Starting phenix.real_space_refine on Thu Jul 2 06:04:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1m_36795/07_2026/8k1m_36795.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1m_36795/07_2026/8k1m_36795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k1m_36795/07_2026/8k1m_36795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1m_36795/07_2026/8k1m_36795.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1m_36795/07_2026/8k1m_36795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1m_36795/07_2026/8k1m_36795.cif" } resolution = 2.9 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= -0.001 sd= 0.064 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 23 5.16 5 C 4573 2.51 5 N 1250 2.21 5 O 1299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 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: 7148 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3847 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 20, 'TRANS': 508} Chain: "C" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1589 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 8, 'TRANS': 202} Chain: "D" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1589 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 8, 'TRANS': 202} Chain: "B" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 123 Unusual residues: {'CDL': 1, 'L9Q': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Time building chain proxies: 1.26, per 1000 atoms: 0.18 Number of scatterers: 7148 At special positions: 0 Unit cell: (67.24, 101.68, 109.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 3 15.00 O 1299 8.00 N 1250 7.00 C 4573 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: 0.43 Conformation dependent library (CDL) restraints added in 252.1 milliseconds 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1678 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 0 sheets defined 56.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 78 through 82 removed outlier: 4.351A pdb=" N ARG D 82 " --> pdb=" O VAL D 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 78 through 82' Processing helix chain 'D' and resid 99 through 109 removed outlier: 4.023A pdb=" N ALA D 107 " --> pdb=" O ILE D 103 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 125 removed outlier: 3.621A pdb=" N GLU D 120 " --> pdb=" O ALA D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 150 removed outlier: 3.670A pdb=" N GLN D 142 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS D 143 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 144 " --> pdb=" O ASN D 140 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 183 removed outlier: 3.909A pdb=" N GLN D 183 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 201 Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'B' and resid 40 through 63 removed outlier: 3.585A pdb=" N TRP B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 48 " --> pdb=" O TRP B 44 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER B 49 " --> pdb=" O VAL B 45 " (cutoff:3.500A) Proline residue: B 51 - end of helix removed outlier: 4.079A pdb=" N THR B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL B 55 " --> pdb=" O PRO B 51 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ALA B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 79 removed outlier: 3.759A pdb=" N ALA B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 87 removed outlier: 4.237A pdb=" N LEU B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 101 through 125 removed outlier: 4.940A pdb=" N MET B 105 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N PHE B 106 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N HIS B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA B 111 " --> pdb=" O HIS B 107 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ALA B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ASP B 125 " --> pdb=" O HIS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 removed outlier: 4.820A pdb=" N ASP B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 169 Processing helix chain 'B' and resid 174 through 200 removed outlier: 4.024A pdb=" N VAL B 178 " --> pdb=" O PRO B 174 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE B 191 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 228 removed outlier: 3.546A pdb=" N GLY B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 236 removed outlier: 4.439A pdb=" N CYS B 236 " --> pdb=" O THR B 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 232 through 236' Processing helix chain 'B' and resid 238 through 244 removed outlier: 3.839A pdb=" N SER B 242 " --> pdb=" O PRO B 238 