Starting phenix.real_space_refine on Thu Jul 2 16:36:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ctc_26985/07_2026/8ctc_26985.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ctc_26985/07_2026/8ctc_26985.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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8ctc_26985/07_2026/8ctc_26985.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ctc_26985/07_2026/8ctc_26985.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ctc_26985/07_2026/8ctc_26985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ctc_26985/07_2026/8ctc_26985.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ctc_26985/07_2026/8ctc_26985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ctc_26985/07_2026/8ctc_26985.map" } 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= 0.012 sd= 0.147 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Hg 3 10.96 5 S 60 5.16 5 Na 9 4.78 5 C 6090 2.51 5 N 1479 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s 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: 9309 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3085 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 11, 'TRANS': 394} Chain breaks: 2 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' HG': 1, ' NA': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1577 SG CYS A 269 83.711 62.418 25.018 1.00 74.49 S ATOM 2858 SG CYS A 441 81.025 63.145 27.129 1.00 85.07 S Restraints were copied for chains: B, C Time building chain proxies: 2.20, per 1000 atoms: 0.24 Number of scatterers: 9309 At special positions: 0 Unit cell: (108.3, 99.636, 73.644, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Hg 3 79.96 S 60 16.00 Na 9 11.00 O 1668 8.00 N 1479 7.00 C 6090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 352.8 milliseconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 3 sheets defined 84.3% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 removed outlier: 4.050A pdb=" N LEU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR A 24 " --> pdb=" O VAL A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 53 through 82 removed outlier: 3.570A pdb=" N ILE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 4.100A pdb=" N LEU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 117 removed outlier: 3.601A pdb=" N TYR A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.839A pdb=" N LEU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.539A pdb=" N ALA A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 230 Processing helix chain 'A' and resid 233 through 268 removed outlier: 3.525A pdb=" N VAL A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 284 through 299 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.864A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 351 through 366 removed outlier: 4.029A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix removed outlier: 4.521A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 390 through 408 removed outlier: 3.524A pdb=" N ILE A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 426 removed outlier: 3.970A pdb=" N VAL A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 438 removed outlier: 3.520A pdb=" N ASP A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A 433 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 437 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ALA A 438 " --> pdb=" O LEU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 465 removed outlier: 3.703A pdb=" N LEU A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'B' and resid 18 through 42 removed outlier: 4.049A pdb=" N LEU B 22 " --> pdb=" O ASN B 18 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR B 24 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 Processing helix chain 'B' and resid 53 through 82 removed outlier: 3.571A pdb=" N ILE B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Proline residue: B 69 - end of helix removed outlier: 4.100A pdb=" N LEU B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 117 removed outlier: 3.600A pdb=" N TYR B 97 " --> pdb=" O ARG B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.839A pdb=" N LEU B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 removed outlier: 3.539A pdb=" N ALA B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 230 Processing helix chain 'B' and resid 233 through 268 removed outlier: 3.526A pdb=" N VAL B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TRP B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Proline residue: B 259 - end of helix