Starting phenix.real_space_refine on Thu Mar 5 06:14:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bcq_12142/03_2026/7bcq_12142.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bcq_12142/03_2026/7bcq_12142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bcq_12142/03_2026/7bcq_12142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bcq_12142/03_2026/7bcq_12142.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bcq_12142/03_2026/7bcq_12142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bcq_12142/03_2026/7bcq_12142.map" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 S 48 5.16 5 C 6453 2.51 5 N 1626 2.21 5 O 1734 1.98 5 H 10299 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20160 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 6697 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 17, 'TRANS': 424} Chain: "B" Number of atoms: 6697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 6697 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 17, 'TRANS': 424} Chain: "C" Number of atoms: 6697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 6697 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 17, 'TRANS': 424} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'TG2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'TG2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'TG2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.31, per 1000 atoms: 0.16 Number of scatterers: 20160 At special positions: 0 Unit cell: (106.26, 105.248, 77.924, 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 48 16.00 O 1734 8.00 N 1626 7.00 C 6453 6.00 H 10299 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 662.7 milliseconds 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2394 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 3 sheets defined 84.5% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 52 through 76 Processing helix chain 'A' and resid 77 through 103 Proline residue: A 83 - end of helix Proline residue: A 92 - end of helix removed outlier: 3.844A pdb=" N ILE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 117 removed outlier: 3.704A pdb=" N ALA A 117 " --> pdb=" O ILE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 154 Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 179 through 191 Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 230 through 248 Processing helix chain 'A' and resid 249 through 291 removed outlier: 3.687A pdb=" N GLU A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU A 254 " --> pdb=" O PRO A 250 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TRP A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 296 through 319 removed outlier: 6.604A pdb=" N LYS A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 330 Processing helix chain 'A' and resid 332 through 339 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 352 through 367 Proline residue: A 358 - end of helix Processing helix chain 'A' and resid 371 through 385 Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 387 through 404 Processing helix chain 'A' and resid 411 through 431 removed outlier: 4.336A pdb=" N VAL A 426 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 429 " --> pdb=" O SER A 425 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE A 431 " --> pdb=" O GLY A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 removed outlier: 4.329A pdb=" N ILE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 458 removed outlier: 3.519A pdb=" N ILE A 456 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 458 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 488 removed outlier: 3.547A pdb=" N VAL A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ARG A 465 " --> pdb=" O TRP A 461 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 52 through 76 Processing helix chain 'B' and resid 77 through 103 Proline residue: B 83 - end of helix Proline residue: B 92 - end of helix removed outlier: 3.843A pdb=" N ILE B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 117 removed outlier: 3.703A pdb=" N ALA B 117 " --> pdb=" O ILE B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 154 Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 179 through 191 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 230 through 248 Processing helix chain 'B' and resid 249 through 291 removed outlier: 3.687A pdb=" N GLU B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TRP