Starting phenix.real_space_refine on Wed Mar 4 09:39:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d9x_27269/03_2026/8d9x_27269_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d9x_27269/03_2026/8d9x_27269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d9x_27269/03_2026/8d9x_27269_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d9x_27269/03_2026/8d9x_27269_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d9x_27269/03_2026/8d9x_27269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d9x_27269/03_2026/8d9x_27269.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 7945 2.51 5 N 2293 2.21 5 O 2384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 12670 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1585 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 205} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1576 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 205} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 4, 'TRP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1585 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 205} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 44 Chain: "D" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1584 Classifications: {'peptide': 210} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 205} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 44 Chain: "E" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1585 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 205} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 44 Chain: "F" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1585 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 205} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 44 Chain: "G" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1585 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 205} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 44 Chain: "H" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1585 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 205} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 44 Time building chain proxies: 2.91, per 1000 atoms: 0.23 Number of scatterers: 12670 At special positions: 0 Unit cell: (85.1, 86.25, 157.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 2384 8.00 N 2293 7.00 C 7945 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: 1.03 Conformation dependent library (CDL) restraints added in 541.6 milliseconds 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3102 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 0 sheets defined 82.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 228 through 259 Processing helix chain 'A' and resid 261 through 273 Processing helix chain 'A' and resid 276 through 290 Processing helix chain 'A' and resid 297 through 310 removed outlier: 3.677A pdb=" N GLN A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 332 through 347 removed outlier: 3.656A pdb=" N GLN A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 361 removed outlier: 3.868A pdb=" N GLN A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 381 Processing helix chain 'A' and resid 384 through 398 Processing helix chain 'A' and resid 405 through 418 Processing helix chain 'A' and resid 420 through 434 Processing helix chain 'B' and resid 229 through 259 Processing helix chain 'B' and resid 261 through 273 Processing helix chain 'B' and resid 276 through 290 Processing helix chain 'B' and resid 297 through 309 Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 332 through 347 removed outlier: 3.898A pdb=" N GLN B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 361 removed outlier: 4.243A pdb=" N GLN B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 381 Processing helix chain 'B' and resid 384 through 398 Processing helix chain 'B' and resid 405 through 418 Processing helix chain 'B' and resid 420 through 431 removed outlier: 3.736A pdb=" N ALA B 429 " --> pdb=" O GLU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 437 removed outlier: 3.593A pdb=" N ALA B 437 " --> pdb=" O GLY B 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 259 Processing helix chain 'C' and resid 261 through 273 Processing helix chain 'C' and resid 276 through 290 Processing helix chain 'C' and resid 297 through 310 removed outlier: 3.752A pdb=" N GLN C 310 " --> pdb=" O LEU C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 325 Processing helix chain 'C' and resid 332 through 348 removed outlier: 3.915A pdb=" N GLN C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 361 removed outlier: 3.768A pdb=" N GLN C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 381 Processing helix chain 'C' and resid 384 through 398 Processing helix chain 'C' and resid 405 through 418 Processing helix chain 'C' and resid 420 through 433 removed outlier: 3.828A pdb=" N ARG C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ALA C 429 " --> pdb=" O GLU C 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 259 Processing helix chain 'D' and resid 261 through 273 Processing helix chain 'D' and resid 276 through 290 Processing helix chain 'D' and resid 297 through 309 Processing helix chain 'D' and resid 312 through 324 Processing helix chain 'D' and resid 332 through 347 removed outlier: 4.091A pdb=" N GLN D 336 " --> pdb=" O ASN D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 361 removed outlier: 3.742A pdb=" N GLN D 354 " --> pdb=" O LEU D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 381 Processing helix chain 'D' and resid 384 through 398 Processing helix chain 'D' and resid 405 through 418 removed outlier: 3.547A pdb=" N LEU D 418 " --> pdb=" O GLN D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 434 Processing helix chain 'E' and resid 229 through 259 Processing helix chain 'E' and resid 261 through 273 Processing helix chain 'E' and resid 276 through 289 Processing helix chain 'E' and resid 297 through 309 Processing helix chain 'E' and resid 312 through 324 Processing helix chain 'E' and resid 332 through 347 removed outlier: 3.770A pdb=" N GLN E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 361 removed outlier: 3.787A pdb=" N GLN E 354 " --> pdb=" O LEU E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 381 Processing helix chain 'E' and resid 384 through 398 Processing helix chain 'E' and resid 405 through 418 Processing helix chain 'E' and resid 422 through 437 removed outlier: 4.295A pdb=" N ALA E 435 " --> pdb=" O PHE E 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 259 Processing helix chain 'F' and resid 261 through 273 Processing helix chain 'F' and resid 276 through 290 Processing helix chain 'F' and resid 297 through 310 removed outlier: 3.802A pdb=" N GLN F 310 " --> pdb=" O LEU F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 325 Processing helix chain 'F' and resid 332 through 347 removed outlier: 3.701A pdb=" N GLN F 336 " --> pdb=" O ASN F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 361 removed outlier: 3.800A pdb=" N GLN F 354 " --> pdb=" O LEU F 350 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA F 355 " --> pdb=" O ARG F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 382 Processing helix chain 'F' and resid 384 through 398 Processing helix chain 'F' and resid 405 through 418 Processing helix chain 'F' and resid 420 through 437 removed outlier: 4.136A pdb=" N ALA F 435 " --> pdb=" O PHE F 431 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 259 Processing helix chain 'G' and resid 261 through 273 Processing helix chain 'G' and resid 276 through 290 Processing helix chain 'G' and resid 297 through 309 Processing helix chain 'G' and resid 312 through 324 Processing helix chain 'G' and resid 332 through 347 removed outlier: 3.835A pdb=" N GLN G 336 " --> pdb=" O ASN G 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 361 removed outlier: 3.718A pdb=" N GLN G 354 " --> pdb=" O LEU G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 381 Processing helix chain 'G' and resid 384 through 398 Processing helix chain 'G' and resid 405 through 418 Processing helix chain 'G' and resid 420 through 434 Processing helix chain 'H' and resid 229 through 259 Processing helix chain 'H' and resid 261 through 273 Processing helix chain 'H' and resid 276 through 289 Processing helix chain 'H' and resid 297 through 309 Processing helix chain 'H' and resid 312 through 324 Processing helix chain 'H' and resid 332 through 347 removed outlier: 3.770A pdb=" N GLN H 336 " --> pdb=" O ASN H 332 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 361 removed outlier: 3.788A pdb=" N GLN H 354 " --> pdb=" O LEU H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 368 through 381 Processing helix chain 'H' and resid 384 through 398 Processing helix chain 'H' and resid 405 through 418 Processing helix chain 'H' and resid 422 through 437 removed outlier: 4.295A pdb=" N ALA H 435 " --> pdb=" O PHE H 431 " (cutoff:3.500A) 995 hydrogen bonds defined for protein. 