Starting phenix.real_space_refine on Mon Aug 25 00:59:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x83_38134/08_2025/8x83_38134_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x83_38134/08_2025/8x83_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_38134/08_2025/8x83_38134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x83_38134/08_2025/8x83_38134.map" model { file = "/net/cci-nas-00/data/ceres_data/8x83_38134/08_2025/8x83_38134_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x83_38134/08_2025/8x83_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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24482 Number of models: 1 Model: "" Number of chains: 9 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: "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} Restraints were copied for chains: B, C, D Time building chain proxies: 6.69, per 1000 atoms: 0.27 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: 2.36 Conformation dependent library (CDL) restraints added in 846.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.41 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: 6.10 Time building geometry restraints manager: 3.30 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: 1.250 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: 0.180 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 27.220 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.600 ------------------------------------------------------------------------------- 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 aren 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 : 0.593 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: 1.5846 time to fit residues: 231.2130 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 : 0.642 ------------------------------------------------------------------------------- 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 = 46)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.111226 restraints weight = 36637.669| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.61 r_work: 0.3074 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- 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 aren 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 3.96080 ( 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 : 0.671 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: 0.7850 (ttt) cc_final: 0.7589 (ttp) REVERT: A 272 LYS cc_start: 0.7326 (tppt) cc_final: 0.6602 (tmmt) REVERT: A 354 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8143 (mm-30) REVERT: B 209 MET cc_start: 0.7860 (ttt) cc_final: 0.7600 (ttp) REVERT: B 272 LYS cc_start: 0.7318 (tppt) cc_final: 0.6592 (tmmt) REVERT: B 354 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8152 (mm-30) REVERT: B 424 ARG cc_start: 0.6366 (mpt90) cc_final: 0.5966 (mtp85) REVERT: C 209 MET cc_start: 0.7857 (ttt) cc_final: 0.7599 (ttp) REVERT: C 272 LYS cc_start: 0.7332 (tppt) cc_final: 0.6603 (tmmt) REVERT: C 354 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8150 (mm-30) REVERT: C 424 ARG cc_start: 0.6368 (mpt90) cc_final: 0.5971 (mtp85) REVERT: D 209 MET cc_start: 0.7847 (ttt) cc_final: 0.7588 (ttp) REVERT: D 272 LYS cc_start: 0.7324 (tppt) cc_final: 0.6597 (tmmt) REVERT: D 354 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8135 (mm-30) REVERT: D 424 ARG cc_start: 0.6363 (mpt90) cc_final: 0.5972 (mtp85) outliers start: 20 outliers final: 8 residues processed: 156 average time/residue: 1.2961 time to fit residues: 220.1732 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 : 0.599 ------------------------------------------------------------------------------- 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: 0.9990 chunk 9 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 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 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 = 0.3588 r_free = 0.3588 target = 0.141957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.113083 restraints weight = 36856.281| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.53 r_work: 0.3080 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1860 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= 0.160 Angle : 0.442 4.276 16668 Z= 0.242 Chirality : 0.034 0.138 2004 Planarity : 0.003 0.036 2032 Dihedral : 4.740 56.846 1760 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.10 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 aren not related in a simple way. whole: 3.04 (0.21), residues: 1504 helix: 2.57 (0.14), residues: 1256 sheet: 0.47 (0.81), residues: 48 loop : -1.42 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 340 TYR 0.007 0.001 TYR A 56 PHE 0.012 0.001 PHE D 11 TRP 0.006 0.001 TRP C 154 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd covalent