Starting phenix.real_space_refine on Mon Dec 30 08:02:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d9x_27269/12_2024/8d9x_27269_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d9x_27269/12_2024/8d9x_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d9x_27269/12_2024/8d9x_27269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d9x_27269/12_2024/8d9x_27269.map" model { file = "/net/cci-nas-00/data/ceres_data/8d9x_27269/12_2024/8d9x_27269_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d9x_27269/12_2024/8d9x_27269_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'TRP:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 44 Time building chain proxies: 7.88, per 1000 atoms: 0.62 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: 3.39 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.01 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: 3.61 Time building geometry restraints manager: 3.74 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: 1.040 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 30.000 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.230 ------------------------------------------------------------------------------- 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= 0.289 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP F 377 HIS 0.011 0.001 HIS G 287 PHE 0.033 0.002 PHE C 250 TYR 0.029 0.002 TYR F 389 ARG 0.016 0.001 ARG A 410 *********************** 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 : 1.345 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: 0.7853 (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: 0.7839 (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: 0.6995 (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: 0.8467 (tp) REVERT: E 237 GLN cc_start: 0.7391 (pp30) cc_final: 0.7144 (pp30) REVERT: E 238 GLN cc_start: 0.8243 (tp40) cc_final: 0.8032 (tp40) REVERT: E 241 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7193 (tp40) REVERT: E 269 GLN cc_start: 0.7548 (mt0) cc_final: 0.7257 (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: 0.8352 (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: 0.7067 (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: 0.7256 (pp30) REVERT: G 245 SER cc_start: 0.8970 (t) cc_final: 0.8749 (t) REVERT: G 287 HIS cc_start: 0.6984 (t-170) cc_final: 0.6628 (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: 0.7172 (tmt170) REVERT: H 237 GLN cc_start: 0.7491 (pp30) cc_final: 0.7283 (pp30) REVERT: H 241 GLN cc_start: 0.7549 (mm-40) cc_final: 0.7291 (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: 0.5995 (ttm) outliers start: 7 outliers final: 6 residues processed: 490 average time/residue: 0.3020 time to fit residues: 198.7477 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 : 1.557 ------------------------------------------------------------------------------- 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 141 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 70 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 chunk 152 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** 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** E 386 GLN F 255 ASN F 289 HIS ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 ASN 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12910 Z= 0.200 Angle : 0.591 7.250 17451 Z= 0.305 Chirality : 0.037 0.133 1878 Planarity : 0.004 0.040 2311 Dihedral : 4.968 53.729 1875 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.20), residues: 1664 helix: 0.62 (0.14), residues: 1376 sheet: None (None), residues: 0 loop : -1.31 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 377 HIS 0.004 0.001 HIS C 289 PHE 0.016 0.001 PHE H 250 TYR 0.022 0.002 TYR C 281 ARG 0.006 0.001 ARG A 337 *********************** 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 521 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 484 time to evaluate : 1.317 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: 0.7678 (pp30) cc_final: 0.7375 (pp30) REVERT: A 238 GLN cc_start: 0.8554 (tp40) cc_final: 0.8259 (tp40) REVERT: A 241 GLN cc_start: 0.7854 (tp-100) cc_final: 0.7582 (tp-100) REVERT: A 274 ARG cc_start: 0.8113 (ptm160) cc_final: 0.7777 (ptp-170) REVERT: A 281 TYR cc_start: 0.8668 (t80) cc_final: 0.8442 (t80) REVERT: A 364 GLU cc_start: 0.7508 (tp30) cc_final: 0.7144 (tp30) REVERT: A 433 MET cc_start: 0.6412 (tpt) cc_final: 0.6135 (tpt) REVERT: B 236 ILE cc_start: 0.8519 (tp) cc_final: 0.8287 (tp) REVERT: B 241 GLN cc_start: 0.7813 (tp-100) cc_final: 0.7365 (tp-100) REVERT: B 281 TYR cc_start: 0.8514 (t80) cc_final: 0.8291 (t80) REVERT: B 386 GLN cc_start: 0.7897 (tp40) cc_final: 0.7364 (tp40) REVERT: B 414 GLN cc_start: 0.6935 (pm20) cc_final: 0.6685 (pm20) REVERT: C 236 ILE cc_start: 0.8483 (tp) cc_final: 0.8259 (tp) REVERT: C 241 GLN cc_start: 0.7809 (mm-40) cc_final: 0.7431 (mm-40) REVERT: C 297 ILE cc_start: 0.8710 (mm) cc_final: 0.8474 (mm) REVERT: C 343 LYS cc_start: 0.8282 (tptm) cc_final: 0.7982 (tptt) REVERT: C 344 GLN cc_start: 0.7674 (tm-30) cc_final: 0.7454 (tm-30) REVERT: C 370 GLN cc_start: 0.7404 (mm-40) cc_final: 0.7189 (mm-40) REVERT: C 386 GLN cc_start: 0.7955 (tp40) cc_final: 0.7468 (tp40) REVERT: C 420 ASN cc_start: 0.8207 (t0) cc_final: 0.7902 (t0) REVERT: C 426 ARG cc_start: 0.6870 (tmt170) cc_final: 0.6620 (tmt170) REVERT: D 236 ILE cc_start: 0.8530 (tp) cc_final: 0.8277 (tp) REVERT: D 251 LEU cc_start: 0.8277 (tp) cc_final: 0.8001 (tp) REVERT: D 305 GLN cc_start: 0.7756 (tp-100) cc_final: 0.7156 (tp-100) REVERT: D 354 GLN cc_start: 0.7047 (mt0) cc_final: 0.6846 (mt0) REVERT: D 396 GLU cc_start: 0.7386 (tm-30) cc_final: 0.6996 (tm-30) REVERT: D 433 MET cc_start: 0.6386 (mmp) cc_final: 0.5979 (mmp) REVERT: E 236 ILE cc_start: 0.8710 (tp) cc_final: 0.8468 (tp) REVERT: E 237 GLN cc_start: 0.7491 (pp30) cc_final: 0.7185 (pp30) REVERT: E 269 GLN cc_start: 0.7611 (mt0) cc_final: 0.7306 (mt0) REVERT: E 304 TYR cc_start: 0.7751 (m-80) cc_final: 0.7225 (m-80) REVERT: E 343 LYS cc_start: 0.8040 (tptm) cc_final: 0.7672 (tptp) REVERT: E 410 ARG cc_start: 0.7321 (tmm160) cc_final: 0.7102 (tmm160) REVERT: E 414 GLN cc_start: 0.6948 (pp30) cc_final: 0.6705 (pp30) REVERT: E 433 MET cc_start: 0.5903 (ttm) cc_final: 0.5437 (ttm) REVERT: F 236 ILE cc_start: 0.8690 (tp) cc_final: 0.8412 (tp) REVERT: F 238 GLN cc_start: 0.8052 (tp40) cc_final: 0.7759 (tp40) REVERT: F 241 GLN cc_start: 0.7494 (mm-40) cc_final: 0.7140 (mm-40) REVERT: F 251 LEU cc_start: 0.8178 (mp) cc_final: 0.7970 (mm) REVERT: F 343 LYS cc_start: 0.8060 (tptp) cc_final: 0.7588 (tptp) REVERT: F 414 GLN cc_start: 0.7416 (pp30) cc_final: 0.6385 (pp30) REVERT: F 420 ASN cc_start: 0.7709 (t0) cc_final: 0.7493 (t0) REVERT: G 237 GLN cc_start: 0.7606 (pp30) cc_final: 0.7359 (pp30) REVERT: G 287 HIS cc_start: 0.7017 (t-170) cc_final: 0.6655 (t-170) REVERT: G 321 ARG cc_start: 0.7473 (ttt90) cc_final: 0.7053 (ttt90) REVERT: G 323 LEU cc_start: 0.8362 (tp) cc_final: 0.8039 (tt) REVERT: G 385 SER