Starting phenix.real_space_refine on Wed Jul 30 17:45:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d9x_27269/07_2025/8d9x_27269_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d9x_27269/07_2025/8d9x_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_27269/07_2025/8d9x_27269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d9x_27269/07_2025/8d9x_27269.map" model { file = "/net/cci-nas-00/data/ceres_data/8d9x_27269/07_2025/8d9x_27269_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d9x_27269/07_2025/8d9x_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 8.18, per 1000 atoms: 0.65 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: 3.18 Conformation dependent library (CDL) restraints added in 1.7 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: 1.16 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: 3.79 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2111 1.30 - 1.43: 3609 1.43 - 1.55: 7126 1.55 - 1.68: 0 1.68 - 1.81: 64 Bond restraints: 12910 Sorted by residual: bond pdb=" CA PHE C 250 " pdb=" C PHE C 250 " ideal model delta sigma weight residual 1.524 1.422 0.102 1.26e-02 6.30e+03 6.55e+01 bond pdb=" CA LEU H 251 " pdb=" C LEU H 251 " ideal model delta sigma weight residual 1.524 1.440 0.084 1.26e-02 6.30e+03 4.39e+01 bond pdb=" CA LEU E 251 " pdb=" C LEU E 251 " ideal model delta sigma weight residual 1.524 1.441 0.083 1.26e-02 6.30e+03 4.37e+01 bond pdb=" CA LEU G 251 " pdb=" C LEU G 251 " ideal model delta sigma weight residual 1.524 1.442 0.082 1.26e-02 6.30e+03 4.21e+01 bond pdb=" CA LEU C 251 " pdb=" C LEU C 251 " ideal model delta sigma weight residual 1.523 1.447 0.077 1.30e-02 5.92e+03 3.49e+01 ... (remaining 12905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 16884 1.74 - 3.48: 471 3.48 - 5.22: 57 5.22 - 6.96: 32 6.96 - 8.70: 7 Bond angle restraints: 17451 Sorted by residual: angle pdb=" C PHE C 250 " pdb=" CA PHE C 250 " pdb=" CB PHE C 250 " ideal model delta sigma weight residual 110.90 102.37 8.53 1.58e+00 4.01e-01 2.91e+01 angle pdb=" N ILE E 297 " pdb=" CA ILE E 297 " pdb=" C ILE E 297 " ideal model delta sigma weight residual 112.96 108.58 4.38 1.00e+00 1.00e+00 1.92e+01 angle pdb=" N ILE H 297 " pdb=" CA ILE H 297 " pdb=" C ILE H 297 " ideal model delta sigma weight residual 112.96 108.61 4.35 1.00e+00 1.00e+00 1.90e+01 angle pdb=" N ILE C 297 " pdb=" CA ILE C 297 " pdb=" C ILE C 297 " ideal model delta sigma weight residual 112.96 108.61 4.35 1.00e+00 1.00e+00 1.90e+01 angle pdb=" N ILE E 393 " pdb=" CA ILE E 393 " pdb=" C ILE E 393 " ideal model delta sigma weight residual 111.00 106.31 4.69 1.09e+00 8.42e-01 1.85e+01 ... (remaining 17446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6847 17.99 - 35.97: 702 35.97 - 53.96: 99 53.96 - 71.95: 10 71.95 - 89.94: 5 Dihedral angle restraints: 7663 sinusoidal: 2793 harmonic: 4870 Sorted by residual: dihedral pdb=" C GLU E 396 " pdb=" N GLU E 396 " pdb=" CA GLU E 396 " pdb=" CB GLU E 396 " ideal model delta harmonic sigma weight residual -122.60 -134.34 11.74 0 2.50e+00 1.60e-01 2.21e+01 dihedral pdb=" C PHE C 250 " pdb=" N PHE C 250 " pdb=" CA PHE C 250 " pdb=" CB PHE C 250 " ideal model delta harmonic sigma weight residual -122.60 -111.53 -11.07 0 2.50e+00 1.60e-01 1.96e+01 dihedral pdb=" N GLU E 396 " pdb=" C GLU E 396 " pdb=" CA GLU E 396 " pdb=" CB GLU E 396 " ideal model delta harmonic sigma weight residual 122.80 133.67 -10.87 0 2.50e+00 1.60e-01 1.89e+01 ... (remaining 7660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1845 0.103 - 0.207: 31 0.207 - 0.310: 1 0.310 - 0.413: 0 0.413 - 0.516: 1 Chirality restraints: 1878 Sorted by residual: chirality pdb=" CA GLU E 396 " pdb=" N GLU E 396 " pdb=" C GLU E 396 " pdb=" CB GLU E 396 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.67e+00 chirality pdb=" CA ARG E 403 " pdb=" N ARG E 403 " pdb=" C ARG E 403 " pdb=" CB ARG E 403 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA ARG A 410 " pdb=" N ARG A 410 " pdb=" C ARG A 410 " pdb=" CB ARG A 410 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.83e-01 ... (remaining 1875 not shown) Planarity restraints: 2311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN E 402 " -0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C GLN E 402 " 0.064 2.00e-02 2.50e+03 pdb=" O GLN E 402 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG E 403 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 250 " 0.016 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C PHE G 250 " -0.059 2.00e-02 2.50e+03 pdb=" O PHE G 250 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU G 251 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 250 " -0.014 2.00e-02 2.50e+03 2.95e-02 8.68e+00 pdb=" C PHE E 250 " 0.051 2.00e-02 2.50e+03 pdb=" O PHE E 250 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU E 251 " -0.017 2.00e-02 2.50e+03 ... (remaining 2308 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2133 2.75 - 3.29: 13506 3.29 - 3.83: 22224 3.83 - 4.36: 23704 4.36 - 4.90: 41000 Nonbonded interactions: 102567 Sorted by model distance: nonbonded pdb=" O ALA F 345 " pdb=" OG SER F 348 " model vdw 2.217 3.040 nonbonded pdb=" OG SER D 432 " pdb=" NH2 ARG H 403 " model vdw 2.222 3.120 nonbonded pdb=" OE1 GLN B 316 " pdb=" NE2 GLN B 344 " model vdw 2.234 3.120 nonbonded pdb=" O ALA C 345 " pdb=" OG SER C 348 " model vdw 2.241 3.040 nonbonded pdb=" O ALA A 345 " pdb=" OG SER A 348 " model vdw 2.253 3.040 ... (remaining 102562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 228 through 425 or (resid 426 and (name N or name CA or na \ me C or name O or name CB )) or resid 427 through 429 or (resid 430 and (name N \ or name CA or name C or name O or name CB )) or resid 431 through 434 or (resid \ 435 and (name N or name CA or name C or name O )) or resid 436 through 437)) selection = (chain 'B' and (resid 228 through 434 or (resid 435 and (name N or name CA or na \ me C or name O )) or resid 436 through 437)) selection = (chain 'C' and (resid 228 through 425 or (resid 426 and (name N or name CA or na \ me C or name O or name CB )) or resid 427 through 429 or (resid 430 and (name N \ or name CA or name C or name O or name CB )) or resid 431 through 434 or (resid \ 435 and (name N or name CA or name C or name O )) or resid 436 through 437)) selection = (chain 'D' and (resid 228 through 425 or (resid 426 and (name N or name CA or na \ me C or name O or name CB )) or resid 427 through 429 or (resid 430 and (name N \ or name CA or name C or name O or name CB )) or resid 431 through 437)) selection = (chain 'E' and (resid 228 through 425 or (resid 426 and (name N or name CA or na \ me C or name O or name CB )) or resid 427 through 429 or (resid 430 and (name N \ or name CA or name C or name O or name CB )) or resid 431 through 434 or (resid \ 435 and (name N or name CA or name C or name O )) or resid 436 through 437)) selection = (chain 'F' and (resid 228 through 425 or (resid 426 and (name N or name CA or na \ me C or name O or name CB )) or resid 427 through 429 or (resid 430 and (name N \ or name CA or name C or name O or name CB )) or resid 431 through 434 or (resid \ 435 and (name N or name CA or name C or name O )) or resid 436 through 437)) selection = (chain 'G' and (resid 228 through 425 or (resid 426 and (name N or name CA or na \ me C or name O or name CB )) or resid 427 through 429 or (resid 430 and (name N \ or name CA or name C or name O or name CB )) or resid 431 through 434 or (resid \ 435 and (name N or name CA or name C or name O )) or resid 436 through 437)) selection = (chain 'H' and (resid 228 through 425 or (resid 426 and (name N or name CA or na \ me C or name O or name CB )) or resid 427 through 429 or (resid 430 and (name N \ or name CA or name C or name O or name CB )) or resid 431 through 434 or (resid \ 435 and (name N or name CA or name C or name O )) or resid 436 through 437)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.340 Find NCS groups from input model: 0.670 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 12910 Z= 0.281 Angle : 0.709 8.701 17451 Z= 0.406 Chirality : 0.042 0.516 1878 Planarity : 0.005 0.068 2311 Dihedral : 13.941 89.936 4561 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.58 % Allowed : 0.49 % Favored : 98.93 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.09962 ( 995) hydrogen bonds : angle 5.18997 ( 2982) covalent geometry : bond 0.00441 (12910) covalent geometry : angle 0.70909 (17451) *********************** 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 : 1.331 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: 0.2906 time to fit residues: 191.7182 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 : 1.399 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.149924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.129702 restraints weight = 21450.