Starting phenix.real_space_refine on Sat Jan 18 17:42:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d9x_27269/01_2025/8d9x_27269_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d9x_27269/01_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_27269/01_2025/8d9x_27269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d9x_27269/01_2025/8d9x_27269.map" model { file = "/net/cci-nas-00/data/ceres_data/8d9x_27269/01_2025/8d9x_27269_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d9x_27269/01_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 12670 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1585 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 205} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1576 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 205} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1585 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 205} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "D" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1584 Classifications: {'peptide': 210} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 205} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "E" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1585 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 205} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "F" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1585 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 205} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "G" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1585 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 205} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "H" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1585 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 205} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 44 Time building chain proxies: 7.26, per 1000 atoms: 0.57 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: 2.99 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: 0.88 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: 3.76 Time building geometry restraints manager: 3.46 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: 0.700 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: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 28.420 Find NCS groups from input model: 0.610 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 12910 Z= 0.289 Angle : 0.709 8.701 17451 Z= 0.406 Chirality : 0.042 0.516 1878 Planarity : 0.005 0.068 2311 Dihedral : 13.941 89.936 4561 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.58 % Allowed : 0.49 % Favored : 98.93 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 1664 helix: 0.46 (0.14), residues: 1352 sheet: None (None), residues: 0 loop : -1.46 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 377 HIS 0.011 0.001 HIS G 287 PHE 0.033 0.002 PHE C 250 TYR 0.029 0.002 TYR F 389 ARG 0.016 0.001 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 488 time to evaluate : 1.379 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: 0.3069 time to fit residues: 200.5240 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 : 1.295 ------------------------------------------------------------------------------- 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 = 0.149925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.129707 restraints weight = 21453.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.134183 restraints weight = 12483.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.137271 restraints weight = 8276.808| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12910 Z= 0.200 Angle : 0.591 7.250 17451 Z= 0.305 Chirality : 0.037 0.133 1878 Planarity : 0.004 0.040 2311 Dihedral : 4.968 53.729 1875 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.05 % Allowed : 16.47 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.20), residues: 1664 helix: 0.62 (0.14), residues: 1376 sheet: None (None), residues: 0 loop : -1.31 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 377 HIS 0.004 0.001 HIS C 289 PHE 0.016 0.001 PHE H 250 TYR 0.022 0.002 TYR C 281 ARG 0.006 0.001 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 484 time to evaluate : 1.258 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: 0.7665 (pp30) cc_final: 0.7341 (pp30) REVERT: A 238 GLN cc_start: 0.8520 (tp40) cc_final: 0.8212 (tp40) REVERT: A 241 GLN cc_start: 0.7888 (tp-100) cc_final: 0.7618 (tp-100) REVERT: A 274 ARG cc_start: 0.8125 (ptm160) cc_final: 0.7780 (ptp-170) REVERT: A 281 TYR