B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 296 through 319 removed outlier: 6.603A pdb=" N LYS B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 330 Processing helix chain 'B' and resid 332 through 339 Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 352 through 367 Proline residue: B 358 - end of helix Processing helix chain 'B' and resid 371 through 385 Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 387 through 404 Processing helix chain 'B' and resid 411 through 431 removed outlier: 4.336A pdb=" N VAL B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA B 429 " --> pdb=" O SER B 425 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY B 430 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE B 431 " --> pdb=" O GLY B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 447 removed outlier: 4.329A pdb=" N ILE B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 458 removed outlier: 3.518A pdb=" N ILE B 456 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 458 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 488 removed outlier: 3.547A pdb=" N VAL B 463 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ARG B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 Processing helix chain 'C' and resid 52 through 76 Processing helix chain 'C' and resid 77 through 103 Proline residue: C 83 - end of helix Proline residue: C 92 - end of helix removed outlier: 3.844A pdb=" N ILE C 103 " --> pdb=" O LEU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 117 removed outlier: 3.704A pdb=" N ALA C 117 " --> pdb=" O ILE C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 154 Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 179 through 191 Processing helix chain 'C' and resid 195 through 200 Processing helix chain 'C' and resid 230 through 248 Processing helix chain 'C' and resid 249 through 291 removed outlier: 3.687A pdb=" N GLU C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU C 254 " --> pdb=" O PRO C 250 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU C 255 " --> pdb=" O GLU C 251 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TRP C 272 " --> pdb=" O VAL C 268 " (cutoff:3.500A) Proline residue: C 278 - end of helix Processing helix chain 'C' and resid 296 through 319 removed outlier: 6.604A pdb=" N LYS C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR C 305 " --> pdb=" O ARG C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 330 Processing helix chain 'C' and resid 332 through 339 Processing helix chain 'C' and resid 340 through 351 Processing helix chain 'C' and resid 352 through 367 Proline residue: C 358 - end of helix Processing helix chain 'C' and resid 371 through 385 Proline residue: C 380 - end of helix Processing helix chain 'C' and resid 387 through 404 Processing helix chain 'C' and resid 411 through 431 removed outlier: 4.337A pdb=" N VAL C 426 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA C 429 " --> pdb=" O SER C 425 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY C 430 " --> pdb=" O VAL C 426 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE C 431 " --> pdb=" O GLY C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 447 removed outlier: 4.329A pdb=" N ILE C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 458 removed outlier: 3.517A pdb=" N ILE C 456 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 458 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 488 removed outlier: 3.547A pdb=" N VAL C 463 " --> pdb=" O VAL C 459 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ARG C 465 " --> pdb=" O TRP C 461 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 209 removed outlier: 3.705A pdb=" N SER A 205 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 202 through 209 removed outlier: 3.704A pdb=" N SER B 205 " --> pdb=" O GLN B 224 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 209 removed outlier: 3.704A pdb=" N SER C 205 " --> pdb=" O GLN C 224 " (cutoff:3.500A) 784 hydrogen bonds defined for protein. 