (mpt90) cc_final: 0.6008 (ttt90) REVERT: C 25 VAL cc_start: 0.7677 (p) cc_final: 0.7424 (p) REVERT: C 272 LYS cc_start: 0.7551 (tppt) cc_final: 0.6772 (tmmt) REVERT: C 354 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7997 (mm-30) REVERT: C 391 ASP cc_start: 0.6148 (OUTLIER) cc_final: 0.5886 (t0) REVERT: C 424 ARG cc_start: 0.6235 (mpt90) cc_final: 0.6006 (ttt90) REVERT: D 25 VAL cc_start: 0.7710 (p) cc_final: 0.7437 (p) REVERT: D 272 LYS cc_start: 0.7536 (tppt) cc_final: 0.6752 (tmmt) REVERT: D 354 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7988 (mm-30) REVERT: D 391 ASP cc_start: 0.6154 (OUTLIER) cc_final: 0.5895 (t0) REVERT: D 424 ARG cc_start: 0.6238 (mpt90) cc_final: 0.5998 (ttt90) outliers start: 20 outliers final: 4 residues processed: 164 average time/residue: 1.0173 time to fit residues: 184.0360 Evaluate side-chains 148 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 124 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN A 113 ASN B 27 ASN B 113 ASN C 27 ASN C 113 ASN D 27 ASN D 113 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.138090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.107547 restraints weight = 36323.001| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.65 r_work: 0.3029 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12284 Z= 0.199 Angle : 0.464 4.231 16668 Z= 0.257 Chirality : 0.035 0.140 2004 Planarity : 0.003 0.036 2032 Dihedral : 5.036 58.997 1760 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.83 % Allowed : 11.31 % Favored : 86.85 % 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: 2.96 (0.21), residues: 1504 helix: 2.50 (0.14), residues: 1256 sheet: 0.58 (0.77), residues: 48 loop : -1.42 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 399 TYR 0.007 0.001 TYR C 56 PHE 0.011 0.002 PHE A 11 TRP 0.009 0.002 TRP A 174 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (12284) covalent geometry : angle 0.46427 / 0.26 (16668) hydrogen bonds : bond 0.04557 / 3.07 ( 1056) hydrogen bonds : angle 3.85226 / 2.79 ( 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 164 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.649 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: A 272 LYS cc_start: 0.7611 (tppt) cc_final: 0.6843 (tmmt) REVERT: A 391 ASP cc_start: 0.6135 (OUTLIER) cc_final: 0.5865 (t0) REVERT: A 424 ARG cc_start: 0.6357 (mpt90) cc_final: 0.6117 (ttt90) REVERT: B 272 LYS cc_start: 0.7628 (tppt) cc_final: 0.6858 (tmmt) REVERT: B 391 ASP cc_start: 0.6143 (OUTLIER) cc_final: 0.5875 (t0) REVERT: B 424 ARG cc_start: 0.6368 (mpt90) cc_final: 0.6129 (ttt90) REVERT: C 272 LYS cc_start: 0.7639 (tppt) cc_final: 0.6870 (tmmt) REVERT: C 391 ASP cc_start: 0.6117 (OUTLIER) cc_final: 0.5841 (t0) REVERT: C 424 ARG cc_start: 0.6358 (mpt90) cc_final: 0.6124 (ttt90) REVERT: D 272 LYS cc_start: 0.7620 (tppt) cc_final: 0.6848 (tmmt) REVERT: D 391 ASP cc_start: 0.6134 (OUTLIER) cc_final: 0.5860 (t0) REVERT: D 424 ARG cc_start: 0.6368 (mpt90) cc_final: 0.6122 (ttt90) outliers start: 24 outliers final: 4 residues processed: 152 average time/residue: 1.1103 time to fit residues: 185.5201 Evaluate side-chains 150 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 134 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 103 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.140152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.109455 restraints weight = 36180.444| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.66 r_work: 0.3075 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12284 Z= 0.135 Angle : 0.417 4.077 16668 Z= 0.230 Chirality : 0.033 0.136 2004 Planarity : 0.003 0.034 2032 Dihedral : 4.827 59.788 1760 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.22 % Allowed : 11.85 % Favored : 86.93 % 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: 3.24 (0.21), residues: 1504 helix: 2.69 (0.14), residues: 1256 sheet: 0.52 (0.76), residues: 48 loop : -1.23 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 399 TYR 0.005 0.001 TYR C 182 PHE 0.012 0.001 PHE A 11 TRP 0.008 0.001 TRP A 174 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (12284) covalent geometry : angle 0.41689 / 0.23 (16668) hydrogen bonds : bond 0.04154 / 2.80 ( 1056) hydrogen bonds : angle 3.69092 / 2.68 ( 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 157 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.628 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: 0.7679 (tppt) cc_final: 0.6941 (tmmt) REVERT: A 391 ASP cc_start: 0.5986 (m-30) cc_final: 0.5764 (t0) REVERT: A 424 ARG cc_start: 0.6366 (mpt90) cc_final: 0.6161 (ttt90) REVERT: B 272 LYS cc_start: 0.7685 (tppt) cc_final: 0.6949 (tmmt) REVERT: B 391 ASP cc_start: 0.6002 (m-30) cc_final: 0.5779 (t0) REVERT: B 424 ARG cc_start: 0.6373 (mpt90) cc_final: 0.6168 (ttt90) REVERT: C 272 LYS cc_start: 0.7695 (tppt) cc_final: 0.6961 (tmmt) REVERT: C 391 ASP cc_start: 0.5946 (m-30) cc_final: 0.5720 (t0) REVERT: C 424 ARG cc_start: 0.6378 (mpt90) cc_final: 0.6175 (ttt90) REVERT: D 272 LYS cc_start: 0.7678 (tppt) cc_final: 0.6942 (tmmt) REVERT: D 391 ASP cc_start: 0.5954 (m-30) cc_final: 0.5731 (t0) REVERT: D 424 ARG cc_start: 0.6374 (mpt90) cc_final: 0.6164 (ttt90) outliers start: 16 outliers final: 12 residues processed: 157 average time/residue: 1.1392 time to fit residues: 197.0605 Evaluate side-chains 160 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 419 LEU Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 419 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 107 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3537 r_free = 0.3537 target = 0.137617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.107332 restraints weight = 36373.111| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.63 r_work: 0.3036 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12284 Z= 0.187 Angle : 0.457 4.204 16668 Z= 0.252 Chirality : 0.035 0.137 2004 Planarity : 0.003 0.036 2032 Dihedral : 5.054 59.565 1760 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.83 % Allowed : 11.85 % Favored : 86.31 % 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: 3.01 (0.21), residues: 1504 helix: 2.53 (0.14), residues: 1256 sheet: 0.49 (0.76), residues: 48 loop : -1.28 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 399 TYR 0.007 0.001 TYR A 182 PHE 0.010 0.002 PHE A 11 TRP 0.011 0.002 TRP D 174 HIS 0.003 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (12284) covalent geometry : angle 0.45681 / 0.25 (16668) hydrogen bonds : bond 0.04482 / 3.02 ( 1056) hydrogen bonds : angle 3.82724 / 2.78 ( 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 173 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.602 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: A 272 LYS cc_start: 0.7688 (tppt) cc_final: 0.6939 (tmmt) REVERT: A 391 ASP cc_start: 0.6055 (OUTLIER) cc_final: 0.5837 (t0) REVERT: B 272 LYS cc_start: 0.7702 (tppt) cc_final: 0.6957 (tmmt) REVERT: B 391 ASP cc_start: 0.6075 (OUTLIER) cc_final: 0.5858 (t0) REVERT: C 272 LYS cc_start: 0.7707 (tppt) cc_final: 0.6960 (tmmt) REVERT: C 391 ASP cc_start: 0.6112 (OUTLIER) cc_final: 0.5886 (t0) REVERT: D 272 LYS cc_start: 0.7692 (tppt) cc_final: 0.6945 (tmmt) REVERT: D 391 ASP cc_start: 0.6134 (OUTLIER) cc_final: 0.5910 (t0) REVERT: D 424 ARG cc_start: 0.6332 (mpt90) cc_final: 0.6129 (ttt90) outliers start: 24 outliers final: 12 residues processed: 165 average time/residue: 1.1607 time to fit residues: 211.6685 Evaluate side-chains 160 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 391 ASP Chi-restraints excluded: chain B residue 113 ASN 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 113 ASN 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 113 ASN 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=2.00 ------------------------------------------------------------------------------- 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: 0.7980 chunk 54 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 139 optimal weight: 0.2980 chunk 144 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.141703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.113199 restraints weight = 37158.663| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.52 r_work: 0.3078 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12284 Z= 0.128 