Processing helix chain 'B' and resid 276 through 282 Processing helix chain 'B' and resid 284 through 299 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 312 through 320 removed outlier: 3.864A pdb=" N PHE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 336 through 347 Processing helix chain 'B' and resid 351 through 366 removed outlier: 4.030A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Proline residue: B 360 - end of helix removed outlier: 4.521A pdb=" N THR B 364 " --> pdb=" O PRO B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 385 Processing helix chain 'B' and resid 390 through 408 removed outlier: 3.524A pdb=" N ILE B 397 " --> pdb=" O GLN B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 426 removed outlier: 3.970A pdb=" N VAL B 422 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 438 removed outlier: 3.520A pdb=" N ASP B 432 " --> pdb=" O PRO B 429 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL B 433 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 437 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ALA B 438 " --> pdb=" O LEU B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 465 removed outlier: 3.703A pdb=" N LEU B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 455 " --> pdb=" O ASN B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'C' and resid 18 through 42 removed outlier: 4.050A pdb=" N LEU C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR C 24 " --> pdb=" O VAL C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 Processing helix chain 'C' and resid 53 through 82 removed outlier: 3.571A pdb=" N ILE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Proline residue: C 69 - end of helix removed outlier: 4.100A pdb=" N LEU C 82 " --> pdb=" O GLY C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 117 removed outlier: 3.601A pdb=" N TYR C 97 " --> pdb=" O ARG C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.839A pdb=" N LEU C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 158 removed outlier: 3.539A pdb=" N ALA C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 230 Processing helix chain 'C' and resid 233 through 268 removed outlier: 3.525A pdb=" N VAL C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TRP C 256 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Proline residue: C 259 - end of helix Processing helix chain 'C' and resid 276 through 282 Processing helix chain 'C' and resid 284 through 299 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 312 through 320 removed outlier: 3.863A pdb=" N PHE C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 336 through 347 Processing helix chain 'C' and resid 351 through 366 removed outlier: 4.029A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Proline residue: C 360 - end of helix removed outlier: 4.520A pdb=" N THR C 364 " --> pdb=" O PRO C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 385 Processing helix chain 'C' and resid 390 through 408 removed outlier: 3.524A pdb=" N ILE C 397 " --> pdb=" O GLN C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 426 removed outlier: 3.969A pdb=" N VAL C 422 " --> pdb=" O THR C 418 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 438 removed outlier: 3.520A pdb=" N ASP C 432 " --> pdb=" O PRO C 429 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL C 433 " --> pdb=" O ALA C 430 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE C 437 " --> pdb=" O THR C 434 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ALA C 438 " --> pdb=" O LEU C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 465 removed outlier: 3.702A pdb=" N LEU C 443 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET C 449 " --> pdb=" O ARG C 445 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP C 455 " --> pdb=" O ASN C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 470 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 167 Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 167 699 hydrogen bonds defined for protein. 