2982 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: 2.03 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2111 1.30 - 1.43: 3609 1.43 - 1.55: 7126 1.55 - 1.68: 0 1.68 - 1.81: 64 Bond restraints: 12910 Sorted by residual: bond pdb=" CA PHE C 250 " pdb=" C PHE C 250 " ideal model delta sigma weight residual 1.524 1.422 0.102 1.26e-02 6.30e+03 6.55e+01 bond pdb=" CA LEU H 251 " pdb=" C LEU H 251 " ideal model delta sigma weight residual 1.524 1.440 0.084 1.26e-02 6.30e+03 4.39e+01 bond pdb=" CA LEU E 251 " pdb=" C LEU E 251 " ideal model delta sigma weight residual 1.524 1.441 0.083 1.26e-02 6.30e+03 4.37e+01 bond pdb=" CA LEU G 251 " pdb=" C LEU G 251 " ideal model delta sigma weight residual 1.524 1.442 0.082 1.26e-02 6.30e+03 4.21e+01 bond pdb=" CA LEU C 251 " pdb=" C LEU C 251 " ideal model delta sigma weight residual 1.523 1.447 0.077 1.30e-02 5.92e+03 3.49e+01 ... (remaining 12905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 16884 1.74 - 3.48: 471 3.48 - 5.22: 57 5.22 - 6.96: 32 6.96 - 8.70: 7 Bond angle restraints: 17451 Sorted by residual: angle pdb=" C PHE C 250 " pdb=" CA PHE C 250 " pdb=" CB PHE C 250 " ideal model delta sigma weight residual 110.90 102.37 8.53 1.58e+00 4.01e-01 2.91e+01 angle pdb=" N ILE E 297 " pdb=" CA ILE E 297 " pdb=" C ILE E 297 " ideal model delta sigma weight residual 112.96 108.58 4.38 1.00e+00 1.00e+00 1.92e+01 angle pdb=" N ILE H 297 " pdb=" CA ILE H 297 " pdb=" C ILE H 297 " ideal model delta sigma weight residual 112.96 108.61 4.35 1.00e+00 1.00e+00 1.90e+01 angle pdb=" N ILE C 297 " pdb=" CA ILE C 297 " pdb=" C ILE C 297 " ideal model delta sigma weight residual 112.96 108.61 4.35 1.00e+00 1.00e+00 1.90e+01 angle pdb=" N ILE E 393 " pdb=" CA ILE E 393 " pdb=" C ILE E 393 " ideal model delta sigma weight residual 111.00 106.31 4.69 1.09e+00 8.42e-01 1.85e+01 ... (remaining 17446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6847 17.99 - 35.97: 702 35.97 - 53.96: 99 53.96 - 71.95: 10 71.95 - 89.94: 5 Dihedral angle restraints: 7663 sinusoidal: 2793 harmonic: 4870 Sorted by residual: dihedral pdb=" C GLU E 396 " pdb=" N GLU E 396 " pdb=" CA GLU E 396 " pdb=" CB GLU E 396 " ideal model delta harmonic sigma weight residual -122.60 -134.34 11.74 0 2.50e+00 1.60e-01 2.21e+01 dihedral pdb=" C PHE C 250 " pdb=" N PHE C 250 " pdb=" CA PHE C 250 " pdb=" CB PHE C 250 " ideal model delta harmonic sigma weight residual -122.60 -111.53 -11.07 0 2.50e+00 1.60e-01 1.96e+01 dihedral pdb=" N GLU E 396 " pdb=" C GLU E 396 " pdb=" CA GLU E 396 " pdb=" CB GLU E 396 " ideal model delta harmonic sigma weight residual 122.80 133.67 -10.87 0 2.50e+00 1.60e-01 1.89e+01 ... (remaining 7660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1845 0.103 - 0.207: 31 0.207 - 0.310: 1 0.310 - 0.413: 0 0.413 - 0.516: 1 Chirality restraints: 1878 Sorted by residual: chirality pdb=" CA GLU E 396 " pdb=" N GLU E 396 " pdb=" C GLU E 396 " pdb=" CB GLU E 396 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.67e+00 chirality pdb=" CA ARG E 403 " pdb=" N ARG E 403 " pdb=" C ARG E 403 " pdb=" CB ARG E 403 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA ARG A 410 " pdb=" N ARG A 410 " pdb=" C ARG A 410 " pdb=" CB ARG A 410 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.83e-01 ... (remaining 1875 not shown) Planarity restraints: 2311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN E 402 " -0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C GLN E 402 " 0.064 2.00e-02 2.50e+03 pdb=" O GLN E 402 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG E 403 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 250 " 0.016 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C PHE G 250 " -0.059 2.00e-02 2.50e+03 pdb=" O PHE G 250 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU G 251 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 250 " -0.014 2.00e-02 2.50e+03 2.95e-02 8.68e+00 pdb=" C PHE E 250 " 0.051 2.00e-02 2.50e+03 pdb=" O PHE E 250 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU E 251 " -0.017 2.00e-02 2.50e+03 ... (remaining 2308 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2133 2.75 - 3.29: 13506 3.29 - 3.83: 22224 3.83 - 4.36: 23704 4.36 - 4.90: 41000 Nonbonded interactions: 102567 Sorted by model distance: nonbonded pdb=" O ALA F 345 " pdb=" OG SER F 348 " model vdw 2.217 3.040 nonbonded pdb=" OG SER D 432 " pdb=" NH2 ARG H 403 " model vdw 2.222 3.120 nonbonded pdb=" OE1 GLN B 316 " pdb=" NE2 GLN B 344 " model vdw 2.234 3.120 nonbonded pdb=" O ALA C 345 " pdb=" OG SER C 348 " model vdw 2.241 3.040 nonbonded pdb=" O ALA A 345 " pdb=" OG SER A 348 " model vdw 2.253 3.040 ... (remaining 102562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 228 through 425 or (resid 426 and (name N or name CA or na \ me C or name O or name CB )) or resid 427 through 429 or (resid 430 and (name N \ or name CA or name C or name O or name CB )) or resid 431 through 434 or (resid \ 435 and (name N or name CA or name C or name O )) or resid 436 through 437)) selection = (chain 'B' and (resid 228 through 434 or (resid 435 and (name N or name CA or na \ me C or name O )) or resid 436 through 437)) selection = (chain 'C' and (resid 228 through 425 or (resid 426 and (name N or name CA or na \ me C or name O or name CB )) or resid 427 through 429 or (resid 430 and (name N \ or name CA or name C or name O or name CB )) or resid 431 through 434 or (resid \ 435 and (name N or name CA or name C or name O )) or resid 436 through 437)) selection = (chain 'D' and (resid 228 through 425 or (resid 426 and (name N or name CA or na \ me C or name O or name CB )) or resid 427 through 429 or (resid 430 and (name N \ or name CA or name C or name O or name CB )) or resid 431 through 437)) selection = (chain 'E' and (resid 228 through 425 or (resid 426 and (name N or name CA or na \ me C or name O or name CB )) or resid 427 through 429 or (resid 430 and (name N \ or name CA or name C or name O or name CB )) or resid 431 through 434 or (resid \ 435 and (name N or name CA or name C or name O )) or resid 436 through 437)) selection = (chain 'F' and (resid 228 through 425 or (resid 426 and (name N or name CA or na \ me C or name O or name CB )) or resid 427 through 429 or (resid 430 and (name N \ or name CA or name C or name O or name CB )) or resid 431 through 434 or (resid \ 435 and (name N or name CA or name C or name O )) or resid 436 through 437)) selection = (chain 'G' and (resid 228 through 425 or (resid 426 and (name N or name CA or na \ me C or name O or name CB )) or resid 427 through 429 or (resid 430 and (name N \ or name CA or name C or name O or name CB )) or resid 431 through 434 or (resid \ 435 and (name N or name CA or name C or name O )) or resid 436 through 437)) selection = (chain 'H' and (resid 228 through 425 or (resid 426 and (name N or name CA or na \ me C or name O or name CB )) or resid 427 through 429 or (resid 430 and (name N \ or name CA or name C or name O or name CB )) or resid 431 through 434 or (resid \ 435 and (name N or name CA or name C or name O )) or resid 436 through 437)) } 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 group one per residue 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.840 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 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 : 0.004 0.102 12910 Z= 0.281 Angle : 0.709 8.701 17451 Z= 0.406 Chirality : 0.042 0.516 1878 Planarity : 0.005 0.068 2311 Dihedral : 13.941 89.936 4561 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.58 % Allowed : 0.49 % Favored : 98.93 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 25.00 % 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: 0.05 (0.20), residues: 1664 helix: 0.46 (0.14), residues: 1352 sheet: None (None), residues: 0 loop : -1.46 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 410 TYR 0.029 0.002 TYR F 389 PHE 0.033 0.002 PHE C 250 TRP 0.006 0.001 TRP F 377 HIS 0.011 0.001 HIS G 287 Details of bonding type rmsd covalent geometry : bond 0.00441 (12910) covalent geometry : angle 0.70909 (17451) hydrogen bonds : bond 0.09962 ( 995) hydrogen bonds : angle 5.18997 ( 2982) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 488 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7534 (pp30) cc_final: 0.7301 (pp30) REVERT: A 241 GLN cc_start: 0.7791 (tp-100) cc_final: 0.7351 (tp-100) REVERT: A 274 ARG cc_start: 0.7905 (ptm160) cc_final: 0.7675 (ptp-170) REVERT: A 281 TYR cc_start: 0.8672 (t80) cc_final: 0.8420 (t80) REVERT: A 364 GLU cc_start: 0.7381 (tp30) cc_final: 0.7152 (tp30) REVERT: A 399 LEU cc_start: 0.8090 (pt) cc_final: 0.7854 (pt) REVERT: A 414 GLN cc_start: 0.6895 (pp30) cc_final: 0.6681 (pp30) REVERT: A 433 MET cc_start: 0.6452 (tpt) cc_final: 0.6198 (tpt) REVERT: B 236 ILE cc_start: 0.8484 (tp) cc_final: 0.8271 (tp) REVERT: B 241 GLN cc_start: 0.7817 (tp-100) cc_final: 0.7422 (tp-100) REVERT: B 305 GLN cc_start: 0.7860 (tp40) cc_final: 0.7340 (tp40) REVERT: C 236 ILE cc_start: 0.8445 (tp) cc_final: 0.8242 (tp) REVERT: C 241 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7133 (mm-40) REVERT: C 363 LYS cc_start: 0.7781 (tmtt) cc_final: 0.7085 (tmtt) REVERT: C 370 GLN cc_start: 0.7329 (mm-40) cc_final: 0.7104 (mm-40) REVERT: C 426 ARG cc_start: 0.6911 (tmt170) cc_final: 0.6578 (tmt170) REVERT: D 236 ILE cc_start: 0.8538 (tp) cc_final: 0.8317 (tp) REVERT: D 241 GLN cc_start: 0.7711 (tp-100) cc_final: 0.7348 (tp-100) REVERT: D 251 LEU cc_start: 0.8261 (tp) cc_final: 0.7930 (tp) REVERT: D 305 GLN cc_start: 0.7616 (tp-100) cc_final: 0.7135 (tp-100) REVERT: D 396 GLU cc_start: 0.7399 (tm-30) cc_final: 0.6994 (tm-30) REVERT: D 433 MET cc_start: 0.6363 (mmp) cc_final: 0.5898 (mmp) REVERT: E 236 ILE cc_start: 0.8668 (tp) cc_final: 0.8468 (tp) REVERT: E 237 GLN cc_start: 0.7392 (pp30) cc_final: 0.7147 (pp30) REVERT: E 238 GLN cc_start: 0.8243 (tp40) cc_final: 0.8037 (tp40) REVERT: E 241 GLN cc_start: 0.7678 (mm-40) cc_final: 0.6924 (tp40) REVERT: E 269 GLN cc_start: 0.7548 (mt0) cc_final: 0.7260 (mt0) REVERT: E 410 ARG cc_start: 0.7273 (tmm160) cc_final: 0.6997 (tmm160) REVERT: E 433 MET cc_start: 0.5963 (ttm) cc_final: 0.5531 (ttm) REVERT: F 235 SER cc_start: 0.8554 (p) cc_final: 0.8351 (p) REVERT: F 236 ILE cc_start: 0.8729 (tp) cc_final: 0.8497 (tp) REVERT: F 238 GLN cc_start: 0.8053 (tp40) cc_final: 0.7701 (tp40) REVERT: F 241 GLN cc_start: 0.7435 (mm-40) cc_final: 0.7066 (mm-40) REVERT: F 274 ARG cc_start: 0.8131 (ptm160) cc_final: 0.7862 (ptm160) REVERT: F 343 LYS cc_start: 0.7999 (tptp) cc_final: 0.7531 (tptp) REVERT: F 386 GLN cc_start: 0.8080 (tp40) cc_final: 0.7601 (tp40) REVERT: F 388 ARG cc_start: 0.7329 (tpp-160) cc_final: 0.7062 (ttm-80) REVERT: F 414 GLN cc_start: 0.7307 (pp30) cc_final: 0.6870 (pp30) REVERT: G 237 GLN cc_start: 0.7516 (pp30) cc_final: 0.7257 (pp30) REVERT: G 245 SER cc_start: 0.8970 (t) cc_final: 0.8748 (t) REVERT: G 287 HIS cc_start: 0.6985 (t-170) cc_final: 0.6629 (t-170) REVERT: G 321 ARG cc_start: 0.7399 (ttt90) cc_final: 0.6919 (ttt90) REVERT: G 323 LEU cc_start: 0.8331 (tp) cc_final: 0.7948 (tt) REVERT: G 420 ASN cc_start: 0.7502 (t0) cc_final: 0.7237 (t0) REVERT: G 426 ARG cc_start: 0.7650 (tmt170) cc_final: 0.7171 (tmt170) REVERT: H 237 GLN cc_start: 0.7491 (pp30) cc_final: 0.7282 (pp30) REVERT: H 241 GLN cc_start: 0.7549 (mm-40) cc_final: 0.7293 (mm-40) REVERT: H 371 ARG cc_start: 0.6906 (ttm110) cc_final: 0.6522 (ttm110) REVERT: H 396 GLU cc_start: 0.6827 (tm-30) cc_final: 0.6419 (tm-30) REVERT: H 433 MET cc_start: 0.6311 (ttm) cc_final: 0.5994 (ttm) outliers start: 7 outliers final: 6 residues processed: 490 average time/residue: 0.1362 time to fit residues: 90.1989 Evaluate side-chains 454 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 448 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 251 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.0980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN B 312 HIS B 354 GLN C 289 HIS C 310 GLN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 HIS ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS E 310 GLN ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 ASN F 289 HIS ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 HIS H 310 GLN ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.150890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.130698 restraints weight = 21638.