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 275 removed outlier: 4.286A pdb=" N LEU B 257 " --> pdb=" O TRP B 253 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 258 " --> pdb=" O TRP B 254 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 306 removed outlier: 3.829A pdb=" N ALA B 304 " --> pdb=" O PRO B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 329 removed outlier: 3.833A pdb=" N SER B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 329 " --> pdb=" O VAL B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 336 removed outlier: 7.145A pdb=" N ASP B 335 " --> pdb=" O HIS B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 350 removed outlier: 4.316A pdb=" N THR B 348 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 388 removed outlier: 3.911A pdb=" N LEU B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 379 " --> pdb=" O PHE B 375 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N HIS B 384 " --> pdb=" O THR B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 397 Processing helix chain 'B' and resid 405 through 436 removed outlier: 6.935A pdb=" N HIS B 409 " --> pdb=" O TRP B 405 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER B 424 " --> pdb=" O ALA B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 467 removed outlier: 4.142A pdb=" N GLN B 453 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Proline residue: B 455 - end of helix removed outlier: 3.696A pdb=" N LEU B 459 " --> pdb=" O PRO B 455 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LEU B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER B 461 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL B 463 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 493 Proline residue: B 476 - end of helix removed outlier: 4.903A pdb=" N TRP B 479 " --> pdb=" O THR B 475 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 488 " --> pdb=" O GLY B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 503 removed outlier: 4.087A pdb=" N ASN B 503 " --> pdb=" O GLN B 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 499 through 503' Processing helix chain 'B' and resid 507 through 510 No H-bonds generated for 'chain 'B' and resid 507 through 510' Processing helix chain 'B' and resid 522 through 540 removed outlier: 3.508A pdb=" N ILE B 529 " --> pdb=" O TRP B 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 78 through 82 removed outlier: 4.389A pdb=" N ARG C 82 " --> pdb=" O VAL C 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 78 through 82' Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 115 through 125 removed outlier: 3.621A pdb=" N GLU C 120 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.671A pdb=" N GLN C 142 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C 143 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL C 144 " --> pdb=" O ASN C 140 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER C 145 " --> pdb=" O ARG C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 183 removed outlier: 3.909A pdb=" N GLN C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 201 286 hydrogen bonds defined for protein. 858 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: 0.70 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1140 1.29 - 1.42: 1755 1.42 - 1.55: 4332 1.55 - 1.68: 6 1.68 - 1.81: 39 Bond restraints: 7272 Sorted by residual: bond pdb=" C ARG C 53 " pdb=" O ARG C 53 " ideal model delta sigma weight residual 1.236 1.162 0.074 1.32e-02 5.74e+03 3.16e+01 bond pdb=" CA ALA D 154 " pdb=" CB ALA D 154 " ideal model delta sigma weight residual 1.530 1.459 0.071 1.55e-02 4.16e+03 2.12e+01 bond pdb=" N VAL D 91 " pdb=" CA VAL D 91 " ideal model delta sigma weight residual 1.456 1.507 -0.051 1.15e-02 7.56e+03 1.99e+01 bond pdb=" C PRO B 300 " pdb=" O PRO B 300 " ideal model delta sigma weight residual 1.234 1.192 0.042 1.00e-02 1.00e+04 1.78e+01 bond pdb=" C PRO B 295 " pdb=" O PRO B 295 " ideal model delta sigma weight residual 1.238 1.179 0.059 1.42e-02 4.96e+03 1.74e+01 ... (remaining 7267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 9499 2.75 - 5.50: 284 5.50 - 8.24: 68 8.24 - 10.99: 8 10.99 - 13.74: 5 Bond angle restraints: 9864 Sorted by residual: angle pdb=" N ARG D 110 " pdb=" CA ARG D 110 " pdb=" C ARG D 110 " ideal model delta sigma weight residual 112.23 102.32 9.91 1.26e+00 6.30e-01 6.19e+01 angle pdb=" N MET C 109 " pdb=" CA MET C 109 " pdb=" C MET C 109 " ideal model delta sigma weight residual 113.89 101.70 12.19 1.58e+00 4.01e-01 5.95e+01 angle pdb=" CA GLU B 299 " pdb=" C GLU B 299 " pdb=" N PRO B 300 " ideal model delta sigma weight residual 117.95 122.97 -5.02 7.70e-01 1.69e+00 4.25e+01 angle pdb=" N LEU D 58 " pdb=" CA LEU D 58 " pdb=" C LEU D 58 " ideal model delta sigma weight residual 111.28 118.35 -7.07 1.09e+00 8.42e-01 4.21e+01 angle pdb=" N LEU C 58 " pdb=" CA LEU C 58 " pdb=" C LEU C 58 " ideal model delta sigma weight residual 111.28 118.34 -7.06 1.09e+00 8.42e-01 4.19e+01 ... (remaining 9859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.48: 4052 23.48 - 46.96: 240 46.96 - 70.44: 33 70.44 - 93.92: 5 93.92 - 117.39: 1 Dihedral angle restraints: 4331 sinusoidal: 1690 harmonic: 2641 Sorted by residual: dihedral pdb=" C VAL D 22 " pdb=" N VAL D 22 " pdb=" CA VAL D 22 " pdb=" CB VAL D 22 " ideal model delta harmonic sigma weight residual -122.00 -136.07 14.07 0 2.50e+00 1.60e-01 3.17e+01 dihedral pdb=" C VAL C 22 " pdb=" N VAL C 22 " pdb=" CA VAL C 22 " pdb=" CB VAL C 22 " ideal model delta harmonic sigma weight residual -122.00 -135.78 13.78 0 2.50e+00 1.60e-01 3.04e+01 dihedral pdb=" CA TRP B 458 " pdb=" C TRP B 458 " pdb=" N LEU B 459 " pdb=" CA LEU B 459 " ideal model delta harmonic sigma weight residual 180.00 153.24 26.76 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 4328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1017 0.076 - 0.153: 132 0.153 - 0.229: 14 0.229 - 0.306: 6 0.306 - 0.382: 4 Chirality restraints: 1173 Sorted by residual: chirality pdb=" CA VAL D 22 " pdb=" N VAL D 22 " pdb=" C VAL D 22 " pdb=" CB VAL D 22 " both_signs ideal model delta sigma weight residual False 2.44 2.06 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CA VAL C 22 " pdb=" N VAL C 22 " pdb=" C VAL C 22 " pdb=" CB VAL C 22 " both_signs ideal model delta sigma weight residual False 2.44 2.08 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA ARG D 108 " pdb=" N ARG D 108 " pdb=" C ARG D 108 " pdb=" CB ARG D 108 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 1170 not shown) Planarity restraints: 1239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 L9Q B 601 " 0.082 2.00e-02 2.50e+03 8.12e-02 6.60e+01 pdb=" C39 L9Q B 601 " -0.084 2.00e-02 2.50e+03 pdb=" C40 L9Q B 601 " -0.079 2.00e-02 2.50e+03 pdb=" C41 L9Q B 601 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 108 " 0.027 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C ARG C 108 " -0.094 2.00e-02 2.50e+03 pdb=" O ARG C 108 " 0.036 2.00e-02 2.50e+03 pdb=" N MET C 109 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 103 " -0.022 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" C ILE D 103 " 0.079 2.00e-02 2.50e+03 pdb=" O ILE D 103 " -0.029 2.00e-02 2.50e+03 pdb=" N ASP D 104 " -0.027 2.00e-02 2.50e+03 ... (remaining 1236 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2138 2.82 - 3.34: 6495 3.34 - 3.86: 10986 3.86 - 4.38: 13216 4.38 - 4.90: 23314 Nonbonded interactions: 56149 Sorted by model distance: nonbonded pdb=" OH TYR B 33 " pdb=" OD1 ASN B 144 " model vdw 2.303 3.040 nonbonded pdb=" O ALA B 290 " pdb=" OG1 THR C 98 " model vdw 2.310 3.040 nonbonded pdb=" OG SER D 192 " pdb=" OE2 GLU D 197 " model vdw 2.345 3.040 nonbonded pdb=" OG SER C 192 " pdb=" OE2 GLU C 197 " model vdw 2.345 3.040 nonbonded pdb=" O PRO B 472 " pdb=" OG1 THR B 475 " model vdw 2.346 3.040 ... (remaining 56144 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } 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: 3.150 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.520 Find NCS groups from input model: 0.040 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:5.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 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 : 0.006 0.074 7272 Z= 0.378 Angle : 1.117 13.740 9864 Z= 0.648 Chirality : 0.057 0.382 1173 Planarity : 0.007 0.115 1239 Dihedral : 14.854 117.395 2653 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.42 % Allowed : 1.25 % Favored : 98.33 % Cbeta Deviations : 0.36 % 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: -1.85 (0.26), residues: 945 helix: -0.06 (0.24), residues: 501 sheet: -1.37 (0.73), residues: 58 loop : -2.83 (0.26), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 544 TYR 0.008 0.001 TYR B 56 PHE 0.026 0.003 PHE D 19 TRP 0.019 0.001 TRP B 44 HIS 0.005 0.002 HIS D 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.38 ( 7272) covalent geometry : angle 1.11659 / 0.65 ( 9864) hydrogen bonds : bond 0.11579 / 6.86 ( 286) hydrogen bonds : angle 6.04476 / 4.37 ( 858) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 287 ARG cc_start: 0.7677 (mtp-110) cc_final: 0.7362 (mtp-110) REVERT: B 296 MET cc_start: 0.8061 (mmt) cc_final: 0.7837 (mmt) REVERT: C 60 LYS cc_start: 0.8993 (tttp) cc_final: 0.8785 (tttp) REVERT: C 215 GLU cc_start: 0.8091 (tp30) cc_final: 0.7005 (mt-10) outliers start: 3 outliers