2043 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.47 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2837 1.34 - 1.46: 1120 1.46 - 1.57: 5352 1.57 - 1.69: 0 1.69 - 1.81: 111 Bond restraints: 9420 Sorted by residual: bond pdb=" N ASP B 275 " pdb=" CA ASP B 275 " ideal model delta sigma weight residual 1.458 1.494 -0.036 9.00e-03 1.23e+04 1.59e+01 bond pdb=" N ASP A 275 " pdb=" CA ASP A 275 " ideal model delta sigma weight residual 1.458 1.494 -0.036 9.00e-03 1.23e+04 1.59e+01 bond pdb=" N ASP C 275 " pdb=" CA ASP C 275 " ideal model delta sigma weight residual 1.458 1.493 -0.035 9.00e-03 1.23e+04 1.50e+01 bond pdb=" N TRP C 276 " pdb=" CA TRP C 276 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.45e+00 bond pdb=" N TRP B 276 " pdb=" CA TRP B 276 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 8.99e+00 ... (remaining 9415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 11892 1.33 - 2.65: 708 2.65 - 3.98: 156 3.98 - 5.30: 18 5.30 - 6.63: 12 Bond angle restraints: 12786 Sorted by residual: angle pdb=" CA GLU C 274 " pdb=" C GLU C 274 " pdb=" O GLU C 274 " ideal model delta sigma weight residual 120.70 116.80 3.90 1.03e+00 9.43e-01 1.44e+01 angle pdb=" CA GLU B 274 " pdb=" C GLU B 274 " pdb=" O GLU B 274 " ideal model delta sigma weight residual 120.70 116.80 3.90 1.03e+00 9.43e-01 1.43e+01 angle pdb=" CA GLU A 274 " pdb=" C GLU A 274 " pdb=" O GLU A 274 " ideal model delta sigma weight residual 120.70 116.84 3.86 1.03e+00 9.43e-01 1.41e+01 angle pdb=" N ARG B 315 " pdb=" CA ARG B 315 " pdb=" C ARG B 315 " ideal model delta sigma weight residual 111.36 107.48 3.88 1.09e+00 8.42e-01 1.26e+01 angle pdb=" N ARG A 315 " pdb=" CA ARG A 315 " pdb=" C ARG A 315 " ideal model delta sigma weight residual 111.36 107.52 3.84 1.09e+00 8.42e-01 1.24e+01 ... (remaining 12781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.44: 4906 14.44 - 28.89: 486 28.89 - 43.33: 176 43.33 - 57.77: 45 57.77 - 72.22: 12 Dihedral angle restraints: 5625 sinusoidal: 2130 harmonic: 3495 Sorted by residual: dihedral pdb=" CG ARG C 147 " pdb=" CD ARG C 147 " pdb=" NE ARG C 147 " pdb=" CZ ARG C 147 " ideal model delta sinusoidal sigma weight residual 180.00 136.17 43.83 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CG ARG A 147 " pdb=" CD ARG A 147 " pdb=" NE ARG A 147 " pdb=" CZ ARG A 147 " ideal model delta sinusoidal sigma weight residual 180.00 136.22 43.78 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CG ARG B 147 " pdb=" CD ARG B 147 " pdb=" NE ARG B 147 " pdb=" CZ ARG B 147 " ideal model delta sinusoidal sigma weight residual 180.00 136.22 43.78 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 5622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1099 0.040 - 0.079: 354 0.079 - 0.119: 124 0.119 - 0.159: 34 0.159 - 0.199: 15 Chirality restraints: 1626 Sorted by residual: chirality pdb=" CA VAL B 273 " pdb=" N VAL B 273 " pdb=" C VAL B 273 " pdb=" CB VAL B 273 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" CA VAL A 273 " pdb=" N VAL A 273 " pdb=" C VAL A 273 " pdb=" CB VAL A 273 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.73e-01 chirality pdb=" CA VAL C 273 " pdb=" N VAL C 273 " pdb=" C VAL C 273 " pdb=" CB VAL C 273 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.67e-01 ... (remaining 1623 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 386 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.96e+00 pdb=" C ASP B 386 " -0.046 2.00e-02 2.50e+03 pdb=" O ASP B 386 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU B 387 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 386 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C ASP A 386 " -0.046 2.00e-02 2.50e+03 pdb=" O ASP A 386 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU A 387 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 386 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C ASP C 386 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP C 386 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU C 387 " -0.016 2.00e-02 2.50e+03 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 46 2.51 - 3.11: 7202 3.11 - 3.71: 14387 3.71 - 4.30: 20421 4.30 - 4.90: 34361 Nonbonded interactions: 76417 Sorted by model distance: nonbonded pdb=" OG1 THR B 102 " pdb="NA NA B 603 " model vdw 1.917 2.470 nonbonded pdb=" OG1 THR A 102 " pdb="NA NA A 603 " model vdw 1.918 2.470 nonbonded pdb=" OG1 THR C 102 " pdb="NA NA C 603 " model vdw 1.918 2.470 nonbonded pdb=" SG CYS B 269 " pdb="HG HG B 604 " model vdw 2.067 2.880 nonbonded pdb=" SG CYS A 269 " pdb="HG HG A 604 " model vdw 2.067 2.880 ... (remaining 76412 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.840 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 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 0.042 9420 Z= 0.362 Angle : 0.736 6.630 12786 Z= 0.505 Chirality : 0.049 0.199 1626 Planarity : 0.003 0.030 1557 Dihedral : 14.007 72.218 3369 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 15.38 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.39 (0.24), residues: 1200 helix: 0.77 (0.17), residues: 948 sheet: -0.59 (0.68), residues: 54 loop : -1.61 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 315 TYR 0.007 0.001 TYR C 257 PHE 0.011 0.001 PHE C 240 TRP 0.006 0.001 TRP B 19 HIS 0.005 0.002 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.36 ( 9420) covalent geometry : angle 0.73569 / 0.51 (12786) hydrogen bonds : bond 0.16870 / 11.35 ( 699) hydrogen bonds : angle 6.14360 / 4.39 ( 2043) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.284 Fit side-chains REVERT: A 353 ARG cc_start: 0.6985 (mtm180) cc_final: 0.6294 (mtp180) REVERT: A 367 MET cc_start: 0.9138 (mtt) cc_final: 0.8746 (mtm) REVERT: B 342 ARG cc_start: 0.7531 (ttm110) cc_final: 0.7173 (ttp-110) REVERT: B 346 GLU cc_start: 0.6736 (mt-10) cc_final: 0.6229 (mm-30) REVERT: B 353 ARG cc_start: 0.7402 (mtm180) cc_final: 0.7067 (mtm180) REVERT: C 275 ASP cc_start: 0.7650 (p0) cc_final: 0.7393 (p0) REVERT: C 367 MET cc_start: 0.8994 (mtt) cc_final: 0.8791 (mtm) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.5768 time to fit residues: 113.5187 Evaluate side-chains 162 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.0980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN A 347 ASN A 385 ASN B 348 ASN C 347 ASN C 385 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.176196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.118192 restraints weight = 3581.385| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.26 r_work: 0.3122 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9420 Z= 0.141 Angle : 0.509 5.219 12786 Z= 0.271 Chirality : 0.038 0.130 1626 Planarity : 0.004 0.034 1557 Dihedral : 4.035 35.034 1281 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.25 % Allowed : 14.69 % Favored : 82.05 % 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: 0.88 (0.24), residues: 1200 helix: 1.20 (0.17), residues: 948 sheet: -0.75 (0.62), residues: 54 loop : -1.84 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 315 TYR 0.008 0.001 TYR C 162 PHE 0.013 0.002 PHE B 240 TRP 0.011 0.001 TRP B 19 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 9420) covalent geometry : angle 0.50913 / 0.27 (12786) hydrogen bonds : bond 0.04956 / 3.37 ( 699) hydrogen bonds : angle 4.69188 / 3.27 ( 2043) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.391 Fit side-chains REVERT: A 256 TRP cc_start: 0.8221 (m-10) cc_final: 0.7573 (m100) REVERT: B 48 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7348 (mt-10) REVERT: B 208 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8129 (m-30) REVERT: B 304 ILE cc_start: 0.7654 (tt) cc_final: 0.7183 (mt) REVERT: B 342 ARG cc_start: 0.6950 (ttm110) cc_final: 0.6697 (ttp-110) REVERT: C 275 ASP cc_start: 0.7410 (p0) cc_final: 0.7076 (p0) REVERT: C 277 GLU cc_start: 0.6711 (mp0) cc_final: 0.6503 (mp0) REVERT: C 318 MET cc_start: 0.7890 (tpt) cc_final: 0.7672 (mmm) REVERT: C 600 GLU cc_start: 0.8483 (mp0) cc_final: 0.7925 (mp0) outliers start: 33 outliers final: 13 residues processed: 180 average time/residue: 0.5148 time to fit residues: 99.7776 Evaluate side-chains 159 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 424 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 7 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN A 347 ASN A 385 ASN B 347 ASN C 347 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.173777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.117588 restraints weight = 3823.581| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.26 r_work: 0.3196 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9420 Z= 0.136 Angle : 0.496 8.427 12786 Z= 0.258 Chirality : 0.038 0.124 1626 Planarity : 0.004 0.032 1557 Dihedral : 3.964 35.176 1281 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.55 % Allowed : 16.27 % Favored : 80.18 % 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: 1.02 (0.24), residues: 1200 helix: 1.30 (0.17), residues: 957 sheet: -0.84 (0.60), residues: 54 loop : -1.92 (0.38), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 310 TYR 0.007 0.001 TYR C 162 PHE 0.020 0.002 PHE A 306 TRP 0.007 0.001 TRP B 19 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 9420) covalent geometry : angle 0.49637 / 0.26 (12786) hydrogen bonds : bond 0.04773 / 3.26 ( 699) hydrogen bonds : angle 4.53973 / 3.17 ( 2043) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.351 Fit side-chains REVERT: A 256 TRP cc_start: 0.8126 (m-10) cc_final: 0.7450 (m100) REVERT: B 62 MET cc_start: 0.8608 (mtp) cc_final: 0.8408 (mtt) REVERT: B 304 ILE cc_start: 0.7618 (tt) cc_final: 0.7169 (mt) REVERT: B 342 ARG cc_start: 0.6811 (ttm110) cc_final: 0.6562 (ttp-110) REVERT: C 113 VAL cc_start: 0.7012 (p) cc_final: 0.6803 (p) REVERT: C 274 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7309 (mp0) REVERT: C 318 MET cc_start: 0.7890 (tpt) cc_final: 0.7647 (mmm) REVERT: B 600 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7810 (mp0) outliers start: 36 outliers final: 17 residues processed: 172 average time/residue: 0.5139 time to fit residues: 95.0791 Evaluate side-chains 161 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain B residue 600 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 113 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.173650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.117053 restraints weight = 3759.697| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.25 r_work: 0.3161 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9420 Z= 0.136 Angle : 0.486 7.449 12786 Z= 0.255 Chirality : 0.038 0.138 1626 Planarity : 0.004 0.031 1557 Dihedral : 3.955 35.629 1281 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.25 % Allowed : 17.75 % Favored : 78.99 % 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: 1.12 (0.24), residues: 1200 helix: 1.37 (0.17), residues: 957 sheet: -0.90 (0.59), residues: 54 loop : -1.86 (0.38), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 61 TYR 0.007 0.001 TYR C 162 PHE 0.012 0.001 PHE B 240 TRP 0.006 0.001 TRP A 19 HIS 0.003 0.001 HIS C 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 9420) covalent geometry : angle 0.48609 / 0.26 (12786) hydrogen bonds : bond 0.04640 / 3.16 ( 699) hydrogen bonds : angle 4.47176 / 3.12 ( 2043) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.395 Fit side-chains REVERT: A 318 MET cc_start: 0.7984 (tpt) cc_final: 0.7630 (mmm) REVERT: A 354 ILE cc_start: 0.6736 (OUTLIER) cc_final: 0.6309 (tp) REVERT: B 62 MET cc_start: 0.8636 (mtp) cc_final: 0.8424 (mtt) REVERT: B 304 ILE cc_start: 0.7730 (tt) cc_final: 0.7253 (mt) REVERT: B 342 ARG cc_start: 0.6872 (ttm110) cc_final: 0.6614 (ttp-110) REVERT: B 400 THR cc_start: 0.8243 (m) cc_final: 0.7672 (p) REVERT: C 274 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: C 277 GLU cc_start: 0.6795 (mp0) cc_final: 0.6551 (mp0) REVERT: C 318 MET cc_start: 0.7898 (tpt) cc_final: 0.7674 (mmm) REVERT: A 600 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: B 600 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7876 (mp0) outliers start: 33 outliers final: 14 residues processed: 166 average time/residue: 0.5228 time to fit residues: 93.4341 Evaluate side-chains 158 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain B residue 600 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 78 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 117 optimal weight: 0.3980 chunk 79 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.173852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.117303 restraints weight = 3676.861| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.24 r_work: 0.3195 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9420 Z= 0.130 Angle : 0.475 7.206 12786 Z= 0.250 Chirality : 0.037 0.126 1626 Planarity : 0.004 0.032 1557 Dihedral : 3.916 35.535 1281 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.45 % Allowed : 17.36 % Favored : 79.19 % 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: 1.17 (0.24), residues: 1200 helix: 1.42 (0.17), residues: 951 sheet: -0.81 (0.59), residues: 54 loop : -1.86 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 61 TYR 0.007 0.001 TYR A 97 PHE 0.020 0.002 PHE A 306 TRP 0.007 0.001 TRP C 19 HIS 0.003 0.001 HIS C 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 9420) covalent geometry : angle 0.47515 / 0.25 (12786) hydrogen bonds : bond 0.04512 / 3.07 ( 699) hydrogen bonds : angle 4.40973 / 3.08 ( 2043) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 0.353 Fit side-chains REVERT: A 318 MET cc_start: 0.7958 (tpt) cc_final: 0.7621 (mmm) REVERT: B 62 MET cc_start: 0.8674 (mtp) cc_final: 0.8441 (mtt) REVERT: B 304 ILE cc_start: 0.7728 (tt) cc_final: 0.7246 (mt) REVERT: B 342 ARG cc_start: 0.6892 (ttm110) cc_final: 0.6623 (ttp-110) REVERT: B 400 THR cc_start: 0.8181 (m) cc_final: 0.7720 (p) REVERT: C 274 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: C 318 MET cc_start: 0.7902 (tpt) cc_final: 0.7681 (mmm) REVERT: C 355 THR cc_start: 0.7572 (OUTLIER) cc_final: 0.7360 (m) REVERT: A 600 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8145 (mp0) REVERT: B 600 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7880 (mp0) REVERT: C 600 