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.135151 restraints weight = 12705.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.138080 restraints weight = 8459.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.140333 restraints weight = 6231.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.142016 restraints weight = 4785.830| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12910 Z= 0.129 Angle : 0.585 7.284 17451 Z= 0.301 Chirality : 0.036 0.132 1878 Planarity : 0.004 0.040 2311 Dihedral : 4.929 52.687 1875 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.05 % Allowed : 16.47 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 0.31 (0.20), residues: 1664 helix: 0.61 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -1.45 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 337 TYR 0.021 0.002 TYR C 281 PHE 0.016 0.001 PHE H 250 TRP 0.003 0.000 TRP B 377 HIS 0.004 0.001 HIS F 289 Details of bonding type rmsd covalent geometry : bond 0.00276 (12910) covalent geometry : angle 0.58473 (17451) hydrogen bonds : bond 0.03706 ( 995) hydrogen bonds : angle 3.80904 ( 2982) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 485 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7620 (pp30) cc_final: 0.7298 (pp30) REVERT: A 238 GLN cc_start: 0.8500 (tp40) cc_final: 0.8215 (tp40) REVERT: A 241 GLN cc_start: 0.7861 (tp-100) cc_final: 0.7563 (tp-100) REVERT: A 274 ARG cc_start: 0.8064 (ptm160) cc_final: 0.7722 (ptp-170) REVERT: A 281 TYR cc_start: 0.8638 (t80) cc_final: 0.8408 (t80) REVERT: A 364 GLU cc_start: 0.7397 (tp30) cc_final: 0.7078 (tp30) REVERT: A 386 GLN cc_start: 0.8197 (tp40) cc_final: 0.7865 (tp40) REVERT: A 433 MET cc_start: 0.6353 (tpt) cc_final: 0.6081 (tpt) REVERT: B 236 ILE cc_start: 0.8579 (tp) cc_final: 0.8333 (tp) REVERT: B 241 GLN cc_start: 0.7812 (tp-100) cc_final: 0.6978 (tp-100) REVERT: B 274 ARG cc_start: 0.7923 (ptm160) cc_final: 0.7130 (ptm160) REVERT: B 305 GLN cc_start: 0.8179 (tp40) cc_final: 0.7368 (tp40) REVERT: B 414 GLN cc_start: 0.6979 (pm20) cc_final: 0.6702 (pm20) REVERT: C 236 ILE cc_start: 0.8529 (tp) cc_final: 0.8300 (tp) REVERT: C 241 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7431 (mm-40) REVERT: C 297 ILE cc_start: 0.8670 (mm) cc_final: 0.8438 (mm) REVERT: C 343 LYS cc_start: 0.8276 (tptm) cc_final: 0.7981 (tptt) REVERT: C 344 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7460 (tm-30) REVERT: C 370 GLN cc_start: 0.7416 (mm-40) cc_final: 0.7188 (mm-40) REVERT: C 386 GLN cc_start: 0.7861 (tp40) cc_final: 0.7429 (tp40) REVERT: C 420 ASN cc_start: 0.8257 (t0) cc_final: 0.7939 (t0) REVERT: C 426 ARG cc_start: 0.6872 (tmt170) cc_final: 0.6624 (tmt170) REVERT: D 236 ILE cc_start: 0.8571 (tp) cc_final: 0.8308 (tp) REVERT: D 251 LEU cc_start: 0.8265 (tp) cc_final: 0.8000 (tp) REVERT: D 305 GLN cc_start: 0.7749 (tp-100) cc_final: 0.7107 (tp-100) REVERT: D 354 GLN cc_start: 0.7047 (mt0) cc_final: 0.6843 (mt0) REVERT: D 385 SER cc_start: 0.8137 (m) cc_final: 0.7403 (t) REVERT: D 396 GLU cc_start: 0.7405 (tm-30) cc_final: 0.7011 (tm-30) REVERT: D 433 MET cc_start: 0.6401 (mmp) cc_final: 0.5976 (mmp) REVERT: E 236 ILE cc_start: 0.8666 (tp) cc_final: 0.8427 (tp) REVERT: E 237 GLN cc_start: 0.7436 (pp30) cc_final: 0.7160 (pp30) REVERT: E 241 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7354 (tp40) REVERT: E 269 GLN cc_start: 0.7560 (mt0) cc_final: 0.7280 (mt0) REVERT: E 274 ARG cc_start: 0.8096 (ptm160) cc_final: 0.7715 (ptm160) REVERT: E 304 TYR cc_start: 0.7771 (m-80) cc_final: 0.7272 (m-80) REVERT: E 343 LYS cc_start: 0.8018 (tptm) cc_final: 0.7684 (tptp) REVERT: E 414 GLN cc_start: 0.6935 (pp30) cc_final: 0.6623 (pp30) REVERT: E 433 MET cc_start: 0.5734 (ttm) cc_final: 0.5302 (ttm) REVERT: F 236 ILE cc_start: 0.8637 (tp) cc_final: 0.8370 (tp) REVERT: F 238 GLN cc_start: 0.8058 (tp40) cc_final: 0.7738 (tp40) REVERT: F 241 GLN cc_start: 0.7548 (mm-40) cc_final: 0.7180 (mm-40) REVERT: F 251 LEU cc_start: 0.8227 (mp) cc_final: 0.7982 (mm) REVERT: F 343 LYS cc_start: 0.8034 (tptp) cc_final: 0.7546 (tptp) REVERT: G 237 GLN cc_start: 0.7587 (pp30) cc_final: 0.7324 (pp30) REVERT: G 281 TYR cc_start: 0.8264 (t80) cc_final: 0.8062 (t80) REVERT: G 287 HIS cc_start: 0.7017 (t-170) cc_final: 0.6702 (t-170) REVERT: G 321 ARG cc_start: 0.7496 (ttt90) cc_final: 0.7012 (ttt90) REVERT: G 323 LEU cc_start: 0.8325 (tp) cc_final: 0.8022 (tt) REVERT: G 385 SER cc_start: 0.8061 (m) cc_final: 0.7377 (p) REVERT: G 386 GLN cc_start: 0.7825 (tp40) cc_final: 0.7445 (tp40) REVERT: G 426 ARG cc_start: 0.7641 (tmt170) cc_final: 0.7166 (tmt170) REVERT: H 237 GLN cc_start: 0.7523 (pp30) cc_final: 0.7269 (pp30) REVERT: H 343 LYS cc_start: 0.8058 (tptm) cc_final: 0.7734 (tptp) REVERT: H 371 ARG cc_start: 0.6953 (ttm110) cc_final: 0.6460 (ttm110) REVERT: H 396 GLU cc_start: 0.6894 (tm-30) cc_final: 0.6503 (tm-30) REVERT: H 433 MET cc_start: 0.6152 (ttm) cc_final: 0.5808 (ttm) outliers start: 37 outliers final: 29 residues processed: 487 average time/residue: 0.1328 time to fit residues: 87.0873 Evaluate side-chains 493 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 464 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain E residue 289 HIS Chi-restraints excluded: chain E residue 305 GLN Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 344 GLN Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 289 HIS Chi-restraints excluded: chain H residue 305 GLN Chi-restraints excluded: chain H residue 344 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 149 optimal weight: 1.9990 chunk 139 optimal weight: 0.0370 chunk 142 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 10 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN D 312 HIS ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 GLN ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 386 GLN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 GLN ** G 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 305 GLN ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.143257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.123582 restraints weight = 21901.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.127882 restraints weight = 12890.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.130898 restraints weight = 8584.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.133077 restraints weight = 6213.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.134726 restraints weight = 4759.782| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12910 Z= 0.159 Angle : 0.573 7.533 17451 Z= 0.300 Chirality : 0.037 0.152 1878 Planarity : 0.004 0.041 2311 Dihedral : 4.610 54.460 1869 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.95 % Allowed : 21.00 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 0.48 (0.20), residues: 1664 helix: 0.74 (0.14), residues: 1376 sheet: None (None), residues: 0 loop : -1.38 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 388 TYR 0.021 0.002 TYR F 281 PHE 0.019 0.001 PHE H 250 TRP 0.003 0.000 TRP D 377 HIS 0.010 0.001 HIS F 289 Details of bonding type rmsd covalent geometry : bond 0.00332 (12910) covalent geometry : angle 0.57293 (17451) hydrogen bonds : bond 0.03733 ( 995) hydrogen bonds : angle 3.69507 ( 2982) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 478 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7678 (pp30) cc_final: 0.7360 (pp30) REVERT: A 238 GLN cc_start: 0.8558 (tp40) cc_final: 0.8345 (tp40) REVERT: A 241 GLN cc_start: 0.7783 (tp-100) cc_final: 0.7368 (tp-100) REVERT: A 274 ARG cc_start: 0.8111 (ptm160) cc_final: 0.7794 (ptm160) REVERT: A 351 ARG cc_start: 0.7177 (ttm-80) cc_final: 0.6699 (ttm-80) REVERT: A 364 GLU cc_start: 0.7480 (tp30) cc_final: 0.7109 (tp30) REVERT: A 433 MET cc_start: 0.6310 (tpt) cc_final: 0.6099 (tpt) REVERT: B 236 ILE cc_start: 0.8624 (tp) cc_final: 0.8358 (tp) REVERT: B 241 GLN cc_start: 0.7779 (tp-100) cc_final: 0.7175 (tp-100) REVERT: B 274 ARG cc_start: 0.8139 (ptm160) cc_final: 0.7437 (ptm160) REVERT: B 386 GLN cc_start: 0.7967 (tp40) cc_final: 0.7537 (tp40) REVERT: C 236 ILE cc_start: 0.8549 (tp) cc_final: 0.8289 (tp) REVERT: C 237 GLN cc_start: 0.7528 (pp30) cc_final: 0.7196 (pp30) REVERT: C 241 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7526 (mm-40) REVERT: C 343 LYS cc_start: 0.8275 (tptm) cc_final: 0.8048 (tptt) REVERT: C 344 GLN cc_start: 0.7741 (tm-30) cc_final: 0.7410 (tm-30) REVERT: C 370 GLN cc_start: 0.7421 (mm-40) cc_final: 0.7132 (mm-40) REVERT: C 386 GLN cc_start: 0.7994 (tp40) cc_final: 0.7794 (tp40) REVERT: D 236 ILE cc_start: 0.8589 (tp) cc_final: 0.8325 (tp) REVERT: D 251 LEU cc_start: 0.8301 (tp) cc_final: 0.8000 (tp) REVERT: D 305 GLN cc_start: 0.7841 (tp-100) cc_final: 0.7188 (tp-100) REVERT: D 337 ARG cc_start: 0.7620 (mpt180) cc_final: 0.6893 (mpt180) REVERT: D 385 SER