Starting phenix.real_space_refine on Wed Feb 4 06:36:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ctc_26985/02_2026/8ctc_26985.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ctc_26985/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ctc_26985/02_2026/8ctc_26985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ctc_26985/02_2026/8ctc_26985.map" model { file = "/net/cci-nas-00/data/ceres_data/8ctc_26985/02_2026/8ctc_26985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ctc_26985/02_2026/8ctc_26985.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= 0.012 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-2.0-5952/lib/python3.9/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: 1.71, per 1000 atoms: 0.18 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: 0.58 Conformation dependent library (CDL) restraints added in 429.5 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: 0.20 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: 1.31 Time building geometry restraints manager: 0.75 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: 0.05 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 8.350 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:5.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 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 covalent geometry : bond 0.00510 ( 9420) covalent geometry : angle 0.73569 (12786) hydrogen bonds : bond 0.16870 ( 699) hydrogen bonds : angle 6.14360 ( 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 : 0.274 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: 0.4869 time to fit residues: 95.6209 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 : 0.300 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 0.7591 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 covalent geometry : bond 0.00315 ( 9420) covalent geometry : angle 0.50913 (12786) hydrogen bonds : bond 0.04956 ( 699) hydrogen bonds : angle 4.69188 ( 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 : 0.379 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: 0.4289 time to fit residues: 83.1327 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 : 0.250 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 0.7445 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 covalent geometry : bond 0.00309 ( 9420) covalent geometry : angle 0.49637 (12786) hydrogen bonds : bond 0.04773 ( 699) hydrogen bonds : angle 4.53973 ( 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 : 0.297 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: 0.4397 time to fit residues: 81.1293 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 : 0.352 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.173624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.116993 restraints weight = 3753.804| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.26 r_work: 0.3162 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2068 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 7.448 12786 Z= 0.255 Chirality : 0.038 0.141 1626 Planarity : 0.004 0.032 1557 Dihedral : 3.956 35.673 1281 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.16 % Allowed : 17.85 % 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 0.013 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 covalent geometry : bond 0.00312 ( 9420) covalent geometry : angle 0.48648 (12786) hydrogen bonds : bond 0.04639 ( 699) hydrogen bonds : angle 4.46997 ( 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 177 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.359 Fit side-chains REVERT: A 318 MET cc_start: 0.7984 (tpt) cc_final: 0.7632 (mmm) REVERT: A 354 ILE cc_start: 0.6739 (OUTLIER) cc_final: 0.6311 (tp) REVERT: B 62 MET cc_start: 0.8640 (mtp) cc_final: 0.8408 (mtt) REVERT: B 304 ILE cc_start: 0.7729 (tt) cc_final: 0.7252 (mt) REVERT: B 342 ARG cc_start: 0.6873 (ttm110) cc_final: 0.6615 (ttp-110) REVERT: B 400 THR cc_start: 0.8244 (m) cc_final: 0.7673 (p) REVERT: C 274 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7316 (mp0) REVERT: C 277 GLU cc_start: 0.6803 (mp0) cc_final: 0.6555 (mp0) REVERT: C 318 MET cc_start: 0.7901 (tpt) cc_final: 0.7676 (mmm) REVERT: A 600 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8122 (mp0) REVERT: B 600 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.7877 (mp0) outliers start: 32 outliers final: 14 residues processed: 166 average time/residue: 0.4282 time to fit residues: 76.6046 Evaluate side-chains 157 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 117 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.173907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.117297 restraints weight = 3683.318| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.25 r_work: 0.3196 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2190 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= 0.128 Angle : 0.474 7.223 12786 Z= 0.250 Chirality : 0.037 0.124 1626 Planarity : 0.004 0.032 1557 Dihedral : 3.914 35.488 1281 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.55 % Allowed : 17.26 % 