final: 1 residues processed: 112 average time/residue: 0.6157 time to fit residues: 71.8220 Evaluate side-chains 73 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 67 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.0040 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 193 HIS D 153 HIS D 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.113254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.093931 restraints weight = 9721.873| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.26 r_work: 0.2920 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7272 Z= 0.128 Angle : 0.600 8.867 9864 Z= 0.301 Chirality : 0.043 0.142 1173 Planarity : 0.004 0.056 1239 Dihedral : 10.823 83.459 1158 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.65 % Allowed : 11.00 % Favored : 86.35 % 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: -1.25 (0.26), residues: 945 helix: 0.56 (0.24), residues: 502 sheet: -1.34 (0.72), residues: 58 loop : -2.72 (0.25), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 13 TYR 0.006 0.001 TYR B 432 PHE 0.014 0.001 PHE B 191 TRP 0.016 0.001 TRP B 44 HIS 0.005 0.001 HIS B 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 7272) covalent geometry : angle 0.59954 / 0.30 ( 9864) hydrogen bonds : bond 0.04226 / 2.79 ( 286) hydrogen bonds : angle 3.72503 / 2.68 ( 858) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.164 Fit side-chains REVERT: B 67 ARG cc_start: 0.7789 (ttt90) cc_final: 0.7546 (ttt90) REVERT: B 135 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7655 (m-30) REVERT: B 287 ARG cc_start: 0.7627 (mtp-110) cc_final: 0.7329 (mtp-110) REVERT: B 296 MET cc_start: 0.8325 (mmt) cc_final: 0.8044 (mmt) REVERT: B 312 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7810 (mp) REVERT: C 124 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7800 (ptp-170) REVERT: C 215 GLU cc_start: 0.8464 (tp30) cc_final: 0.6977 (mt-10) REVERT: D 67 ARG cc_start: 0.8347 (mtm180) cc_final: 0.7305 (mtp85) REVERT: D 212 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7937 (mttm) outliers start: 19 outliers final: 6 residues processed: 87 average time/residue: 0.5939 time to fit residues: 53.8949 Evaluate side-chains 78 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 212 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 7 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 93 optimal weight: 0.1980 chunk 85 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 88 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.114360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.094868 restraints weight = 9679.229| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.26 r_work: 0.2938 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7272 Z= 0.105 Angle : 0.526 8.680 9864 Z= 0.265 Chirality : 0.041 0.139 1173 Planarity : 0.004 0.036 1239 Dihedral : 9.226 59.469 1154 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.79 % Allowed : 12.95 % Favored : 84.26 % 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: -0.94 (0.27), residues: 945 helix: 0.81 (0.24), residues: 505 sheet: -1.07 (0.73), residues: 58 loop : -2.61 (0.26), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 402 TYR 0.004 0.001 TYR B 489 PHE 0.013 0.001 PHE B 191 TRP 0.014 0.001 TRP B 44 HIS 0.003 0.001 HIS B 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 7272) covalent geometry : angle 0.52644 / 0.26 ( 9864) hydrogen bonds : bond 0.03488 / 2.31 ( 286) hydrogen bonds : angle 3.35195 / 2.39 ( 858) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.186 Fit side-chains REVERT: B 67 ARG cc_start: 0.7716 (ttt90) cc_final: 0.7485 (ttt90) REVERT: B 135 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7586 (m-30) REVERT: B 272 ARG cc_start: 0.6918 (mmp-170) cc_final: 0.6547 (tpp-160) REVERT: B 287 ARG cc_start: 0.7555 (mtp-110) cc_final: 0.7133 (mtp-110) REVERT: B 296 MET cc_start: 0.8354 (mmt) cc_final: 0.8019 (mmt) REVERT: B 312 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7681 (mp) REVERT: B 360 PHE cc_start: 0.7287 (t80) cc_final: 0.7016 (t80) REVERT: C 124 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7781 (ptp-110) REVERT: C 180 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6926 (tm-30) REVERT: D 67 ARG cc_start: 0.8232 (mtm180) cc_final: 0.7267 (mtp85) REVERT: D 109 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.8045 (mmt) outliers start: 20 outliers final: 6 residues processed: 85 average time/residue: 0.5431 time to fit residues: 48.5649 Evaluate side-chains 81 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain D residue 109 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 89 