geometry : bond 0.00343 (12284) covalent geometry : angle 0.44165 (16668) hydrogen bonds : bond 0.04377 ( 1056) hydrogen bonds : angle 3.80870 ( 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 174 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.617 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 LYS cc_start: 0.7415 (tppt) cc_final: 0.6631 (tmmt) REVERT: A 354 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8131 (mm-30) REVERT: A 424 ARG cc_start: 0.6197 (mpt90) cc_final: 0.5909 (ttt90) REVERT: B 272 LYS cc_start: 0.7428 (tppt) cc_final: 0.6643 (tmmt) REVERT: B 354 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8136 (mm-30) REVERT: B 424 ARG cc_start: 0.6180 (mpt90) cc_final: 0.5886 (ttt90) REVERT: C 354 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8142 (mm-30) REVERT: C 424 ARG cc_start: 0.6173 (mpt90) cc_final: 0.5885 (ttt90) REVERT: D 354 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8125 (mm-30) REVERT: D 424 ARG cc_start: 0.6192 (mpt90) cc_final: 0.5896 (ttt90) outliers start: 24 outliers final: 8 residues processed: 166 average time/residue: 1.0183 time to fit residues: 185.7598 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 : 0.506 ------------------------------------------------------------------------------- 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: 3.9990 chunk 135 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 115 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.142800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.114006 restraints weight = 36870.054| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.53 r_work: 0.3083 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2041 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= 0.141 Angle : 0.420 4.074 16668 Z= 0.231 Chirality : 0.033 0.135 2004 Planarity : 0.003 0.036 2032 Dihedral : 4.717 58.269 1760 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.92 % Allowed : 11.31 % 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 aren not related in a simple way. whole: 3.26 (0.21), residues: 1504 helix: 2.70 (0.14), residues: 1256 sheet: 0.63 (0.79), residues: 48 loop : -1.25 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 399 TYR 0.006 0.001 TYR A 56 PHE 0.012 0.001 PHE A 11 TRP 0.006 0.001 TRP D 154 HIS 0.002 0.000 HIS D 337 Details of bonding type rmsd covalent geometry : bond 0.00297 (12284) covalent geometry : angle 0.42027 (16668) hydrogen bonds : bond 0.04173 ( 1056) hydrogen bonds : angle 3.72379 ( 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 164 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.603 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: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7761 (mt-10) REVERT: A 272 LYS cc_start: 0.7475 (tppt) cc_final: 0.6683 (tmmt) REVERT: A 391 ASP cc_start: 0.6119 (OUTLIER) cc_final: 0.5903 (t0) REVERT: A 424 ARG cc_start: 0.6266 (mpt90) cc_final: 0.6004 (ttt90) REVERT: B 33 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7763 (mt-10) REVERT: B 272 LYS cc_start: 0.7481 (tppt) cc_final: 0.6690 (tmmt) REVERT: B 391 ASP cc_start: 0.6120 (OUTLIER) cc_final: 0.5887 (t0) REVERT: B 424 ARG cc_start: 0.6246 (mpt90) cc_final: 0.6004 (ttt90) REVERT: C 33 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7759 (mt-10) REVERT: C 272 LYS cc_start: 0.7484 (tppt) cc_final: 0.6693 (tmmt) REVERT: C 391 ASP cc_start: 0.6106 (OUTLIER) cc_final: 0.5872 (t0) REVERT: C 424 ARG cc_start: 0.6236 (mpt90) cc_final: 0.6002 (ttt90) REVERT: D 33 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7754 (mt-10) REVERT: D 272 LYS cc_start: 0.7473 (tppt) cc_final: 0.6678 (tmmt) REVERT: D 391 ASP cc_start: 0.6180 (OUTLIER) cc_final: 0.5941 (t0) REVERT: D 424 ARG cc_start: 0.6246 (mpt90) cc_final: 0.6002 (ttt90) outliers start: 12 outliers final: 4 residues processed: 160 average time/residue: 1.1696 time to fit residues: 205.0542 Evaluate side-chains 156 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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: 2.9990 chunk 16 optimal weight: 0.0010 chunk 121 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.7192 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.139163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.108262 restraints weight = 36145.782| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.66 r_work: 0.3047 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2263 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= 0.170 Angle : 0.442 4.195 16668 Z= 0.244 Chirality : 0.034 0.140 2004 Planarity : 0.003 0.036 2032 Dihedral : 4.925 59.083 1760 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.83 % Allowed : 11.16 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.14 (0.21), residues: 1504 helix: 2.61 (0.14), residues: 1256 sheet: 