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: 1.18 (0.24), residues: 1200 helix: 1.43 (0.17), residues: 951 sheet: -0.80 (0.59), residues: 54 loop : -1.87 (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 0.021 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 covalent geometry : bond 0.00289 ( 9420) covalent geometry : angle 0.47394 (12786) hydrogen bonds : bond 0.04486 ( 699) hydrogen bonds : angle 4.40672 ( 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: 36 poor density : 143 time to evaluate : 0.310 Fit side-chains REVERT: A 318 MET cc_start: 0.7965 (tpt) cc_final: 0.7611 (mmm) REVERT: B 62 MET cc_start: 0.8695 (mtp) cc_final: 0.8467 (mtt) REVERT: B 304 ILE cc_start: 0.7744 (tt) cc_final: 0.7262 (mt) REVERT: B 342 ARG cc_start: 0.6902 (ttm110) cc_final: 0.6633 (ttp-110) REVERT: B 400 THR cc_start: 0.8187 (m) cc_final: 0.7728 (p) REVERT: C 200 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.7107 (m-10) REVERT: C 274 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: C 277 GLU cc_start: 0.6815 (mp0) cc_final: 0.6118 (mp0) REVERT: C 318 MET cc_start: 0.7906 (tpt) cc_final: 0.7686 (mmm) REVERT: C 355 THR cc_start: 0.7592 (OUTLIER) cc_final: 0.7373 (m) REVERT: A 600 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: B 600 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: C 600 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8031 (mp0) outliers start: 36 outliers final: 17 residues processed: 161 average time/residue: 0.4726 time to fit residues: 81.6756 Evaluate side-chains 161 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 200 TYR 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: 0.7980 chunk 114 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.171772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.114969 restraints weight = 3571.313| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.22 r_work: 0.3102 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9420 Z= 0.163 Angle : 0.510 7.004 12786 Z= 0.269 Chirality : 0.039 0.125 1626 Planarity : 0.004 0.033 1557 Dihedral : 4.014 37.487 1281 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.34 % Allowed : 17.46 % Favored : 78.21 % 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: 0.99 (0.24), residues: 1200 helix: 1.31 (0.17), residues: 951 sheet: -0.90 (0.59), residues: 54 loop : -1.95 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 61 TYR 0.007 0.001 TYR A 97 PHE 0.015 0.002 PHE A 240 TRP 0.008 0.001 TRP C 19 HIS 0.004 0.001 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 9420) covalent geometry : angle 0.50958 (12786) hydrogen bonds : bond 0.05081 ( 699) hydrogen bonds : angle 4.50215 ( 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 192 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.284 Fit side-chains REVERT: A 318 MET cc_start: 0.7971 (tpt) cc_final: 0.7633 (mmm) REVERT: A 354 ILE cc_start: 0.6737 (OUTLIER) cc_final: 0.6302 (tp) REVERT: B 276 TRP cc_start: 0.5975 (m100) cc_final: 0.5465 (m-10) REVERT: B 304 ILE cc_start: 0.7744 (tt) cc_final: 0.7278 (mt) REVERT: B 342 ARG cc_start: 0.6878 (ttm110) cc_final: 0.6597 (ttp-110) REVERT: C 274 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: C 279 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.7253 (t80) REVERT: C 318 MET cc_start: 0.7960 (tpt) cc_final: 0.7728 (mmm) REVERT: C 355 THR cc_start: 0.7518 (OUTLIER) cc_final: 0.7303 (m) REVERT: A 600 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: B 600 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7803 (mp0) REVERT: C 600 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7940 (mp0) outliers start: 44 outliers final: 22 residues processed: 171 average time/residue: 0.4436 time to fit residues: 81.5912 Evaluate side-chains 171 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU 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 355 THR Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain C residue 103 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 65 optimal weight: 0.0370 chunk 56 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 55 optimal weight: 0.0980 chunk 16 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 322 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.174909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.118463 restraints weight = 3640.863| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.24 r_work: 0.3130 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2392 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= 0.122 Angle : 0.482 6.734 12786 Z= 0.255 Chirality : 0.037 0.124 1626 Planarity : 0.004 0.034 1557 Dihedral : 3.894 35.872 1281 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.25 % Allowed : 19.03 % 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: 1.29 (0.24), residues: 1200 helix: 1.56 (0.17), residues: 942 sheet: -0.78 (0.60), residues: 54 loop : -1.95 (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 B 162 PHE 0.022 0.001 PHE A 306 TRP 0.013 0.001 TRP C 19 HIS 0.003 0.001 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9420) covalent