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.134190 restraints weight = 12486.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.137267 restraints weight = 8280.667| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.1532 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= 0.143 Angle : 0.591 7.247 17451 Z= 0.305 Chirality : 0.037 0.133 1878 Planarity : 0.004 0.040 2311 Dihedral : 4.968 53.745 1875 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.05 % Allowed : 16.39 % Favored : 80.56 % 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 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 995) hydrogen bonds : angle 3.82680 ( 2982) covalent geometry : bond 0.00303 (12910) covalent geometry : angle 0.59090 (17451) *********************** 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 : 1.255 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: 0.7662 (pp30) cc_final: 0.7339 (pp30) REVERT: A 238 GLN cc_start: 0.8519 (tp40) cc_final: 0.8212 (tp40) REVERT: A 241 GLN cc_start: 0.7886 (tp-100) cc_final: 0.7617 (tp-100) REVERT: A 274 ARG cc_start: 0.8128 (ptm160) cc_final: 0.7783 (ptp-170) REVERT: A 281 TYR cc_start: 0.8669 (t80) cc_final: 0.8458 (t80) REVERT: A 364 GLU cc_start: 0.7481 (tp30) cc_final: 0.7132 (tp30) REVERT: A 399 LEU cc_start: 0.8224 (pt) cc_final: 0.8023 (pt) REVERT: A 433 MET cc_start: 0.6508 (tpt) cc_final: 0.6214 (tpt) REVERT: B 236 ILE cc_start: 0.8575 (tp) cc_final: 0.8334 (tp) REVERT: B 241 GLN cc_start: 0.7831 (tp-100) cc_final: 0.7386 (tp-100) REVERT: B 281 TYR cc_start: 0.8535 (t80) cc_final: 0.8324 (t80) REVERT: B 386 GLN cc_start: 0.7885 (tp40) cc_final: 0.7319 (tp40) REVERT: B 414 GLN cc_start: 0.6992 (pm20) cc_final: 0.6698 (pm20) REVERT: C 236 ILE cc_start: 0.8523 (tp) cc_final: 0.8293 (tp) REVERT: C 241 GLN cc_start: 0.7795 (mm-40) cc_final: 0.7423 (mm-40) REVERT: C 297 ILE cc_start: 0.8706 (mm) cc_final: 0.8501 (mm) REVERT: C 343 LYS cc_start: 0.8304 (tptm) cc_final: 0.7994 (tptt) REVERT: C 344 GLN cc_start: 0.7700 (tm-30) cc_final: 0.7481 (tm-30) REVERT: C 370 GLN cc_start: 0.7461 (mm-40) cc_final: 0.7231 (mm-40) REVERT: C 386 GLN cc_start: 0.7888 (tp40) cc_final: 0.7407 (tp40) REVERT: C 420 ASN cc_start: 0.8227 (t0) cc_final: 0.7908 (t0) REVERT: C 426 ARG cc_start: 0.6975 (tmt170) cc_final: 0.6717 (tmt170) REVERT: D 236 ILE cc_start: 0.8573 (tp) cc_final: 0.8311 (tp) REVERT: D 251 LEU cc_start: 0.8262 (tp) cc_final: 0.7992 (tp) REVERT: D 305 GLN cc_start: 0.7790 (tp-100) cc_final: 0.7208 (tp-100) REVERT: D 354 GLN cc_start: 0.7103 (mt0) cc_final: 0.6895 (mt0) REVERT: D 396 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7046 (tm-30) REVERT: D 433 MET cc_start: 0.6528 (mmp) cc_final: 0.6102 (mmp) REVERT: E 236 ILE cc_start: 0.8643 (tp) cc_final: 0.8409 (tp) REVERT: E 237 GLN cc_start: 0.7499 (pp30) cc_final: 0.7212 (pp30) REVERT: E 269 GLN cc_start: 0.7637 (mt0) cc_final: 0.7329 (mt0) REVERT: E 304 TYR cc_start: 0.7757 (m-80) cc_final: 0.7226 (m-80) REVERT: E 343 LYS cc_start: 0.8089 (tptm) cc_final: 0.7690 (tptp) REVERT: E 414 GLN cc_start: 0.6977 (pp30) cc_final: 0.6711 (pp30) REVERT: E 433 MET cc_start: 0.5854 (ttm) cc_final: 0.5406 (ttm) REVERT: F 236 ILE cc_start: 0.8659 (tp) cc_final: 0.8387 (tp) REVERT: F 238 GLN cc_start: 0.8091 (tp40) cc_final: 0.7803 (tp40) REVERT: F 241 GLN cc_start: 0.7564 (mm-40) cc_final: 0.7189 (mm-40) REVERT: F 251 LEU cc_start: 0.8239 (mp) cc_final: 0.8035 (mm) REVERT: F 343 LYS cc_start: 0.8044 (tptp) cc_final: 0.7565 (tptp) REVERT: F 414 GLN cc_start: 0.7499 (pp30) cc_final: 0.6467 (pp30) REVERT: F 420 ASN cc_start: 0.7701 (t0) cc_final: 0.7479 (t0) REVERT: G 237 GLN cc_start: 0.7622 (pp30) cc_final: 0.7375 (pp30) REVERT: G 281 TYR cc_start: 0.8316 (t80) cc_final: 0.8113 (t80) REVERT: G 287 HIS cc_start: 0.7063 (t-170) cc_final: 0.6679 (t-170) REVERT: G 321 ARG cc_start: 0.7499 (ttt90) cc_final: 0.7035 (ttt90) REVERT: G 323 LEU cc_start: 0.8325 (tp) cc_final: 0.8006 (tt) REVERT: G 385 SER cc_start: 0.8098 (m) cc_final: 0.7410 (p) REVERT: G 386 GLN cc_start: 0.7872 (tp40) cc_final: 0.7488 (tp40) REVERT: G 426 ARG cc_start: 0.7664 (tmt170) cc_final: 0.7189 (tmt170) REVERT: H 237 GLN cc_start: 0.7562 (pp30) cc_final: 0.7320 (pp30) REVERT: H 281 TYR cc_start: 0.8570 (t80) cc_final: 0.8307 (t80) REVERT: H 343 LYS cc_start: 0.8121 (tptm) cc_final: 0.7777 (tptp) REVERT: H 371 ARG cc_start: 0.7044 (ttm110) cc_final: 0.6523 (ttm110) REVERT: H 396 GLU cc_start: 0.6926 (tm-30) cc_final: 0.6513 (tm-30) REVERT: H 433 MET cc_start: 0.6307 (ttm) cc_final: 0.5933 (ttm) outliers start: 37 outliers final: 29 residues processed: 486 average time/residue: 0.3065 time to fit residues: 198.7770 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 : 1.250 ------------------------------------------------------------------------------- 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 133 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 386 GLN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.142877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.123285 restraints weight = 21738.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.127574 restraints weight = 12880.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.130599 restraints weight = 8616.721| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12910 Z= 0.163 Angle : 0.575 7.342 17451 Z= 0.301 Chirality : 0.037 0.156 1878 Planarity : 0.004 0.040 2311 Dihedral : 4.648 54.861 1869 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.20 % Allowed : 21.25 % Favored : 74.55 % 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: 0.45 (0.20), residues: 1664 helix: 0.72 (0.14), residues: 1376 sheet: None (None), residues: 0 loop : -1.39 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 377 HIS 0.010 0.001 HIS F 289 PHE 0.019 0.001 PHE H 250 TYR 0.019 0.002 TYR F 281 ARG 0.005 0.000 ARG E 410 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 995) hydrogen bonds : angle 3.71956 ( 2982) covalent geometry : bond 0.00342 (12910) covalent geometry : angle 0.57525 (17451) *********************** 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 534 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 483 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7703 (pp30) cc_final: 0.7400 (pp30) REVERT: A 238 GLN cc_start: 0.8574 (tp40) cc_final: 0.8369 (tp40) REVERT: A 241 GLN cc_start: 0.7829 (tp-100) cc_final: 0.7353 (tp-100) REVERT: A 274 ARG cc_start: 0.8116 (ptm160) cc_final: 0.7791 (ptm160) REVERT: A 351 ARG cc_start: 0.7311 (ttm-80) cc_final: 0.6836 (ttm-80) REVERT: A 364 GLU cc_start: 0.7571 (tp30) cc_final: 0.7194 (tp30) REVERT: A 399 LEU cc_start: 0.8202 (pt) cc_final: 0.7969 (pt) REVERT: A 433 MET cc_start: 0.6505 (tpt) cc_final: 0.6230 (tpt) REVERT: B 236 ILE cc_start: 0.8634 (tp) cc_final: 0.8364 (tp) REVERT: B 241 GLN cc_start: 0.7802 (tp-100) cc_final: 0.7169 (tp-100) REVERT: B 274 ARG cc_start: 0.8157 (ptm160) cc_final: 0.7422 (ptm160) REVERT: B 386 GLN cc_start: 0.7961 (tp40) cc_final: 0.7646 (tp40) REVERT: B 414 GLN cc_start: 0.6935 (OUTLIER) cc_final: 0.6488 (pm20) REVERT: C 236 ILE cc_start: 0.8554 (tp) cc_final: 0.8296 (tp) REVERT: C 237 GLN cc_start: 0.7549 (pp30) cc_final: 0.7241 (pp30) REVERT: C 241 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7509 (mm-40) REVERT: C 343 LYS cc_start: 0.8306 (tptm) cc_final: 0.8071 (tptt) REVERT: C 344 GLN cc_start: 0.7768 (tm-30) cc_final: 0.7454 (tm-30) REVERT: C 370 GLN cc_start: 0.7456 (mm-40) cc_final: 0.7162 (mm-40) REVERT: C 386 GLN cc_start: 0.8025 (tp40) cc_final: 0.7762 (tp40) REVERT: C 420 ASN cc_start: 0.8146 (t0) cc_final: 0.7876 (t0) REVERT: D 236 ILE cc_start: 0.8613 (tp) cc_final: 0.8342 (tp) REVERT: D 251 LEU cc_start: 0.8289 (tp) cc_final: 0.7988 (tp) REVERT: D 305 GLN cc_start: 0.7855 (tp-100) cc_final: 0.7201 (tp-100) REVERT: D 337 ARG cc_start: 0.7671 (mpt180) cc_final: 0.6922 (mpt180) REVERT: D 385 SER cc_start: 0.8254 (m) cc_final: 0.7526 (t) REVERT: D 386 GLN cc_start: 0.8020 (tp40) cc_final: 0.7781 (tp40) REVERT: D 396 GLU cc_start: 0.7425 (tm-30) cc_final: 0.6974 (tm-30) REVERT: D 433 MET cc_start: 0.6673 (mmp) cc_final: 0.6331 (mmp) REVERT: E 236 ILE cc_start: 0.8770 (tp) cc_final: 0.8498 (tp) REVERT: E 237 GLN cc_start: 