0.57 (0.81), residues: 48 loop : -1.22 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 399 TYR 0.007 0.001 TYR A 182 PHE 0.011 0.001 PHE A 11 TRP 0.007 0.001 TRP D 174 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd covalent geometry : bond 0.00371 (12284) covalent geometry : angle 0.44199 (16668) hydrogen bonds : bond 0.04396 ( 1056) hydrogen bonds : angle 3.77401 ( 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 176 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.448 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 VAL cc_start: 0.7750 (p) cc_final: 0.7503 (p) REVERT: A 272 LYS cc_start: 0.7613 (tppt) cc_final: 0.6841 (tmmt) REVERT: A 391 ASP cc_start: 0.6243 (OUTLIER) cc_final: 0.5896 (t0) REVERT: A 424 ARG cc_start: 0.6392 (mpt90) cc_final: 0.6119 (ttt90) REVERT: B 25 VAL cc_start: 0.7756 (p) cc_final: 0.7512 (p) REVERT: B 272 LYS cc_start: 0.7627 (tppt) cc_final: 0.6854 (tmmt) REVERT: B 391 ASP cc_start: 0.6202 (OUTLIER) cc_final: 0.5885 (t0) REVERT: B 424 ARG cc_start: 0.6369 (mpt90) cc_final: 0.6111 (ttt90) REVERT: C 25 VAL cc_start: 0.7759 (p) cc_final: 0.7513 (p) REVERT: C 272 LYS cc_start: 0.7636 (tppt) cc_final: 0.6867 (tmmt) REVERT: C 391 ASP cc_start: 0.6198 (OUTLIER) cc_final: 0.5881 (t0) REVERT: C 424 ARG cc_start: 0.6349 (mpt90) cc_final: 0.6115 (ttt90) REVERT: D 25 VAL cc_start: 0.7758 (p) cc_final: 0.7511 (p) REVERT: D 272 LYS cc_start: 0.7622 (tppt) cc_final: 0.6847 (tmmt) REVERT: D 391 ASP cc_start: 0.6216 (OUTLIER) cc_final: 0.5877 (t0) REVERT: D 424 ARG cc_start: 0.6355 (mpt90) cc_final: 0.6106 (ttt90) outliers start: 24 outliers final: 8 residues processed: 168 average time/residue: 1.0504 time to fit residues: 193.6385 Evaluate side-chains 165 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 108 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.137745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.107076 restraints weight = 36350.345| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.65 r_work: 0.3030 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12284 Z= 0.197 Angle : 0.461 4.237 16668 Z= 0.256 Chirality : 0.035 0.139 2004 Planarity : 0.003 0.036 2032 Dihedral : 5.120 59.908 1760 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.45 % Allowed : 10.09 % 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 aren not related in a simple way. whole: 2.91 (0.21), residues: 1504 helix: 2.45 (0.14), residues: 1256 sheet: 0.54 (0.81), residues: 48 loop : -1.31 (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 0.011 0.002 PHE D 11 TRP 0.010 0.002 TRP A 174 HIS 0.003 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00439 (12284) covalent geometry : angle 0.46123 (16668) hydrogen bonds : bond 0.04573 ( 1056) hydrogen bonds : angle 3.86776 ( 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: 32 poor density : 156 time to evaluate : 0.407 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: 0.7619 (tppt) cc_final: 0.6862 (tmmt) REVERT: A 391 ASP cc_start: 0.6131 (OUTLIER) cc_final: 0.5805 (t0) REVERT: A 424 ARG cc_start: 0.6398 (mpt90) cc_final: 0.6169 (ttt90) REVERT: B 272 LYS cc_start: 0.7632 (tppt) cc_final: 0.6875 (tmmt) REVERT: B 391 ASP cc_start: 0.6050 (OUTLIER) cc_final: 0.5795 (t0) REVERT: B 424 ARG cc_start: 0.6388 (mpt90) cc_final: 0.6161 (ttt90) REVERT: C 272 LYS cc_start: 0.7642 (tppt) cc_final: 0.6887 (tmmt) REVERT: C 391 ASP cc_start: 0.6022 (OUTLIER) cc_final: 0.5765 (t0) REVERT: C 424 ARG cc_start: 0.6373 (mpt90) cc_final: 0.6151 (ttt90) REVERT: D 272 LYS cc_start: 0.7627 (tppt) cc_final: 0.6868 (tmmt) REVERT: D 391 ASP cc_start: 0.6115 (OUTLIER) cc_final: 0.5816 (t0) REVERT: D 424 ARG cc_start: 0.6386 (mpt90) cc_final: 0.6157 (ttt90) outliers start: 32 outliers final: 16 residues processed: 172 average time/residue: 1.0551 time to fit residues: 199.0749 Evaluate side-chains 176 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR 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 75 THR 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 75 THR 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 75 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 107 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 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: 1.9990 chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.138751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.108043 restraints weight = 36156.857| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.66 r_work: 0.3049 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12284 Z= 0.163 Angle : 0.452 4.158 16668 Z= 0.250 Chirality : 0.034 0.135 2004 Planarity : 0.003 0.036 2032 Dihedral : 4.115 30.439 1752 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.22 % Allowed : 12.54 % 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 