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 3 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 183 GLN D 193 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.091679 restraints weight = 9821.430| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.34 r_work: 0.2883 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7272 Z= 0.138 Angle : 0.554 8.687 9864 Z= 0.277 Chirality : 0.042 0.146 1173 Planarity : 0.004 0.040 1239 Dihedral : 8.881 58.127 1154 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 4.04 % Allowed : 12.67 % Favored : 83.29 % 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: -0.96 (0.27), residues: 945 helix: 0.78 (0.23), residues: 514 sheet: -1.03 (0.73), residues: 58 loop : -2.69 (0.25), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 123 TYR 0.005 0.001 TYR D 86 PHE 0.014 0.001 PHE B 191 TRP 0.012 0.001 TRP B 44 HIS 0.004 0.001 HIS B 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 7272) covalent geometry : angle 0.55388 / 0.28 ( 9864) hydrogen bonds : bond 0.04012 / 2.71 ( 286) hydrogen bonds : angle 3.34327 / 2.39 ( 858) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: B 135 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7593 (m-30) REVERT: B 272 ARG cc_start: 0.6951 (mmp-170) cc_final: 0.6560 (tpp-160) REVERT: B 287 ARG cc_start: 0.7600 (mtp-110) cc_final: 0.7179 (mtp-110) REVERT: B 312 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7593 (mp) REVERT: B 350 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.6944 (mtm) REVERT: B 491 LEU cc_start: 0.5795 (OUTLIER) cc_final: 0.5474 (mm) REVERT: C 13 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7183 (ptp90) REVERT: C 25 LEU cc_start: 0.7990 (mm) cc_final: 0.7740 (mm) REVERT: C 124 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7709 (ptp-110) REVERT: C 180 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6854 (tm-30) REVERT: D 25 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7366 (mm) REVERT: D 67 ARG cc_start: 0.8266 (mtm180) cc_final: 0.7280 (mtp85) REVERT: D 109 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7895 (mmp) outliers start: 29 outliers final: 10 residues processed: 90 average time/residue: 0.5141 time to fit residues: 48.5426 Evaluate side-chains 88 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 212 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 45 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 56 optimal weight: 0.0970 chunk 36 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 88 optimal weight: 0.1980 chunk 91 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 183 GLN C 193 HIS D 38 HIS D 193 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.113798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.094114 restraints weight = 9730.869| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.27 r_work: 0.2940 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7272 Z= 0.099 Angle : 0.512 8.522 9864 Z= 0.258 Chirality : 0.040 0.138 1173 Planarity : 0.004 0.029 1239 Dihedral : 8.564 59.191 1154 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.62 % Allowed : 13.79 % Favored : 82.59 % 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: -0.71 (0.27), residues: 945 helix: 0.97 (0.24), residues: 515 sheet: -0.88 (0.74), residues: 58 loop : -2.57 (0.26), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 13 TYR 0.004 0.001 TYR D 86 PHE 0.011 0.001 PHE B 191 TRP 0.014 0.001 TRP B 44 HIS 0.003 0.001 HIS B 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 7272) covalent geometry : angle 0.51213 / 0.26 ( 9864) hydrogen bonds : bond 0.03328 / 2.24 ( 286) hydrogen bonds : angle 3.21977 / 2.29 ( 858) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: B 135 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7614 (m-30) REVERT: B 272 ARG cc_start: 0.6980 (mmp-170) cc_final: 0.6574 (tpp-160) REVERT: B 287 ARG cc_start: 0.7633 (mtp-110) cc_final: 0.7262 (mtp-110) REVERT: B 296 MET cc_start: 0.8431 (mmt) cc_final: 0.8040 (mmt) REVERT: B 312 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7731 (mp) REVERT: B 350 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.6967 (mtm) REVERT: B 360 PHE cc_start: 0.7304 (t80) cc_final: 0.7073 (t80) REVERT: B 491 LEU cc_start: 0.5782 (OUTLIER) cc_final: 0.5483 (mm) REVERT: C 13 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7135 (ptp90) REVERT: C 25 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7819 (mm) REVERT: C 180 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6985 (tm-30) REVERT: D 25 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7311 (mm) REVERT: D 67 ARG cc_start: 0.8261 (mtm180) cc_final: 0.7348 (mtp85) REVERT: D 109 