cc_start: 0.8274 (m) cc_final: 0.7537 (t) REVERT: D 386 GLN cc_start: 0.7980 (tp40) cc_final: 0.7727 (tp40) REVERT: D 396 GLU cc_start: 0.7385 (tm-30) cc_final: 0.6926 (tm-30) REVERT: D 433 MET cc_start: 0.6537 (mmp) cc_final: 0.6202 (mmp) REVERT: E 236 ILE cc_start: 0.8749 (tp) cc_final: 0.8482 (tp) REVERT: E 237 GLN cc_start: 0.7484 (pp30) cc_final: 0.7143 (pp30) REVERT: E 269 GLN cc_start: 0.7477 (mt0) cc_final: 0.7223 (mt0) REVERT: E 304 TYR cc_start: 0.7748 (m-80) cc_final: 0.7222 (m-80) REVERT: E 343 LYS cc_start: 0.8012 (tptm) cc_final: 0.7739 (tptp) REVERT: E 410 ARG cc_start: 0.6831 (tmm160) cc_final: 0.6374 (tmm160) REVERT: E 433 MET cc_start: 0.5757 (ttm) cc_final: 0.5339 (ttm) REVERT: F 236 ILE cc_start: 0.8700 (tp) cc_final: 0.8394 (tp) REVERT: F 241 GLN cc_start: 0.7543 (mm-40) cc_final: 0.7288 (mm-40) REVERT: F 251 LEU cc_start: 0.8236 (mp) cc_final: 0.7964 (mm) REVERT: F 343 LYS cc_start: 0.8023 (tptp) cc_final: 0.7490 (tptp) REVERT: G 237 GLN cc_start: 0.7617 (pp30) cc_final: 0.7346 (pp30) REVERT: G 287 HIS cc_start: 0.6978 (t-170) cc_final: 0.6605 (t-170) REVERT: G 321 ARG cc_start: 0.7455 (ttt90) cc_final: 0.6982 (ttt90) REVERT: G 323 LEU cc_start: 0.8348 (tp) cc_final: 0.8018 (tt) REVERT: G 385 SER cc_start: 0.8056 (m) cc_final: 0.7404 (p) REVERT: G 386 GLN cc_start: 0.7818 (tp40) cc_final: 0.7428 (tp40) REVERT: G 426 ARG cc_start: 0.7630 (tmt170) cc_final: 0.7128 (tmt170) REVERT: H 237 GLN cc_start: 0.7579 (pp30) cc_final: 0.7234 (pp30) REVERT: H 250 PHE cc_start: 0.8716 (t80) cc_final: 0.8513 (t80) REVERT: H 343 LYS cc_start: 0.7983 (tptm) cc_final: 0.7769 (tptp) REVERT: H 396 GLU cc_start: 0.6923 (tm-30) cc_final: 0.6564 (tm-30) REVERT: H 433 MET cc_start: 0.6335 (ttm) cc_final: 0.5933 (ttm) outliers start: 48 outliers final: 32 residues processed: 487 average time/residue: 0.1377 time to fit residues: 90.1054 Evaluate side-chains 502 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 470 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain E residue 305 GLN Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 305 GLN Chi-restraints excluded: chain F residue 344 GLN Chi-restraints excluded: chain G residue 244 VAL Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 344 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 76 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 88 optimal weight: 0.0070 chunk 52 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN C 289 HIS C 310 GLN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 HIS D 316 GLN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN E 289 HIS E 310 GLN ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 287 HIS F 289 HIS ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 HIS H 310 GLN ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.150807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.129252 restraints weight = 21522.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.133639 restraints weight = 12909.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.136730 restraints weight = 8796.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.138918 restraints weight = 6513.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.140645 restraints weight = 5135.211| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12910 Z= 0.134 Angle : 0.558 7.447 17451 Z= 0.289 Chirality : 0.036 0.156 1878 Planarity : 0.004 0.041 2311 Dihedral : 4.103 19.958 1863 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.11 % Allowed : 23.56 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 0.49 (0.20), residues: 1664 helix: 0.76 (0.14), residues: 1400 sheet: None (None), residues: 0 loop : -1.65 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 388 TYR 0.019 0.002 TYR F 281 PHE 0.014 0.001 PHE H 250 TRP 0.004 0.000 TRP B 377 HIS 0.003 0.001 HIS G 312 Details of bonding type rmsd covalent geometry : bond 0.00286 (12910) covalent geometry : angle 0.55834 (17451) hydrogen bonds : bond 0.03519 ( 995) hydrogen bonds : angle 3.59453 ( 2982) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 469 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7712 (pp30) cc_final: 0.7313 (pp30) REVERT: A 241 GLN cc_start: 0.7798 (tp-100) cc_final: 0.7491 (tp-100) REVERT: A 274 ARG cc_start: 0.8082 (ptm160) cc_final: 0.7756 (ptp-170) REVERT: A 278 LYS cc_start: 0.8089 (mtmm) cc_final: 0.7535 (mtmm) REVERT: A 281 TYR cc_start: 0.8628 (t80) cc_final: 0.8408 (t80) REVERT: A 343 LYS cc_start: 0.8243 (tptp) cc_final: 0.7664 (tptp) REVERT: A 385 SER cc_start: 0.8002 (m) cc_final: 0.7556 (p) REVERT: A 396 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7273 (tm-30) REVERT: B 236 ILE cc_start: 0.8592 (tp) cc_final: 0.8311 (tp) REVERT: B 241 GLN cc_start: 0.7809 (tp-100) cc_final: 0.7035 (tp-100) REVERT: B 274 ARG cc_start: 0.8154 (ptm160) cc_final: 0.7402 (ptm160) REVERT: C 236 ILE cc_start: 0.8481 (tp) cc_final: 0.8242 (tp) REVERT: C 237 GLN cc_start: 0.7576 (pp30) cc_final: 0.7239 (pp30) REVERT: C 241 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7588 (mm-40) REVERT: C 324 LEU cc_start: 0.8142 (tp) cc_final: 0.7873 (tt) REVERT: C 343 LYS cc_start: 0.8308 (tptm) cc_final: 0.8097 (tptt) REVERT: C 344 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7483 (tm-30) REVERT: C 386 GLN cc_start: 0.7990 (tp40) cc_final: 0.7564 (tp40) REVERT: D 236 ILE cc_start: 0.8568 (tp) cc_final: 0.8304 (tp) REVERT: D 251 LEU cc_start: 0.8345 (tp) cc_final: 0.8058 (tp) REVERT: D 274 ARG cc_start: 0.8022 (ptm160) cc_final: 0.7752 (mtp85) REVERT: D 305 GLN cc_start: 0.7872 (tp-100) cc_final: 0.7250 (tp-100) REVERT: D 337 ARG cc_start: 0.7647 (mpt180) cc_final: 0.6905 (mpt180) REVERT: D 344 GLN cc_start: 0.7920 (pp30) cc_final: 0.7463 (pp30) REVERT: D 385 SER cc_start: 0.8264 (m) cc_final: 0.7523 (t) REVERT: D 396 GLU cc_start: 0.7384 (tm-30) cc_final: 0.6934 (tm-30) REVERT: D 433 MET cc_start: 0.6643 (mmp) cc_final: 0.6357 (mmp) REVERT: E 236 ILE cc_start: 0.8689 (tp) cc_final: 0.8415 (tp) REVERT: E 237 GLN cc_start: 0.7542 (pp30) cc_final: 0.7179 (pp30) REVERT: E 269 GLN cc_start: 0.7500 (mt0) cc_final: 0.7240 (mt0) REVERT: E 304 TYR cc_start: 0.7811 (m-80) cc_final: 0.7360 (m-80) REVERT: E 343 LYS cc_start: 0.8022 (tptm) cc_final: 0.7726 (tptp) REVERT: E 410 ARG cc_start: 0.6963 (tmm160) cc_final: 0.6447 (tmm160) REVERT: E 433 MET cc_start: 0.5969 (ttm) cc_final: 0.5403 (ttm) REVERT: F 236 ILE cc_start: 0.8661 (tp) cc_final: 0.8363 (tp) REVERT: F 241 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7309 (mm-40) REVERT: F 251 LEU cc_start: 0.8306 (mp) cc_final: 0.8027 (mm) REVERT: F 321 ARG cc_start: 0.7440 (tmt-80) cc_final: 0.6709 (tmt-80) REVERT: F 343 LYS cc_start: 0.8036 (tptp) cc_final: 0.7732 (tptt) REVERT: G 237 GLN cc_start: 0.7665 (pp30) cc_final: 0.7339 (pp30) REVERT: G 287 HIS cc_start: 0.6900 (t-170) cc_final: 0.6464 (t-170) REVERT: G 321 ARG cc_start: 0.7661 (ttt90) cc_final: 0.7174 (ttt90) REVERT: G 323 LEU cc_start: 0.8342 (tp) cc_final: 0.8004 (tt) REVERT: G 343 LYS cc_start: 0.7969 (tptp) cc_final: 0.7760 (tptp) REVERT: G 385 SER cc_start: 0.8151 (m) cc_final: 0.7516 (p) REVERT: G 386 GLN cc_start: 0.7881 (tp40) cc_final: 0.7530 (tp40) REVERT: G 426 ARG cc_start: 0.7625 (tmt170) cc_final: 0.7158 (tmt170) REVERT: H 237 GLN cc_start: 0.7630 (pp30) cc_final: 0.7289 (pp30) REVERT: H 250 PHE cc_start: 0.8757 (t80) cc_final: 0.8447 (t80) REVERT: H 321 ARG cc_start: 0.7392 (tmt-80) cc_final: 0.6520 (tmt-80) REVERT: H 343 LYS cc_start: 0.8108 (tptm) cc_final: 0.7800 (tptp) REVERT: H 396 GLU cc_start: 0.6949 (tm-30) cc_final: 0.6579 (tm-30) REVERT: H 433 MET cc_start: 0.6480 (ttm) cc_final: 0.6124 (ttm) outliers start: 62 outliers final: 42 residues processed: 480 average time/residue: 0.1353 time to fit residues: 87.0248 Evaluate side-chains 509 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 466 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain E residue 289 HIS Chi-restraints excluded: chain E residue 305 GLN Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 305 GLN Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 344 GLN Chi-restraints excluded: chain F residue 409 LEU Chi-restraints excluded: chain G residue 244 VAL Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 289 HIS Chi-restraints excluded: chain H residue 305 GLN Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain H residue 415 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 131 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 HIS ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 HIS C 289 HIS C 310 GLN C 316 GLN C 354 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN D 312 HIS ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN E 289 HIS E 310 GLN ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN F 289 HIS ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 GLN ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 HIS H 310 GLN ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.157541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136203 restraints weight = 21571.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.140536 restraints weight = 12793.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.143610 restraints weight = 8671.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.145834 restraints weight = 6401.