2307 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: 5.58 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 10278 1.03 - 1.23: 32 1.23 - 1.42: 3970 1.42 - 1.62: 5988 1.62 - 1.81: 75 Bond restraints: 20343 Sorted by residual: bond pdb=" C12 TG2 B 601 " pdb=" C13 TG2 B 601 " ideal model delta sigma weight residual 1.385 1.536 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C12 TG2 C 601 " pdb=" C13 TG2 C 601 " ideal model delta sigma weight residual 1.385 1.535 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" C12 TG2 A 601 " pdb=" C13 TG2 A 601 " ideal model delta sigma weight residual 1.385 1.535 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" C11 TG2 B 601 " pdb=" C16 TG2 B 601 " ideal model delta sigma weight residual 1.396 1.533 -0.137 2.00e-02 2.50e+03 4.68e+01 bond pdb=" C11 TG2 C 601 " pdb=" C16 TG2 C 601 " ideal model delta sigma weight residual 1.396 1.533 -0.137 2.00e-02 2.50e+03 4.66e+01 ... (remaining 20338 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.15: 36838 5.15 - 10.30: 101 10.30 - 15.45: 6 15.45 - 20.60: 0 20.60 - 25.75: 36 Bond angle restraints: 36981 Sorted by residual: angle pdb=" CD1 LEU C 269 " pdb=" CG LEU C 269 " pdb=" HG LEU C 269 " ideal model delta sigma weight residual 108.00 82.25 25.75 3.00e+00 1.11e-01 7.37e+01 angle pdb=" CD1 LEU B 269 " pdb=" CG LEU B 269 " pdb=" HG LEU B 269 " ideal model delta sigma weight residual 108.00 82.59 25.41 3.00e+00 1.11e-01 7.17e+01 angle pdb=" CD1 LEU A 269 " pdb=" CG LEU A 269 " pdb=" HG LEU A 269 " ideal model delta sigma weight residual 108.00 82.60 25.40 3.00e+00 1.11e-01 7.17e+01 angle pdb=" CD2 LEU B 149 " pdb=" CG LEU B 149 " pdb=" HG LEU B 149 " ideal model delta sigma weight residual 108.00 83.02 24.98 3.00e+00 1.11e-01 6.93e+01 angle pdb=" CD2 LEU A 149 " pdb=" CG LEU A 149 " pdb=" HG LEU A 149 " ideal model delta sigma weight residual 108.00 83.03 24.97 3.00e+00 1.11e-01 6.93e+01 ... (remaining 36976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 8228 17.39 - 34.79: 836 34.79 - 52.18: 232 52.18 - 69.57: 164 69.57 - 86.96: 44 Dihedral angle restraints: 9504 sinusoidal: 5226 harmonic: 4278 Sorted by residual: dihedral pdb=" CA ASN C 190 " pdb=" C ASN C 190 " pdb=" N ILE C 191 " pdb=" CA ILE C 191 " ideal model delta harmonic sigma weight residual 180.00 155.15 24.85 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ASN B 190 " pdb=" C ASN B 190 " pdb=" N ILE B 191 " pdb=" CA ILE B 191 " ideal model delta harmonic sigma weight residual 180.00 155.15 24.85 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ASN A 190 " pdb=" C ASN A 190 " pdb=" N ILE A 191 " pdb=" CA ILE A 191 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 9501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.349: 1692 0.349 - 0.697: 0 0.697 - 1.046: 0 1.046 - 1.394: 0 1.394 - 1.743: 12 Chirality restraints: 1704 Sorted by residual: chirality pdb=" CG LEU B 149 " pdb=" CB LEU B 149 " pdb=" CD1 LEU B 149 " pdb=" CD2 LEU B 149 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.59e+01 chirality pdb=" CG LEU A 149 " pdb=" CB LEU A 149 " pdb=" CD1 LEU A 149 " pdb=" CD2 LEU A 149 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.59e+01 chirality pdb=" CG LEU C 149 " pdb=" CB LEU C 149 " pdb=" CD1 LEU C 149 " pdb=" CD2 LEU C 149 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.59e+01 ... (remaining 1701 not shown) Planarity restraints: 2979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 335 " 0.144 9.50e-02 1.11e+02 5.51e-02 1.90e+01 pdb=" NE ARG C 335 " -0.050 2.00e-02 2.50e+03 pdb=" CZ ARG C 335 " 0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG C 335 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 335 " 0.031 2.00e-02 2.50e+03 pdb="HH11 ARG C 335 " 0.019 2.00e-02 2.50e+03 pdb="HH12 ARG C 335 " -0.028 2.00e-02 2.50e+03 pdb="HH21 ARG C 335 " 0.006 2.00e-02 2.50e+03 pdb="HH22 ARG C 335 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 335 " 0.144 9.50e-02 1.11e+02 5.52e-02 1.88e+01 pdb=" NE ARG A 335 " -0.050 2.00e-02 2.50e+03 pdb=" CZ ARG A 335 " 0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG A 335 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 335 " 0.030 2.00e-02 2.50e+03 pdb="HH11 ARG A 335 " 0.019 2.00e-02 2.50e+03 pdb="HH12 ARG A 335 " -0.028 2.00e-02 2.50e+03 pdb="HH21 ARG A 335 " 0.006 2.00e-02 2.50e+03 pdb="HH22 ARG A 335 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 335 " -0.143 9.50e-02 1.11e+02 5.48e-02 1.86e+01 pdb=" NE ARG B 335 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG B 335 " -0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG B 335 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 335 " -0.031 2.00e-02 2.50e+03 pdb="HH11 ARG B 335 " -0.019 2.00e-02 2.50e+03 pdb="HH12 ARG B 335 " 0.028 2.00e-02 2.50e+03 pdb="HH21 ARG B 335 " -0.006 2.00e-02 2.50e+03 pdb="HH22 ARG B 335 " 0.025 2.00e-02 