Angle : 0.428 3.993 16668 Z= 0.235 Chirality : 0.033 0.131 2004 Planarity : 0.003 0.033 2032 Dihedral : 3.880 26.734 1752 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.22 % Allowed : 12.39 % Favored : 86.39 % 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: 3.33 (0.21), residues: 1504 helix: 2.74 (0.14), residues: 1256 sheet: 0.43 (0.76), residues: 48 loop : -1.10 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 399 TYR 0.005 0.001 TYR D 182 PHE 0.011 0.001 PHE D 11 TRP 0.008 0.001 TRP C 174 HIS 0.003 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (12284) covalent geometry : angle 0.42767 / 0.24 (16668) hydrogen bonds : bond 0.04125 / 2.78 ( 1056) hydrogen bonds : angle 3.67072 / 2.67 ( 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 162 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.472 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 127 ARG cc_start: 0.6477 (ttt180) cc_final: 0.6276 (ttt180) REVERT: A 209 MET cc_start: 0.7752 (ttt) cc_final: 0.7434 (ttm) REVERT: A 272 LYS cc_start: 0.7561 (tppt) cc_final: 0.6780 (tmmt) REVERT: A 391 ASP cc_start: 0.6078 (OUTLIER) cc_final: 0.5865 (t0) REVERT: B 127 ARG cc_start: 0.6471 (ttt180) cc_final: 0.6271 (ttt180) REVERT: B 209 MET cc_start: 0.7745 (ttt) cc_final: 0.7430 (ttm) REVERT: B 272 LYS cc_start: 0.7579 (tppt) cc_final: 0.6798 (tmmt) REVERT: B 391 ASP cc_start: 0.6102 (OUTLIER) cc_final: 0.5890 (t0) REVERT: C 272 LYS cc_start: 0.7570 (tppt) cc_final: 0.6788 (tmmt) REVERT: C 391 ASP cc_start: 0.6101 (OUTLIER) cc_final: 0.5859 (t0) REVERT: D 127 ARG cc_start: 0.6480 (ttt180) cc_final: 0.6277 (ttt180) REVERT: D 272 LYS cc_start: 0.7575 (tppt) cc_final: 0.6793 (tmmt) REVERT: D 391 ASP cc_start: 0.6113 (OUTLIER) cc_final: 0.5875 (t0) REVERT: D 424 ARG cc_start: 0.6251 (mpt90) cc_final: 0.6043 (ttt90) outliers start: 16 outliers final: 8 residues processed: 158 average time/residue: 1.0349 time to fit residues: 180.0476 Evaluate side-chains 158 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 391 ASP 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 182 TYR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 391 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 12 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.136547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.106229 restraints weight = 36563.749| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.64 r_work: 0.3023 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12284 Z= 0.215 Angle : 0.478 4.270 16668 Z= 0.265 Chirality : 0.036 0.140 2004 Planarity : 0.003 0.036 2032 Dihedral : 4.312 32.778 1752 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.22 % Allowed : 12.31 % Favored : 86.47 % 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: 2.83 (0.21), residues: 1504 helix: 2.41 (0.14), residues: 1256 sheet: 0.39 (0.78), residues: 48 loop : -1.37 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 399 TYR 0.007 0.002 TYR C 326 PHE 0.010 0.002 PHE A 11 TRP 0.013 0.002 TRP D 174 HIS 0.003 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.22 (12284) covalent geometry : angle 0.47792 / 0.26 (16668) hydrogen bonds : bond 0.04646 / 3.13 ( 1056) hydrogen bonds : angle 3.88178 / 2.82 ( 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 166 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.489 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: A 272 LYS cc_start: 0.7700 (tppt) cc_final: 0.6980 (tmmt) REVERT: A 391 ASP cc_start: 0.6339 (OUTLIER) cc_final: 0.6023 (t0) REVERT: B 272 LYS cc_start: 0.7719 (tppt) cc_final: 0.7004 (tmmt) REVERT: B 391 ASP cc_start: 0.6359 (OUTLIER) cc_final: 0.6043 (t0) REVERT: C 272 LYS cc_start: 0.7713 (tppt) cc_final: 0.6997 (tmmt) REVERT: C 391 ASP cc_start: 0.6301 (OUTLIER) cc_final: 0.5976 (t0) REVERT: D 272 LYS cc_start: 0.7717 (tppt) cc_final: 0.7000 (tmmt) REVERT: D 391 ASP cc_start: 0.6319 (OUTLIER) cc_final: 0.5993 (t0) REVERT: D 424 ARG cc_start: 0.6403 (mpt90) cc_final: 0.6134 (ttt90) outliers start: 16 outliers final: 8 residues processed: 162 average time/residue: 1.0104 time to fit residues: 181.5338 Evaluate side-chains 154 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 