aren not related in a simple way. whole: 3.06 (0.21), residues: 1504 helix: 2.54 (0.14), residues: 1256 sheet: 0.65 (0.80), residues: 48 loop : -1.19 (0.40), 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 182 PHE 0.012 0.001 PHE A 11 TRP 0.010 0.001 TRP C 174 HIS 0.003 0.001 HIS D 337 Details of bonding type rmsd covalent geometry : bond 0.00351 (12284) covalent geometry : angle 0.45224 (16668) hydrogen bonds : bond 0.04375 ( 1056) hydrogen bonds : angle 3.78067 ( 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 176 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.516 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: 0.7688 (tppt) cc_final: 0.6951 (tmmt) REVERT: A 391 ASP cc_start: 0.6030 (m-30) cc_final: 0.5775 (t0) REVERT: A 424 ARG cc_start: 0.6368 (mpt90) cc_final: 0.6157 (ttt90) REVERT: B 272 LYS cc_start: 0.7703 (tppt) cc_final: 0.6967 (tmmt) REVERT: C 272 LYS cc_start: 0.7712 (tppt) cc_final: 0.6977 (tmmt) REVERT: D 272 LYS cc_start: 0.7703 (tppt) cc_final: 0.6966 (tmmt) REVERT: D 391 ASP cc_start: 0.6053 (m-30) cc_final: 0.5828 (t0) REVERT: D 424 ARG cc_start: 0.6373 (mpt90) cc_final: 0.6171 (ttt90) outliers start: 16 outliers final: 8 residues processed: 176 average time/residue: 1.0291 time to fit residues: 199.1396 Evaluate side-chains 151 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 C residue 182 TYR Chi-restraints excluded: chain C residue 189 GLN 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: 0.9980 chunk 112 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 144 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.139119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.109540 restraints weight = 37713.899| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.62 r_work: 0.3056 rms_B_bonded: 2.23 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: 0.7718 moved from start: 0.2566 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= 0.131 Angle : 0.418 4.081 16668 Z= 0.230 Chirality : 0.033 0.138 2004 Planarity : 0.003 0.035 2032 Dihedral : 3.764 23.461 1752 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.92 % Allowed : 12.69 % 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 aren not related in a simple way. whole: 3.32 (0.21), residues: 1504 helix: 2.72 (0.14), residues: 1256 sheet: 0.78 (0.76), residues: 48 loop : -1.12 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 399 TYR 0.005 0.001 TYR A 182 PHE 0.011 0.001 PHE C 11 TRP 0.009 0.001 TRP C 174 HIS 0.003 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00275 (12284) covalent geometry : angle 0.41829 (16668) hydrogen bonds : bond 0.04102 ( 1056) hydrogen bonds : angle 3.64729 ( 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: 12 poor density : 158 time to evaluate : 0.506 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: 0.7688 (p) cc_final: 0.7426 (p) REVERT: A 209 MET cc_start: 0.7886 (ttt) cc_final: 0.7589 (ttm) REVERT: A 272 LYS cc_start: 0.7667 (tppt) cc_final: 0.6928 (tmmt) REVERT: A 391 ASP cc_start: 0.5992 (m-30) cc_final: 0.5709 (t0) REVERT: A 424 ARG cc_start: 0.6319 (mpt90) cc_final: 0.6105 (ttt90) REVERT: B 25 VAL cc_start: 0.7697 (p) cc_final: 0.7418 (p) REVERT: B 209 MET cc_start: 0.7865 (ttt) cc_final: 0.7568 (ttm) REVERT: B 272 LYS cc_start: 0.7679 (tppt) cc_final: 0.6940 (tmmt) REVERT: C 25 VAL cc_start: 0.7698 (p) cc_final: 0.7421 (p) REVERT: C 209 MET cc_start: 0.7890 (ttt) cc_final: 0.7593 (ttm) REVERT: C 272 LYS cc_start: 0.7671 (tppt) cc_final: 0.6933 (tmmt) REVERT: D 25 VAL cc_start: 0.7673 (p) cc_final: 0.7414 (p) REVERT: D 209 MET cc_start: 0.7890 (ttt) cc_final: 0.7592 (ttm) REVERT: D 272 LYS cc_start: 0.7678 (tppt) cc_final: 0.6943 (tmmt) REVERT: D 424 ARG cc_start: 0.6328 (mpt90) cc_final: 0.6111 (ttt90) outliers start: 12 outliers final: 8 residues processed: 170 average time/residue: 1.2210 time to fit residues: 225.1774 Evaluate side-chains 154 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 C residue 182 TYR Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 189 GLN 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: 0.0870 chunk 79 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.9564 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.137554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.107770 restraints weight = 36455.478| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.57 r_work: 0.3036 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12284 Z= 0.186 Angle : 0.461 4.242 16668 Z= 0.255 Chirality : 0.035 0.136 2004 Planarity : 0.003 0.036 2032 Dihedral : 4.124 29.964 1752 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.92 % Allowed : 12.61 % 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 aren not related in a simple way. whole: 3.02 (0.21), residues: 1504 helix: 2.51 (0.14), residues: 