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8043 (mmp) outliers start: 26 outliers final: 10 residues processed: 83 average time/residue: 0.5442 time to fit residues: 47.3276 Evaluate side-chains 88 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 212 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 75 optimal weight: 0.0020 chunk 49 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 183 GLN C 193 HIS D 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.113750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.094131 restraints weight = 9781.779| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.27 r_work: 0.2935 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7272 Z= 0.105 Angle : 0.506 7.993 9864 Z= 0.255 Chirality : 0.041 0.136 1173 Planarity : 0.004 0.049 1239 Dihedral : 8.400 59.896 1154 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.06 % Allowed : 14.48 % Favored : 82.45 % 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: -0.65 (0.27), residues: 945 helix: 1.00 (0.24), residues: 516 sheet: -0.86 (0.74), residues: 58 loop : -2.52 (0.26), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 124 TYR 0.005 0.001 TYR B 432 PHE 0.012 0.001 PHE B 191 TRP 0.012 0.001 TRP B 44 HIS 0.003 0.001 HIS B 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.10 ( 7272) covalent geometry : angle 0.50619 / 0.25 ( 9864) hydrogen bonds : bond 0.03341 / 2.25 ( 286) hydrogen bonds : angle 3.17804 / 2.26 ( 858) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: B 105 MET cc_start: 0.8087 (mmm) cc_final: 0.7836 (mmp) REVERT: B 135 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7654 (m-30) REVERT: B 272 ARG cc_start: 0.6979 (mmp-170) cc_final: 0.6565 (tpp-160) REVERT: B 287 ARG cc_start: 0.7644 (mtp-110) cc_final: 0.7282 (mtp-110) REVERT: B 312 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7732 (mp) REVERT: B 350 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.6894 (mtm) REVERT: B 385 GLN cc_start: 0.7765 (mt0) cc_final: 0.7542 (mt0) REVERT: B 491 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.5486 (mm) REVERT: C 13 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7125 (ptp90) REVERT: C 25 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7834 (mm) REVERT: C 180 GLU cc_start: 0.7325 (mt-10) cc_final: 0.7040 (tm-30) REVERT: C 183 GLN cc_start: 0.8348 (pt0) cc_final: 0.8001 (mp10) REVERT: D 25 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7374 (mm) REVERT: D 67 ARG cc_start: 0.8332 (mtm180) cc_final: 0.7413 (mtp85) outliers start: 22 outliers final: 9 residues processed: 84 average time/residue: 0.5145 time to fit residues: 45.4763 Evaluate side-chains 85 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 212 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 90 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 HIS C 193 HIS D 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.113507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.093926 restraints weight = 9731.757| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.26 r_work: 0.2936 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7272 Z= 0.104 Angle : 0.502 8.282 9864 Z= 0.252 Chirality : 0.040 0.136 1173 Planarity : 0.004 0.040 1239 Dihedral : 8.283 59.619 1154 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.65 % Allowed : 15.74 % Favored : 81.62 % 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: -0.64 (0.27), residues: 945 helix: 1.04 (0.24), residues: 512 sheet: -0.84 (0.74), residues: 58 loop : -2.54 (0.26), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 124 TYR 0.005 0.001 TYR D 86 PHE 0.012 0.001 PHE B 191 TRP 0.012 0.001 TRP B 44 HIS 0.003 0.001 HIS B 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.10 ( 7272) covalent geometry : angle 0.50153 / 0.25 ( 9864) hydrogen bonds : bond 0.03333 / 2.24 ( 286) hydrogen bonds : angle 3.16335 / 2.25 ( 858) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: B 105 MET cc_start: 0.8028 (mmm) cc_final: 0.7786 (mmp) REVERT: B 135 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7596 (m-30) REVERT: B 272 ARG cc_start: 0.6892 (mmp-170) cc_final: 0.6471 (tpp-160) REVERT: B 287 ARG cc_start: 0.7658 (mtp-110) cc_final: 0.7305 (mtp-110) REVERT: B 296 MET cc_start: 0.8369 (mmt) cc_final: 0.7980 (mmt) REVERT: B 312 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7634 (mp) REVERT: B 350 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.6888 (mtm) REVERT: B 385 GLN cc_start: 0.7718 (mt0) cc_final: 0.7506 (mt0) REVERT: B 491 LEU cc_start: 0.5676 (OUTLIER) cc_final: 0.5394 (mm) REVERT: C 13 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7170 (ptp90) REVERT: C 25 