cc_start: 0.8107 (m) cc_final: 0.7435 (p) REVERT: G 386 GLN cc_start: 0.7945 (tp40) cc_final: 0.7567 (tp40) REVERT: G 426 ARG cc_start: 0.7615 (tmt170) cc_final: 0.7199 (tmt170) REVERT: H 237 GLN cc_start: 0.7590 (pp30) cc_final: 0.7363 (pp30) REVERT: H 281 TYR cc_start: 0.8516 (t80) cc_final: 0.8260 (t80) REVERT: H 343 LYS cc_start: 0.8094 (tptm) cc_final: 0.7772 (tptp) REVERT: H 371 ARG cc_start: 0.7010 (ttm110) cc_final: 0.6511 (ttm110) REVERT: H 396 GLU cc_start: 0.6898 (tm-30) cc_final: 0.6489 (tm-30) REVERT: H 433 MET cc_start: 0.6256 (ttm) cc_final: 0.5886 (ttm) outliers start: 37 outliers final: 29 residues processed: 486 average time/residue: 0.3168 time to fit residues: 204.4968 Evaluate side-chains 491 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 462 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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 84 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 165 optimal weight: 0.4980 chunk 136 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 52 optimal weight: 0.2980 chunk 122 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN A 390 HIS ** 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 241 GLN ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 ASN G 269 GLN ** G 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 305 GLN ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.1909 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= 0.177 Angle : 0.559 7.703 17451 Z= 0.288 Chirality : 0.036 0.148 1878 Planarity : 0.004 0.040 2311 Dihedral : 4.564 54.060 1869 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.04 % Allowed : 21.33 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.20), residues: 1664 helix: 0.75 (0.14), residues: 1392 sheet: None (None), residues: 0 loop : -1.20 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 377 HIS 0.008 0.001 HIS E 289 PHE 0.019 0.001 PHE H 250 TYR 0.024 0.002 TYR G 281 ARG 0.009 0.000 ARG F 388 *********************** 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 531 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 482 time to evaluate : 1.344 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: 0.7714 (pp30) cc_final: 0.7434 (pp30) REVERT: A 238 GLN cc_start: 0.8574 (tp40) cc_final: 0.8325 (tp40) REVERT: A 241 GLN cc_start: 0.7837 (tp-100) cc_final: 0.7348 (tp-100) REVERT: A 274 ARG cc_start: 0.8111 (ptm160) cc_final: 0.7800 (ptm160) REVERT: A 281 TYR cc_start: 0.8648 (t80) cc_final: 0.8429 (t80) REVERT: A 351 ARG cc_start: 0.7173 (ttm-80) cc_final: 0.6770 (ttm-80) REVERT: A 364 GLU cc_start: 0.7572 (tp30) cc_final: 0.7179 (tp30) REVERT: A 433 MET cc_start: 0.6397 (tpt) cc_final: 0.6131 (tpt) REVERT: B 236 ILE cc_start: 0.8538 (tp) cc_final: 0.8273 (tp) REVERT: B 239 LEU cc_start: 0.8544 (tp) cc_final: 0.8304 (tp) REVERT: B 241 GLN cc_start: 0.7809 (tp-100) cc_final: 0.7196 (tp-100) REVERT: B 274 ARG cc_start: 0.8175 (ptm160) cc_final: 0.7501 (ptm160) REVERT: B 386 GLN cc_start: 0.7953 (tp40) cc_final: 0.7718 (tp40) REVERT: B 414 GLN cc_start: 0.6830 (OUTLIER) cc_final: 0.6371 (pm20) REVERT: C 236 ILE cc_start: 0.8472 (tp) cc_final: 0.8234 (tp) REVERT: C 241 GLN cc_start: 0.7771 (mm-40) cc_final: 0.7472 (mm-40) REVERT: C 343 LYS cc_start: 0.8275 (tptm) cc_final: 0.8047 (tptt) REVERT: C 344 GLN cc_start: 0.7751 (tm-30) cc_final: 0.7390 (tm-30) REVERT: D 236 ILE cc_start: 0.8530 (tp) cc_final: 0.8279 (tp) REVERT: D 251 LEU cc_start: 0.8316 (tp) cc_final: 0.8023 (tp) REVERT: D 305 GLN cc_start: 0.7775 (tp-100) cc_final: 0.7130 (tp-100) REVERT: D 337 ARG cc_start: 0.7615 (mpt180) cc_final: 0.6885 (mpt180) REVERT: D 385 SER cc_start: 0.8275 (m) cc_final: 0.7534 (t) REVERT: D 396 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6942 (tm-30) REVERT: D 433 MET cc_start: 0.6531 (mmp) cc_final: 0.6196 (mmp) REVERT: E 236 ILE cc_start: 0.8724 (tp) cc_final: 0.8455 (tp) REVERT: E 237 GLN cc_start: 0.7546 (pp30) cc_final: 0.7193 (pp30) REVERT: E 269 GLN cc_start: 0.7528 (mt0) cc_final: 0.7254 (mt0) REVERT: E 304 TYR cc_start: 0.7796 (m-80) cc_final: 0.7315 (m-80) REVERT: E 343 LYS cc_start: 0.8011 (tptm) cc_final: 0.7720 (tptp) REVERT: E 414 GLN cc_start: 0.6963 (pp30) cc_final: 0.6698 (pp30) REVERT: E 433 MET cc_start: 0.5894 (ttm) cc_final: 0.5406 (ttm) REVERT: F 236 ILE cc_start: 0.8712 (tp) cc_final: 0.8397 (tp) REVERT: F 241 GLN cc_start: 0.7518 (mm-40) cc_final: 0.7287 (mm-40) REVERT: F 251 LEU cc_start: 0.8244 (mp) cc_final: 0.7971 (mm) REVERT: F 343 LYS cc_start: 0.8050 (tptp) cc_final: 0.7513 (tptp) REVERT: G 237 GLN cc_start: 0.7625 (pp30) cc_final: 0.7376 (pp30) REVERT: G 287 HIS cc_start: 0.6892 (t-170) cc_final: 0.6529 (t-170) REVERT: G 321 ARG cc_start: 0.7462 (ttt90) cc_final: 0.7036 (ttt90) REVERT: G 323 LEU cc_start: 0.8368 (tp) cc_final: 0.8052 (tt) REVERT: G 385 SER cc_start: 0.8107 (m) cc_final: 0.7467 (p) REVERT: G 386 GLN cc_start: 0.7956 (tp40) cc_final: 0.7592 (tp40) REVERT: G 426 ARG cc_start: 0.7621 (tmt170) cc_final: 0.7208 (tmt170) REVERT: H 237 GLN cc_start: 0.7639 (pp30) cc_final: 0.7316 (pp30) REVERT: H 281 TYR cc_start: 0.8481 (t80) cc_final: 0.8209 (t80) REVERT: H 304 TYR cc_start: 0.7814 (m-80) cc_final: 0.7313 (m-80) REVERT: H 343 LYS cc_start: 0.8001 (tptm) cc_final: 0.7782 (tptp) REVERT: H 371 ARG cc_start: 0.6980 (ttm110) cc_final: 0.6495 (ttm110) REVERT: H 386 GLN cc_start: 0.8244 (tp40) cc_final: 0.7899 (tp-100) REVERT: H 396 GLU cc_start: 0.6904 (tm-30) cc_final: 0.6592 (tm-30) REVERT: H 433 MET cc_start: 0.6331 (ttm) cc_final: 0.5928 (ttm) outliers start: 49 outliers final: 33 residues processed: 490 average time/residue: 0.3208 time to fit residues: 208.4725 Evaluate side-chains 504 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 470 time to evaluate : 1.413 ------------------------------------------------------------------------------- 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 289 HIS Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain C residue 337 ARG 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 385 SER 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 251 LEU 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 344 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 72 optimal weight: 0.0980 chunk 102 optimal weight: 0.9980 chunk 153 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 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 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 HIS ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 289 HIS E 310 GLN ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 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 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 280 GLN H 289 HIS H 310 GLN ** H 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12910 Z= 0.194 Angle : 0.560 7.317 17451 Z= 0.290 Chirality : 0.036 0.159 1878 Planarity : 0.004 0.040 2311 Dihedral : 4.279 53.470 1865 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.11 % Allowed : 23.64 