1256 sheet: 0.79 (0.79), residues: 48 loop : -1.25 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 399 TYR 0.007 0.001 TYR B 182 PHE 0.012 0.002 PHE A 392 TRP 0.014 0.002 TRP D 174 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd covalent geometry : bond 0.00414 (12284) covalent geometry : angle 0.46082 (16668) hydrogen bonds : bond 0.04466 ( 1056) hydrogen bonds : angle 3.79645 ( 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 161 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.486 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: 0.7628 (tppt) cc_final: 0.6885 (tmmt) REVERT: B 272 LYS cc_start: 0.7636 (tppt) cc_final: 0.6893 (tmmt) REVERT: C 272 LYS cc_start: 0.7637 (tppt) cc_final: 0.6899 (tmmt) REVERT: D 272 LYS cc_start: 0.7633 (tppt) cc_final: 0.6892 (tmmt) REVERT: D 424 ARG cc_start: 0.6258 (mpt90) cc_final: 0.5984 (ttt90) outliers start: 12 outliers final: 12 residues processed: 157 average time/residue: 1.0925 time to fit residues: 187.9893 Evaluate side-chains 161 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 113 ASN 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 74 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 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: 1.9990 chunk 48 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.138799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.110257 restraints weight = 37072.411| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.52 r_work: 0.3042 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 12284 Z= 0.240 Angle : 1.228 59.199 16668 Z= 0.759 Chirality : 0.047 0.719 2004 Planarity : 0.003 0.036 2032 Dihedral : 4.178 29.983 1752 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.15 % Allowed : 12.69 % Favored : 86.16 % 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 aren not related in a simple way. whole: 3.00 (0.21), residues: 1504 helix: 2.50 (0.14), residues: 1256 sheet: 0.78 (0.80), residues: 48 loop : -1.26 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 205 TYR 0.007 0.001 TYR C 182 PHE 0.012 0.002 PHE A 392 TRP 0.012 0.002 TRP D 174 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd covalent geometry : bond 0.00498 (12284) covalent geometry : angle 1.22755 (16668) hydrogen bonds : bond 0.04459 ( 1056) hydrogen bonds : angle 3.80310 ( 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: 15 poor density : 149 time to evaluate : 0.580 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: 0.7589 (p) cc_final: 0.7339 (p) REVERT: A 113 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7702 (t0) REVERT: A 272 LYS cc_start: 0.7592 (tppt) cc_final: 0.6844 (tmmt) REVERT: B 25 VAL cc_start: 0.7582 (p) cc_final: 0.7333 (p) REVERT: B 113 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7698 (t0) REVERT: B 272 LYS cc_start: 0.7608 (tppt) cc_final: 0.6861 (tmmt) REVERT: C 25 VAL cc_start: 0.7588 (p) cc_final: 0.7338 (p) REVERT: C 113 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.7687 (t0) REVERT: C 272 LYS cc_start: 0.7607 (tppt) cc_final: 0.6864 (tmmt) REVERT: D 25 VAL cc_start: 0.7590 (p) cc_final: 0.7338 (p) REVERT: D 113 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7629 (t0) REVERT: D 272 LYS cc_start: 0.7610 (tppt) cc_final: 0.6863 (tmmt) REVERT: D 424 ARG cc_start: 0.6214 (mpt90) cc_final: 0.5936 (ttt90) outliers start: 15 outliers final: 8 residues processed: 160 average time/residue: 0.9622 time to fit residues: 169.1176 Evaluate side-chains 162 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 113 ASN 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: 0.9990 chunk 83 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.139271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.110797 restraints weight = 37257.729| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.51 r_work: 0.3043 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 12284 Z= 0.238 Angle : 1.126 59.129 16668 Z= 0.706 Chirality : 0.047 0.734 2004 Planarity : 0.004 0.117 2032 Dihedral : 4.178 29.983 1752 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.92 % Allowed : 12.92 % Favored : 86.16 % 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 aren not related in a simple way. whole: 3.00 (0.21), residues: 1504 helix: 2.50 (0.14), residues: 1256 sheet: 0.78 (0.80), residues: 48 loop : -1.26 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 205 TYR 0.007 0.001 TYR C 182 PHE 0.012 0.002 PHE A 392 TRP 0.012 0.002 TRP D 174 HIS 0.003 0.001 HIS C 337 Details of bonding type rmsd covalent geometry : bond 0.00492 (12284) covalent geometry : angle 1.12590 (16668) hydrogen bonds : bond 0.04459 ( 1056) hydrogen bonds : angle 3.80310 ( 3168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7109.98 seconds wall clock time: 121 minutes 16.83 seconds (7276.83 seconds total)