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.147475 restraints weight = 5012.747| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12910 Z= 0.154 Angle : 0.556 7.290 17451 Z= 0.293 Chirality : 0.036 0.164 1878 Planarity : 0.004 0.041 2311 Dihedral : 4.132 20.323 1863 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 5.44 % Allowed : 25.04 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 0.51 (0.20), residues: 1664 helix: 0.78 (0.14), residues: 1400 sheet: None (None), residues: 0 loop : -1.68 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 388 TYR 0.024 0.002 TYR G 281 PHE 0.015 0.001 PHE D 356 TRP 0.003 0.000 TRP D 377 HIS 0.007 0.001 HIS H 289 Details of bonding type rmsd covalent geometry : bond 0.00325 (12910) covalent geometry : angle 0.55620 (17451) hydrogen bonds : bond 0.03618 ( 995) hydrogen bonds : angle 3.63053 ( 2982) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 464 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7736 (pp30) cc_final: 0.7315 (pp30) REVERT: A 241 GLN cc_start: 0.7773 (tp-100) cc_final: 0.7471 (tp-100) REVERT: A 274 ARG cc_start: 0.8076 (ptm160) cc_final: 0.7711 (ptp-170) REVERT: A 281 TYR cc_start: 0.8664 (t80) cc_final: 0.8394 (t80) REVERT: A 343 LYS cc_start: 0.8224 (tptp) cc_final: 0.7674 (tptp) REVERT: A 378 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8072 (tp) REVERT: A 385 SER cc_start: 0.8058 (m) cc_final: 0.7616 (p) REVERT: A 386 GLN cc_start: 0.8423 (tp40) cc_final: 0.8187 (tp40) REVERT: A 396 GLU cc_start: 0.7577 (pp20) cc_final: 0.7292 (tm-30) REVERT: B 236 ILE cc_start: 0.8564 (tp) cc_final: 0.8291 (tp) REVERT: B 241 GLN cc_start: 0.7824 (tp-100) cc_final: 0.6922 (tp-100) REVERT: B 274 ARG cc_start: 0.8140 (ptm160) cc_final: 0.7410 (ptm160) REVERT: C 236 ILE cc_start: 0.8499 (tp) cc_final: 0.8257 (tp) REVERT: C 241 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7495 (mm-40) REVERT: C 324 LEU cc_start: 0.8160 (tp) cc_final: 0.7904 (tt) REVERT: C 343 LYS cc_start: 0.8369 (tptm) cc_final: 0.8105 (tptt) REVERT: C 344 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7563 (tm-30) REVERT: C 370 GLN cc_start: 0.7451 (mm-40) cc_final: 0.7137 (mm-40) REVERT: D 236 ILE cc_start: 0.8570 (tp) cc_final: 0.8311 (tp) REVERT: D 244 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8319 (p) REVERT: D 251 LEU cc_start: 0.8382 (tp) cc_final: 0.8097 (tp) REVERT: D 274 ARG cc_start: 0.8078 (ptm160) cc_final: 0.7853 (mtp85) REVERT: D 337 ARG cc_start: 0.7681 (mpt180) cc_final: 0.6926 (mpt180) REVERT: D 344 GLN cc_start: 0.7956 (pp30) cc_final: 0.7361 (pp30) REVERT: D 385 SER cc_start: 0.8222 (m) cc_final: 0.7467 (t) REVERT: D 386 GLN cc_start: 0.8043 (tp40) cc_final: 0.7488 (tp40) REVERT: D 396 GLU cc_start: 0.7377 (tm-30) cc_final: 0.6936 (tm-30) REVERT: D 433 MET cc_start: 0.6665 (mmp) cc_final: 0.6394 (mmp) REVERT: E 236 ILE cc_start: 0.8716 (tp) cc_final: 0.8450 (tp) REVERT: E 237 GLN cc_start: 0.7580 (pp30) cc_final: 0.7159 (pp30) REVERT: E 269 GLN cc_start: 0.7482 (mt0) cc_final: 0.7223 (mt0) REVERT: E 343 LYS cc_start: 0.8027 (tptm) cc_final: 0.7725 (tptp) REVERT: E 396 GLU cc_start: 0.7740 (tt0) cc_final: 0.7421 (tt0) REVERT: E 433 MET cc_start: 0.6017 (ttm) cc_final: 0.5468 (ttm) REVERT: F 236 ILE cc_start: 0.8686 (tp) cc_final: 0.8389 (tp) REVERT: F 241 GLN cc_start: 0.7554 (mm-40) cc_final: 0.7236 (mm-40) REVERT: F 280 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7517 (mt0) REVERT: F 321 ARG cc_start: 0.7415 (tmt-80) cc_final: 0.6721 (tmt-80) REVERT: F 343 LYS cc_start: 0.8010 (tptp) cc_final: 0.7639 (tptp) REVERT: G 237 GLN cc_start: 0.7685 (pp30) cc_final: 0.7343 (pp30) REVERT: G 293 THR cc_start: 0.7887 (m) cc_final: 0.7404 (p) REVERT: G 321 ARG cc_start: 0.7630 (ttt90) cc_final: 0.7174 (ttt90) REVERT: G 323 LEU cc_start: 0.8341 (tp) cc_final: 0.8015 (tt) REVERT: G 343 LYS cc_start: 0.7950 (tptp) cc_final: 0.7716 (tptp) REVERT: G 385 SER cc_start: 0.8166 (m) cc_final: 0.7502 (p) REVERT: G 426 ARG cc_start: 0.7590 (tmt170) cc_final: 0.7138 (tmt170) REVERT: H 237 GLN cc_start: 0.7622 (pp30) cc_final: 0.7260 (pp30) REVERT: H 250 PHE cc_start: 0.8785 (t80) cc_final: 0.8371 (t80) REVERT: H 321 ARG cc_start: 0.7390 (tmt-80) cc_final: 0.6556 (tmt-80) REVERT: H 343 LYS cc_start: 0.8127 (tptm) cc_final: 0.7799 (tptp) REVERT: H 385 SER cc_start: 0.8052 (m) cc_final: 0.7430 (t) REVERT: H 387 SER cc_start: 0.8252 (m) cc_final: 0.7715 (p) REVERT: H 396 GLU cc_start: 0.6973 (tm-30) cc_final: 0.6626 (tm-30) REVERT: H 433 MET cc_start: 0.6570 (ttm) cc_final: 0.6251 (ttm) outliers start: 66 outliers final: 49 residues processed: 480 average time/residue: 0.1428 time to fit residues: 91.9177 Evaluate side-chains 511 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 459 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 337 ARG Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain E residue 289 HIS Chi-restraints excluded: chain E residue 305 GLN Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 266 SER Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 305 GLN Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 344 GLN Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain G residue 244 VAL Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain H residue 241 GLN Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 289 HIS Chi-restraints excluded: chain H residue 305 GLN Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain H residue 415 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 122 optimal weight: 0.1980 chunk 72 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 83 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN C 289 HIS C 310 GLN C 316 GLN C 354 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS E 310 GLN ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 GLN F 289 HIS ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 GLN G 289 HIS ** G 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 HIS H 310 GLN H 312 HIS ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.158133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.136968 restraints weight = 21579.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.141256 restraints weight = 12702.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.144356 restraints weight = 8593.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.146530 restraints weight = 6351.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.148137 restraints weight = 4985.584| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12910 Z= 0.139 Angle : 0.557 7.634 17451 Z= 0.290 Chirality : 0.036 0.155 1878 Planarity : 0.004 0.042 2311 Dihedral : 4.106 19.967 1863 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 5.27 % Allowed : 26.52 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 0.57 (0.20), residues: 1664 helix: 0.82 (0.14), residues: 1400 sheet: None (None), residues: 0 loop : -1.71 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 388 TYR 0.025 0.002 TYR B 281 PHE 0.011 0.001 PHE H 250 TRP 0.003 0.000 TRP D 377 HIS 0.005 0.001 HIS E 289 Details of bonding type rmsd covalent geometry : bond 0.00295 (12910) covalent geometry : angle 0.55694 (17451) hydrogen bonds : bond 0.03528 ( 995) hydrogen bonds : angle 3.60199 ( 2982) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 466 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7762 (pp30) cc_final: 0.7370 (pp30) REVERT: A 241 GLN cc_start: 0.7736 (tp-100) cc_final: 0.7194 (tp-100) REVERT: A 244 VAL cc_start: 0.8756 (p) cc_final: 0.8345 (p) REVERT: A 274 ARG cc_start: 0.8125 (ptm160) cc_final: 0.7624 (mtp85) REVERT: A 278 LYS cc_start: 0.8101 (mtmm) cc_final: 0.7385 (mtmm) REVERT: A 281 TYR cc_start: 0.8670 (t80) cc_final: 0.8440 (t80) REVERT: A 343 LYS cc_start: 0.8201 (tptp) cc_final: 0.7614 (tptp) REVERT: A 364 GLU cc_start: 0.7604 (tp30) cc_final: 0.7258 (tp30) REVERT: A 378 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8041 (tp) REVERT: A 385 SER cc_start: 0.8143 (m) cc_final: 0.7705 (p) REVERT: A 386 GLN cc_start: 0.8415 (tp40) cc_final: 0.8143 (tp40) REVERT: B 236 ILE cc_start: 0.8566 (tp) cc_final: 0.8300 (tp) REVERT: B 241 GLN cc_start: 0.7828 (tp-100) cc_final: 0.6874 (tp-100) REVERT: B 274 ARG cc_start: 0.8064 (ptm160) cc_final: 0.7175 (ptm160) REVERT: C 236 ILE cc_start: 0.8485 (tp) cc_final: 0.8241 (tp) REVERT: C 241 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7466 (mm-40) REVERT: C 343 LYS cc_start: 0.8386 (tptm) cc_final: 0.8128 (tptt) REVERT: C 344 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7577 (tm-30) REVERT: C 370 GLN cc_start: 0.7451 (mm-40) cc_final: 0.7140 (mm-40) REVERT: C 385 SER cc_start: 0.8098 (m) cc_final: 0.7528 (p) REVERT: D 236 ILE cc_start: 0.8547 (tp) cc_final: 0.8291 (tp) REVERT: D 244 VAL cc_start: 0.8772 (OUTLIER) cc_final: 0.8202 (p) REVERT: D 337 ARG cc_start: 0.7707 (mpt180) cc_final: 0.6917 (mpt180) REVERT: D 385 SER cc_start: 0.8176 (m) cc_final: 0.7397 (t) REVERT: D 386 GLN cc_start: 0.8042 (tp40) cc_final: 0.7758 (tp-100) REVERT: D 396 GLU cc_start: 0.7384 (tm-30) cc_final: 0.6910 (tm-30) REVERT: D 433 MET cc_start: 0.6714 (mmp) cc_final: 0.6443 (mmp) REVERT: E 236 ILE cc_start: 0.8699 (tp) cc_final: 0.8433 (tp) REVERT: E 237 GLN cc_start: 0.7580 (pp30) cc_final: 0.7159 (pp30) REVERT: E 269 GLN cc_start: 0.7487 (mt0) cc_final: 0.7127 (mt0) REVERT: E 343 LYS cc_start: 0.8031 (tptm) cc_final: 0.7765 (tptp) REVERT: E 396 GLU cc_start: 0.7736 (tt0) cc_final: 0.7427 (tt0) REVERT: E 433 MET cc_start: 0.6023 (ttm) cc_final: 0.5479 (ttm) REVERT: F 236 ILE cc_start: 0.8684 (tp) cc_final: 0.8388 (tp) REVERT: F 241 GLN cc_start: 0.7551 (mm-40) cc_final: 0.7227 (mm-40) REVERT: F 321 ARG cc_start: 0.7428 (tmt-80) cc_final: 0.6690 (tmt-80) REVERT: F 343 LYS cc_start: 0.8049 (tptp) cc_final: 0.7716 (tptp) REVERT: G 237 GLN cc_start: 0.7689 (pp30) cc_final: 0.7333 (pp30) REVERT: G 287 HIS cc_start: 0.6825 (m-70) cc_final: 0.6605 (m170) REVERT: G 321 ARG cc_start: 0.7642 (ttt90) cc_final: 0.7117 (ttt90) REVERT: G 323 LEU cc_start: 0.8373 (tp) cc_final: 0.7993 (tt) REVERT: G 343 LYS cc_start: 0.7941 (tptp) cc_final: 0.7727 (tptp) REVERT: G 385 SER cc_start: 0.8148 (m) cc_final: 0.7457 (p) REVERT: G 426 ARG cc_start: 0.7601 (tmt170) cc_final: 0.7137 (tmt170) REVERT: H 237 GLN cc_start: 0.7630 (pp30) cc_final: 0.7280 (pp30) REVERT: H 250 PHE cc_start: 0.8768 (t80) cc_final: 0.8355 (t80) REVERT: H 281 TYR cc_start: 0.8542 (t80) cc_final: 0.8285 (t80) REVERT: H 321 ARG cc_start: 0.7376 (tmt-80) cc_final: 0.6552 (tmt-80) REVERT: H 343 LYS cc_start: 0.8117 (tptm) cc_final: 0.7777 (tptp) REVERT: H 385 SER cc_start: 0.8038 (m) cc_final: 0.7402 (t) REVERT: H 387 SER cc_start: 0.8257 (m) cc_final: 0.7714 (p) REVERT: H 396 GLU cc_start: 0.6965 (tm-30) cc_final: 0.6661 (tm-30) REVERT: H 433 MET cc_start: 0.6634 (ttm) cc_final: 0.6323 (ttm) outliers start: 64 outliers final: 54 residues processed: 478 average time/residue: 0.1316 time to fit residues: 84.6158 Evaluate side-chains 516 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 460 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 305 GLN Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 337 ARG Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 426 ARG Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain E residue 289 HIS Chi-restraints excluded: chain E residue 305 GLN Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 414 GLN Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 305 GLN Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 344 GLN Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 289 HIS Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain H residue 241 GLN Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 289 HIS Chi-restraints excluded: chain H residue 305 GLN Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain H residue 415 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 30 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.0370 chunk 16 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 46 optimal weight: 0.0010 chunk 111 optimal weight: 0.4980 chunk 138 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 overall best weight: 0.