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.21), residues: 1664 helix: 0.81 (0.14), residues: 1392 sheet: None (None), residues: 0 loop : -1.21 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP F 377 HIS 0.002 0.001 HIS E 390 PHE 0.013 0.001 PHE B 356 TYR 0.022 0.002 TYR G 281 ARG 0.005 0.000 ARG F 388 *********************** 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 : 1.393 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: symmetry clash REVERT: A 237 GLN cc_start: 0.7763 (pp30) cc_final: 0.7402 (pp30) REVERT: A 241 GLN cc_start: 0.7778 (tp-100) cc_final: 0.7498 (tp-100) REVERT: A 274 ARG cc_start: 0.8088 (ptm160) cc_final: 0.7760 (ptp-170) REVERT: A 278 LYS cc_start: 0.8074 (mtmm) cc_final: 0.7495 (mtmm) REVERT: A 343 LYS cc_start: 0.8211 (tptp) cc_final: 0.7656 (tptp) REVERT: A 385 SER cc_start: 0.8053 (m) cc_final: 0.7595 (p) REVERT: A 396 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7230 (tm-30) REVERT: A 433 MET cc_start: 0.6347 (tpt) cc_final: 0.6139 (tpt) REVERT: B 236 ILE cc_start: 0.8541 (tp) cc_final: 0.8270 (tp) REVERT: B 241 GLN cc_start: 0.7812 (tp-100) cc_final: 0.7031 (tp-100) REVERT: B 274 ARG cc_start: 0.8166 (ptm160) cc_final: 0.7421 (ptm160) REVERT: B 386 GLN cc_start: 0.8001 (tp40) cc_final: 0.7635 (tp40) REVERT: C 236 ILE cc_start: 0.8470 (tp) cc_final: 0.8224 (tp) REVERT: C 237 GLN cc_start: 0.7587 (pp30) cc_final: 0.7240 (pp30) REVERT: C 241 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7582 (mm-40) REVERT: C 343 LYS cc_start: 0.8294 (tptm) cc_final: 0.8045 (tptt) REVERT: C 344 GLN cc_start: 0.7864 (tm-30) cc_final: 0.7503 (tm-30) REVERT: C 370 GLN cc_start: 0.7392 (mm-40) cc_final: 0.7148 (mm-40) REVERT: D 236 ILE cc_start: 0.8552 (tp) cc_final: 0.8293 (tp) REVERT: D 251 LEU cc_start: 0.8350 (tp) cc_final: 0.8065 (tp) REVERT: D 274 ARG cc_start: 0.8024 (ptm160) cc_final: 0.7784 (mtp85) REVERT: D 281 TYR cc_start: 0.8435 (t80) cc_final: 0.8154 (t80) REVERT: D 305 GLN cc_start: 0.7853 (tp-100) cc_final: 0.7240 (tp-100) REVERT: D 337 ARG cc_start: 0.7629 (mpt180) cc_final: 0.6904 (mpt180) REVERT: D 385 SER cc_start: 0.8253 (m) cc_final: 0.7531 (t) REVERT: D 386 GLN cc_start: 0.8035 (tp40) cc_final: 0.7621 (tp40) REVERT: D 396 GLU cc_start: 0.7364 (tm-30) cc_final: 0.6937 (tm-30) REVERT: D 433 MET cc_start: 0.6564 (mmp) cc_final: 0.6281 (mmp) REVERT: E 236 ILE cc_start: 0.8733 (tp) cc_final: 0.8464 (tp) REVERT: E 237 GLN cc_start: 0.7574 (pp30) cc_final: 0.7202 (pp30) REVERT: E 241 GLN cc_start: 0.8013 (mm110) cc_final: 0.7404 (tp40) REVERT: E 269 GLN cc_start: 0.7524 (mt0) cc_final: 0.7260 (mt0) REVERT: E 274 ARG cc_start: 0.8295 (ptm160) cc_final: 0.7650 (ptp-110) REVERT: E 343 LYS cc_start: 0.8025 (tptm) cc_final: 0.7728 (tptp) REVERT: E 386 GLN cc_start: 0.8376 (tp40) cc_final: 0.8139 (tp-100) REVERT: E 433 MET cc_start: 0.6026 (ttm) cc_final: 0.5456 (ttm) REVERT: F 236 ILE cc_start: 0.8723 (tp) cc_final: 0.8416 (tp) REVERT: F 241 GLN cc_start: 0.7515 (mm-40) cc_final: 0.7278 (mm-40) REVERT: F 251 LEU cc_start: 0.8271 (mp) cc_final: 0.8006 (mm) REVERT: F 343 LYS cc_start: 0.8057 (tptp) cc_final: 0.7744 (tptt) REVERT: G 237 GLN cc_start: 0.7682 (pp30) cc_final: 0.7370 (pp30) REVERT: G 321 ARG cc_start: 0.7634 (ttt90) cc_final: 0.7121 (ttt90) REVERT: G 323 LEU cc_start: 0.8384 (tp) cc_final: 0.8019 (tt) REVERT: G 385 SER cc_start: 0.8196 (m) cc_final: 0.7528 (p) REVERT: G 386 GLN cc_start: 0.7982 (tp40) cc_final: 0.7620 (tp40) REVERT: G 426 ARG cc_start: 0.7585 (tmt170) cc_final: 0.7183 (tmt170) REVERT: H 237 GLN cc_start: 0.7656 (pp30) cc_final: 0.7300 (pp30) REVERT: H 281 TYR cc_start: 0.8500 (t80) cc_final: 0.8286 (t80) REVERT: H 304 TYR cc_start: 0.7802 (m-80) cc_final: 0.7273 (m-80) REVERT: H 321 ARG cc_start: 0.7370 (tmt-80) cc_final: 0.6538 (tmt-80) REVERT: H 343 LYS cc_start: 0.8123 (tptm) cc_final: 0.7826 (tptp) REVERT: H 396 GLU cc_start: 0.6941 (tm-30) cc_final: 0.6565 (tm-30) REVERT: H 433 MET cc_start: 0.6476 (ttm) cc_final: 0.6111 (ttm) outliers start: 62 outliers final: 43 residues processed: 481 average time/residue: 0.3248 time to fit residues: 207.0484 Evaluate side-chains 510 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 466 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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 289 HIS Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 GLN 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 C residue 405 LEU 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 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 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 135 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 269 GLN B 287 HIS 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 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 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 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 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 280 GLN ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12910 Z= 0.272 Angle : 0.583 7.296 17451 Z= 0.311 Chirality : 0.038 0.175 1878 Planarity : 0.004 0.041 2311 Dihedral : 4.248 20.966 1863 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.77 % Allowed : 24.55 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.20), residues: 1664 helix: 0.75 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -1.88 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP D 377 HIS 0.010 0.001 HIS H 289 PHE 0.015 0.001 PHE E 265 TYR 0.022 0.002 TYR G 281 ARG 0.004 0.000 ARG F 388 *********************** 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 544 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 474 time to evaluate : 1.313 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: 0.7799 (pp30) cc_final: 0.7441 (pp30) REVERT: A 241 GLN cc_start: 0.7761 (tp-100) cc_final: 0.7245 (tp-100) REVERT: A 274 ARG cc_start: 0.8159 (ptm160) cc_final: 0.7574 (mtp85) REVERT: A 278 LYS cc_start: 0.8115 (mtmm) cc_final: 0.7466 (mtmm) REVERT: A 281 TYR cc_start: 0.8663 (t80) cc_final: 0.8434 (t80) REVERT: A 343 LYS cc_start: 0.8258 (tptp) cc_final: 0.7705 (tptp) REVERT: A 364 GLU cc_start: 0.7706 (tp30) cc_final: 0.7329 (tp30) REVERT: A 378 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8074 (tp) REVERT: A 385 SER cc_start: 0.8093 (m) cc_final: 0.7628 (p) REVERT: A 396 GLU cc_start: 0.7632 (pp20) cc_final: 0.7336 (tm-30) REVERT: A 410 ARG cc_start: 0.7408 (ptt180) cc_final: 0.7043 (pmt170) REVERT: A 414 GLN cc_start: 0.7229 (pp30) cc_final: 0.6872 (pp30) REVERT: B 236 ILE cc_start: 0.8550 (tp) cc_final: 0.8276 (tp) REVERT: B 241 GLN cc_start: 0.7813 (tp-100) cc_final: 0.6882 (tp-100) REVERT: B 274 ARG cc_start: 0.8145 (ptm160) cc_final: 0.7378 (ptm160) REVERT: C 236 ILE cc_start: 0.8474 (tp) cc_final: 0.8234 (tp) REVERT: C 237 GLN cc_start: 0.7633 (pp30) cc_final: 0.7242 (pp30) REVERT: C 241 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7531 (mm-40) REVERT: C 343 LYS cc_start: 0.8365 (tptm) cc_final: 