2.50e+03 ... (remaining 2976 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 3445 2.29 - 2.87: 46601 2.87 - 3.44: 54414 3.44 - 4.02: 71435 4.02 - 4.60: 110452 Nonbonded interactions: 286347 Sorted by model distance: nonbonded pdb="HH11 ARG B 189 " pdb=" OE1 GLU C 94 " model vdw 1.711 2.450 nonbonded pdb="HD21 ASN A 195 " pdb=" O ALA B 200 " model vdw 1.713 2.450 nonbonded pdb=" OE2 GLU A 227 " pdb="HH12 ARG C 202 " model vdw 1.716 2.450 nonbonded pdb=" O ARG A 189 " pdb="HH21 ARG B 98 " model vdw 1.725 2.450 nonbonded pdb=" O ALA A 200 " pdb="HD21 ASN C 195 " model vdw 1.734 2.450 ... (remaining 286342 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.130 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.950 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 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 : 0.011 0.151 10044 Z= 0.472 Angle : 1.074 11.942 13692 Z= 0.523 Chirality : 0.154 1.743 1704 Planarity : 0.007 0.092 1707 Dihedral : 14.625 86.732 3543 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -0.68 (0.22), residues: 1320 helix: 0.21 (0.15), residues: 975 sheet: -3.09 (0.47), residues: 42 loop : -1.95 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.002 ARG C 335 TYR 0.018 0.003 TYR C 325 PHE 0.045 0.003 PHE A 393 TRP 0.025 0.004 TRP B 338 HIS 0.007 0.002 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.01125 (10044) covalent geometry : angle 1.07388 (13692) hydrogen bonds : bond 0.12762 ( 784) hydrogen bonds : angle 6.37715 ( 2307) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 417 ILE cc_start: 0.7452 (mt) cc_final: 0.7069 (tp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1593 time to fit residues: 21.4468 Evaluate side-chains 79 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.228816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.4016 r_free = 0.4016 target = 0.181800 restraints weight = 27653.106| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.14 r_work: 0.3773 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10044 Z= 0.139 Angle : 0.696 10.552 13692 Z= 0.321 Chirality : 0.146 1.745 1704 Planarity : 0.005 0.044 1707 Dihedral : 9.328 85.314 1473 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % 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: 0.63 (0.23), residues: 1320 helix: 1.16 (0.16), residues: 987 sheet: -2.79 (0.51), residues: 42 loop : -1.51 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 376 TYR 0.008 0.001 TYR C 204 PHE 0.020 0.001 PHE A 393 TRP 0.015 0.001 TRP B 461 HIS 0.002 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00308 (10044) covalent geometry : angle 0.69600 (13692) hydrogen bonds : bond 0.04495 ( 784) hydrogen bonds : angle 5.11421 ( 2307) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 ILE cc_start: 0.7712 (mt) cc_final: 0.7268 (tp) REVERT: B 417 ILE cc_start: 0.7257 (mt) cc_final: 0.6909 (tp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1627 time to fit residues: 21.5228 Evaluate side-chains 82 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 115 optimal weight: 0.9980 chunk 99 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.227829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.178823 restraints weight = 28573.172| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.00 r_work: 0.3677 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10044 Z= 0.147 Angle : 0.672 10.959 13692 Z= 0.308 Chirality : 0.146 1.719 1704 Planarity : 0.004 0.040 1707 Dihedral : 8.545 83.621 1473 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.10 % Allowed : 5.44 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.24), residues: 1320 helix: 1.65 (0.17), residues: 981 sheet: None (None), residues: 0 loop : -1.57 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 376 TYR 0.007 0.001 TYR C 325 PHE 0.022 0.001 PHE A 393 TRP 0.020 0.001 TRP B 461 HIS 0.002 0.001 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00331 (10044) covalent geometry : angle 0.67175 (13692) hydrogen bonds : bond 0.03968 ( 784) hydrogen bonds : angle 4.84263 ( 2307) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.7805 (tpp) cc_final: 0.7549 (tpp) REVERT: A 417 ILE cc_start: 0.7548 (mt) cc_final: 0.7060 (tp) REVERT: B 288 LYS cc_start: 0.7414 (mmtt) cc_final: 0.7161 (mptt) REVERT: B 417 ILE cc_start: 0.7293 (mt) cc_final: 0.6882 (tp) REVERT: C 417 ILE cc_start: 0.7254 (mt) cc_final: 0.6624 (tp) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.1750 