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8032 (mp0) outliers start: 35 outliers final: 17 residues processed: 162 average time/residue: 0.5328 time to fit residues: 92.9587 Evaluate side-chains 160 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain C residue 600 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 95 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.173621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.117000 restraints weight = 3612.368| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.24 r_work: 0.3160 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9420 Z= 0.135 Angle : 0.484 6.957 12786 Z= 0.255 Chirality : 0.038 0.126 1626 Planarity : 0.004 0.032 1557 Dihedral : 3.920 36.020 1281 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.55 % Allowed : 17.95 % Favored : 78.50 % 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: 1.22 (0.24), residues: 1200 helix: 1.45 (0.17), residues: 951 sheet: -0.81 (0.59), residues: 54 loop : -1.76 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 61 TYR 0.007 0.001 TYR A 97 PHE 0.014 0.002 PHE B 306 TRP 0.009 0.001 TRP C 19 HIS 0.003 0.001 HIS C 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 9420) covalent geometry : angle 0.48411 / 0.26 (12786) hydrogen bonds : bond 0.04592 / 3.12 ( 699) hydrogen bonds : angle 4.39897 / 3.07 ( 2043) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.379 Fit side-chains REVERT: A 318 MET cc_start: 0.7960 (tpt) cc_final: 0.7627 (mmm) REVERT: A 354 ILE cc_start: 0.6722 (OUTLIER) cc_final: 0.6288 (tp) REVERT: B 276 TRP cc_start: 0.5969 (m100) cc_final: 0.5469 (m-10) REVERT: B 304 ILE cc_start: 0.7743 (tt) cc_final: 0.7259 (mt) REVERT: B 342 ARG cc_start: 0.6909 (ttm110) cc_final: 0.6635 (ttp-110) REVERT: C 274 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7410 (mp0) REVERT: C 277 GLU cc_start: 0.6770 (mp0) cc_final: 0.6520 (mp0) REVERT: C 279 PHE cc_start: 0.7522 (OUTLIER) cc_final: 0.7229 (t80) REVERT: C 318 MET cc_start: 0.7911 (tpt) cc_final: 0.7696 (mmm) REVERT: C 355 THR cc_start: 0.7573 (OUTLIER) cc_final: 0.7361 (m) REVERT: A 600 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8158 (mp0) REVERT: B 600 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: C 600 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8022 (mp0) outliers start: 36 outliers final: 22 residues processed: 160 average time/residue: 0.5267 time to fit residues: 90.7025 Evaluate side-chains 162 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain C residue 600 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 65 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.174561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.117943 restraints weight = 3647.002| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.24 r_work: 0.3123 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9420 Z= 0.124 Angle : 0.473 6.741 12786 Z= 0.249 Chirality : 0.037 0.124 1626 Planarity : 0.004 0.032 1557 Dihedral : 3.881 35.498 1281 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.55 % Allowed : 18.74 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.31 (0.24), residues: 1200 helix: 1.58 (0.17), residues: 942 sheet: -0.78 (0.60), residues: 54 loop : -1.97 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 310 TYR 0.007 0.001 TYR A 97 PHE 0.021 0.002 PHE A 306 TRP 0.011 0.001 TRP C 19 HIS 0.003 0.001 HIS C 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 9420) covalent geometry : angle 0.47271 / 0.25 (12786) hydrogen bonds : bond 0.04372 / 2.97 ( 699) hydrogen bonds : angle 4.35115 / 3.03 ( 2043) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.350 Fit side-chains REVERT: A 279 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.7100 (t80) REVERT: A 318 MET cc_start: 0.7780 (tpt) cc_final: 0.7455 (mmm) REVERT: A 354 ILE cc_start: 0.6686 (OUTLIER) cc_final: 0.6258 (tp) REVERT: B 304 ILE cc_start: 0.7679 (tt) cc_final: 0.7201 (mt) REVERT: B 342 ARG cc_start: 0.6849 (ttm110) cc_final: 0.6576 (ttp-110) REVERT: C 274 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7462 (mp0) REVERT: C 277 GLU cc_start: 0.6864 (mp0) cc_final: 0.6216 (mp0) REVERT: C 279 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.7207 (t80) REVERT: C 318 MET cc_start: 0.7894 (tpt) cc_final: 0.7679 (mmm) REVERT: C 346 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6218 (mm-30) REVERT: C 355 THR cc_start: 0.7523 (OUTLIER) cc_final: 0.7314 (m) REVERT: A 600 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8140 (mp0) REVERT: B 600 