0.8146 (tptt) REVERT: C 344 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7578 (tm-30) REVERT: C 370 GLN cc_start: 0.7423 (mm-40) cc_final: 0.7098 (mm-40) REVERT: D 236 ILE cc_start: 0.8564 (tp) cc_final: 0.8295 (tp) REVERT: D 244 VAL cc_start: 0.8814 (OUTLIER) cc_final: 0.8346 (p) REVERT: D 274 ARG cc_start: 0.8105 (ptm160) cc_final: 0.7901 (mtp85) REVERT: D 337 ARG cc_start: 0.7666 (mpt180) cc_final: 0.6928 (mpt180) REVERT: D 385 SER cc_start: 0.8189 (m) cc_final: 0.7453 (t) REVERT: D 386 GLN cc_start: 0.8092 (tp40) cc_final: 0.7874 (tp-100) REVERT: D 396 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6902 (tm-30) REVERT: D 433 MET cc_start: 0.6636 (mmp) cc_final: 0.6403 (mmp) REVERT: E 236 ILE cc_start: 0.8745 (tp) cc_final: 0.8481 (tp) REVERT: E 237 GLN cc_start: 0.7612 (pp30) cc_final: 0.7194 (pp30) REVERT: E 269 GLN cc_start: 0.7563 (mt0) cc_final: 0.7274 (mt0) REVERT: E 343 LYS cc_start: 0.8131 (tptm) cc_final: 0.7785 (tptp) REVERT: E 387 SER cc_start: 0.8560 (m) cc_final: 0.8112 (p) REVERT: E 396 GLU cc_start: 0.7824 (tt0) cc_final: 0.7567 (tt0) REVERT: E 433 MET cc_start: 0.6159 (ttm) cc_final: 0.5596 (ttm) REVERT: F 236 ILE cc_start: 0.8751 (tp) cc_final: 0.8444 (tp) REVERT: F 241 GLN cc_start: 0.7503 (mm-40) cc_final: 0.7186 (mm-40) REVERT: F 251 LEU cc_start: 0.8297 (mp) cc_final: 0.8060 (mm) REVERT: F 280 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7510 (mt0) REVERT: F 297 ILE cc_start: 0.8501 (mm) cc_final: 0.8234 (mm) REVERT: F 321 ARG cc_start: 0.7475 (tmt-80) cc_final: 0.6686 (tmt-80) REVERT: F 343 LYS cc_start: 0.8114 (tptp) cc_final: 0.7790 (tptp) REVERT: G 237 GLN cc_start: 0.7666 (pp30) cc_final: 0.7328 (pp30) REVERT: G 278 LYS cc_start: 0.8207 (mttt) cc_final: 0.7765 (mtmm) REVERT: G 293 THR cc_start: 0.7986 (m) cc_final: 0.7486 (p) REVERT: G 321 ARG cc_start: 0.7654 (ttt90) cc_final: 0.7163 (ttt90) REVERT: G 323 LEU cc_start: 0.8412 (tp) cc_final: 0.8051 (tt) REVERT: G 385 SER cc_start: 0.8212 (m) cc_final: 0.7528 (p) REVERT: G 426 ARG cc_start: 0.7578 (tmt170) cc_final: 0.7219 (tmt170) REVERT: H 237 GLN cc_start: 0.7655 (pp30) cc_final: 0.7295 (pp30) REVERT: H 281 TYR cc_start: 0.8559 (t80) cc_final: 0.8337 (t80) REVERT: H 321 ARG cc_start: 0.7407 (tmt-80) cc_final: 0.6592 (tmt-80) REVERT: H 343 LYS cc_start: 0.8241 (tptm) cc_final: 0.7856 (tptp) REVERT: H 385 SER cc_start: 0.8095 (m) cc_final: 0.7517 (t) REVERT: H 387 SER cc_start: 0.8348 (m) cc_final: 0.7798 (p) REVERT: H 433 MET cc_start: 0.6622 (ttm) cc_final: 0.6297 (ttm) outliers start: 70 outliers final: 50 residues processed: 493 average time/residue: 0.3387 time to fit residues: 221.0798 Evaluate side-chains 523 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 470 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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 242 LEU 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 401 VAL Chi-restraints excluded: chain B residue 414 GLN 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 388 ARG Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 405 LEU 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 D residue 426 ARG 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 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 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 54 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 162 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 269 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 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 305 GLN 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 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 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2696 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= 0.210 Angle : 0.581 9.815 17451 Z= 0.300 Chirality : 0.037 0.164 1878 Planarity : 0.004 0.043 2311 Dihedral : 4.201 20.509 1863 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 5.44 % Allowed : 26.85 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.20), residues: 1664 helix: 0.78 (0.14), residues: 1392 sheet: None (None), residues: 0 loop : -1.82 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 377 HIS 0.002 0.001 HIS G 287 PHE 0.012 0.001 PHE B 265 TYR 0.023 0.002 TYR G 281 ARG 0.004 0.000 ARG F 388 *********************** 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 544 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 478 time to evaluate : 1.535 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: A 237 GLN cc_start: 0.7801 (pp30) cc_final: 0.7423 (pp30) REVERT: A 241 GLN cc_start: 0.7746 (tp-100) cc_final: 0.7258 (tp-100) REVERT: A 244 VAL cc_start: 0.8785 (p) cc_final: 0.8374 (p) REVERT: A 274 ARG cc_start: 0.8133 (ptm160) cc_final: 0.7618 (mtp85) REVERT: A 278 LYS cc_start: 0.8086 (mtmm) cc_final: 0.7395 (mtmm) REVERT: A 281 TYR cc_start: 0.8660 (t80) cc_final: 0.8430 (t80) REVERT: A 343 LYS cc_start: 0.8235 (tptp) cc_final: 0.7668 (tptp) REVERT: A 351 ARG cc_start: 0.7337 (ttm-80) cc_final: 0.6833 (ttm-80) REVERT: A 364 GLU cc_start: 0.7680 (tp30) cc_final: 0.7292 (tp30) REVERT: A 378 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8043 (tp) REVERT: A 385 SER cc_start: 0.8067 (m) cc_final: 0.7618 (p) REVERT: A 410 ARG cc_start: 0.7359 (ptt180) cc_final: 0.7100 (pmt170) REVERT: A 414 GLN cc_start: 0.7157 (pp30) cc_final: 0.6930 (pp30) REVERT: B 236 ILE cc_start: 0.8548 (tp) cc_final: 0.8291 (tp) REVERT: B 241 GLN cc_start: 0.7833 (tp-100) cc_final: 0.6864 (tp-100) REVERT: B 274 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7248 (ptm160) REVERT: B 378 LEU cc_start: 0.8516 (tt) cc_final: 0.8202 (pp) REVERT: C 236 ILE cc_start: 0.8488 (tp) cc_final: 0.8239 (tp) REVERT: C 237 GLN cc_start: 0.7615 (pp30) cc_final: 0.7253 (pp30) REVERT: C 241 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7500 (mm-40) REVERT: C 343 LYS cc_start: 0.8387 (tptm) cc_final: 0.8116 (tptt) REVERT: C 344 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7580 (tm-30) REVERT: C 370 GLN cc_start: 0.7402 (mm-40) cc_final: 0.7082 (mm-40) REVERT: C 385 SER cc_start: 0.8136 (m) cc_final: 0.7522 (p) REVERT: D 236 ILE cc_start: 0.8556 (tp) cc_final: 0.8299 (tp) REVERT: D 244 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8541 (p) REVERT: D 337 ARG cc_start: 0.7672 (mpt180) cc_final: 0.6888 (mpt180) REVERT: D 385 SER cc_start: 0.8189 (m) cc_final: 0.7432 (t) REVERT: D 386 GLN cc_start: 0.8123 (tp40) cc_final: 0.7865 (tp-100) REVERT: D 396 GLU cc_start: 0.7362 (tm-30) cc_final: 0.6863 (tm-30) REVERT: D 433 MET cc_start: 0.6658 (mmp) cc_final: 0.6412 (mmp) REVERT: E 236 ILE cc_start: 0.8724 (tp) cc_final: 0.8449 (tp) REVERT: E 237 GLN cc_start: 0.7608 (pp30) cc_final: 0.7188 (pp30) REVERT: E 269 GLN cc_start: 0.7549 (mt0) cc_final: 0.7272 (mt0) REVERT: E 343 LYS cc_start: 0.8071 (tptm) cc_final: 0.7745 (tptp) REVERT: E 387 SER cc_start: 0.8569 (m) cc_final: 0.8144 (p) REVERT: E 396 GLU cc_start: 0.7766 (tt0) cc_final: 0.7540 (tt0) REVERT: E 433 MET