0.7531 (pp30) cc_final: 0.7196 (pp30) REVERT: E 241 GLN cc_start: 0.7991 (mm110) cc_final: 0.7287 (tp40) REVERT: E 269 GLN cc_start: 0.7512 (mt0) cc_final: 0.7251 (mt0) REVERT: E 274 ARG cc_start: 0.8332 (ptm160) cc_final: 0.7918 (ptm160) REVERT: E 304 TYR cc_start: 0.7774 (m-80) cc_final: 0.7262 (m-80) REVERT: E 343 LYS cc_start: 0.8064 (tptm) cc_final: 0.7776 (tptp) REVERT: E 410 ARG cc_start: 0.6848 (tmm160) cc_final: 0.6348 (tmm160) REVERT: E 433 MET cc_start: 0.5886 (ttm) cc_final: 0.5364 (ttm) REVERT: F 236 ILE cc_start: 0.8711 (tp) cc_final: 0.8409 (tp) REVERT: F 241 GLN cc_start: 0.7557 (mm-40) cc_final: 0.7289 (mm-40) REVERT: F 251 LEU cc_start: 0.8252 (mp) cc_final: 0.7972 (mm) REVERT: F 343 LYS cc_start: 0.8057 (tptp) cc_final: 0.7760 (tptt) REVERT: G 237 GLN cc_start: 0.7643 (pp30) cc_final: 0.7384 (pp30) REVERT: G 287 HIS cc_start: 0.7006 (t-170) cc_final: 0.6603 (t-170) REVERT: G 321 ARG cc_start: 0.7463 (ttt90) cc_final: 0.7011 (ttt90) REVERT: G 323 LEU cc_start: 0.8342 (tp) cc_final: 0.8008 (tt) REVERT: G 385 SER cc_start: 0.8084 (m) cc_final: 0.7449 (p) REVERT: G 386 GLN cc_start: 0.7857 (tp40) cc_final: 0.7462 (tp40) REVERT: G 426 ARG cc_start: 0.7626 (tmt170) cc_final: 0.7136 (tmt170) REVERT: H 237 GLN cc_start: 0.7612 (pp30) cc_final: 0.7266 (pp30) REVERT: H 250 PHE cc_start: 0.8718 (t80) cc_final: 0.8481 (t80) REVERT: H 281 TYR cc_start: 0.8538 (t80) cc_final: 0.8311 (t80) REVERT: H 343 LYS cc_start: 0.8052 (tptm) cc_final: 0.7818 (tptp) REVERT: H 396 GLU cc_start: 0.6922 (tm-30) cc_final: 0.6577 (tm-30) REVERT: H 433 MET cc_start: 0.6440 (ttm) cc_final: 0.6057 (ttm) outliers start: 51 outliers final: 36 residues processed: 492 average time/residue: 0.3068 time to fit residues: 200.7061 Evaluate side-chains 509 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 472 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain C residue 242 LEU 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 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 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 305 GLN Chi-restraints excluded: chain F residue 344 GLN Chi-restraints excluded: chain G residue 244 VAL Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 344 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 95 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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** ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 287 HIS F 289 HIS ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 GLN ** G 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 280 GLN H 289 HIS H 310 GLN ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.157837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.136675 restraints weight = 21393.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.140983 restraints weight = 12715.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.144045 restraints weight = 8641.472| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12910 Z= 0.160 Angle : 0.569 7.596 17451 Z= 0.299 Chirality : 0.037 0.161 1878 Planarity : 0.004 0.042 2311 Dihedral : 4.182 20.588 1863 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.44 % Allowed : 23.39 % Favored : 71.17 % 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: 0.38 (0.20), residues: 1664 helix: 0.73 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -1.82 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP F 377 HIS 0.003 0.001 HIS G 312 PHE 0.014 0.001 PHE H 250 TYR 0.022 0.002 TYR G 281 ARG 0.005 0.000 ARG F 388 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 995) hydrogen bonds : angle 3.66966 ( 2982) covalent geometry : bond 0.00334 (12910) covalent geometry : angle 0.56887 (17451) *********************** 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 537 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 471 time to evaluate : 1.380 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: symmetry clash REVERT: A 237 GLN cc_start: 0.7767 (pp30) cc_final: 0.7387 (pp30) REVERT: A 241 GLN cc_start: 0.7784 (tp-100) cc_final: 0.7327 (tp-100) REVERT: A 274 ARG cc_start: 0.8085 (ptm160) cc_final: 0.7482 (mtp85) REVERT: A 281 TYR cc_start: 0.8705 (t80) cc_final: 0.8442 (t80) REVERT: A 343 LYS cc_start: 0.8240 (tptp) cc_final: 0.7674 (tptp) REVERT: A 351 ARG cc_start: 0.7303 (ttm-80) cc_final: 0.6831 (ttm-80) REVERT: A 385 SER cc_start: 0.8123 (m) cc_final: 0.7675 (p) REVERT: A 396 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7348 (tm-30) REVERT: A 399 LEU cc_start: 0.8131 (pt) cc_final: 0.7864 (pt) REVERT: A 414 GLN cc_start: 0.7198 (pp30) cc_final: 0.6668 (pp30) REVERT: A 433 MET cc_start: 0.6454 (tpt) cc_final: 0.6213 (tpt) REVERT: B 236 ILE cc_start: 0.8568 (tp) cc_final: 0.8291 (tp) REVERT: B 241 GLN cc_start: 0.7846 (tp-100) cc_final: 0.7018 (tp-100) REVERT: B 274 ARG cc_start: 0.8123 (ptm160) cc_final: 0.7331 (ptm160) REVERT: B 386 GLN cc_start: 0.7975 (tp40) cc_final: 0.7500 (tp40) REVERT: C 236 ILE cc_start: 0.8475 (tp) cc_final: 0.8236 (tp) REVERT: C 241 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7445 (mm-40) REVERT: C 324 LEU cc_start: 0.8167 (tp) cc_final: 0.7890 (tt) REVERT: C 337 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7321 (mpt180) REVERT: C 344 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7524 (tm-30) REVERT: C 370 GLN cc_start: 0.7463 (mm-40) cc_final: 0.7164 (mm-40) REVERT: C 386 GLN cc_start: 0.8012 (tp40) cc_final: 0.7684 (tp40) REVERT: C 420 ASN cc_start: 0.8104 (t0) cc_final: 0.7715 (t0) REVERT: D 236 ILE cc_start: 0.8567 (tp) cc_final: 0.8298 (tp) REVERT: D 244 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8408 (p) REVERT: D 251 LEU cc_start: 0.8318 (tp) cc_final: 0.8030 (tp) REVERT: D 274 ARG cc_start: 0.8047 (ptm160) cc_final: 0.7802 (mtp85) REVERT: D 281 TYR cc_start: 0.8555 (t80) cc_final: 0.8315 (t80) REVERT: D 337 ARG cc_start: 0.7721 (mpt180) cc_final: 0.6954 (mpt180) REVERT: D 344 GLN cc_start: 0.7961 (pp30) cc_final: 0.7480 (pp30) REVERT: D 385 SER cc_start: 0.8255 (m) cc_final: 0.7516 (t) REVERT: D 396 GLU cc_start: 0.7414 (tm-30) cc_final: 0.6971 (tm-30) REVERT: D 433 MET cc_start: 0.6759 (mmp) cc_final: 0.6464 (mmp) REVERT: E 236 ILE cc_start: 0.8726 (tp) cc_final: 0.8462 (tp) REVERT: E 237 GLN cc_start: 0.7585 (pp30) cc_final: 0.7196 (pp30) REVERT: E 241 GLN cc_start: 0.7943 (mm110) cc_final: 0.7215 (tp40) REVERT: E 269 GLN cc_start: 0.7537 (mt0) cc_final: 0.7268 (mt0) REVERT: E 274 ARG cc_start: 0.8286 (ptm160) cc_final: 0.7880 (ptm160) REVERT: E 304 TYR cc_start: 0.7845 (m-80) cc_final: 0.7392 (m-80) REVERT: E 343 LYS cc_start: 0.8069 (tptm) cc_final: 0.7761 (tptp) REVERT: E 387 SER cc_start: 0.8601 (m) cc_final: 0.8110 (p) REVERT: E 388 ARG cc_start: 0.7221 (ttt90) cc_final: 0.7017 (ttm-80) REVERT: E 410 ARG cc_start: 0.6960 (tmm160) cc_final: 0.6396 (tmm160) REVERT: E 433 MET cc_start: 0.6073 (ttm) cc_final: 0.5509 (ttm) REVERT: F 236 ILE cc_start: 0.8696 (tp) cc_final: 0.8401 (tp) REVERT: F 241 GLN cc_start: 0.7565 (mm-40) cc_final: 0.7281 (mm-40) REVERT: F 251 LEU cc_start: 0.8262 (mp) cc_final: 0.8009 (mm) REVERT: F 321 ARG cc_start: 0.7434 (tmt-80) cc_final: 0.6696 (tmt-80) REVERT: F 343 LYS cc_start: 0.8083 (tptp) cc_final: 0.7711 (tptp) REVERT: G 237 GLN cc_start: 0.7677 (pp30) cc_final: 0.7381 (pp30) REVERT: G 321 ARG cc_start: 0.7648 (ttt90) cc_final: 0.7186 (ttt90) REVERT: G 323 LEU cc_start: 0.8345 (tp) cc_final: 0.7982 (tt) REVERT: G 385 SER cc_start: 0.8173 (m) cc_final: 0.7525 (p) REVERT: G 426 ARG cc_start: 0.7665 (tmt170) cc_final: 0.7123 (tmt170) REVERT: H 237 GLN cc_start: 0.7647 (pp30) cc_final: 0.7317 (pp30) REVERT: H 250 PHE cc_start: 0.8774 (t80) cc_final: 0.8426 (t80) REVERT: H 281 TYR cc_start: 0.8537 (t80) cc_final: 0.8291 (t80) REVERT: H 321 ARG cc_start: 0.7376 (tmt-80) cc_final: 0.6544 (tmt-80) REVERT: H 343 LYS cc_start: 0.8180 (tptm) cc_final: 0.7856 (tptp) REVERT: H 385 SER cc_start: 0.8131 (m) cc_final: 0.7529 (t) REVERT: H 387 SER cc_start: 0.8301 (m) cc_final: 0.7770 (p) REVERT: H 396 GLU cc_start: 0.6979 (tm-30) cc_final: 0.6658 (tm-30) REVERT: H 433 MET cc_start: 0.6628 (ttm) cc_final: 0.6296 (ttm) outliers start: 66 outliers final: 45 residues processed: 488 average time/residue: 0.3172 time to fit residues: 204.5485 Evaluate side-chains 516 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 468 time to evaluate : 1.396 ------------------------------------------------------------------------------- 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 278 LYS Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 287 HIS 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 289 HIS 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 246 ILE Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain E residue 289 HIS Chi-restraints excluded: chain E residue 305 GLN Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 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 G residue 427 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 415 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 32 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS E 310 GLN ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 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 289 HIS H 310 GLN ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.157208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.136136 restraints weight = 21448.