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 HIS C 310 GLN C 312 HIS C 316 GLN C 354 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS E 305 GLN E 310 GLN ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 289 HIS ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 289 HIS ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 HIS H 310 GLN H 386 GLN ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.152590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.131668 restraints weight = 21441.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.136037 restraints weight = 12549.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.139161 restraints weight = 8404.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.141383 restraints weight = 6144.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.143029 restraints weight = 4766.343| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12910 Z= 0.116 Angle : 0.559 8.331 17451 Z= 0.285 Chirality : 0.035 0.144 1878 Planarity : 0.004 0.042 2311 Dihedral : 4.050 19.292 1863 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.86 % Allowed : 28.17 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 0.73 (0.20), residues: 1664 helix: 0.97 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -1.71 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 351 TYR 0.026 0.002 TYR B 281 PHE 0.010 0.001 PHE H 250 TRP 0.006 0.000 TRP B 377 HIS 0.005 0.001 HIS E 289 Details of bonding type rmsd covalent geometry : bond 0.00250 (12910) covalent geometry : angle 0.55905 (17451) hydrogen bonds : bond 0.03340 ( 995) hydrogen bonds : angle 3.55606 ( 2982) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 454 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7748 (pp30) cc_final: 0.7300 (pp30) REVERT: A 241 GLN cc_start: 0.7739 (tp-100) cc_final: 0.7289 (tp-100) REVERT: A 244 VAL cc_start: 0.8742 (p) cc_final: 0.8332 (p) REVERT: A 274 ARG cc_start: 0.8121 (ptm160) cc_final: 0.7641 (mtp85) REVERT: A 278 LYS cc_start: 0.8079 (mtmm) cc_final: 0.7374 (mtmm) REVERT: A 281 TYR cc_start: 0.8642 (t80) cc_final: 0.8429 (t80) REVERT: A 343 LYS cc_start: 0.8224 (tptp) cc_final: 0.7609 (tptp) REVERT: A 364 GLU cc_start: 0.7611 (tp30) cc_final: 0.7221 (tp30) REVERT: A 378 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8047 (tp) REVERT: A 385 SER cc_start: 0.8117 (m) cc_final: 0.7723 (p) REVERT: A 386 GLN cc_start: 0.8361 (tp40) cc_final: 0.8079 (tp40) REVERT: B 236 ILE cc_start: 0.8603 (tp) cc_final: 0.8332 (tp) REVERT: B 241 GLN cc_start: 0.7816 (tp-100) cc_final: 0.6890 (tp-100) REVERT: B 274 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7333 (ptm160) REVERT: B 377 TRP cc_start: 0.6763 (t60) cc_final: 0.6562 (t60) REVERT: C 236 ILE cc_start: 0.8481 (tp) cc_final: 0.8216 (tp) REVERT: C 241 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7490 (mm-40) REVERT: C 304 TYR cc_start: 0.8112 (m-80) cc_final: 0.7759 (m-80) REVERT: C 343 LYS cc_start: 0.8307 (tptm) cc_final: 0.8018 (tptt) REVERT: C 344 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7566 (tm-30) REVERT: C 385 SER cc_start: 0.8084 (m) cc_final: 0.7503 (p) REVERT: D 236 ILE cc_start: 0.8533 (tp) cc_final: 0.8273 (tp) REVERT: D 251 LEU cc_start: 0.8432 (tp) cc_final: 0.8099 (tp) REVERT: D 319 TYR cc_start: 0.7417 (t80) cc_final: 0.7147 (t80) REVERT: D 337 ARG cc_start: 0.7599 (mpt180) cc_final: 0.6839 (mpt180) REVERT: D 385 SER cc_start: 0.8181 (m) cc_final: 0.7405 (t) REVERT: D 386 GLN cc_start: 0.8100 (tp40) cc_final: 0.7792 (tp-100) REVERT: D 396 GLU cc_start: 0.7349 (tm-30) cc_final: 0.6891 (tm-30) REVERT: D 433 MET cc_start: 0.6697 (mmp) cc_final: 0.6418 (mmp) REVERT: E 236 ILE cc_start: 0.8663 (tp) cc_final: 0.8402 (tp) REVERT: E 237 GLN cc_start: 0.7595 (pp30) cc_final: 0.7170 (pp30) REVERT: E 241 GLN cc_start: 0.7863 (mm110) cc_final: 0.7211 (tp40) REVERT: E 269 GLN cc_start: 0.7493 (mt0) cc_final: 0.7228 (mt0) REVERT: E 274 ARG cc_start: 0.8162 (ptp-170) cc_final: 0.7422 (ptm160) REVERT: E 343 LYS cc_start: 0.8018 (tptm) cc_final: 0.7717 (tptp) REVERT: E 387 SER cc_start: 0.8435 (m) cc_final: 0.8012 (p) REVERT: E 396 GLU cc_start: 0.7734 (tt0) cc_final: 0.7424 (tt0) REVERT: E 433 MET cc_start: 0.6079 (ttm) cc_final: 0.5531 (ttm) REVERT: F 236 ILE cc_start: 0.8715 (tp) cc_final: 0.8398 (tp) REVERT: F 241 GLN cc_start: 0.7531 (mm-40) cc_final: 0.7034 (mm-40) REVERT: F 274 ARG cc_start: 0.8283 (ptm160) cc_final: 0.7694 (ptm160) REVERT: F 321 ARG cc_start: 0.7469 (tmt-80) cc_final: 0.6738 (tmt-80) REVERT: F 343 LYS cc_start: 0.8089 (tptp) cc_final: 0.7699 (tptp) REVERT: F 433 MET cc_start: 0.6856 (mtm) cc_final: 0.6297 (mtm) REVERT: G 237 GLN cc_start: 0.7682 (pp30) cc_final: 0.7317 (pp30) REVERT: G 287 HIS cc_start: 0.6841 (OUTLIER) cc_final: 0.6542 (m170) REVERT: G 321 ARG cc_start: 0.7671 (ttt90) cc_final: 0.7093 (ttt90) REVERT: G 385 SER cc_start: 0.8141 (m) cc_final: 0.7467 (p) REVERT: G 386 GLN cc_start: 0.7926 (tp40) cc_final: 0.7605 (tp40) REVERT: G 426 ARG cc_start: 0.7582 (tmt170) cc_final: 0.7136 (tmt170) REVERT: H 237 GLN cc_start: 0.7606 (pp30) cc_final: 0.7231 (pp30) REVERT: H 250 PHE cc_start: 0.8757 (t80) cc_final: 0.8346 (t80) REVERT: H 304 TYR cc_start: 0.7781 (m-80) cc_final: 0.7308 (m-80) REVERT: H 321 ARG cc_start: 0.7360 (tmt-80) cc_final: 0.6532 (tmt-80) REVERT: H 343 LYS cc_start: 0.8105 (tptm) cc_final: 0.7743 (tptp) REVERT: H 396 GLU cc_start: 0.6972 (tm-30) cc_final: 0.6647 (tm-30) REVERT: H 433 MET cc_start: 0.6641 (ttm) cc_final: 0.6335 (ttm) outliers start: 59 outliers final: 46 residues processed: 465 average time/residue: 0.1361 time to fit residues: 84.0405 Evaluate side-chains 499 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 450 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 289 HIS Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 414 GLN Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 305 GLN Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 344 GLN Chi-restraints excluded: chain F residue 427 LEU Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 287 HIS Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 289 HIS Chi-restraints excluded: chain G residue 305 GLN Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain H residue 241 GLN Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 289 HIS Chi-restraints excluded: chain H residue 305 GLN Chi-restraints excluded: chain H residue 344 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 62 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 HIS C 310 GLN ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN D 312 HIS ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS E 310 GLN ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 289 HIS ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 289 HIS ** G 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 HIS H 310 GLN ** H 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.157422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.136098 restraints weight = 21374.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.140428 restraints weight = 12595.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.143466 restraints weight = 8510.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145641 restraints weight = 6304.