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7816 (mm) REVERT: C 180 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6994 (tm-30) REVERT: C 183 GLN cc_start: 0.8332 (pt0) cc_final: 0.7990 (mp10) REVERT: D 25 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7368 (mm) REVERT: D 67 ARG cc_start: 0.8303 (mtm180) cc_final: 0.7299 (mtp85) outliers start: 19 outliers final: 9 residues processed: 77 average time/residue: 0.5297 time to fit residues: 42.7301 Evaluate side-chains 81 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 212 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 29 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 72 optimal weight: 0.0870 chunk 71 optimal weight: 0.0980 chunk 79 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 54 optimal weight: 0.0270 chunk 89 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.2016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 107 HIS C 193 HIS D 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.117731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.098157 restraints weight = 9754.949| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.28 r_work: 0.2997 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7272 Z= 0.079 Angle : 0.458 8.411 9864 Z= 0.233 Chirality : 0.039 0.122 1173 Planarity : 0.004 0.031 1239 Dihedral : 7.883 59.377 1154 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.37 % Allowed : 16.02 % Favored : 81.62 % 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 (0.27), residues: 945 helix: 1.22 (0.24), residues: 513 sheet: -0.59 (0.76), residues: 58 loop : -2.42 (0.26), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 124 TYR 0.004 0.000 TYR D 136 PHE 0.010 0.001 PHE B 191 TRP 0.015 0.001 TRP B 44 HIS 0.002 0.000 HIS B 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00169 / 0.08 ( 7272) covalent geometry : angle 0.45786 / 0.23 ( 9864) hydrogen bonds : bond 0.02546 / 1.71 ( 286) hydrogen bonds : angle 2.99966 / 2.13 ( 858) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.202 Fit side-chains REVERT: B 67 ARG cc_start: 0.7656 (ttt90) cc_final: 0.7356 (ttt90) REVERT: B 93 ASP cc_start: 0.8691 (p0) cc_final: 0.7799 (p0) REVERT: B 272 ARG cc_start: 0.6798 (mmp-170) cc_final: 0.6364 (tpp-160) REVERT: B 287 ARG cc_start: 0.7640 (mtp-110) cc_final: 0.7304 (mtp-110) REVERT: B 296 MET cc_start: 0.8385 (mmt) cc_final: 0.8006 (mmt) REVERT: B 350 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7402 (mtm) REVERT: C 13 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7080 (ptp90) REVERT: C 25 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7802 (mm) REVERT: C 180 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6988 (tm-30) REVERT: C 183 GLN cc_start: 0.8271 (pt0) cc_final: 0.7925 (mp10) REVERT: D 25 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7281 (mm) REVERT: D 67 ARG cc_start: 0.8237 (mtm180) cc_final: 0.7281 (mtp85) REVERT: D 134 ARG cc_start: 0.8630 (ttp-110) cc_final: 0.8368 (ptp90) REVERT: D 212 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7710 (mttm) outliers start: 17 outliers final: 5 residues processed: 86 average time/residue: 0.5001 time to fit residues: 45.1997 Evaluate side-chains 80 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 212 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.0040 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 193 HIS D 193 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.114164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.094545 restraints weight = 9704.912| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.27 r_work: 0.2943 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7272 Z= 0.113 Angle : 0.504 7.984 9864 Z= 0.252 Chirality : 0.041 0.128 1173 Planarity : 0.004 0.038 1239 Dihedral : 7.897 58.574 1154 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.81 % Allowed : 16.85 % Favored : 81.34 % 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: -0.47 (0.27), residues: 945 helix: 1.16 (0.24), residues: 514 sheet: -0.66 (0.76), residues: 58 loop : -2.47 (0.26), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 124 TYR 0.005 0.001 TYR B 91 PHE 0.012 0.001 PHE B 191 TRP 0.008 0.001 TRP B 44 HIS 0.003 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 ( 7272) covalent geometry : angle 0.50364 / 0.25 ( 9864) hydrogen bonds : bond 0.03341 / 2.25 ( 286) hydrogen bonds : angle 3.11882 / 2.22 ( 858) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.167 Fit side-chains REVERT: B 67 ARG cc_start: 0.7729 (ttt90) cc_final: 0.7482 (ttt90) REVERT: B 272 ARG cc_start: 0.7050 (mmp-170) cc_final: 0.6617 (tpp-160) REVERT: B 287 ARG cc_start: 0.7668 (mtp-110) cc_final: 