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.140506 restraints weight = 12603.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.143555 restraints weight = 8491.780| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2498 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= 0.150 Angle : 0.556 7.185 17451 Z= 0.292 Chirality : 0.036 0.162 1878 Planarity : 0.004 0.042 2311 Dihedral : 4.164 20.651 1863 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 5.60 % Allowed : 24.79 % Favored : 69.60 % 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: 0.48 (0.20), residues: 1664 helix: 0.81 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -1.83 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 377 HIS 0.005 0.001 HIS H 289 PHE 0.015 0.001 PHE D 356 TYR 0.023 0.002 TYR G 281 ARG 0.004 0.000 ARG F 388 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 995) hydrogen bonds : angle 3.63942 ( 2982) covalent geometry : bond 0.00315 (12910) covalent geometry : angle 0.55595 (17451) *********************** 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 538 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 470 time to evaluate : 1.338 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: 0.7788 (pp30) cc_final: 0.7395 (pp30) REVERT: A 241 GLN cc_start: 0.7763 (tp-100) cc_final: 0.7532 (tp-100) REVERT: A 244 VAL cc_start: 0.8784 (p) cc_final: 0.8527 (p) REVERT: A 274 ARG cc_start: 0.8070 (ptm160) cc_final: 0.7751 (ptp-170) REVERT: A 281 TYR cc_start: 0.8699 (t80) cc_final: 0.8437 (t80) REVERT: A 293 THR cc_start: 0.7094 (m) cc_final: 0.6893 (m) REVERT: A 343 LYS cc_start: 0.8288 (tptp) cc_final: 0.7710 (tptp) REVERT: A 378 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8097 (tp) REVERT: A 385 SER cc_start: 0.8119 (m) cc_final: 0.7679 (p) REVERT: A 396 GLU cc_start: 0.7639 (pp20) cc_final: 0.7351 (tm-30) REVERT: A 399 LEU cc_start: 0.8124 (pt) cc_final: 0.7845 (pt) REVERT: A 414 GLN cc_start: 0.7132 (pp30) cc_final: 0.6842 (pp30) REVERT: A 433 MET cc_start: 0.6541 (tpt) cc_final: 0.6336 (tpt) REVERT: B 236 ILE cc_start: 0.8542 (tp) cc_final: 0.8267 (tp) REVERT: B 241 GLN cc_start: 0.7857 (tp-100) cc_final: 0.6908 (tp-100) REVERT: B 274 ARG cc_start: 0.8145 (ptm160) cc_final: 0.7385 (ptm160) REVERT: B 386 GLN cc_start: 0.7999 (tp40) cc_final: 0.7730 (tp40) REVERT: C 236 ILE cc_start: 0.8472 (tp) cc_final: 0.8233 (tp) REVERT: C 237 GLN cc_start: 0.7622 (pp30) cc_final: 0.7265 (pp30) REVERT: C 241 GLN cc_start: 0.7761 (mm-40) cc_final: 0.7540 (mm-40) REVERT: C 324 LEU cc_start: 0.8142 (tp) cc_final: 0.7861 (tt) REVERT: C 337 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7105 (mpt180) REVERT: C 343 LYS cc_start: 0.8482 (tptt) cc_final: 0.8274 (tptt) REVERT: C 344 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7540 (tm-30) REVERT: C 370 GLN cc_start: 0.7489 (mm-40) cc_final: 0.7160 (mm-40) REVERT: C 385 SER cc_start: 0.8132 (m) cc_final: 0.7639 (p) REVERT: C 420 ASN cc_start: 0.8085 (t0) cc_final: 0.7881 (t0) REVERT: D 236 ILE cc_start: 0.8562 (tp) cc_final: 0.8280 (tp) REVERT: D 244 VAL cc_start: 0.8816 (OUTLIER) cc_final: 0.8319 (p) REVERT: D 251 LEU cc_start: 0.8388 (tp) cc_final: 0.8111 (tp) REVERT: D 274 ARG cc_start: 0.8038 (ptm160) cc_final: 0.7822 (mtp85) REVERT: D 337 ARG cc_start: 0.7740 (mpt180) cc_final: 0.6955 (mpt180) REVERT: D 344 GLN cc_start: 0.7987 (pp30) cc_final: 0.7413 (pp30) REVERT: D 385 SER cc_start: 0.8236 (m) cc_final: 0.7477 (t) REVERT: D 386 GLN cc_start: 0.8108 (tp40) cc_final: 0.7851 (tp-100) REVERT: D 396 GLU cc_start: 0.7402 (tm-30) cc_final: 0.6957 (tm-30) REVERT: D 433 MET cc_start: 0.6763 (mmp) cc_final: 0.6489 (mmp) REVERT: E 236 ILE cc_start: 0.8741 (tp) cc_final: 0.8470 (tp) REVERT: E 237 GLN cc_start: 0.7591 (pp30) cc_final: 0.7175 (pp30) REVERT: E 241 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7585 (tp40) REVERT: E 269 GLN cc_start: 0.7521 (mt0) cc_final: 0.7176 (mt0) REVERT: E 343 LYS cc_start: 0.8114 (tptm) cc_final: 0.7740 (tptp) REVERT: E 387 SER cc_start: 0.8584 (m) cc_final: 0.8100 (p) REVERT: E 433 MET cc_start: 0.6120 (ttm) cc_final: 0.5552 (ttm) REVERT: F 236 ILE cc_start: 0.8692 (tp) cc_final: 0.8386 (tp) REVERT: F 241 GLN cc_start: 0.7553 (mm-40) cc_final: 0.7270 (mm-40) REVERT: F 251 LEU cc_start: 0.8272 (mp) cc_final: 0.8029 (mm) REVERT: F 280 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7509 (mt0) REVERT: F 321 ARG cc_start: 0.7429 (tmt-80) cc_final: 0.6690 (tmt-80) REVERT: F 343 LYS cc_start: 0.8057 (tptp) cc_final: 0.7661 (tptp) REVERT: G 237 GLN cc_start: 0.7677 (pp30) cc_final: 0.7338 (pp30) REVERT: G 278 LYS cc_start: 0.8211 (mttt) cc_final: 0.7726 (mtmm) REVERT: G 293 THR cc_start: 0.7994 (m) cc_final: 0.7765 (p) REVERT: G 321 ARG cc_start: 0.7634 (ttt90) cc_final: 0.7162 (ttt90) REVERT: G 323 LEU cc_start: 0.8356 (tp) cc_final: 0.7984 (tt) REVERT: G 385 SER cc_start: 0.8200 (m) cc_final: 0.7510 (p) REVERT: G 426 ARG cc_start: 0.7639 (tmt170) cc_final: 0.7171 (tmt170) REVERT: H 237 GLN cc_start: 0.7652 (pp30) cc_final: 0.7303 (pp30) REVERT: H 250 PHE cc_start: 0.8763 (t80) cc_final: 0.8347 (t80) REVERT: H 281 TYR cc_start: 0.8509 (t80) cc_final: 0.8274 (t80) REVERT: H 304 TYR cc_start: 0.7763 (m-80) cc_final: 0.7243 (m-80) REVERT: H 321 ARG cc_start: 0.7375 (tmt-80) cc_final: 0.6543 (tmt-80) REVERT: H 343 LYS cc_start: 0.8147 (tptm) cc_final: 0.7820 (tptp) REVERT: H 385 SER cc_start: 0.8102 (m) cc_final: 0.7505 (t) REVERT: H 387 SER cc_start: 0.8297 (m) cc_final: 0.7741 (p) REVERT: H 396 GLU cc_start: 0.6998 (tm-30) cc_final: 0.6662 (tm-30) REVERT: H 433 MET cc_start: 0.6636 (ttm) cc_final: 0.6321 (ttm) outliers start: 68 outliers final: 53 residues processed: 485 average time/residue: 0.3204 time to fit residues: 205.2957 Evaluate side-chains 530 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 472 time to evaluate : 1.349 ------------------------------------------------------------------------------- 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 278 LYS 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 287 HIS 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 337 ARG Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain E residue 289 HIS Chi-restraints excluded: chain E residue 305 GLN Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain F residue 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 F residue 409 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 344 GLN Chi-restraints excluded: chain G residue 415 SER 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 391 LEU 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 32 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 105 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 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 312 HIS ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS E 310 GLN ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 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** ** 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.156653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.135513 restraints weight = 21699.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.139880 restraints weight = 12654.