cc_start: 0.6144 (ttm) cc_final: 0.5588 (ttm) REVERT: F 236 ILE cc_start: 0.8741 (tp) cc_final: 0.8419 (tp) REVERT: F 241 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7185 (mm-40) REVERT: F 251 LEU cc_start: 0.8291 (mp) cc_final: 0.8060 (mm) REVERT: F 297 ILE cc_start: 0.8475 (mm) cc_final: 0.8226 (mm) REVERT: F 321 ARG cc_start: 0.7480 (tmt-80) cc_final: 0.6735 (tmt-80) REVERT: F 343 LYS cc_start: 0.8139 (tptp) cc_final: 0.7778 (tptp) REVERT: F 357 LEU cc_start: 0.7630 (tp) cc_final: 0.7417 (tp) REVERT: G 237 GLN cc_start: 0.7651 (pp30) cc_final: 0.7310 (pp30) REVERT: G 278 LYS cc_start: 0.8194 (mttt) cc_final: 0.7720 (mtmm) REVERT: G 287 HIS cc_start: 0.6830 (m-70) cc_final: 0.6609 (m170) REVERT: G 293 THR cc_start: 0.8012 (m) cc_final: 0.7769 (p) REVERT: G 321 ARG cc_start: 0.7660 (ttt90) cc_final: 0.7167 (ttt90) REVERT: G 323 LEU cc_start: 0.8422 (tp) cc_final: 0.8030 (tt) REVERT: G 385 SER cc_start: 0.8180 (m) cc_final: 0.7498 (p) REVERT: G 386 GLN cc_start: 0.8135 (tp40) cc_final: 0.7701 (tp40) REVERT: G 426 ARG cc_start: 0.7576 (tmt170) cc_final: 0.7195 (tmt170) REVERT: H 237 GLN cc_start: 0.7648 (pp30) cc_final: 0.7288 (pp30) REVERT: H 281 TYR cc_start: 0.8512 (t80) cc_final: 0.8278 (t80) REVERT: H 343 LYS cc_start: 0.8196 (tptm) cc_final: 0.7838 (tptp) REVERT: H 385 SER cc_start: 0.8052 (m) cc_final: 0.7419 (t) REVERT: H 387 SER cc_start: 0.8345 (m) cc_final: 0.7787 (p) REVERT: H 388 ARG cc_start: 0.7037 (ttt90) cc_final: 0.6816 (ttt90) REVERT: H 433 MET cc_start: 0.6817 (ttm) cc_final: 0.6506 (ttm) outliers start: 66 outliers final: 51 residues processed: 494 average time/residue: 0.3389 time to fit residues: 222.5269 Evaluate side-chains 526 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 472 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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 266 SER Chi-restraints excluded: chain B residue 274 ARG 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 B residue 414 GLN 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 405 LEU 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 E residue 288 GLU 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 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 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 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 156 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 118 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 90 optimal weight: 0.0980 chunk 161 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 289 HIS ** F 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 289 HIS G 310 GLN G 414 GLN H 289 HIS ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12910 Z= 0.190 Angle : 0.577 7.978 17451 Z= 0.295 Chirality : 0.036 0.164 1878 Planarity : 0.004 0.043 2311 Dihedral : 4.154 20.038 1863 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 5.52 % Allowed : 27.68 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.20), residues: 1664 helix: 0.87 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -1.81 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 377 HIS 0.006 0.001 HIS E 289 PHE 0.011 0.001 PHE H 265 TYR 0.026 0.002 TYR G 281 ARG 0.005 0.000 ARG E 295 *********************** 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 543 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 476 time to evaluate : 1.617 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: 0.7811 (pp30) cc_final: 0.7428 (pp30) REVERT: A 241 GLN cc_start: 0.7729 (tp-100) cc_final: 0.7247 (tp-100) REVERT: A 244 VAL cc_start: 0.8782 (p) cc_final: 0.8485 (p) REVERT: A 274 ARG cc_start: 0.8132 (ptm160) cc_final: 0.7616 (mtp85) REVERT: A 278 LYS cc_start: 0.8076 (mtmm) cc_final: 0.7383 (mtmm) REVERT: A 281 TYR cc_start: 0.8663 (t80) cc_final: 0.8418 (t80) REVERT: A 343 LYS cc_start: 0.8217 (tptp) cc_final: 0.7654 (tptp) REVERT: A 364 GLU cc_start: 0.7667 (tp30) cc_final: 0.7254 (tp30) REVERT: A 378 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8067 (tp) REVERT: A 385 SER cc_start: 0.8068 (m) cc_final: 0.7618 (p) REVERT: A 410 ARG cc_start: 0.7345 (ptt180) cc_final: 0.7079 (pmt170) REVERT: B 236 ILE cc_start: 0.8544 (tp) cc_final: 0.8281 (tp) REVERT: B 241 GLN cc_start: 0.7834 (tp-100) cc_final: 0.6879 (tp-100) REVERT: B 274 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7276 (ptm160) REVERT: B 378 LEU cc_start: 0.8496 (tt) cc_final: 0.8192 (pp) REVERT: C 236 ILE cc_start: 0.8486 (tp) cc_final: 0.8227 (tp) REVERT: C 237 GLN cc_start: 0.7617 (pp30) cc_final: 0.7240 (pp30) REVERT: C 343 LYS cc_start: 0.8377 (tptm) cc_final: 0.8118 (tptt) REVERT: C 344 GLN cc_start: 0.7905 (tm-30) cc_final: 0.7603 (tm-30) REVERT: C 385 SER cc_start: 0.8136 (m) cc_final: 0.7525 (p) REVERT: D 236 ILE cc_start: 0.8566 (tp) cc_final: 0.8298 (tp) REVERT: D 244 VAL cc_start: 0.8748 (OUTLIER) cc_final: 0.8524 (p) REVERT: D 319 TYR cc_start: 0.7428 (t80) cc_final: 0.7199 (t80) REVERT: D 337 ARG cc_start: 0.7630 (mpt180) cc_final: 0.6850 (mpt180) REVERT: D 385 SER cc_start: 0.8187 (m) cc_final: 0.7404 (t) REVERT: D 386 GLN cc_start: 0.8147 (tp40) cc_final: 0.7837 (tp-100) REVERT: D 396 GLU cc_start: 0.7348 (tm-30) cc_final: 0.6909 (tm-30) REVERT: D 414 GLN cc_start: 0.6982 (pp30) cc_final: 0.6604 (pp30) REVERT: D 433 MET cc_start: 0.6654 (mmp) cc_final: 0.6422 (mmp) REVERT: E 236 ILE cc_start: 0.8706 (tp) cc_final: 0.8422 (tp) REVERT: E 237 GLN cc_start: 0.7599 (pp30) cc_final: 0.7161 (pp30) REVERT: E 269 GLN cc_start: 0.7532 (mt0) cc_final: 0.7155 (mt0) REVERT: E 343 LYS cc_start: 0.8061 (tptm) cc_final: 0.7730 (tptp) REVERT: E 363 LYS cc_start: 0.8093 (tmtt) cc_final: 0.7706 (tmtt) REVERT: E 387 SER cc_start: 0.8524 (m) cc_final: 0.8159 (p) REVERT: E 433 MET cc_start: 0.6177 (ttm) cc_final: 0.5615 (ttm) REVERT: F 236 ILE cc_start: 0.8764 (tp) cc_final: 0.8440 (tp) REVERT: F 241 GLN cc_start: 0.7491 (mm-40) cc_final: 0.6989 (mm-40) REVERT: F 251 LEU cc_start: 0.8281 (mp) cc_final: 0.8053 (mm) REVERT: F 274 ARG cc_start: 0.8350 (ptm160) cc_final: 0.7772 (ptm160) REVERT: F 321 ARG cc_start: 0.7471 (tmt-80) cc_final: 0.6707 (tmt-80) REVERT: F 343 LYS cc_start: 0.8120 (tptp) cc_final: 0.7739 (tptp) REVERT: F 357 LEU cc_start: 0.7639 (tp) cc_final: 0.7426 (tp) REVERT: F 433 MET cc_start: 0.6847 (mtm) cc_final: 0.6322 (mtm) REVERT: G 237 GLN cc_start: 0.7664 (pp30) cc_final: 0.7300 (pp30) REVERT: G 278 LYS cc_start: 0.8189 (mttt) cc_final: 0.7601 (mtmm) REVERT: G 287 HIS cc_start: 0.6819 (m-70) cc_final: 0.6608 (m170) REVERT: G 293 THR cc_start: 0.8050 (m) cc_final: 0.7799 (p) REVERT: G 321 ARG cc_start: 0.7643 (ttt90) cc_final: 0.7161 (ttt180) REVERT: G 363 LYS cc_start: 0.8182 (tmtt) cc_final: 0.7573 (tmtt) REVERT: G 385 SER cc_start: 0.8185 (m) cc_final: 0.7516 (p) REVERT: G 426 ARG cc_start: 0.7563 (tmt170) cc_final: 0.7161 (tmt170) REVERT: H 237 GLN cc_start: 0.7640 (pp30) cc_final: 0.7252 (pp30) REVERT: H 281 TYR cc_start: 0.8506 (t80) cc_final: 0.8279 (t80) REVERT: H 304 TYR cc_start: 0.7738 (m-80) cc_final: 0.7221 (m-80) REVERT: H 343 LYS cc_start: 0.8188 (tptm) cc_final: 0.7809 (tptp) REVERT: H 363 LYS cc_start: 0.8046 (tmtt) cc_final: 0.7693 (tmtt) REVERT: H 396 GLU cc_start: 0.6963 (tm-30) cc_final: 0.6618 (tm-30) REVERT: H 433 MET cc_start: 0.6797 (ttm) cc_final: 0.6460 (ttm) outliers start: 67 outliers final: 54 residues processed: 488 average time/residue: 0.3567 time to fit residues: 231.9458 Evaluate side-chains 532 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 475 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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 242 LEU Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 274 ARG 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 401 VAL Chi-restraints excluded: chain B residue 414 GLN 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 388 ARG Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 405 LEU 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 426 ARG Chi-restraints excluded: chain E residue 241 GLN 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 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 Chi-restraints excluded: chain H residue 391 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 0.0270 chunk 102 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 332 ASN ** 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 316 GLN ** 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** H 289 HIS ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12910 Z= 0.202 Angle : 0.591 8.362 17451 Z= 0.302 Chirality : 0.037 0.161 1878 Planarity : 0.004 0.044 2311 Dihedral : 4.149 20.156 1863 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 5.68 % Allowed : 28.25 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.20), residues: 1664 helix: 0.90 (0.14), residues: 1376 sheet: None (None), residues: 0 loop : -1.34 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP F 377 HIS 0.003 0.001 HIS H 289 PHE 0.011 0.001 PHE H 265 TYR 0.024 0.002 TYR G 281 ARG 0.005 0.000 ARG E 295 *********************** 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 540 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 471 time to evaluate : 1.223 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: 0.7821 (pp30) cc_final: 0.7423 (pp30) REVERT: A 244 VAL cc_start: 0.8781 (p) cc_final: 0.8501 (p) REVERT: A 274 ARG cc_start: 0.8121 (ptm160) cc_final: 0.7808 (ptp-170) REVERT: A 278 LYS cc_start: 0.8086 (mtmm) cc_final: 0.7408 (mtmm) REVERT: A 281 TYR cc_start: 0.8667 (t80) cc_final: 0.8448 (t80) REVERT: A 343 LYS cc_start: 0.8236 (tptp) cc_final: 0.7647 (tptp) REVERT: A 351 ARG cc_start: 0.7327 (ttm-80) cc_final: 0.6815 (ttm-80) REVERT: A 364 GLU cc_start: 0.7632 (tp30) cc_final: 0.7261 (tp30) REVERT: A 378 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8052 (tp) REVERT: A 385 SER cc_start: 0.8084 (m) cc_final: 0.7624 (p) REVERT: A 410 ARG cc_start: 0.7368 (ptt180) cc_final: 0.7094 (pmt170) REVERT: B 236 ILE cc_start: 0.8543 (tp) cc_final: 0.8279 (tp) REVERT: B 241 GLN cc_start: 0.7833 (tp-100) cc_final: 0.6880 (tp-100) REVERT: B 274 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7273 (ptm160) REVERT: C 236 ILE cc_start: 0.8486 (tp) cc_final: 0.8215 (tp) REVERT: C 241 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7596 (tp40) REVERT: C 274 ARG cc_start: 0.8065 (ptp-110) cc_final: 0.7655 (mtp85) REVERT: C 343 LYS cc_start: 0.8384 (tptm) cc_final: 0.8101 (tptt) REVERT: C 344 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7608 (tm-30) REVERT: C 385 SER cc_start: 0.8094 (m) cc_final: 0.7448 (p) REVERT: D 236 ILE cc_start: 0.8567 (tp) cc_final: 0.8304 (tp) REVERT: D 244 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8519 (p) REVERT: D 337 ARG cc_start: 0.7592 (mpt180) cc_final: 0.6882 (mpt180) REVERT: D 385 SER cc_start: 0.8193 (m) cc_final: 0.7423 (t) REVERT: D 386 GLN cc_start: 0.8154 (tp40) cc_final: 0.7835 (tp-100) REVERT: D 396 GLU cc_start: 0.7343 (tm-30) cc_final: 0.6918 (tm-30) REVERT: D 433 MET cc_start: 0.6682 (mmp) cc_final: 0.6454 (mmp) REVERT: E 236 ILE cc_start: 0.8703 (tp) cc_final: 0.8418 (tp) REVERT: E 237 GLN cc_start: 0.7618 (pp30) cc_final: 0.7191 (pp30) REVERT: E 269 GLN cc_start: 0.7528 (mt0) cc_final: 0.7268 (mt0) REVERT: E 343 LYS cc_start: 0.8074 (tptm) cc_final: 0.7762 (tptp) REVERT: E 363 LYS cc_start: 0.8105 (tmtt) cc_final: 0.7708 (tmtt) REVERT: E 387 SER cc_start: 0.8502 (m) cc_final: 0.8163 (p) REVERT: E 396 GLU cc_start: 0.7785 (tt0) cc_final: 0.7479 (tt0) REVERT: E 433 MET cc_start: 0.6231 (ttm) cc_final: 0.5677 (ttm) REVERT: F 236 ILE cc_start: 0.8761 (tp) cc_final: 0.8426 (tp) REVERT: F 241 GLN cc_start: 0.7499 (mm-40) cc_final: 0.7042 (mm-40) REVERT: F 251 LEU cc_start: 0.8275 (mp) cc_final: 0.8031 (mm) REVERT: F 274 ARG cc_start: 0.8351 (ptm160) cc_final: 0.7770 (ptm160) REVERT: F 297 ILE cc_start: 0.8448 (mm) cc_final: 0.8230 (mm) REVERT: F 321 ARG cc_start: 0.7474 (tmt-80) cc_final: 0.6700 (tmt-80) REVERT: F 343 LYS cc_start: 0.8151 (tptp) cc_final: 0.7769 (tptp) REVERT: F 357 LEU cc_start: 0.7651 (tp) cc_final: 0.7425 (tp) REVERT: F 433 MET cc_start: 0.6861 (mtm) cc_final: 0.6325 (mtm) REVERT: G 237 GLN cc_start: 0.7672 (pp30) cc_final: 0.7311 (pp30) REVERT: G 278 LYS cc_start: 0.8204 (mttt) cc_final: 0.7618 (mtmm) REVERT: G 293 THR cc_start: 0.8034 (m) cc_final: 0.7775 (p) REVERT: G 321 ARG cc_start: 0.7645 (ttt90) cc_final: 0.7155 (ttt90) REVERT: G 385 SER cc_start: 0.8189 (m) cc_final: 0.7521 (p) REVERT: G 426 ARG cc_start: 0.7557 (tmt170) cc_final: 0.7165 (tmt170) REVERT: H 237 GLN cc_start: 0.7642 (pp30) cc_final: 0.7255 (pp30) REVERT: H 281 TYR cc_start: 0.8496 (t80) cc_final: 0.8294 (t80) REVERT: H 304 TYR cc_start: 0.7753 (m-80) cc_final: 0.7221 (m-80) REVERT: H 343 LYS cc_start: 0.8202 (tptm) cc_final: 0.7818 (tptp) REVERT: H 363 LYS cc_start: 0.8043 (tmtt) cc_final: 0.7680 (tmtt) REVERT: H 396 GLU cc_start: 0.6948 (tm-30) cc_final: 0.6654 (tm-30) REVERT: H 433 MET cc_start: 0.6810 (ttm) cc_final: 0.6454 (ttm) outliers start: 69 outliers final: 59 residues processed: 483 average time/residue: 0.3249 time to fit residues: 207.9619 Evaluate side-chains 532 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 470 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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 242 LEU 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 305 GLN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 GLN 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 C residue 405 LEU 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 E residue 241 GLN Chi-restraints excluded: chain E residue 251 LEU 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 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 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 Chi-restraints excluded: chain H residue 391 LEU Chi-restraints excluded: chain H residue 415 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 150 optimal weight: 0.5980 chunk 90 optimal weight: 0.0980 chunk 65 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 159 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 305 GLN 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 332 ASN ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 289 HIS F 312 HIS ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 287 HIS 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 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.2989 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= 0.188 Angle : 0.593 8.630 17451 Z= 0.301 Chirality : 0.036 0.156 1878 Planarity : 0.004 0.044 2311 Dihedral : 4.119 19.935 1863 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.35 % Allowed : 29.