0.7343 (mtp-110) REVERT: B 296 MET cc_start: 0.8464 (mmt) cc_final: 0.8077 (mmt) REVERT: B 350 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7036 (mtm) REVERT: C 13 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7222 (ptp90) REVERT: C 25 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7876 (mm) REVERT: C 72 ASP cc_start: 0.8265 (p0) cc_final: 0.8021 (p0) REVERT: C 76 ASP cc_start: 0.7675 (m-30) cc_final: 0.7465 (m-30) REVERT: C 180 GLU cc_start: 0.7293 (mt-10) cc_final: 0.7081 (tm-30) REVERT: C 183 GLN cc_start: 0.8319 (pt0) cc_final: 0.7976 (mp10) REVERT: D 25 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7443 (mm) REVERT: D 67 ARG cc_start: 0.8377 (mtm180) cc_final: 0.7405 (mtp85) REVERT: D 109 MET cc_start: 0.8688 (mmt) cc_final: 0.8467 (mmp) outliers start: 13 outliers final: 7 residues processed: 76 average time/residue: 0.5105 time to fit residues: 40.6617 Evaluate side-chains 78 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 212 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 193 HIS D 193 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.113925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.094377 restraints weight = 9647.450| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.26 r_work: 0.2944 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7272 Z= 0.108 Angle : 0.504 8.205 9864 Z= 0.253 Chirality : 0.041 0.128 1173 Planarity : 0.004 0.039 1239 Dihedral : 7.850 59.413 1154 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.09 % Allowed : 16.57 % Favored : 81.34 % 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: -0.50 (0.27), residues: 945 helix: 1.12 (0.23), residues: 519 sheet: -0.68 (0.76), residues: 58 loop : -2.51 (0.26), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 124 TYR 0.005 0.001 TYR D 86 PHE 0.012 0.001 PHE B 191 TRP 0.010 0.001 TRP B 44 HIS 0.003 0.001 HIS B 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 7272) covalent geometry : angle 0.50447 / 0.25 ( 9864) hydrogen bonds : bond 0.03304 / 2.23 ( 286) hydrogen bonds : angle 3.13906 / 2.23 ( 858) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.157 Fit side-chains REVERT: B 67 ARG cc_start: 0.7749 (ttt90) cc_final: 0.7504 (ttt90) REVERT: B 272 ARG cc_start: 0.7028 (mmp-170) cc_final: 0.6590 (tpp-160) REVERT: B 287 ARG cc_start: 0.7678 (mtp-110) cc_final: 0.7364 (mtp-110) REVERT: B 296 MET cc_start: 0.8461 (mmt) cc_final: 0.8080 (mmt) REVERT: C 13 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7188 (ptp90) REVERT: C 25 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7865 (mm) REVERT: C 72 ASP cc_start: 0.8280 (p0) cc_final: 0.8043 (p0) REVERT: C 76 ASP cc_start: 0.7671 (m-30) cc_final: 0.7454 (m-30) REVERT: C 180 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7084 (tm-30) REVERT: C 183 GLN cc_start: 0.8296 (pt0) cc_final: 0.7972 (mp10) REVERT: D 13 ARG cc_start: 0.7823 (pmt-80) cc_final: 0.7566 (pmt-80) REVERT: D 25 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7463 (mm) REVERT: D 67 ARG cc_start: 0.8367 (mtm180) cc_final: 0.7397 (mtp85) outliers start: 15 outliers final: 7 residues processed: 75 average time/residue: 0.4966 time to fit residues: 39.0722 Evaluate side-chains 75 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 212 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 13 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 93 optimal weight: 0.1980 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 23 optimal weight: 0.0470 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 385 GLN C 193 HIS D 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.094934 restraints weight = 9716.528| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.28 r_work: 0.2953 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7272 Z= 0.099 Angle : 0.494 8.278 9864 Z= 0.248 Chirality : 0.040 0.126 1173 Planarity : 0.004 0.040 1239 Dihedral : 7.725 59.410 1154 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.81 % Allowed : 16.99 % Favored : 81.20 % 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: -0.45 (0.27), residues: 945 helix: 1.17 (0.23), residues: 519 sheet: -0.63 (0.76), residues: 58 loop : -2.51 (0.26), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 124 TYR 0.004 0.001 TYR D 86 PHE 0.011 0.001 PHE B 191 TRP 0.011 0.001 TRP B 44 HIS 0.003 0.001 HIS B 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 7272) covalent geometry : angle 0.49442 / 0.25 ( 9864) hydrogen bonds : bond 0.03150 / 2.13 ( 286) hydrogen bonds : angle 3.11567 / 2.21 ( 858) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1962.83 seconds wall clock time: 34 minutes 8.58 seconds (2048.58 seconds total)