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.142954 restraints weight = 8499.025| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2651 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= 0.144 Angle : 0.558 7.521 17451 Z= 0.291 Chirality : 0.036 0.157 1878 Planarity : 0.004 0.042 2311 Dihedral : 4.146 20.433 1863 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 6.18 % Allowed : 25.86 % Favored : 67.96 % 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: 0.54 (0.20), residues: 1664 helix: 0.81 (0.14), residues: 1400 sheet: None (None), residues: 0 loop : -1.76 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 377 HIS 0.008 0.001 HIS C 289 PHE 0.012 0.001 PHE D 356 TYR 0.023 0.002 TYR G 281 ARG 0.004 0.000 ARG F 388 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 995) hydrogen bonds : angle 3.61272 ( 2982) covalent geometry : bond 0.00305 (12910) covalent geometry : angle 0.55827 (17451) *********************** 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 552 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 477 time to evaluate : 1.334 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: 0.7790 (pp30) cc_final: 0.7398 (pp30) REVERT: A 241 GLN cc_start: 0.7741 (tp-100) cc_final: 0.7267 (tp-100) REVERT: A 244 VAL cc_start: 0.8784 (p) cc_final: 0.8357 (p) REVERT: A 274 ARG cc_start: 0.8134 (ptm160) cc_final: 0.7632 (mtp85) REVERT: A 281 TYR cc_start: 0.8695 (t80) cc_final: 0.8456 (t80) REVERT: A 343 LYS cc_start: 0.8292 (tptp) cc_final: 0.7679 (tptp) REVERT: A 364 GLU cc_start: 0.7701 (tp30) cc_final: 0.7322 (tp30) REVERT: A 378 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8080 (tp) REVERT: A 385 SER cc_start: 0.8132 (m) cc_final: 0.7683 (p) REVERT: A 396 GLU cc_start: 0.7573 (pp20) cc_final: 0.7309 (tm-30) REVERT: A 399 LEU cc_start: 0.8098 (pt) cc_final: 0.7807 (pt) REVERT: A 410 ARG cc_start: 0.7317 (ptt180) cc_final: 0.6940 (pmt170) REVERT: B 236 ILE cc_start: 0.8533 (tp) cc_final: 0.8265 (tp) REVERT: B 241 GLN cc_start: 0.7862 (tp-100) cc_final: 0.6881 (tp-100) REVERT: B 274 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7217 (ptm160) REVERT: B 378 LEU cc_start: 0.8516 (tt) cc_final: 0.8191 (pp) REVERT: B 386 GLN cc_start: 0.8024 (tp40) cc_final: 0.7718 (tp40) REVERT: C 236 ILE cc_start: 0.8484 (tp) cc_final: 0.8233 (tp) REVERT: C 237 GLN cc_start: 0.7628 (pp30) cc_final: 0.7265 (pp30) REVERT: C 241 GLN cc_start: 0.7744 (mm-40) cc_final: 0.7506 (mm-40) REVERT: C 281 TYR cc_start: 0.8660 (t80) cc_final: 0.8256 (t80) REVERT: C 337 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7088 (mpt180) REVERT: C 343 LYS cc_start: 0.8483 (tptt) cc_final: 0.8171 (tptt) REVERT: C 344 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7619 (tm-30) REVERT: C 370 GLN cc_start: 0.7510 (mm-40) cc_final: 0.7162 (mm-40) REVERT: C 385 SER cc_start: 0.8152 (m) cc_final: 0.7653 (p) REVERT: C 420 ASN cc_start: 0.8016 (t0) cc_final: 0.7812 (t0) REVERT: D 236 ILE cc_start: 0.8563 (tp) cc_final: 0.8286 (tp) REVERT: D 244 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8560 (p) REVERT: D 281 TYR cc_start: 0.8491 (t80) cc_final: 0.8252 (t80) REVERT: D 337 ARG cc_start: 0.7733 (mpt180) cc_final: 0.6920 (mpt180) REVERT: D 385 SER cc_start: 0.8241 (m) cc_final: 0.7483 (t) REVERT: D 386 GLN cc_start: 0.8101 (tp40) cc_final: 0.7819 (tp-100) REVERT: D 396 GLU cc_start: 0.7394 (tm-30) cc_final: 0.6942 (tm-30) REVERT: D 433 MET cc_start: 0.6802 (mmp) cc_final: 0.6542 (mmp) REVERT: E 236 ILE cc_start: 0.8730 (tp) cc_final: 0.8454 (tp) REVERT: E 237 GLN cc_start: 0.7578 (pp30) cc_final: 0.7174 (pp30) REVERT: E 241 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7580 (tp40) REVERT: E 269 GLN cc_start: 0.7526 (mt0) cc_final: 0.7177 (mt0) REVERT: E 343 LYS cc_start: 0.8094 (tptm) cc_final: 0.7771 (tptp) REVERT: E 387 SER cc_start: 0.8552 (m) cc_final: 0.8081 (p) REVERT: E 396 GLU cc_start: 0.7770 (tt0) cc_final: 0.7524 (tt0) REVERT: E 433 MET cc_start: 0.6134 (ttm) cc_final: 0.5561 (ttm) REVERT: F 236 ILE cc_start: 0.8726 (tp) cc_final: 0.8416 (tp) REVERT: F 241 GLN cc_start: 0.7549 (mm-40) cc_final: 0.7267 (mm-40) REVERT: F 251 LEU cc_start: 0.8266 (mp) cc_final: 0.8015 (mm) REVERT: F 321 ARG cc_start: 0.7432 (tmt-80) cc_final: 0.6668 (tmt-80) REVERT: F 343 LYS cc_start: 0.8042 (tptp) cc_final: 0.7709 (tptp) REVERT: F 433 MET cc_start: 0.7007 (mtm) cc_final: 0.6445 (mtm) REVERT: G 237 GLN cc_start: 0.7665 (pp30) cc_final: 0.7304 (pp30) REVERT: G 278 LYS cc_start: 0.8202 (mttt) cc_final: 0.7707 (mtmm) REVERT: G 287 HIS cc_start: 0.6831 (OUTLIER) cc_final: 0.6621 (m170) REVERT: G 293 THR cc_start: 0.8016 (m) cc_final: 0.7730 (p) REVERT: G 321 ARG cc_start: 0.7644 (ttt90) cc_final: 0.7154 (ttt90) REVERT: G 323 LEU cc_start: 0.8350 (tp) cc_final: 0.7960 (tt) REVERT: G 385 SER cc_start: 0.8192 (m) cc_final: 0.7488 (p) REVERT: G 426 ARG cc_start: 0.7645 (tmt170) cc_final: 0.7178 (tmt170) REVERT: H 237 GLN cc_start: 0.7643 (pp30) cc_final: 0.7285 (pp30) REVERT: H 250 PHE cc_start: 0.8769 (t80) cc_final: 0.8322 (t80) REVERT: H 321 ARG cc_start: 0.7379 (tmt-80) cc_final: 0.6504 (tmt-80) REVERT: H 343 LYS cc_start: 0.8145 (tptm) cc_final: 0.7806 (tptp) REVERT: H 396 GLU cc_start: 0.6970 (tm-30) cc_final: 0.6664 (tm-30) REVERT: H 433 MET cc_start: 0.6836 (ttm) cc_final: 0.6529 (ttm) outliers start: 75 outliers final: 56 residues processed: 493 average time/residue: 0.3140 time to fit residues: 205.4852 Evaluate side-chains 537 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 475 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 278 LYS 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 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 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 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 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 378 LEU 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 251 LEU Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain G residue 287 HIS Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 289 HIS Chi-restraints excluded: chain G residue 305 GLN Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 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 136 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 90 optimal weight: 0.3980 chunk 61 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 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 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** ** 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.156283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.135380 restraints weight = 21566.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.139672 restraints weight = 12604.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.142718 restraints weight = 8477.889| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12910 Z= 0.168 Angle : 0.582 7.800 17451 Z= 0.303 Chirality : 0.037 0.157 1878 Planarity : 0.004 0.042 2311 Dihedral : 4.184 20.701 1863 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.93 % Allowed : 27.02 % Favored : 67.05 % 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: 0.49 (0.20), residues: 1664 helix: 0.81 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -1.83 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 377 HIS 0.009 0.001 HIS C 289 PHE 0.013 0.001 PHE E 265 TYR 0.026 0.002 TYR G 281 ARG 0.004 0.000 ARG C 351 Details of bonding type rmsd hydrogen bonds : bond 0.03690 ( 995) hydrogen bonds : angle 3.63615 ( 2982) covalent geometry : bond 0.00351 (12910) covalent geometry : angle 0.58161 (17451) *********************** 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 548 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 476 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: A 237 GLN cc_start: 0.7816 (pp30) cc_final: 0.7398 (pp30) REVERT: A 244 VAL cc_start: 0.8796 (p) cc_final: 0.8492 (p) REVERT: A 274 ARG cc_start: 0.8128 (ptm160) cc_final: 0.7835 (ptp-170) REVERT: A 281 TYR cc_start: 0.8701 (t80) cc_final: 0.8437 (t80) REVERT: A 343 LYS cc_start: 0.8287 (tptp) cc_final: 0.7690 (tptp) REVERT: A 364 GLU cc_start: 0.7692 (tp30) cc_final: 0.7278 (tp30) REVERT: A 378 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8097 (tp) REVERT: A 385 SER cc_start: 0.8149 (m) cc_final: 0.7690 (p) REVERT: A 396 GLU cc_start: 0.7776 (pp20) cc_final: 0.7490 (tm-30) REVERT: A 399 LEU cc_start: 0.8108 (pt) cc_final: 0.7812 (pt) REVERT: A 410 ARG cc_start: 0.7370 (ptt180) cc_final: 0.7090 (pmt170) REVERT: B 236 ILE cc_start: 0.8569 (tp) cc_final: 0.8301 (tp) REVERT: B 241 GLN cc_start: 0.7846 (tp-100) cc_final: 0.6897 (tp-100) REVERT: B 274 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7279 (ptm160) REVERT: C 236 ILE cc_start: 0.8468 (tp) cc_final: 0.8209 (tp) REVERT: C 237 GLN cc_start: 0.7656 (pp30) cc_final: 0.7268 (pp30) REVERT: C 241 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7539 (mm-40) REVERT: C 337 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7109 (mpt180) REVERT: C 343 LYS cc_start: 0.8481 (tptt) cc_final: 0.8241 (tptt) REVERT: C 344 GLN cc_start: 0.7902 (tm-30) cc_final: 0.7542 (tm-30) REVERT: C 370 GLN cc_start: 0.7499 (mm-40) cc_final: 0.7153 (mm-40) REVERT: C 385 SER cc_start: 0.8174 (m) cc_final: 0.7644 (p) REVERT: C 420 ASN cc_start: 0.8005 (t0) cc_final: 0.7765 (t0) REVERT: D 236 ILE cc_start: 0.8560 (tp) cc_final: 0.8284 (tp) REVERT: D 244 VAL cc_start: 0.8769 (OUTLIER) cc_final: 0.8538 (p) REVERT: D 337 ARG cc_start: 0.7738 (mpt180) cc_final: 0.6932 (mpt180) REVERT: D 385 SER cc_start: 0.8230 (m) cc_final: 0.7461 (t) REVERT: D 386 GLN cc_start: 0.8078 (tp40) cc_final: 0.7792 (tp-100) REVERT: D 396 GLU cc_start: 0.7396 (tm-30) cc_final: 0.6950 (tm-30) REVERT: D 433 MET cc_start: 0.6839 (mmp) cc_final: 0.6600 (mmp) REVERT: E 236 ILE cc_start: 0.8713 (tp) cc_final: 0.8450 (tp) REVERT: E 237 GLN cc_start: 0.7616 (pp30) cc_final: 0.7165 (pp30) REVERT: E 241 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7562 (tp40) REVERT: E 269 GLN cc_start: 0.7481 (mt0) cc_final: 0.7151 (mt0) REVERT: E 319 TYR cc_start: 0.7907 (t80) cc_final: 0.7679 (t80) REVERT: E 343 LYS cc_start: 0.8126 (tptm) cc_final: 0.7804 (tptp) REVERT: E 363 LYS cc_start: 0.8143 (tmtt) cc_final: 0.7730 (tmtt) REVERT: E 396 GLU cc_start: 0.7803 (tt0) cc_final: 0.7513 (tt0) REVERT: E 433 MET cc_start: 0.6183 (ttm) cc_final: 0.5596 (ttm) REVERT: F 236 ILE cc_start: 0.8702 (tp) cc_final: 0.8385 (tp) REVERT: F 241 GLN cc_start: 0.7561 (mm-40) cc_final: 0.7046 (mm-40) REVERT: F 251 LEU cc_start: 0.8277 (mp) cc_final: 0.8036 (mm) REVERT: F 274 ARG cc_start: 0.8312 (ptm160) cc_final: 0.7725 (ptm160) REVERT: F 297 ILE cc_start: 0.8520 (mm) cc_final: 0.8267 (mm) REVERT: F 321 ARG cc_start: 0.7476 (tmt-80) cc_final: 0.6725 (tmt-80) REVERT: F 343 LYS cc_start: 0.8189 (tptp) cc_final: 0.7817 (tptp) REVERT: F 433 MET cc_start: 0.7002 (mtm) cc_final: 0.6433 (mtm) REVERT: G 237 GLN cc_start: 0.7694 (pp30) cc_final: 0.7342 (pp30) REVERT: G 278 LYS cc_start: 0.8247 (mttt) cc_final: 0.7759 (mtmm) REVERT: G 293 THR cc_start: 0.8078 (m) cc_final: 0.7839 (p) REVERT: G 321 ARG cc_start: 0.7657 (ttt90) cc_final: 0.7187 (ttt90) REVERT: G 323 LEU cc_start: 0.8348 (tp) cc_final: 0.7949 (tt) REVERT: G 363 LYS cc_start: 0.8193 (tmtt) cc_final: 0.7590 (tmtt) REVERT: G 385 SER cc_start: 0.8176 (m) cc_final: 0.7483 (p) REVERT: G 426 ARG cc_start: 0.7625 (tmt170) cc_final: 0.7161 (tmt170) REVERT: H 237 GLN cc_start: 0.7660 (pp30) cc_final: 0.7282 (pp30) REVERT: H 250 PHE cc_start: 0.8794 (t80) cc_final: 0.8309 (t80) REVERT: H 343 LYS cc_start: 0.8187 (tptm) cc_final: 0.7821 (tptp) REVERT: H 363 LYS cc_start: 0.8066 (tmtt) cc_final: 0.7718 (tmtt) REVERT: H 388 ARG cc_start: 0.7022 (ttt90) cc_final: 0.6797 (ttt90) REVERT: H 433 MET cc_start: 0.6813 (ttm) cc_final: 0.6475 (ttm) outliers start: 72 outliers final: 60 residues processed: 490 average time/residue: 0.3130 time to fit residues: 203.6559 Evaluate side-chains 538 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 473 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 278 LYS 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 287 HIS Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 305 GLN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 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 337 ARG Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 246 ILE 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 378 LEU 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 256 MET Chi-restraints excluded: chain G residue 287 HIS Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 289 HIS Chi-restraints excluded: chain G residue 305 GLN Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 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 391 LEU Chi-restraints excluded: chain H residue 415 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 88 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 136 optimal weight: 0.3980 chunk 135 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 287 HIS 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 310 GLN D 312 HIS ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN F 289 HIS ** F 316 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.157029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135602 restraints weight = 21659.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.139953 restraints weight = 12636.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.143056 restraints weight = 8517.981| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2883 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= 0.147 Angle : 0.585 8.446 17451 Z= 0.302 Chirality : 0.037 0.172 1878 Planarity : 0.004 0.043 2311 Dihedral : 4.166 20.209 1863 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 6.18 % Allowed : 27.68 % Favored : 66.14 % 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: 0.52 (0.20), residues: 1664 helix: 0.84 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -1.84 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 377 HIS 0.007 0.001 HIS C 289 PHE 0.011 0.001 PHE E 265 TYR 0.024 0.002 TYR G 281 ARG 0.004 0.000 ARG E 351 Details of bonding type rmsd hydrogen bonds : bond 0.03602 ( 995) hydrogen bonds : angle 3.61326 ( 2982) covalent geometry : bond 0.00314 (12910) covalent geometry : angle 0.58534 (17451) *********************** 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 546 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 471 time to evaluate : 1.359 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 241 GLN cc_start: 0.7840 (tp-100) cc_final: 0.7542 (tp-100) REVERT: A 244 VAL cc_start: 0.8808 (p) cc_final: 0.8372 (p) REVERT: A 281 TYR cc_start: 0.8680 (t80) cc_final: 0.8427 (t80) REVERT: A 343 LYS cc_start: 0.8297 (tptp) cc_final: 0.7680 (tptp) REVERT: A 351 ARG cc_start: 0.7362 (ttm-80) cc_final: 0.6783 (ttm-80) REVERT: A 364 GLU cc_start: 0.7686 (tp30) cc_final: 0.7299 (tp30) REVERT: A 378 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8083 (tp) REVERT: A 385 SER cc_start: 0.8208 (m) cc_final: 0.7773 (p) REVERT: A 386 GLN cc_start: 0.8521 (tp40) cc_final: 0.8201 (tp40) REVERT: A 399 LEU cc_start: 0.8090 (pt) cc_final: 0.7793 (pt) REVERT: A 410 ARG cc_start: 0.7368 (ptt180) cc_final: 0.7079 (pmt170) REVERT: B 236 ILE cc_start: 0.8548 (tp) cc_final: 0.8282 (tp) REVERT: B 241 GLN cc_start: 0.7866 (tp-100) cc_final: 0.6873 (tp-100) REVERT: B 274 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7254 (ptm160) REVERT: C 236 ILE cc_start: 0.8445 (tp) cc_final: 0.8194 (tp) REVERT: C 237 GLN cc_start: 0.7630 (pp30) cc_final: 0.7275 (pp30) REVERT: C 241 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7516 (mm-40) REVERT: C 324 LEU cc_start: 0.8186 (tp) cc_final: 0.7980 (tt) REVERT: C 337 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7128 (mpt180) REVERT: C 343 LYS cc_start: 0.8488 (tptt) cc_final: 0.8202 (tptt) REVERT: C 344 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7558 (tm-30) REVERT: C 370 GLN cc_start: 0.7497 (mm-40) cc_final: 0.7125 (mm-40) REVERT: C 385 SER cc_start: 0.8172 (m) cc_final: 0.7534 (p) REVERT: C 386 GLN cc_start: 0.7866 (tp40) cc_final: 0.7508 (tp40) REVERT: D 236 ILE cc_start: 0.8545 (tp) cc_final: 0.8274 (tp) REVERT: D 244 VAL cc_start: 0.8749 (OUTLIER) cc_final: 0.8520 (p) REVERT: D 337 ARG cc_start: 0.7737 (mpt180) cc_final: 0.6913 (mpt180) REVERT: D 385 SER cc_start: 0.8223 (m) cc_final: 0.7444 (t) REVERT: D 386 GLN cc_start: 0.8044 (tp40) cc_final: 0.7758 (tp-100) REVERT: D 396 GLU cc_start: 0.7394 (tm-30) cc_final: 0.6941 (tm-30) REVERT: D 433 MET cc_start: 0.6904 (mmp) cc_final: 0.6651 (mmp) REVERT: E 236 ILE cc_start: 0.8689 (tp) cc_final: 0.8424 (tp) REVERT: E 237 GLN cc_start: 0.7612 (pp30) cc_final: 0.7196 (pp30) REVERT: E 241 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7535 (tp40) REVERT: E 269 GLN cc_start: 0.7510 (mt0) cc_final: 0.7162 (mt0) REVERT: E 343 LYS cc_start: 0.8142 (tptm) cc_final: 0.7807 (tptp) REVERT: E 363 LYS cc_start: 0.8120 (tmtt) cc_final: 0.7702 (tmtt) REVERT: E 396 GLU cc_start: 0.7811 (tt0) cc_final: 0.7533 (tt0) REVERT: E 433 MET cc_start: 0.6239 (ttm) cc_final: 0.5656 (ttm) REVERT: F 236 ILE cc_start: 0.8710 (tp) cc_final: 0.8388 (tp) REVERT: F 241 GLN cc_start: 0.7569 (mm-40) cc_final: 0.7063 (mm-40) REVERT: F 251 LEU cc_start: 0.8289 (mp) cc_final: 0.8051 (mm) REVERT: F 274 ARG cc_start: 0.8307 (ptm160) cc_final: 0.7733 (ptm160) REVERT: F 280 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7533 (mt0) REVERT: F 297 ILE cc_start: 0.8534 (mm) cc_final: 0.8298 (mm) REVERT: F 321 ARG cc_start: 0.7485 (tmt-80) cc_final: 0.6705 (tmt-80) REVERT: F 343 LYS cc_start: 0.8203 (tptp) cc_final: 0.7822 (tptp) REVERT: F 433 MET cc_start: 0.6984 (mtm) cc_final: 0.6428 (mtm) REVERT: G 237 GLN cc_start: 0.7706 (pp30) cc_final: 0.7333 (pp30) REVERT: G 278 LYS cc_start: 0.8222 (mttt) cc_final: 0.7611 (mtmm) REVERT: G 293 THR cc_start: 0.8036 (m) cc_final: 0.7789 (p) REVERT: G 321 ARG cc_start: 0.7665 (ttt90) cc_final: 0.7173 (ttt90) REVERT: G 323 LEU cc_start: 0.8393 (tp) cc_final: 0.7993 (tt) REVERT: G 385 SER cc_start: 0.8171 (m) cc_final: 0.7469 (p) REVERT: G 426 ARG cc_start: 0.7643 (tmt170) cc_final: 0.7152 (tmt170) REVERT: H 237 GLN cc_start: 0.7658 (pp30) cc_final: 0.7287 (pp30) REVERT: H 250 PHE cc_start: 0.8791 (t80) cc_final: 0.8296 (t80) REVERT: H 343 LYS cc_start: 0.8201 (tptm) cc_final: 0.7812 (tptp) REVERT: H 363 LYS cc_start: 0.8072 (tmtt) cc_final: 0.7704 (tmtt) REVERT: H 396 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6676 (tm-30) REVERT: H 433 MET cc_start: 0.6816 (ttm) cc_final: 0.6441 (ttm) outliers start: 75 outliers final: 61 residues processed: 487 average time/residue: 0.3115 time to fit residues: 200.6013 Evaluate side-chains 538 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 471 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 278 LYS 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 287 HIS Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 305 GLN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain 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 337 ARG Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 246 ILE 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 E residue 427 LEU 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 378 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 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 150 optimal weight: 0.4980 chunk 93 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 269 GLN B 287 HIS 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 305 GLN D 310 GLN ** 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** ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 289 HIS ** F 316 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.157118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.135969 restraints weight = 21335.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.140304 restraints weight = 12490.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.143358 restraints weight = 8386.949| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2977 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= 0.151 Angle : 0.592 8.718 17451 Z= 0.306 Chirality : 0.037 0.169 1878 Planarity : 0.004 0.042 2311 Dihedral : 4.183 20.224 1863 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.77 % Allowed : 29.00 % Favored : 65.24 % 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: 0.52 (0.20), residues: 1664 helix: 0.86 (0.14), residues: 1376 sheet: None (None), residues: 0 loop : -1.92 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 377 HIS 0.008 0.001 HIS C 289 PHE 0.013 0.001 PHE A 268 TYR 0.022 0.002 TYR G 281 ARG 0.007 0.000 ARG B 295 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 995) hydrogen bonds : angle 3.62085 ( 2982) covalent geometry : bond 0.00323 (12910) covalent geometry : angle 0.59182 (17451) *********************** 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 541 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 471 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7790 (pp30) cc_final: 0.7424 (pp30) REVERT: A 281 TYR cc_start: 0.8671 (t80) cc_final: 0.8390 (t80) REVERT: A 343 LYS cc_start: 0.8299 (tptp) cc_final: 0.7667 (tptp) REVERT: A 351 ARG cc_start: 0.7352 (ttm-80) cc_final: 0.6786 (ttm-80) REVERT: A 364 GLU cc_start: 0.7655 (tp30) cc_final: 0.7275 (tp30) REVERT: A 378 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8080 (tp) REVERT: A 385 SER cc_start: 0.8207 (m) cc_final: 0.7798 (p) REVERT: A 399 LEU cc_start: 0.8088 (pt) cc_final: 0.7774 (pt) REVERT: A 410 ARG cc_start: 0.7379 (ptt180) cc_final: 0.7092 (pmt170) REVERT: B 236 ILE cc_start: 0.8540 (tp) cc_final: 0.8260 (tp) REVERT: B 241 GLN cc_start: 0.7861 (tp-100) cc_final: 0.6884 (tp-100) REVERT: B 274 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7193 (ptm160) REVERT: B 377 TRP cc_start: 0.6832 (t60) cc_final: 0.6599 (t60) REVERT: C 236 ILE cc_start: 0.8436 (tp) cc_final: 0.8180 (tp) REVERT: C 241 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7467 (mm-40) REVERT: C 337 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7118 (mpt180) REVERT: C 343 LYS cc_start: 0.8461 (tptt) cc_final: 0.8195 (tptt) REVERT: C 344 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7566 (tm-30) REVERT: C 370 GLN cc_start: 0.7497 (mm-40) cc_final: 0.7141 (mm-40) REVERT: C 385 SER cc_start: 0.8156 (m) cc_final: 0.7511 (p) REVERT: C 386 GLN cc_start: 0.7894 (tp40) cc_final: 0.7517 (tp40) REVERT: D 236 ILE cc_start: 0.8553 (tp) cc_final: 0.8281 (tp) REVERT: D 244 VAL cc_start: 0.8743 (OUTLIER) cc_final: 0.8510 (p) REVERT: D 337 ARG cc_start: 0.7740 (mpt180) cc_final: 0.6980 (mpt180) REVERT: D 385 SER cc_start: 0.8227 (m) cc_final: 0.7447 (t) REVERT: D 386 GLN cc_start: 0.8025 (tp40) cc_final: 0.7726 (tp40) REVERT: D 396 GLU cc_start: 0.7392 (tm-30) cc_final: 0.6940 (tm-30) REVERT: D 433 MET cc_start: 0.6892 (mmp) cc_final: 0.6632 (mmp) REVERT: E 236 ILE cc_start: 0.8684 (tp) cc_final: 0.8416 (tp) REVERT: E 237 GLN cc_start: 0.7612 (pp30) cc_final: 0.7211 (pp30) REVERT: E 241 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7171 (tp40) REVERT: E 269 GLN cc_start: 0.7503 (mt0) cc_final: 0.7144 (mt0) REVERT: E 274 ARG cc_start: 0.8279 (ptm160) cc_final: 0.7538 (ptm160) REVERT: E 343 LYS cc_start: 0.8133 (tptm) cc_final: 0.7787 (tptp) REVERT: E 363 LYS cc_start: 0.8125 (tmtt) cc_final: 0.7696 (tmtt) REVERT: E 387 SER cc_start: 0.8532 (m) cc_final: 0.8115 (p) REVERT: E 433 MET cc_start: 0.6269 (ttm) cc_final: 0.5720 (ttm) REVERT: F 236 ILE cc_start: 0.8692 (tp) cc_final: 0.8372 (tp) REVERT: F 241 GLN cc_start: 0.7564 (mm-40) cc_final: 0.7081 (mm-40) REVERT: F 274 ARG cc_start: 0.8304 (ptm160) cc_final: 0.7786 (ptm160) REVERT: F 297 ILE cc_start: 0.8552 (mm) cc_final: 0.8329 (mm) REVERT: F 321 ARG cc_start: 0.7487 (tmt-80) cc_final: 0.6713 (tmt-80) REVERT: F 343 LYS cc_start: 0.8195 (tptp) cc_final: 0.7792 (tptp) REVERT: F 433 MET cc_start: 0.6973 (mtm) cc_final: 0.6436 (mtm) REVERT: G 237 GLN cc_start: 0.7715 (pp30) cc_final: 0.7349 (pp30) REVERT: G 278 LYS cc_start: 0.8253 (mttt) cc_final: 0.7704 (mtmm) REVERT: G 289 HIS cc_start: 0.7450 (OUTLIER) cc_final: 0.7120 (m90) REVERT: G 321 ARG cc_start: 0.7661 (ttt90) cc_final: 0.7181 (ttt90) REVERT: G 323 LEU cc_start: 0.8408 (tp) cc_final: 0.7996 (tt) REVERT: G 385 SER cc_start: 0.8179 (m) cc_final: 0.7494 (p) REVERT: G 414 GLN cc_start: 0.7199 (pt0) cc_final: 0.6812 (pm20) REVERT: G 426 ARG cc_start: 0.7624 (tmt170) cc_final: 0.7154 (tmt170) REVERT: H 237 GLN cc_start: 0.7657 (pp30) cc_final: 0.7282 (pp30) REVERT: H 250 PHE cc_start: 0.8786 (t80) cc_final: 0.8288 (t80) REVERT: H 343 LYS cc_start: 0.8197 (tptm) cc_final: 0.7803 (tptp) REVERT: H 363 LYS cc_start: 0.8067 (tmtt) cc_final: 0.7733 (tmtt) REVERT: H 396 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6678 (tm-30) REVERT: H 433 MET cc_start: 0.6840 (ttm) cc_final: 0.6451 (ttm) outliers start: 70 outliers final: 61 residues processed: 484 average time/residue: 0.3172 time to fit residues: 204.7936 Evaluate side-chains 537 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 470 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 278 LYS 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 287 HIS Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 305 GLN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain 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 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 306 LEU Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 289 HIS Chi-restraints excluded: chain E residue 302 LEU 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 E residue 427 LEU Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 305 GLN Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 344 GLN Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 427 LEU Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain G residue 287 HIS Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 289 HIS Chi-restraints excluded: chain G residue 305 GLN Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain H residue 241 GLN Chi-restraints excluded: chain H residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 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 287 HIS 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 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** F 280 GLN F 289 HIS ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 287 HIS G 289 HIS ** G 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 310 GLN ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.149099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.127999 restraints weight = 21532.