time to fit residues: 28.7957 Evaluate side-chains 98 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 61 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.223562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.179610 restraints weight = 28292.567| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 2.02 r_work: 0.3695 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10044 Z= 0.124 Angle : 0.654 10.727 13692 Z= 0.296 Chirality : 0.146 1.708 1704 Planarity : 0.004 0.040 1707 Dihedral : 8.514 84.168 1473 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.29 % Allowed : 7.00 % Favored : 92.71 % 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: 1.55 (0.24), residues: 1320 helix: 1.85 (0.17), residues: 981 sheet: None (None), residues: 0 loop : -1.49 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 376 TYR 0.007 0.001 TYR C 334 PHE 0.015 0.001 PHE C 393 TRP 0.009 0.001 TRP B 461 HIS 0.001 0.000 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00283 (10044) covalent geometry : angle 0.65425 (13692) hydrogen bonds : bond 0.03698 ( 784) hydrogen bonds : angle 4.65870 ( 2307) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.7828 (tpp) cc_final: 0.7604 (tpp) REVERT: A 417 ILE cc_start: 0.7581 (mt) cc_final: 0.7060 (tp) REVERT: A 473 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8243 (tm-30) REVERT: B 417 ILE cc_start: 0.7341 (mt) cc_final: 0.6961 (tp) REVERT: C 417 ILE cc_start: 0.7310 (mt) cc_final: 0.6707 (tp) outliers start: 3 outliers final: 1 residues processed: 106 average time/residue: 0.1602 time to fit residues: 26.2733 Evaluate side-chains 99 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 105 optimal weight: 0.0980 chunk 23 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.226724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.189200 restraints weight = 28258.709| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 1.26 r_work: 0.3821 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10044 Z= 0.123 Angle : 0.652 11.054 13692 Z= 0.294 Chirality : 0.146 1.705 1704 Planarity : 0.004 0.041 1707 Dihedral : 8.365 83.333 1473 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.29 % Allowed : 7.58 % Favored : 92.13 % 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: 1.64 (0.24), residues: 1320 helix: 1.89 (0.17), residues: 996 sheet: None (None), residues: 0 loop : -1.51 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 376 TYR 0.007 0.001 TYR A 334 PHE 0.014 0.001 PHE C 393 TRP 0.006 0.001 TRP B 275 HIS 0.001 0.000 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00283 (10044) covalent geometry : angle 0.65201 (13692) hydrogen bonds : bond 0.03587 ( 784) hydrogen bonds : angle 4.58518 ( 2307) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.7991 (tpp) cc_final: 0.7720 (tpp) REVERT: A 417 ILE cc_start: 0.7695 (mt) cc_final: 0.7198 (tp) REVERT: A 473 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8413 (tm-30) REVERT: B 417 ILE cc_start: 0.7458 (mt) cc_final: 0.7106 (tp) REVERT: C 417 ILE cc_start: 0.7523 (mt) cc_final: 0.6939 (tp) outliers start: 3 outliers final: 1 residues processed: 110 average time/residue: 0.1791 time to fit residues: 29.7628 Evaluate side-chains 105 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 95 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.217902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3893 r_free = 0.3893 target = 0.171161 restraints weight = 28639.774| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.05 r_work: 0.3595 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10044 Z= 0.200 Angle : 0.716 11.329 13692 Z= 0.337 Chirality : 0.148 1.717 1704 Planarity : 0.004 0.041 1707 Dihedral : 8.218 80.173 1473 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.39 % Allowed : 7.87 % Favored : 91.74 % 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 (0.24), residues: 1320 helix: 1.60 (0.16), residues: 996 sheet: None (None), residues: 0 loop : -1.62 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 376 TYR 0.010 0.002 TYR A 334 PHE 0.016 0.002 PHE A 348 TRP 0.008 0.001 TRP A 130 HIS 0.002 0.001 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00473 (10044) covalent geometry : angle 0.71630 (13692) hydrogen bonds : bond 0.04072 ( 784) hydrogen bonds : angle 4.84056 ( 2307) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.7792 (mptt) cc_final: 0.7514 (mptt) REVERT: A 360 MET cc_start: 0.8195 (tpp) cc_final: 0.7888 (tpt) REVERT: A 417 ILE cc_start: 0.7640 (mt) cc_final: 0.7093 (tp) REVERT: A 473 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8309 (tm-30) REVERT: B 224 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7464 (pt0) outliers start: 4 outliers final: 1 residues processed: 126 average time/residue: 0.1807 time to fit residues: 34.1740 Evaluate side-chains 121 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 224 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 119 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.218814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.169972 restraints weight = 28604.138| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.31 r_work: 0.3577 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10044 Z= 0.166 Angle : 0.685 11.174 13692 Z= 0.316 Chirality : 0.147 1.706 1704 Planarity : 0.004 0.040 1707 Dihedral : 8.181 79.402 1473 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.68 % Allowed : 8.16 % Favored : 91.16 % 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: 1.39 (0.24), residues: 1320 helix: 1.70 (0.17), residues: 996 sheet: None (None), residues: 0 loop : -1.58 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 376 TYR 0.009 0.001 TYR A 334 PHE 0.013 0.001 PHE A 348 TRP 0.008 0.001 TRP A 338 HIS 0.002 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00386 (10044) covalent geometry : angle 0.68521 (13692) hydrogen bonds : bond 0.03839 ( 784) hydrogen bonds : angle 4.76832 ( 2307) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6848 (tp) REVERT: A 288 LYS cc_start: 0.7789 (mptt) cc_final: 0.7507 (mptt) REVERT: A 360 MET cc_start: 0.8302 (tpp) cc_final: 0.7895 (tpt) REVERT: A 417 ILE cc_start: 0.7598 (mt) cc_final: 0.7073 (tp) REVERT: A 473 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8263 (tm-30) REVERT: C 224 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7409 (pt0) outliers start: 7 outliers final: 4 residues processed: 125 average time/residue: 0.1790 time to fit residues: 33.4948 Evaluate side-chains 122 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 393 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 224 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.220447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.170364 restraints weight = 28469.197| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.18 r_work: 0.3630 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10044 Z= 0.141 Angle : 0.673 11.070 13692 Z= 0.307 Chirality : 0.147 1.720 1704 Planarity : 0.004 0.040 1707 Dihedral : 8.009 78.002 1473 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.68 % Allowed : 8.07 % Favored : 91.25 % 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: 1.47 (0.24), residues: 1320 helix: 1.75 (0.17), residues: 996 sheet: None (None), residues: 0 loop : -1.50 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 376 TYR 0.010 0.001 TYR A 334 PHE 0.013 0.001 PHE A 348 TRP 0.011 0.001 TRP A 275 HIS 0.001 0.000 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00324 (10044) covalent geometry : angle 0.67256 (13692) hydrogen bonds : bond 0.03668 ( 784) hydrogen bonds : angle 4.69020 ( 2307) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6659 (tp) REVERT: A 360 MET cc_start: 0.8290 (tpp) cc_final: 0.7905 (tpt) REVERT: A 417 ILE cc_start: 0.7623 (mt) cc_final: 0.7083 (tp) REVERT: A 473 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8358 (tm-30) REVERT: B 224 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7568 (pt0) REVERT: C 224 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7413 (pt0) outliers start: 7 outliers final: 4 residues processed: 123 average time/residue: 0.1816 time to fit residues: 33.3159 Evaluate side-chains 123 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 393 PHE Chi-restraints excluded: chain C residue 224 GLN Chi-restraints excluded: chain C residue 393 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 64 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 124 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.219613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.169457 restraints weight = 28312.738| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.13 r_work: 0.3658 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10044 Z= 0.117 Angle : 0.661 10.984 13692 Z= 0.298 Chirality : 0.146 1.702 1704 Planarity : 0.004 0.042 1707 Dihedral : 7.885 77.036 