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: C 600 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8023 (mp0) outliers start: 36 outliers final: 18 residues processed: 167 average time/residue: 0.4929 time to fit residues: 88.6592 Evaluate side-chains 160 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain C residue 600 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.173757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.116902 restraints weight = 3626.134| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.24 r_work: 0.3170 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9420 Z= 0.135 Angle : 0.489 6.641 12786 Z= 0.257 Chirality : 0.038 0.122 1626 Planarity : 0.004 0.032 1557 Dihedral : 3.894 36.055 1281 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.35 % Allowed : 19.13 % Favored : 77.51 % 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: 1.32 (0.24), residues: 1200 helix: 1.58 (0.17), residues: 939 sheet: -0.82 (0.59), residues: 54 loop : -1.86 (0.38), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 61 TYR 0.008 0.001 TYR A 97 PHE 0.018 0.002 PHE B 306 TRP 0.015 0.001 TRP C 19 HIS 0.004 0.001 HIS C 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 9420) covalent geometry : angle 0.48931 / 0.26 (12786) hydrogen bonds : bond 0.04572 / 3.11 ( 699) hydrogen bonds : angle 4.37353 / 3.05 ( 2043) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.244 Fit side-chains REVERT: A 279 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.7151 (t80) REVERT: A 318 MET cc_start: 0.7829 (tpt) cc_final: 0.7461 (mmm) REVERT: A 354 ILE cc_start: 0.6710 (OUTLIER) cc_final: 0.6277 (tp) REVERT: B 304 ILE cc_start: 0.7724 (tt) cc_final: 0.7244 (mt) REVERT: B 342 ARG cc_start: 0.6872 (ttm110) cc_final: 0.6589 (ttp-110) REVERT: B 465 LEU cc_start: 0.7685 (mt) cc_final: 0.7435 (mt) REVERT: C 274 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7487 (mp0) REVERT: C 277 GLU cc_start: 0.6880 (mp0) cc_final: 0.6281 (mp0) REVERT: C 279 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.7241 (t80) REVERT: C 318 MET cc_start: 0.7909 (tpt) cc_final: 0.7687 (mmm) REVERT: C 346 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6239 (mm-30) REVERT: C 355 THR cc_start: 0.7520 (OUTLIER) cc_final: 0.7292 (m) REVERT: A 600 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8158 (mp0) REVERT: B 600 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7884 (mp0) REVERT: C 600 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8018 (mp0) outliers start: 34 outliers final: 20 residues processed: 159 average time/residue: 0.4680 time to fit residues: 79.8638 Evaluate side-chains 165 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain C residue 600 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 86 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.174366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.117581 restraints weight = 3611.509| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.24 r_work: 0.3200 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9420 Z= 0.131 Angle : 0.493 6.563 12786 Z= 0.259 Chirality : 0.038 0.127 1626 Planarity : 0.004 0.033 1557 Dihedral : 3.893 35.964 1281 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.25 % Allowed : 19.13 % Favored : 77.61 % 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: 1.38 (0.24), residues: 1200 helix: 1.55 (0.17), residues: 948 sheet: -0.80 (0.60), residues: 54 loop : -1.57 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 310 TYR 0.008 0.001 TYR A 97 PHE 0.023 0.002 PHE A 306 TRP 0.017 0.001 TRP C 19 HIS 0.003 0.001 HIS C 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 9420) covalent geometry : angle 0.49313 / 0.26 (12786) hydrogen bonds : bond 0.04459 / 3.03 ( 699) hydrogen bonds : angle 4.36790 / 3.05 ( 2043) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.215 Fit side-chains REVERT: A 279 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.7103 (t80) REVERT: A 318 MET cc_start: 0.7830 (tpt) cc_final: 0.7471 (mmm) REVERT: A 354 ILE cc_start: 0.6692 (OUTLIER) cc_final: 0.6257 (tp) REVERT: B 304 ILE cc_start: 0.7717 (tt) cc_final: 0.7227 (mt) REVERT: B 342 ARG cc_start: 0.6976 (ttm110) cc_final: 0.6701 (ttp-110) REVERT: B 465 LEU cc_start: 0.7686 (mt) cc_final: 0.7424 (mt) REVERT: C 142 MET cc_start: 0.8311 (tpp) cc_final: 0.8075 (mmm) REVERT: C 274 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7443 (mp0) REVERT: C 276 TRP cc_start: 0.6359 (m100) cc_final: 0.6121 (m-10) REVERT: C 277 GLU cc_start: 0.6873 (mp0) cc_final: 0.6258 (mp0) REVERT: C 