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.132390 restraints weight = 12730.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.135499 restraints weight = 8539.588| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 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 0.034 12910 Z= 0.159 Angle : 0.609 10.416 17451 Z= 0.313 Chirality : 0.037 0.169 1878 Planarity : 0.004 0.041 2311 Dihedral : 4.215 20.308 1863 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 6.43 % Allowed : 28.42 % Favored : 65.16 % 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: 0.52 (0.20), residues: 1664 helix: 0.87 (0.14), residues: 1376 sheet: None (None), residues: 0 loop : -1.93 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 377 HIS 0.009 0.001 HIS C 289 PHE 0.013 0.001 PHE H 265 TYR 0.023 0.002 TYR B 281 ARG 0.008 0.000 ARG B 295 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 995) hydrogen bonds : angle 3.63850 ( 2982) covalent geometry : bond 0.00339 (12910) covalent geometry : angle 0.60859 (17451) ********************** 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 550 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 472 time to evaluate : 1.391 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: 0.7777 (pp30) cc_final: 0.7404 (pp30) REVERT: A 305 GLN cc_start: 0.8479 (tp40) cc_final: 0.8216 (tp40) REVERT: A 343 LYS cc_start: 0.8310 (tptp) cc_final: 0.7678 (tptp) REVERT: A 364 GLU cc_start: 0.7680 (tp30) cc_final: 0.7291 (tp30) REVERT: A 378 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8084 (tp) REVERT: A 385 SER cc_start: 0.8175 (m) cc_final: 0.7772 (p) REVERT: A 386 GLN cc_start: 0.8551 (tp40) cc_final: 0.8121 (tp40) REVERT: A 399 LEU cc_start: 0.8088 (pt) cc_final: 0.7766 (pt) REVERT: A 410 ARG cc_start: 0.7486 (ptt180) cc_final: 0.7178 (pmt170) REVERT: B 236 ILE cc_start: 0.8591 (tp) cc_final: 0.8308 (tp) REVERT: B 241 GLN cc_start: 0.7854 (tp-100) cc_final: 0.6880 (tp-100) REVERT: B 274 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7223 (ptm160) REVERT: B 321 ARG cc_start: 0.7352 (mmp-170) cc_final: 0.7150 (mmp-170) REVERT: B 377 TRP cc_start: 0.6892 (t60) cc_final: 0.6634 (t60) REVERT: C 236 ILE cc_start: 0.8458 (tp) cc_final: 0.8199 (tp) REVERT: C 241 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7437 (mm-40) REVERT: C 337 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7068 (mpt180) REVERT: C 344 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7549 (tm-30) REVERT: C 370 GLN cc_start: 0.7486 (mm-40) cc_final: 0.7109 (mm-40) REVERT: C 385 SER cc_start: 0.8154 (m) cc_final: 0.7516 (p) REVERT: C 386 GLN cc_start: 0.7929 (tp40) cc_final: 0.7558 (tp40) REVERT: D 236 ILE cc_start: 0.8585 (tp) cc_final: 0.8306 (tp) REVERT: D 244 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8508 (p) REVERT: D 337 ARG cc_start: 0.7684 (mpt180) cc_final: 0.6963 (mpt180) REVERT: D 385 SER cc_start: 0.8237 (m) cc_final: 0.7472 (t) REVERT: D 386 GLN cc_start: 0.8074 (tp40) cc_final: 0.7771 (tp40) REVERT: D 396 GLU cc_start: 0.7380 (tm-30) cc_final: 0.6924 (tm-30) REVERT: D 433 MET cc_start: 0.6923 (mmp) cc_final: 0.6679 (mmp) REVERT: E 236 ILE cc_start: 0.8663 (tp) cc_final: 0.8410 (tp) REVERT: E 237 GLN cc_start: 0.7620 (pp30) cc_final: 0.7242 (pp30) REVERT: E 241 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7168 (tp40) REVERT: E 269 GLN cc_start: 0.7524 (mt0) cc_final: 0.7258 (mt0) REVERT: E 274 ARG cc_start: 0.8312 (ptm160) cc_final: 0.7542 (ptm160) REVERT: E 343 LYS cc_start: 0.8141 (tptm) cc_final: 0.7782 (tptp) REVERT: E 363 LYS cc_start: 0.8149 (tmtt) cc_final: 0.7703 (tmtt) REVERT: E 387 SER cc_start: 0.8562 (m) cc_final: 0.8158 (p) REVERT: E 433 MET cc_start: 0.6348 (ttm) cc_final: 0.5788 (ttm) REVERT: F 236 ILE cc_start: 0.8703 (tp) cc_final: 0.8371 (tp) REVERT: F 241 GLN cc_start: 0.7536 (mm-40) cc_final: 0.7079 (mm-40) REVERT: F 274 ARG cc_start: 0.8308 (ptm160) cc_final: 0.7799 (ptm160) REVERT: F 280 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7517 (mt0) REVERT: F 297 ILE cc_start: 0.8561 (mm) cc_final: 0.8347 (mm) REVERT: F 321 ARG cc_start: 0.7506 (tmt-80) cc_final: 0.6728 (tmt-80) REVERT: F 343 LYS cc_start: 0.8179 (tptp) cc_final: 0.7779 (tptp) REVERT: F 433 MET cc_start: 0.7060 (mtm) cc_final: 0.6519 (mtm) REVERT: G 237 GLN cc_start: 0.7720 (pp30) cc_final: 0.7358 (pp30) REVERT: G 250 PHE cc_start: 0.8827 (t80) cc_final: 0.8511 (t80) REVERT: G 278 LYS cc_start: 0.8281 (mttt) cc_final: 0.7740 (mtmm) REVERT: G 289 HIS cc_start: 0.7483 (OUTLIER) cc_final: 0.7137 (m90) REVERT: G 321 ARG cc_start: 0.7708 (ttt90) cc_final: 0.7192 (ttt90) REVERT: G 385 SER cc_start: 0.8164 (m) cc_final: 0.7486 (p) REVERT: G 414 GLN cc_start: 0.7221 (pt0) cc_final: 0.6822 (pm20) REVERT: G 426 ARG cc_start: 0.7601 (tmt170) cc_final: 0.7152 (tmt170) REVERT: H 237 GLN cc_start: 0.7651 (pp30) cc_final: 0.7275 (pp30) REVERT: H 250 PHE cc_start: 0.8783 (t80) cc_final: 0.8273 (t80) REVERT: H 343 LYS cc_start: 0.8213 (tptm) cc_final: 0.7817 (tptp) REVERT: H 363 LYS cc_start: 0.8089 (tmtt) cc_final: 0.7730 (tmtt) REVERT: H 433 MET cc_start: 0.6836 (ttm) cc_final: 0.6440 (ttm) outliers start: 78 outliers final: 65 residues processed: 494 average time/residue: 0.3111 time to fit residues: 204.0214 Evaluate side-chains 541 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 469 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 278 LYS 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 287 HIS Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 305 GLN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 337 ARG Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 287 HIS 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 415 SER Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 246 ILE 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 302 LEU 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 E residue 427 LEU 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 378 LEU Chi-restraints excluded: chain F residue 427 LEU Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain G residue 287 HIS Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 289 HIS Chi-restraints excluded: chain G residue 305 GLN Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 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 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 78 optimal weight: 3.9990 chunk 10 optimal weight: 0.0970 chunk 126 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 287 HIS 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 287 HIS D 310 GLN ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS ** E 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.150166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.131525 restraints weight = 21458.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.135717 restraints weight = 12663.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.138699 restraints weight = 8454.299| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12910 Z= 0.177 Angle : 0.624 10.262 17451 Z= 0.324 Chirality : 0.038 0.170 1878 Planarity : 0.004 0.041 2311 Dihedral : 4.251 20.569 1863 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 6.43 % Allowed : 28.83 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.41 (0.20), residues: 1664 helix: 0.79 (0.14), residues: 1376 sheet: None (None), residues: 0 loop : -2.02 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP H 377 HIS 0.009 0.001 HIS C 289 PHE 0.013 0.001 PHE H 265 TYR 0.022 0.002 TYR B 281 ARG 0.007 0.000 ARG B 295 Details of bonding type rmsd hydrogen bonds : bond 0.03779 ( 995) hydrogen bonds : angle 3.67840 ( 2982) covalent geometry : bond 0.00372 (12910) covalent geometry : angle 0.62362 (17451) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4792.74 seconds wall clock time: 83 minutes 32.65 seconds (5012.65 seconds total)