391 ASP 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 182 TYR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 391 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 74 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 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: 0.6980 chunk 48 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 126 optimal weight: 0.1980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3550 r_free = 0.3550 target = 0.138930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.109462 restraints weight = 37447.197| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.62 r_work: 0.3057 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2689 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= 0.125 Angle : 0.413 4.006 16668 Z= 0.228 Chirality : 0.033 0.135 2004 Planarity : 0.003 0.035 2032 Dihedral : 3.760 23.719 1752 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.22 % Allowed : 12.39 % Favored : 86.39 % 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: 3.33 (0.21), residues: 1504 helix: 2.74 (0.14), residues: 1256 sheet: 0.52 (0.78), residues: 48 loop : -1.12 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 111 TYR 0.005 0.001 TYR D 96 PHE 0.012 0.001 PHE A 11 TRP 0.008 0.001 TRP D 174 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (12284) covalent geometry : angle 0.41264 / 0.23 (16668) hydrogen bonds : bond 0.04057 / 2.74 ( 1056) hydrogen bonds : angle 3.65808 / 2.66 ( 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 164 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.452 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 127 ARG cc_start: 0.6801 (ttt180) cc_final: 0.6591 (ttt180) REVERT: A 209 MET cc_start: 0.7880 (ttt) cc_final: 0.7573 (ttm) REVERT: A 272 LYS cc_start: 0.7641 (tppt) cc_final: 0.6914 (tmmt) REVERT: A 391 ASP cc_start: 0.6219 (OUTLIER) cc_final: 0.5937 (t0) REVERT: B 127 ARG cc_start: 0.6800 (ttt180) cc_final: 0.6593 (ttt180) REVERT: B 272 LYS cc_start: 0.7660 (tppt) cc_final: 0.6935 (tmmt) REVERT: B 391 ASP cc_start: 0.6244 (OUTLIER) cc_final: 0.5962 (t0) REVERT: C 272 LYS cc_start: 0.7645 (tppt) cc_final: 0.6920 (tmmt) REVERT: C 391 ASP cc_start: 0.6197 (OUTLIER) cc_final: 0.5910 (t0) REVERT: D 127 ARG cc_start: 0.6807 (ttt180) cc_final: 0.6586 (ttt180) REVERT: D 272 LYS cc_start: 0.7660 (tppt) cc_final: 0.6937 (tmmt) REVERT: D 391 ASP cc_start: 0.6171 (OUTLIER) cc_final: 0.5886 (t0) REVERT: D 424 ARG cc_start: 0.6333 (mpt90) cc_final: 0.6091 (ttt90) outliers start: 16 outliers final: 12 residues processed: 160 average time/residue: 1.2115 time to fit residues: 212.3949 Evaluate side-chains 158 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 391 ASP Chi-restraints excluded: chain B residue 113 ASN 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 113 ASN 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 113 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 52 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.139131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.109569 restraints weight = 37577.510| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.63 r_work: 0.3057 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.175 12284 Z= 0.235 Angle : 1.219 59.199 16668 Z= 0.760 Chirality : 0.059 1.086 2004 Planarity : 0.003 0.036 2032 Dihedral : 3.824 23.735 1752 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.22 % Allowed : 12.77 % Favored : 86.01 % Cbeta Deviations : 0.28 % 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: 3.31 (0.21), residues: 1504 helix: 2.72 (0.14), residues: 1256 sheet: 0.54 (0.78), residues: 48 loop : -1.12 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 399 TYR 0.005 0.001 TYR A 96 PHE 0.011 0.001 PHE B 11 TRP 0.007 0.001 TRP B 174 HIS 0.003 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.24 (12284) covalent geometry : angle 1.21859 / 0.76 (16668) hydrogen bonds : bond 0.04130 / 2.79 ( 1056) hydrogen bonds : angle 3.68905 / 2.68 ( 3168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6886.63 seconds wall clock time: 117 minutes 24.52 seconds (7044.52 seconds total)