geometry : angle 0.48187 (12786) hydrogen bonds : bond 0.04297 ( 699) hydrogen bonds : angle 4.35754 ( 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 183 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.351 Fit side-chains REVERT: A 318 MET cc_start: 0.7822 (tpt) cc_final: 0.7496 (mmm) REVERT: A 346 GLU cc_start: 0.6691 (mt-10) cc_final: 0.6338 (pt0) REVERT: A 354 ILE cc_start: 0.6658 (OUTLIER) cc_final: 0.6219 (tp) REVERT: B 304 ILE cc_start: 0.7668 (tt) cc_final: 0.7191 (mt) REVERT: B 342 ARG cc_start: 0.6853 (ttm110) cc_final: 0.6577 (ttp-110) REVERT: C 274 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: C 277 GLU cc_start: 0.6735 (mp0) cc_final: 0.6496 (mp0) REVERT: C 279 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.7195 (t80) REVERT: C 318 MET cc_start: 0.7897 (tpt) cc_final: 0.7682 (mmm) REVERT: C 346 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6218 (mm-30) REVERT: C 355 THR cc_start: 0.7525 (OUTLIER) cc_final: 0.7321 (m) REVERT: A 600 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8157 (mp0) REVERT: B 600 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: C 600 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8015 (mp0) outliers start: 33 outliers final: 16 residues processed: 169 average time/residue: 0.4558 time to fit residues: 82.7789 Evaluate side-chains 167 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 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 309 VAL Chi-restraints excluded: chain B residue 322 GLN 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 83 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.174003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117470 restraints weight = 3623.149| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.23 r_work: 0.3197 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9420 Z= 0.135 Angle : 0.502 6.656 12786 Z= 0.264 Chirality : 0.038 0.123 1626 Planarity : 0.004 0.033 1557 Dihedral : 3.904 36.319 1281 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.45 % Allowed : 19.33 % Favored : 77.22 % 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: 1.30 (0.24), residues: 1200 helix: 1.56 (0.17), residues: 939 sheet: -0.82 (0.59), residues: 54 loop : -1.85 (0.38), residues: 207 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 0.012 0.001 PHE A 240 TRP 0.014 0.001 TRP C 19 HIS 0.003 0.001 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9420) covalent geometry : angle 0.50162 (12786) hydrogen bonds : bond 0.04501 ( 699) hydrogen bonds : angle 4.36453 ( 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 180 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.369 Fit side-chains REVERT: A 318 MET cc_start: 0.7835 (tpt) cc_final: 0.7508 (mmm) REVERT: A 346 GLU cc_start: 0.6733 (mt-10) cc_final: 0.6375 (pt0) REVERT: A 354 ILE cc_start: 0.6698 (OUTLIER) cc_final: 0.6258 (tp) REVERT: B 304 ILE cc_start: 0.7726 (tt) cc_final: 0.7248 (mt) REVERT: B 342 ARG cc_start: 0.6895 (ttm110) cc_final: 0.6611 (ttp-110) REVERT: C 274 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: C 277 GLU cc_start: 0.6864 (mp0) cc_final: 0.6208 (mp0) REVERT: C 279 PHE cc_start: 0.7521 (OUTLIER) cc_final: 0.7238 (t80) REVERT: C 318 MET cc_start: 0.7925 (tpt) cc_final: 0.7703 (mmm) REVERT: C 346 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6210 (mm-30) REVERT: C 355 THR cc_start: 0.7534 (OUTLIER) cc_final: 0.7306 (m) REVERT: A 600 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: B 600 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: C 600 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8037 (mp0) outliers start: 35 outliers final: 18 residues processed: 164 average time/residue: 0.5001 time to fit residues: 87.9087 Evaluate side-chains 168 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 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 208 ASP 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 109 optimal weight: 0.0570 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 322 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.174036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.117345 restraints weight = 3596.023| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.23 r_work: 0.3141 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9420 Z= 0.134 Angle : 0.503 6.602 12786 Z= 0.264 Chirality : 0.038 0.125 1626 Planarity : 0.004 0.033 1557 Dihedral : 3.906 36.213 1281 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.25 % Allowed : 19.33 % Favored : 77.42 % 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: 1.33 (0.24), residues: 1200 helix: 1.57 (0.17), residues: 939 sheet: -0.82 (0.59), residues: 54 loop : -1.78 (0.38), residues: 207 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 0.015 0.001 TRP C 19 HIS 0.003 0.001 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9420) covalent geometry : angle 0.50301 (12786) hydrogen bonds : bond 0.04507 ( 699) hydrogen bonds : angle 4.37438 ( 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 176 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.303 