1473 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.78 % Allowed : 8.94 % Favored : 90.28 % 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: 1.69 (0.24), residues: 1320 helix: 1.89 (0.17), residues: 999 sheet: None (None), residues: 0 loop : -1.37 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 376 TYR 0.011 0.001 TYR A 334 PHE 0.019 0.001 PHE A 348 TRP 0.012 0.001 TRP A 275 HIS 0.001 0.000 HIS C 373 Details of bonding type rmsd covalent geometry : bond 0.00265 (10044) covalent geometry : angle 0.66085 (13692) hydrogen bonds : bond 0.03459 ( 784) hydrogen bonds : angle 4.56717 ( 2307) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7313 (pt0) REVERT: A 360 MET cc_start: 0.8249 (tpp) cc_final: 0.7927 (tpp) REVERT: A 417 ILE cc_start: 0.7615 (mt) cc_final: 0.7102 (tp) REVERT: A 473 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8408 (tm-30) REVERT: B 224 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7441 (pt0) REVERT: B 417 ILE cc_start: 0.7473 (mt) cc_final: 0.7054 (tp) outliers start: 8 outliers final: 5 residues processed: 120 average time/residue: 0.1816 time to fit residues: 32.4870 Evaluate side-chains 120 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 393 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 393 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 48 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 94 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 105 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: ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.220317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.172655 restraints weight = 28330.880| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.04 r_work: 0.3671 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10044 Z= 0.116 Angle : 0.659 10.976 13692 Z= 0.296 Chirality : 0.146 1.704 1704 Planarity : 0.004 0.040 1707 Dihedral : 7.704 75.364 1473 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.49 % Allowed : 9.43 % Favored : 90.09 % 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: 1.81 (0.24), residues: 1320 helix: 1.99 (0.17), residues: 996 sheet: None (None), residues: 0 loop : -1.36 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 376 TYR 0.008 0.001 TYR A 334 PHE 0.019 0.001 PHE A 348 TRP 0.016 0.001 TRP A 275 HIS 0.001 0.001 HIS C 373 Details of bonding type rmsd covalent geometry : bond 0.00266 (10044) covalent geometry : angle 0.65937 (13692) hydrogen bonds : bond 0.03376 ( 784) hydrogen bonds : angle 4.50715 ( 2307) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.8240 (tpp) cc_final: 0.7911 (tpt) REVERT: A 417 ILE cc_start: 0.7600 (mt) cc_final: 0.7102 (tp) REVERT: A 473 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8280 (tm-30) REVERT: B 224 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7431 (pt0) REVERT: B 417 ILE cc_start: 0.7467 (mt) cc_final: 0.7055 (tp) outliers start: 5 outliers final: 4 residues processed: 121 average time/residue: 0.1850 time to fit residues: 33.5810 Evaluate side-chains 117 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 393 PHE Chi-restraints excluded: chain C residue 393 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.0570 chunk 50 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 123 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.222246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.3918 r_free = 0.3918 target = 0.174205 restraints weight = 28564.209| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.08 r_work: 0.3661 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10044 Z= 0.131 Angle : 0.670 11.035 13692 Z= 0.302 Chirality : 0.147 1.705 1704 Planarity : 0.004 0.046 1707 Dihedral : 7.603 73.993 1473 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.68 % Allowed : 9.72 % Favored : 89.60 % 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: 1.77 (0.24), residues: 1320 helix: 1.96 (0.17), residues: 996 sheet: None (None), residues: 0 loop : -1.38 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 376 TYR 0.008 0.001 TYR A 334 PHE 0.018 0.001 PHE A 348 TRP 0.014 0.001 TRP A 275 HIS 0.001 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00303 (10044) covalent geometry : angle 0.67043 (13692) hydrogen bonds : bond 0.03436 ( 784) hydrogen bonds : angle 4.53985 ( 2307) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3827.03 seconds wall clock time: 65 minutes 43.61 seconds (3943.61 seconds total)