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.21), residues: 1664 helix: 0.94 (0.14), residues: 1376 sheet: None (None), residues: 0 loop : -1.35 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP B 377 HIS 0.006 0.001 HIS F 289 PHE 0.011 0.001 PHE C 268 TYR 0.025 0.002 TYR G 281 ARG 0.005 0.000 ARG E 295 *********************** 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 534 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 469 time to evaluate : 1.403 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: 0.7781 (pp30) cc_final: 0.7411 (pp30) REVERT: A 241 GLN cc_start: 0.7811 (tp-100) cc_final: 0.7585 (tp-100) REVERT: A 244 VAL cc_start: 0.8797 (p) cc_final: 0.8407 (p) REVERT: A 278 LYS cc_start: 0.8076 (mtmm) cc_final: 0.7387 (mtmm) REVERT: A 281 TYR cc_start: 0.8669 (t80) cc_final: 0.8456 (t80) REVERT: A 305 GLN cc_start: 0.8451 (tp40) cc_final: 0.8106 (tp40) REVERT: A 343 LYS cc_start: 0.8258 (tptp) cc_final: 0.7671 (tptp) REVERT: A 351 ARG cc_start: 0.7256 (ttm-80) cc_final: 0.6779 (ttm-80) REVERT: A 364 GLU cc_start: 0.7629 (tp30) cc_final: 0.7255 (tp30) REVERT: A 378 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8056 (tp) REVERT: A 385 SER cc_start: 0.8140 (m) cc_final: 0.7719 (p) REVERT: A 410 ARG cc_start: 0.7389 (ptt180) cc_final: 0.7094 (pmt170) REVERT: B 236 ILE cc_start: 0.8539 (tp) cc_final: 0.8276 (tp) REVERT: B 239 LEU cc_start: 0.8578 (tp) cc_final: 0.8344 (tp) REVERT: B 241 GLN cc_start: 0.7832 (tp-100) cc_final: 0.6908 (tp-100) REVERT: B 274 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7306 (ptm160) REVERT: C 236 ILE cc_start: 0.8472 (tp) cc_final: 0.8211 (tp) REVERT: C 241 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7692 (tp40) REVERT: C 343 LYS cc_start: 0.8358 (tptm) cc_final: 0.8088 (tptt) REVERT: C 344 GLN cc_start: 0.7873 (tm-30) cc_final: 0.7606 (tm-30) REVERT: C 385 SER cc_start: 0.8138 (m) cc_final: 0.7495 (p) REVERT: D 236 ILE cc_start: 0.8566 (tp) cc_final: 0.8297 (tp) REVERT: D 244 VAL cc_start: 0.8749 (OUTLIER) cc_final: 0.8523 (p) REVERT: D 337 ARG cc_start: 0.7623 (mpt180) cc_final: 0.6921 (mpt180) REVERT: D 385 SER cc_start: 0.8202 (m) cc_final: 0.7414 (t) REVERT: D 386 GLN cc_start: 0.8148 (tp40) cc_final: 0.7811 (tp-100) REVERT: D 396 GLU cc_start: 0.7338 (tm-30) cc_final: 0.6924 (tm-30) REVERT: D 433 MET cc_start: 0.6710 (mmp) cc_final: 0.6468 (mmp) REVERT: E 236 ILE cc_start: 0.8700 (tp) cc_final: 0.8434 (tp) REVERT: E 237 GLN cc_start: 0.7613 (pp30) cc_final: 0.7206 (pp30) REVERT: E 241 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7199 (tp40) REVERT: E 269 GLN cc_start: 0.7528 (mt0) cc_final: 0.7258 (mt0) REVERT: E 274 ARG cc_start: 0.8296 (ptm160) cc_final: 0.7723 (ptm160) REVERT: E 343 LYS cc_start: 0.8071 (tptm) cc_final: 0.7747 (tptp) REVERT: E 363 LYS cc_start: 0.8092 (tmtt) cc_final: 0.7699 (tmtt) REVERT: E 386 GLN cc_start: 0.8318 (tp40) cc_final: 0.7929 (tp40) REVERT: E 387 SER cc_start: 0.8467 (m) cc_final: 0.8149 (p) REVERT: E 396 GLU cc_start: 0.7817 (tt0) cc_final: 0.7486 (tt0) REVERT: E 433 MET cc_start: 0.6286 (ttm) cc_final: 0.5718 (ttm) REVERT: F 236 ILE cc_start: 0.8746 (tp) cc_final: 0.8411 (tp) REVERT: F 241 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7066 (mm-40) REVERT: F 274 ARG cc_start: 0.8350 (ptm160) cc_final: 0.7893 (ptm160) REVERT: F 321 ARG cc_start: 0.7485 (tmt-80) cc_final: 0.6729 (tmt-80) REVERT: F 343 LYS cc_start: 0.8149 (tptp) cc_final: 0.7759 (tptp) REVERT: F 357 LEU cc_start: 0.7626 (tp) cc_final: 0.7400 (tp) REVERT: F 433 MET cc_start: 0.6858 (mtm) cc_final: 0.6324 (mtm) REVERT: G 237 GLN cc_start: 0.7673 (pp30) cc_final: 0.7307 (pp30) REVERT: G 250 PHE cc_start: 0.8721 (t80) cc_final: 0.8190 (t80) REVERT: G 278 LYS cc_start: 0.8196 (mttt) cc_final: 0.7715 (mtmm) REVERT: G 321 ARG cc_start: 0.7637 (ttt90) cc_final: 0.7160 (ttt180) REVERT: G 385 SER cc_start: 0.8163 (m) cc_final: 0.7561 (p) REVERT: G 414 GLN cc_start: 0.7153 (pt0) cc_final: 0.6770 (pm20) REVERT: G 426 ARG cc_start: 0.7550 (tmt170) cc_final: 0.7105 (tmt170) REVERT: G 427 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.6401 (mt) REVERT: H 237 GLN cc_start: 0.7634 (pp30) cc_final: 0.7248 (pp30) REVERT: H 281 TYR cc_start: 0.8466 (t80) cc_final: 0.8235 (t80) REVERT: H 304 TYR cc_start: 0.7814 (m-80) cc_final: 0.7287 (m-80) REVERT: H 343 LYS cc_start: 0.8180 (tptm) cc_final: 0.7781 (tptp) REVERT: H 363 LYS cc_start: 0.8018 (tmtt) cc_final: 0.7692 (tmtt) REVERT: H 396 GLU cc_start: 0.6941 (tm-30) cc_final: 0.6641 (tm-30) REVERT: H 433 MET cc_start: 0.6811 (ttm) cc_final: 0.6420 (ttm) outliers start: 65 outliers final: 54 residues processed: 480 average time/residue: 0.3222 time to fit residues: 205.1311 Evaluate side-chains 527 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 468 time to evaluate : 1.329 ------------------------------------------------------------------------------- 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 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 401 VAL Chi-restraints excluded: chain B residue 414 GLN 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 C residue 405 LEU 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 E residue 241 GLN Chi-restraints excluded: chain E residue 251 LEU 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 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 427 LEU Chi-restraints excluded: chain G residue 246 ILE 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 375 TYR 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 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 97 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 167 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 81 optimal weight: 0.2980 chunk 105 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 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** ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 280 GLN F 289 HIS ** F 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 GLN ** 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 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.3064 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= 0.208 Angle : 0.604 8.673 17451 Z= 0.309 Chirality : 0.037 0.157 1878 Planarity : 0.004 0.042 2311 Dihedral : 4.146 20.097 1863 