Fit side-chains REVERT: A 318 MET cc_start: 0.7828 (tpt) cc_final: 0.7467 (mmm) REVERT: A 354 ILE cc_start: 0.6687 (OUTLIER) cc_final: 0.6251 (tp) REVERT: B 304 ILE cc_start: 0.7710 (tt) cc_final: 0.7222 (mt) REVERT: B 342 ARG cc_start: 0.7002 (ttm110) cc_final: 0.6705 (ttp-110) REVERT: B 465 LEU cc_start: 0.7686 (mt) cc_final: 0.7442 (mt) REVERT: C 142 MET cc_start: 0.8317 (tpp) cc_final: 0.8066 (mmm) REVERT: C 274 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: C 276 TRP cc_start: 0.6247 (m100) cc_final: 0.6023 (m-10) REVERT: C 277 GLU cc_start: 0.6883 (mp0) cc_final: 0.6259 (mp0) REVERT: C 279 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.7231 (t80) REVERT: C 318 MET cc_start: 0.7914 (tpt) cc_final: 0.7694 (mmm) REVERT: C 346 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6212 (mm-30) REVERT: C 355 THR cc_start: 0.7523 (OUTLIER) cc_final: 0.7294 (m) REVERT: A 600 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8165 (mp0) REVERT: B 600 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: C 600 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8035 (mp0) outliers start: 33 outliers final: 23 residues processed: 160 average time/residue: 0.4828 time to fit residues: 82.8514 Evaluate side-chains 171 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 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 322 GLN 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 322 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.174525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.117830 restraints weight = 3620.746| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.24 r_work: 0.3156 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9420 Z= 0.130 Angle : 0.507 7.279 12786 Z= 0.266 Chirality : 0.038 0.132 1626 Planarity : 0.004 0.033 1557 Dihedral : 3.903 36.072 1281 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.35 % Allowed : 19.53 % Favored : 77.12 % 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: 1.41 (0.24), residues: 1200 helix: 1.56 (0.17), residues: 948 sheet: -0.79 (0.59), residues: 54 loop : -1.52 (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 0.011 0.001 PHE A 240 TRP 0.018 0.001 TRP C 19 HIS 0.003 0.001 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9420) covalent geometry : angle 0.50685 (12786) hydrogen bonds : bond 0.04412 ( 699) hydrogen bonds : angle 4.37623 ( 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 175 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.287 Fit side-chains REVERT: A 276 TRP cc_start: 0.6160 (m100) cc_final: 0.5848 (m-10) REVERT: A 318 MET cc_start: 0.7832 (tpt) cc_final: 0.7478 (mmm) REVERT: A 354 ILE cc_start: 0.6681 (OUTLIER) cc_final: 0.6245 (tp) REVERT: B 304 ILE cc_start: 0.7701 (tt) cc_final: 0.7210 (mt) REVERT: B 342 ARG cc_start: 0.6972 (ttm110) cc_final: 0.6693 (ttp-110) REVERT: B 465 LEU cc_start: 0.7661 (mt) cc_final: 0.7401 (mt) REVERT: C 142 MET cc_start: 0.8306 (tpp) cc_final: 0.8075 (mmm) REVERT: C 274 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: C 276 TRP cc_start: 0.6375 (m100) cc_final: 0.6102 (m-10) REVERT: C 277 GLU cc_start: 0.6909 (mp0) cc_final: 0.6272 (mp0) REVERT: C 279 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.7233 (t80) REVERT: C 318 MET cc_start: 0.7912 (tpt) cc_final: 0.7694 (mmm) REVERT: C 346 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6263 (mm-30) REVERT: C 355 THR cc_start: 0.7521 (OUTLIER) cc_final: 0.7289 (m) REVERT: A 600 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: B 600 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: C 600 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8030 (mp0) outliers start: 34 outliers final: 21 residues processed: 159 average time/residue: 0.5061 time to fit residues: 86.1343 Evaluate side-chains 169 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 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 322 GLN 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 50 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.173583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.116698 restraints weight = 3555.821| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.23 r_work: 0.3147 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9420 Z= 0.147 Angle : 0.525 8.514 12786 Z= 0.275 Chirality : 0.038 0.160 1626 Planarity : 0.004 0.033 1557 Dihedral : 3.938 36.629 1281 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.45 % Allowed : 19.33 % Favored : 77.22 % 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: 1.49 (0.17), residues: 948 sheet: -0.85 (0.59), residues: 54 loop : -1.53 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.008 0.001 TYR A 97 PHE 0.023 0.002 PHE A 306 TRP 0.020 0.001 TRP C 19 HIS 0.004 0.001 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9420) covalent geometry : angle 0.52542 (12786) hydrogen bonds : bond 0.04685 ( 699) hydrogen bonds : angle 4.42195 ( 2043) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2966.91 seconds wall clock time: 51 minutes 1.18 seconds (3061.18 seconds total)