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.147239 restraints weight = 4961.413| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12910 Z= 0.150 Angle : 0.574 8.297 17451 Z= 0.298 Chirality : 0.036 0.150 1878 Planarity : 0.004 0.039 2311 Dihedral : 4.093 19.815 1863 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 5.19 % Allowed : 28.17 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 0.67 (0.20), residues: 1664 helix: 0.92 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -1.70 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 351 TYR 0.026 0.002 TYR B 281 PHE 0.010 0.001 PHE C 268 TRP 0.004 0.000 TRP B 377 HIS 0.006 0.001 HIS E 289 Details of bonding type rmsd covalent geometry : bond 0.00319 (12910) covalent geometry : angle 0.57434 (17451) hydrogen bonds : bond 0.03522 ( 995) hydrogen bonds : angle 3.59093 ( 2982) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 460 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.7729 (tp-100) cc_final: 0.7241 (tp-100) REVERT: A 244 VAL cc_start: 0.8755 (p) cc_final: 0.8457 (p) REVERT: A 274 ARG cc_start: 0.8117 (ptm160) cc_final: 0.7616 (mtp85) REVERT: A 278 LYS cc_start: 0.8113 (mtmm) cc_final: 0.7450 (mtmm) REVERT: A 281 TYR cc_start: 0.8656 (t80) cc_final: 0.8386 (t80) REVERT: A 343 LYS cc_start: 0.8227 (tptp) cc_final: 0.7611 (tptp) REVERT: A 351 ARG cc_start: 0.7315 (ttm-80) cc_final: 0.6769 (ttm-80) REVERT: A 364 GLU cc_start: 0.7645 (tp30) cc_final: 0.7296 (tp30) REVERT: A 378 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8058 (tp) REVERT: A 385 SER cc_start: 0.8180 (m) cc_final: 0.7775 (p) REVERT: A 386 GLN cc_start: 0.8453 (tp40) cc_final: 0.8160 (tp40) REVERT: A 410 ARG cc_start: 0.7307 (ptt180) cc_final: 0.7061 (pmt170) REVERT: B 236 ILE cc_start: 0.8563 (tp) cc_final: 0.8305 (tp) REVERT: B 241 GLN cc_start: 0.7824 (tp-100) cc_final: 0.6915 (tp-100) REVERT: B 274 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7213 (ptm160) REVERT: C 236 ILE cc_start: 0.8466 (tp) cc_final: 0.8207 (tp) REVERT: C 237 GLN cc_start: 0.7602 (pp30) cc_final: 0.7231 (pp30) REVERT: C 241 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7554 (mm-40) REVERT: C 343 LYS cc_start: 0.8367 (tptm) cc_final: 0.8072 (tptt) REVERT: C 344 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7565 (tm-30) REVERT: C 370 GLN cc_start: 0.7448 (mm-40) cc_final: 0.7130 (mm-40) REVERT: C 385 SER cc_start: 0.8123 (m) cc_final: 0.7520 (p) REVERT: D 236 ILE cc_start: 0.8541 (tp) cc_final: 0.8281 (tp) REVERT: D 319 TYR cc_start: 0.7471 (t80) cc_final: 0.7252 (t80) REVERT: D 332 ASN cc_start: 0.7227 (p0) cc_final: 0.6965 (p0) REVERT: D 337 ARG cc_start: 0.7661 (mpt180) cc_final: 0.6869 (mpt180) REVERT: D 385 SER cc_start: 0.8195 (m) cc_final: 0.7419 (t) REVERT: D 386 GLN cc_start: 0.8078 (tp40) cc_final: 0.7786 (tp-100) REVERT: D 396 GLU cc_start: 0.7397 (tm-30) cc_final: 0.6910 (tm-30) REVERT: D 433 MET cc_start: 0.6746 (mmp) cc_final: 0.6488 (mmp) REVERT: E 236 ILE cc_start: 0.8690 (tp) cc_final: 0.8435 (tp) REVERT: E 237 GLN cc_start: 0.7610 (pp30) cc_final: 0.7175 (pp30) REVERT: E 241 GLN cc_start: 0.7884 (mm110) cc_final: 0.7119 (tp40) REVERT: E 242 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8052 (mp) REVERT: E 269 GLN cc_start: 0.7486 (mt0) cc_final: 0.7225 (mt0) REVERT: E 274 ARG cc_start: 0.8112 (ptp-170) cc_final: 0.7300 (ptm160) REVERT: E 343 LYS cc_start: 0.8082 (tptm) cc_final: 0.7777 (tptp) REVERT: E 363 LYS cc_start: 0.8073 (tmtt) cc_final: 0.7659 (tmtt) REVERT: E 387 SER cc_start: 0.8510 (m) cc_final: 0.8111 (p) REVERT: E 396 GLU cc_start: 0.7788 (tt0) cc_final: 0.7406 (tt0) REVERT: E 433 MET cc_start: 0.6118 (ttm) cc_final: 0.5580 (ttm) REVERT: F 236 ILE cc_start: 0.8708 (tp) cc_final: 0.8389 (tp) REVERT: F 241 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7073 (mm-40) REVERT: F 274 ARG cc_start: 0.8288 (ptm160) cc_final: 0.7702 (ptm160) REVERT: F 321 ARG cc_start: 0.7460 (tmt-80) cc_final: 0.6714 (tmt-80) REVERT: F 343 LYS cc_start: 0.8148 (tptp) cc_final: 0.7784 (tptp) REVERT: F 433 MET cc_start: 0.6889 (mtm) cc_final: 0.6326 (mtm) REVERT: G 287 HIS cc_start: 0.6901 (m-70) cc_final: 0.6655 (m170) REVERT: G 321 ARG cc_start: 0.7641 (ttt90) cc_final: 0.7100 (ttt90) REVERT: G 385 SER cc_start: 0.8149 (m) cc_final: 0.7463 (p) REVERT: G 426 ARG cc_start: 0.7588 (tmt170) cc_final: 0.7121 (tmt170) REVERT: H 237 GLN cc_start: 0.7627 (pp30) cc_final: 0.7233 (pp30) REVERT: H 250 PHE cc_start: 0.8771 (t80) cc_final: 0.8330 (t80) REVERT: H 321 ARG cc_start: 0.7377 (tmt-80) cc_final: 0.6551 (tmt-80) REVERT: H 343 LYS cc_start: 0.8127 (tptm) cc_final: 0.7770 (tptp) REVERT: H 385 SER cc_start: 0.8023 (m) cc_final: 0.7367 (t) REVERT: H 387 SER cc_start: 0.8237 (m) cc_final: 0.7749 (p) REVERT: H 396 GLU cc_start: 0.6983 (tm-30) cc_final: 0.6666 (tm-30) REVERT: H 433 MET cc_start: 0.6801 (ttm) cc_final: 0.6486 (ttm) outliers start: 63 outliers final: 52 residues processed: 473 average time/residue: 0.1459 time to fit residues: 91.6983 Evaluate side-chains 516 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 461 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 337 ARG Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 289 HIS Chi-restraints excluded: chain E residue 305 GLN Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 414 GLN Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 305 GLN Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 344 GLN Chi-restraints excluded: chain F residue 427 LEU Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 289 HIS Chi-restraints excluded: chain G residue 305 GLN Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain H residue 241 GLN Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 289 HIS Chi-restraints excluded: chain H residue 305 GLN Chi-restraints excluded: chain H residue 344 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 137 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 162 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 HIS C 310 GLN C 312 HIS C 316 GLN C 354 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS E 310 GLN ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 289 HIS ** F 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 289 HIS ** G 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 HIS H 310 GLN H 312 HIS ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.150612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.131877 restraints weight = 21457.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.136239 restraints weight = 12593.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.138520 restraints weight = 8326.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.140921 restraints weight = 6305.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.142522 restraints weight = 4814.614| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12910 Z= 0.184 Angle : 0.611 16.405 17451 Z= 0.316 Chirality : 0.038 0.158 1878 Planarity : 0.004 0.040 2311 Dihedral : 4.186 20.249 1863 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 5.77 % Allowed : 28.75 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 0.51 (0.20), residues: 1664 helix: 0.82 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -1.83 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 388 TYR 0.026 0.002 TYR B 281 PHE 0.012 0.001 PHE E 265 TRP 0.005 0.000 TRP B 377 HIS 0.009 0.001 HIS E 289 Details of bonding type rmsd covalent geometry : bond 0.00383 (12910) covalent geometry : angle 0.61097 (17451) hydrogen bonds : bond 0.03733 ( 995) hydrogen bonds : angle 3.68291 ( 2982) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 469 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7833 (pp30) cc_final: 0.7452 (pp30) REVERT: A 244 VAL cc_start: 0.8730 (p) cc_final: 0.8418 (p) REVERT: A 274 ARG cc_start: 0.8109 (ptm160) cc_final: 0.7794 (ptp-170) REVERT: A 278 LYS cc_start: 0.8119 (mtmm) cc_final: 0.7475 (mtmm) REVERT: A 343 LYS cc_start: 0.8317 (tptp) cc_final: 0.7692 (tptp) REVERT: A 351 ARG cc_start: 0.7339 (ttm-80) cc_final: 0.6762 (ttm-80) REVERT: A 364 GLU cc_start: 0.7705 (tp30) cc_final: 0.7330 (tp30) REVERT: A 378 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8055 (tp) REVERT: A 385 SER cc_start: 0.8263 (m) cc_final: 0.7809 (p) REVERT: A 410 ARG cc_start: 0.7411 (ptt180) cc_final: 0.7115 (pmt170) REVERT: B 236 ILE cc_start: 0.8490 (tp) cc_final: 0.8245 (tp) REVERT: B 239 LEU cc_start: 0.8580 (tp) cc_final: 0.8363 (tp) REVERT: B 241 GLN cc_start: 0.7826 (tp-100) cc_final: 0.6966 (tp-100) REVERT: B 274 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7284 (ptm160) REVERT: B 321 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.7049 (mmp-170) REVERT: C 236 ILE cc_start: 0.8462 (tp) cc_final: 0.8213 (tp) REVERT: C 237 GLN cc_start: 0.7632 (pp30) cc_final: 0.7238 (pp30) REVERT: C 343 LYS cc_start: 0.8450 (tptm) cc_final: 0.8164 (tptt) REVERT: C 344 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7645 (tm-30) REVERT: C 369 GLU cc_start: 0.8439 (mp0) cc_final: 0.8226 (mp0) REVERT: C 370 GLN cc_start: 0.7467 (mm-40) cc_final: 0.7097 (mm-40) REVERT: C 385 SER cc_start: 0.8109 (m) cc_final: 0.7483 (p) REVERT: D 236 ILE cc_start: 0.8493 (tp) cc_final: 0.8257 (tp) REVERT: D 244 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8499 (p) REVERT: D 319 TYR cc_start: 0.7547 (t80) cc_final: 0.6921 (t80) REVERT: D 332 ASN cc_start: 0.7203 (p0) cc_final: 0.6909 (p0) REVERT: D 337 ARG cc_start: 0.7686 (mpt180) cc_final: 0.6936 (mpt180) REVERT: D 385 SER cc_start: 0.8163 (m) cc_final: 0.7402 (t) REVERT: D 386 GLN cc_start: 0.7946 (tp40) cc_final: 0.7676 (tp-100) REVERT: D 396 GLU cc_start: 0.7391 (tm-30) cc_final: 0.6896 (tm-30) REVERT: D 433 MET cc_start: 0.6688 (mmp) cc_final: 0.6461 (mmp) REVERT: E 236 ILE cc_start: 0.8633 (tp) cc_final: 0.8393 (tp) REVERT: E 237 GLN cc_start: 0.7647 (pp30) cc_final: 0.7234 (pp30) REVERT: E 241 GLN cc_start: 0.7893 (mm110) cc_final: 0.7493 (tp40) REVERT: E 242 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7992 (mp) REVERT: E 274 ARG cc_start: 0.8142 (ptp-170) cc_final: 0.7689 (ptm160) REVERT: E 343 LYS cc_start: 0.8162 (tptm) cc_final: 0.7816 (tptp) REVERT: E 363 LYS cc_start: 0.8055 (tmtt) cc_final: 0.7613 (tmtt) REVERT: E 387 SER cc_start: 0.8494 (m) cc_final: 0.8096 (p) REVERT: E 396 GLU cc_start: 0.7794 (tt0) cc_final: 0.7545 (tt0) REVERT: E 433 MET cc_start: 0.6131 (ttm) cc_final: 0.5617 (ttm) REVERT: F 236 ILE cc_start: 0.8627 (tp) cc_final: 0.8314 (tp) REVERT: F 241 GLN cc_start: 0.7564 (mm-40) cc_final: 0.7025 (mm-40) REVERT: F 274 ARG cc_start: 0.8316 (ptm160) cc_final: 0.7649 (ptm160) REVERT: F 321 ARG cc_start: 0.7522 (tmt-80) cc_final: 0.6742 (tmt-80) REVERT: F 343 LYS cc_start: 0.8233 (tptp) cc_final: 0.7832 (tptp) REVERT: F 433 MET cc_start: 0.6799 (mtm) cc_final: 0.6264 (mtm) REVERT: G 237 GLN cc_start: 0.7759 (pp30) cc_final: 0.7418 (pp30) REVERT: G 278 LYS cc_start: 0.8253 (mttt) cc_final: 0.8001 (mttt) REVERT: G 321 ARG cc_start: 0.7615 (ttt90) cc_final: 0.7160 (ttt90) REVERT: G 385 SER cc_start: 0.8142 (m) cc_final: 0.7467 (p) REVERT: G 414 GLN cc_start: 0.7232 (pt0) cc_final: 0.6789 (pm20) REVERT: G 426 ARG cc_start: 0.7616 (tmt170) cc_final: 0.7145 (tmt170) REVERT: H 237 GLN cc_start: 0.7650 (pp30) cc_final: 0.7271 (pp30) REVERT: H 250 PHE cc_start: 0.8786 (t80) cc_final: 0.8275 (t80) REVERT: H 343 LYS cc_start: 0.8230 (tptm) cc_final: 0.7817 (tptp) REVERT: H 385 SER cc_start: 0.8049 (m) cc_final: 0.7408 (t) REVERT: H 387 SER cc_start: 0.8229 (m) cc_final: 0.7754 (p) REVERT: H 433 MET cc_start: 0.6750 (ttm) cc_final: 0.6390 (ttm) outliers start: 70 outliers final: 58 residues processed: 486 average time/residue: 0.1377 time to fit residues: 89.1822 Evaluate side-chains 531 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 468 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 305 GLN Chi-restraints excluded: chain B residue 321 ARG Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 337 ARG Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 289 HIS Chi-restraints excluded: chain E residue 305 GLN Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 305 GLN Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 344 GLN Chi-restraints excluded: chain F residue 427 LEU Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 289 HIS Chi-restraints excluded: chain G residue 305 GLN Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 375 TYR Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain H residue 241 GLN Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 289 HIS Chi-restraints excluded: chain H residue 305 GLN Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain H residue 414 GLN Chi-restraints excluded: chain H residue 415 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 154 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 HIS C 310 GLN C 312 HIS ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS E 310 GLN ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 289 HIS G 287 HIS G 289 HIS ** G 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 HIS H 310 GLN ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.156923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135602 restraints weight = 21491.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.139937 restraints weight = 12615.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.142979 restraints weight = 8512.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.145149 restraints weight = 6292.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.146731 restraints weight = 4940.177| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12910 Z= 0.148 Angle : 0.604 8.736 17451 Z= 0.311 Chirality : 0.037 0.167 1878 Planarity : 0.004 0.040 2311 Dihedral : 4.164 19.748 1863 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.77 % Allowed : 29.24 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 0.55 (0.20), residues: 1664 helix: 0.86 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -1.84 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 295 TYR 0.027 0.002 TYR D 281 PHE 0.012 0.001 PHE H 265 TRP 0.003 0.000 TRP B 377 HIS 0.007 0.001 HIS E 289 Details of bonding type rmsd covalent geometry : bond 0.00317 (12910) covalent geometry : angle 0.60398 (17451) hydrogen bonds : bond 0.03585 ( 995) hydrogen bonds : angle 3.64228 ( 2982) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 466 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7769 (pp30) cc_final: 0.7367 (pp30) REVERT: A 241 GLN cc_start: 0.7830 (tp-100) cc_final: 0.7604 (tp-100) REVERT: A 244 VAL cc_start: 0.8771 (p) cc_final: 0.8359 (p) REVERT: A 278 LYS cc_start: 0.8117 (mtmm) cc_final: 0.7389 (mtmm) REVERT: A 343 LYS cc_start: 0.8269 (tptp) cc_final: 0.7653 (tptp) REVERT: A 364 GLU cc_start: 0.7591 (tp30) cc_final: 0.7242 (tp30) REVERT: A 378 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8069 (tp) REVERT: A 385 SER cc_start: 0.8231 (m) cc_final: 0.7769 (p) REVERT: A 410 ARG cc_start: 0.7383 (ptt180) cc_final: 0.7092 (pmt170) REVERT: B 236 ILE cc_start: 0.8548 (tp) cc_final: 0.8286 (tp) REVERT: B 241 GLN cc_start: 0.7844 (tp-100) cc_final: 0.6856 (tp-100) REVERT: B 274 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7251 (ptm160) REVERT: C 236 ILE cc_start: 0.8449 (tp) cc_final: 0.8193 (tp) REVERT: C 237 GLN cc_start: 0.7646 (pp30) cc_final: 0.7229 (pp30) REVERT: C 238 GLN cc_start: 0.8562 (tp40) cc_final: 0.8259 (tp40) REVERT: C 343 LYS cc_start: 0.8362 (tptm) cc_final: 0.8090 (tptt) REVERT: C 344 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7519 (tm-30) REVERT: C 370 GLN cc_start: 0.7433 (mm-40) cc_final: 0.7091 (mm-40) REVERT: C 385 SER cc_start: 0.8122 (m) cc_final: 0.7470 (p) REVERT: C 386 GLN cc_start: 0.7886 (tp40) cc_final: 0.7566 (tp40) REVERT: D 236 ILE cc_start: 0.8530 (tp) cc_final: 0.8282 (tp) REVERT: D 244 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8527 (p) REVERT: D 319 TYR cc_start: 0.7459 (t80) cc_final: 0.7258 (t80) REVERT: D 332 ASN cc_start: 0.7250 (p0) cc_final: 0.6979 (p0) REVERT: D 337 ARG cc_start: 0.7687 (mpt180) cc_final: 0.6909 (mpt180) REVERT: D 385 SER cc_start: 0.8198 (m) cc_final: 0.7411 (t) REVERT: D 386 GLN cc_start: 0.8023 (tp40) cc_final: 0.7734 (tp-100) REVERT: D 396 GLU cc_start: 0.7355 (tm-30) cc_final: 0.6881 (tm-30) REVERT: D 433 MET cc_start: 0.6764 (mmp) cc_final: 0.6539 (mmp) REVERT: E 236 ILE cc_start: 0.8694 (tp) cc_final: 0.8433 (tp) REVERT: E 237 GLN cc_start: 0.7606 (pp30) cc_final: 0.7175 (pp30) REVERT: E 242 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8028 (mp) REVERT: E 269 GLN cc_start: 0.7500 (mt0) cc_final: 0.7242 (mt0) REVERT: E 274 ARG cc_start: 0.8075 (ptp-170) cc_final: 0.7457 (ptm160) REVERT: E 343 LYS cc_start: 0.8077 (tptm) cc_final: 0.7755 (tptp) REVERT: E 363 LYS cc_start: 0.8084 (tmtt) cc_final: 0.7666 (tmtt) REVERT: E 387 SER cc_start: 0.8457 (m) cc_final: 0.8110 (p) REVERT: E 396 GLU cc_start: 0.7784 (tt0) cc_final: 0.7578 (tt0) REVERT: E 433 MET cc_start: 0.6247 (ttm) cc_final: 0.5701 (ttm) REVERT: F 236 ILE cc_start: 0.8715 (tp) cc_final: 0.8390 (tp) REVERT: F 241 GLN cc_start: 0.7508 (mm-40) cc_final: 0.7031 (mm-40) REVERT: F 274 ARG cc_start: 0.8274 (ptm160) cc_final: 0.7701 (ptm160) REVERT: F 321 ARG cc_start: 0.7471 (tmt-80) cc_final: 0.6712 (tmt-80) REVERT: F 343 LYS cc_start: 0.8135 (tptp) cc_final: 0.7770 (tptp) REVERT: F 433 MET cc_start: 0.6888 (mtm) cc_final: 0.6337 (mtm) REVERT: G 237 GLN cc_start: 0.7688 (pp30) cc_final: 0.7317 (pp30) REVERT: G 278 LYS cc_start: 0.8228 (mttt) cc_final: 0.7988 (mttt) REVERT: G 289 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.7122 (m90) REVERT: G 321 ARG cc_start: 0.7564 (ttt90) cc_final: 0.7062 (ttt90) REVERT: G 385 SER cc_start: 0.8144 (m) cc_final: 0.7463 (p) REVERT: G 414 GLN cc_start: 0.7185 (pt0) cc_final: 0.6763 (pm20) REVERT: G 426 ARG cc_start: 0.7581 (tmt170) cc_final: 0.7071 (tmt170) REVERT: G 427 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.6372 (mt) REVERT: H 237 GLN cc_start: 0.7625 (pp30) cc_final: 0.7236 (pp30) REVERT: H 250 PHE cc_start: 0.8800 (t80) cc_final: 0.8303 (t80) REVERT: H 343 LYS cc_start: 0.8149 (tptm) cc_final: 0.7774 (tptp) REVERT: H 385 SER cc_start: 0.8050 (m) cc_final: 0.7372 (t) REVERT: H 387 SER cc_start: 0.8227 (m) cc_final: 0.7758 (p) REVERT: H 433 MET cc_start: 0.6781 (ttm) cc_final: 0.6382 (ttm) outliers start: 70 outliers final: 59 residues processed: 480 average time/residue: 0.1432 time to fit residues: 91.3852 Evaluate side-chains 536 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 471 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 305 GLN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 337 ARG Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 426 ARG Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 289 HIS Chi-restraints excluded: chain E residue 305 GLN Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 414 GLN Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 305 GLN Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 344 GLN Chi-restraints excluded: chain F residue 427 LEU Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain G residue 287 HIS Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 289 HIS Chi-restraints excluded: chain G residue 305 GLN Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain H residue 241 GLN Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 289 HIS Chi-restraints excluded: chain H residue 305 GLN Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain H residue 414 GLN Chi-restraints excluded: chain H residue 415 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 49 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 138 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS A 312 HIS ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN C 289 HIS C 310 GLN C 312 HIS ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 HIS D 310 GLN ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 289 HIS ** F 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 287 HIS G 289 HIS ** G 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 HIS H 310 GLN ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.153087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.134669 restraints weight = 21406.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.138898 restraints weight = 12521.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.141830 restraints weight = 8296.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.143884 restraints weight = 5968.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.145463 restraints weight = 4559.147| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12910 Z= 0.164 Angle : 0.614 8.731 17451 Z= 0.318 Chirality : 0.038 0.171 1878 Planarity : 0.004 0.041 2311 Dihedral : 4.203 20.227 1863 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.60 % Allowed : 29.65 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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 (0.20), residues: 1664 helix: 0.86 (0.14), residues: 1376 sheet: None (None), residues: 0 loop : -1.97 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 295 TYR 0.026 0.002 TYR D 281 PHE 0.025 0.001 PHE B 356 TRP 0.003 0.000 TRP D 377 HIS 0.006 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00347 (12910) covalent geometry : angle 0.61443 (17451) hydrogen bonds : bond 0.03688 ( 995) hydrogen bonds : angle 3.66320 ( 2982) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2250.38 seconds wall clock time: 39 minutes 41.14 seconds (2381.14 seconds total)