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 5.77 % Allowed : 28.91 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.20), residues: 1664 helix: 0.97 (0.14), residues: 1368 sheet: None (None), residues: 0 loop : -1.46 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP B 377 HIS 0.006 0.001 HIS F 289 PHE 0.011 0.001 PHE H 265 TYR 0.025 0.002 TYR G 281 ARG 0.005 0.000 ARG E 295 ********************** 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 538 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 468 time to evaluate : 1.782 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 278 LYS cc_start: 0.8105 (mtmm) cc_final: 0.7490 (mtmm) REVERT: A 281 TYR cc_start: 0.8671 (t80) cc_final: 0.8396 (t80) REVERT: A 305 GLN cc_start: 0.8479 (tp40) cc_final: 0.8126 (tp40) REVERT: A 343 LYS cc_start: 0.8239 (tptp) cc_final: 0.7653 (tptp) REVERT: A 351 ARG cc_start: 0.7333 (ttm-80) cc_final: 0.6834 (ttm-80) REVERT: A 364 GLU cc_start: 0.7630 (tp30) cc_final: 0.7314 (tp30) REVERT: A 378 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8055 (tp) REVERT: A 385 SER cc_start: 0.8187 (m) cc_final: 0.7733 (p) REVERT: A 410 ARG cc_start: 0.7418 (ptt180) cc_final: 0.7108 (pmt170) REVERT: B 236 ILE cc_start: 0.8543 (tp) cc_final: 0.8274 (tp) REVERT: B 239 LEU cc_start: 0.8633 (tp) cc_final: 0.8382 (tp) REVERT: B 241 GLN cc_start: 0.7825 (tp-100) cc_final: 0.6885 (tp-100) REVERT: B 274 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7298 (ptm160) REVERT: C 236 ILE cc_start: 0.8473 (tp) cc_final: 0.8219 (tp) REVERT: C 241 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7616 (mm-40) REVERT: C 343 LYS cc_start: 0.8348 (tptm) cc_final: 0.8102 (tptt) REVERT: C 344 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7585 (tm-30) REVERT: C 385 SER cc_start: 0.8149 (m) cc_final: 0.7493 (p) REVERT: D 236 ILE cc_start: 0.8567 (tp) cc_final: 0.8300 (tp) REVERT: D 244 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8401 (p) REVERT: D 337 ARG cc_start: 0.7635 (mpt180) cc_final: 0.6930 (mpt180) REVERT: D 385 SER cc_start: 0.8208 (m) cc_final: 0.7421 (t) REVERT: D 386 GLN cc_start: 0.8154 (tp40) cc_final: 0.7825 (tp-100) REVERT: D 396 GLU cc_start: 0.7349 (tm-30) cc_final: 0.6906 (tm-30) REVERT: D 433 MET cc_start: 0.6733 (mmp) cc_final: 0.6508 (mmp) REVERT: E 236 ILE cc_start: 0.8700 (tp) cc_final: 0.8429 (tp) REVERT: E 237 GLN cc_start: 0.7628 (pp30) cc_final: 0.7183 (pp30) REVERT: E 269 GLN cc_start: 0.7478 (mt0) cc_final: 0.7114 (mt0) REVERT: E 274 ARG cc_start: 0.8318 (ptm160) cc_final: 0.8099 (ptm160) REVERT: E 343 LYS cc_start: 0.8092 (tptm) cc_final: 0.7753 (tptp) REVERT: E 363 LYS cc_start: 0.8043 (tmtt) cc_final: 0.7635 (tmtt) REVERT: E 386 GLN cc_start: 0.8314 (tp40) cc_final: 0.7953 (tp40) REVERT: E 387 SER cc_start: 0.8476 (m) cc_final: 0.8174 (p) REVERT: E 396 GLU cc_start: 0.7842 (tt0) cc_final: 0.7466 (tt0) REVERT: E 433 MET cc_start: 0.6356 (ttm) cc_final: 0.5786 (ttm) REVERT: F 236 ILE cc_start: 0.8749 (tp) cc_final: 0.8401 (tp) REVERT: F 241 GLN cc_start: 0.7470 (mm-40) cc_final: 0.7059 (mm-40) REVERT: F 274 ARG cc_start: 0.8344 (ptm160) cc_final: 0.7891 (ptm160) REVERT: F 280 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7488 (mt0) REVERT: F 321 ARG cc_start: 0.7482 (tmt-80) cc_final: 0.6719 (tmt-80) REVERT: F 343 LYS cc_start: 0.8151 (tptp) cc_final: 0.7767 (tptp) REVERT: F 357 LEU cc_start: 0.7636 (tp) cc_final: 0.7415 (tp) REVERT: F 433 MET cc_start: 0.6840 (mtm) cc_final: 0.6309 (mtm) REVERT: G 237 GLN cc_start: 0.7676 (pp30) cc_final: 0.7322 (pp30) REVERT: G 250 PHE cc_start: 0.8741 (t80) cc_final: 0.8172 (t80) REVERT: G 278 LYS cc_start: 0.8216 (mttt) cc_final: 0.7667 (mtmm) REVERT: G 289 HIS cc_start: 0.7302 (OUTLIER) cc_final: 0.7011 (m90) REVERT: G 321 ARG cc_start: 0.7639 (ttt90) cc_final: 0.7167 (ttt180) REVERT: G 385 SER cc_start: 0.8168 (m) cc_final: 0.7583 (p) REVERT: G 414 GLN cc_start: 0.7212 (pt0) cc_final: 0.6793 (pm20) REVERT: G 426 ARG cc_start: 0.7565 (tmt170) cc_final: 0.7169 (tmt170) REVERT: H 237 GLN cc_start: 0.7638 (pp30) cc_final: 0.7257 (pp30) REVERT: H 281 TYR cc_start: 0.8473 (t80) cc_final: 0.8262 (t80) REVERT: H 304 TYR cc_start: 0.7763 (m-80) cc_final: 0.7203 (m-80) REVERT: H 343 LYS cc_start: 0.8205 (tptm) cc_final: 0.7787 (tptp) REVERT: H 363 LYS cc_start: 0.8034 (tmtt) cc_final: 0.7691 (tmtt) REVERT: H 433 MET cc_start: 0.6796 (ttm) cc_final: 0.6391 (ttm) outliers start: 70 outliers final: 60 residues processed: 483 average time/residue: 0.3611 time to fit residues: 230.4421 Evaluate side-chains 532 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 467 time to evaluate : 1.339 ------------------------------------------------------------------------------- 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 289 HIS Chi-restraints excluded: chain B residue 305 GLN Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 GLN 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 C residue 405 LEU 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 287 HIS 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 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 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 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 409 LEU Chi-restraints excluded: chain F residue 427 LEU Chi-restraints excluded: chain G residue 246 ILE 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 375 TYR 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 Chi-restraints excluded: chain H residue 391 LEU 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 40 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 312 HIS ** 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 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 289 HIS F 312 HIS ** F 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 GLN ** 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 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3887 r_free = 0.3887 target = 0.149135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.128072 restraints weight = 21475.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.132344 restraints weight = 12833.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.135379 restraints weight = 8727.255| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3097 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= 0.223 Angle : 0.608 8.459 17451 Z= 0.313 Chirality : 0.037 0.159 1878 Planarity : 0.004 0.043 2311 Dihedral : 4.186 20.274 1863 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.44 % Allowed : 29.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.20), residues: 1664 helix: 0.95 (0.14), residues: 1368 sheet: None (None), residues: 0 loop : -1.48 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 377 HIS 0.007 0.001 HIS A 287 PHE 0.027 0.001 PHE B 356 TYR 0.025 0.002 TYR G 281 ARG 0.005 0.000 ARG E 295 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3703.06 seconds wall clock time: 67 minutes 59.12 seconds (4079.12 seconds total)