279 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.7245 (t80) REVERT: C 318 MET cc_start: 0.7909 (tpt) cc_final: 0.7687 (mmm) REVERT: C 346 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6224 (mm-30) REVERT: C 355 THR cc_start: 0.7530 (OUTLIER) cc_final: 0.7305 (m) REVERT: A 600 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: B 600 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: C 600 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8026 (mp0) outliers start: 33 outliers final: 22 residues processed: 158 average time/residue: 0.4463 time to fit residues: 75.8612 Evaluate side-chains 169 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain B residue 600 GLU Chi-restraints excluded: chain C residue 600 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 16 optimal weight: 0.0170 chunk 38 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.175228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118722 restraints weight = 3625.831| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.24 r_work: 0.3206 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9420 Z= 0.122 Angle : 0.486 7.242 12786 Z= 0.255 Chirality : 0.037 0.127 1626 Planarity : 0.004 0.033 1557 Dihedral : 3.848 35.450 1281 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.25 % Allowed : 19.43 % Favored : 77.32 % 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: 1.48 (0.24), residues: 1200 helix: 1.61 (0.17), residues: 948 sheet: -0.74 (0.60), residues: 54 loop : -1.50 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 310 TYR 0.007 0.001 TYR A 97 PHE 0.019 0.001 PHE B 306 TRP 0.022 0.002 TRP C 19 HIS 0.003 0.001 HIS C 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9420) covalent geometry : angle 0.48615 / 0.26 (12786) hydrogen bonds : bond 0.04240 / 2.87 ( 699) hydrogen bonds : angle 4.32357 / 3.01 ( 2043) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.373 Fit side-chains REVERT: A 276 TRP cc_start: 0.6183 (m100) cc_final: 0.5911 (m-10) REVERT: A 279 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.7083 (t80) REVERT: A 318 MET cc_start: 0.7941 (tpt) cc_final: 0.7616 (mmm) REVERT: A 354 ILE cc_start: 0.6672 (OUTLIER) cc_final: 0.6313 (tp) REVERT: B 304 ILE cc_start: 0.7716 (tt) cc_final: 0.7225 (mt) REVERT: B 342 ARG cc_start: 0.6895 (ttm110) cc_final: 0.6611 (ttp-110) REVERT: B 465 LEU cc_start: 0.7594 (mt) cc_final: 0.7359 (mt) REVERT: C 274 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: C 276 TRP cc_start: 0.6254 (m100) cc_final: 0.5939 (m-10) REVERT: C 279 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.7241 (t80) REVERT: C 318 MET cc_start: 0.7874 (tpt) cc_final: 0.7654 (mmm) REVERT: C 346 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6271 (mm-30) REVERT: C 355 THR cc_start: 0.7522 (OUTLIER) cc_final: 0.7294 (m) REVERT: A 600 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8183 (mp0) REVERT: B 600 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.7913 (mp0) outliers start: 33 outliers final: 16 residues processed: 160 average time/residue: 0.4924 time to fit residues: 84.6904 Evaluate side-chains 157 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 279 PHE Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain B residue 600 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 50 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 107 optimal weight: 0.2980 chunk 24 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.174633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.118050 restraints weight = 3568.206| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.23 r_work: 0.3155 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9420 Z= 0.131 Angle : 0.511 8.168 12786 Z= 0.266 Chirality : 0.038 0.157 1626 Planarity : 0.004 0.032 1557 Dihedral : 3.873 35.738 1281 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.76 % Allowed : 20.32 % Favored : 76.92 % 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: 1.44 (0.24), residues: 1200 helix: 1.58 (0.17), residues: 948 sheet: -0.78 (0.60), residues: 54 loop : -1.50 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 61 TYR 0.007 0.001 TYR B 162 PHE 0.023 0.002 PHE A 306 TRP 0.025 0.002 TRP C 19 HIS 0.003 0.001 HIS C 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 9420) covalent geometry : angle 0.51083 / 0.27 (12786) hydrogen bonds : bond 0.04420 / 3.00 ( 699) hydrogen bonds : angle 4.35579 / 3.04 ( 2043) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3322.70 seconds wall clock time: 57 minutes 18.07 seconds (3438.07 seconds total)