cc_start: 0.8669 (t80) cc_final: 0.8456 (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: 0.6509 (tpt) cc_final: 0.6215 (tpt) REVERT: B 236 ILE cc_start: 0.8577 (tp) cc_final: 0.8336 (tp) REVERT: B 241 GLN cc_start: 0.7830 (tp-100) cc_final: 0.7385 (tp-100) REVERT: B 281 TYR cc_start: 0.8536 (t80) cc_final: 0.8325 (t80) REVERT: B 386 GLN cc_start: 0.7884 (tp40) cc_final: 0.7319 (tp40) REVERT: B 414 GLN cc_start: 0.6990 (pm20) cc_final: 0.6697 (pm20) REVERT: C 236 ILE cc_start: 0.8526 (tp) cc_final: 0.8296 (tp) REVERT: C 241 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7422 (mm-40) REVERT: C 297 ILE cc_start: 0.8706 (mm) cc_final: 0.8469 (mm) REVERT: C 343 LYS cc_start: 0.8303 (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: 0.7462 (mm-40) cc_final: 0.7231 (mm-40) REVERT: C 386 GLN cc_start: 0.7887 (tp40) cc_final: 0.7406 (tp40) REVERT: C 420 ASN cc_start: 0.8230 (t0) cc_final: 0.7911 (t0) REVERT: C 426 ARG cc_start: 0.6971 (tmt170) cc_final: 0.6713 (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: 0.7993 (tp) REVERT: D 305 GLN cc_start: 0.7788 (tp-100) cc_final: 0.7205 (tp-100) REVERT: D 354 GLN cc_start: 0.7100 (mt0) cc_final: 0.6890 (mt0) REVERT: D 396 GLU cc_start: 0.7444 (tm-30) cc_final: 0.7049 (tm-30) REVERT: D 433 MET cc_start: 0.6530 (mmp) cc_final: 0.6104 (mmp) REVERT: E 236 ILE cc_start: 0.8647 (tp) cc_final: 0.8411 (tp) REVERT: E 237 GLN cc_start: 0.7497 (pp30) cc_final: 0.7209 (pp30) REVERT: E 269 GLN cc_start: 0.7637 (mt0) cc_final: 0.7328 (mt0) REVERT: E 304 TYR cc_start: 0.7756 (m-80) cc_final: 0.7226 (m-80) REVERT: E 343 LYS cc_start: 0.8090 (tptm) cc_final: 0.7691 (tptp) REVERT: E 414 GLN cc_start: 0.6976 (pp30) cc_final: 0.6709 (pp30) REVERT: E 433 MET cc_start: 0.5854 (ttm) cc_final: 0.5408 (ttm) REVERT: F 236 ILE cc_start: 0.8660 (tp) cc_final: 0.8388 (tp) REVERT: F 238 GLN cc_start: 0.8090 (tp40) cc_final: 0.7803 (tp40) REVERT: F 241 GLN cc_start: 0.7564 (mm-40) cc_final: 0.7188 (mm-40) REVERT: F 251 LEU cc_start: 0.8240 (mp) cc_final: 0.8030 (mm) REVERT: F 343 LYS cc_start: 0.8045 (tptp) cc_final: 0.7566 (tptp) REVERT: F 414 GLN cc_start: 0.7500 (pp30) cc_final: 0.6468 (pp30) REVERT: F 420 ASN cc_start: 0.7698 (t0) cc_final: 0.7479 (t0) REVERT: G 237 GLN cc_start: 0.7621 (pp30) cc_final: 0.7374 (pp30) REVERT: G 281 TYR cc_start: 0.8316 (t80) cc_final: 0.8112 (t80) REVERT: G 287 HIS cc_start: 0.7063 (t-170) cc_final: 0.6677 (t-170) REVERT: G 321 ARG cc_start: 0.7495 (ttt90) cc_final: 0.7030 (ttt90) REVERT: G 323 LEU cc_start: 0.8326 (tp) cc_final: 0.8006 (tt) REVERT: G 385 SER cc_start: 0.8097 (m) cc_final: 0.7411 (p) REVERT: G 386 GLN cc_start: 0.7871 (tp40) cc_final: 0.7486 (tp40) REVERT: G 426 ARG cc_start: 0.7662 (tmt170) cc_final: 0.7195 (tmt170) REVERT: H 237 GLN cc_start: 0.7563 (pp30) cc_final: 0.7320 (pp30) REVERT: H 281 TYR cc_start: 0.8572 (t80) cc_final: 0.8309 (t80) REVERT: H 343 LYS cc_start: 0.8120 (tptm) cc_final: 0.7776 (tptp) REVERT: H 371 ARG cc_start: 0.7045 (ttm110) cc_final: 0.6523 (ttm110) REVERT: H 396 GLU cc_start: 0.6924 (tm-30) cc_final: 0.6513 (tm-30) REVERT: H 433 MET cc_start: 0.6302 (ttm) cc_final: 0.5928 (ttm) outliers start: 37 outliers final: 29 residues processed: 486 average time/residue: 0.3194 time to fit residues: 205.3200 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 : 1.309 ------------------------------------------------------------------------------- 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: 0.4980 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: 0.5980 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.148476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.128762 restraints weight = 21808.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.133153 restraints weight = 12715.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.136043 restraints weight = 8407.648| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12910 Z= 0.209 Angle : 0.570 7.387 17451 Z= 0.297 Chirality : 0.037 0.153 1878 Planarity : 0.004 0.040 2311 Dihedral : 4.620 54.590 1869 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.12 % Allowed : 21.42 % Favored : 74.46 % 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: 0.75 (0.14), residues: 1376 sheet: None (None), residues: 0 loop : -1.37 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 377 HIS 0.008 0.001 HIS F 289 PHE 0.020 0.001 PHE H 250 TYR 0.019 0.002 TYR F 281 ARG 0.004 0.000 ARG F 388 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 480 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7703 (pp30) cc_final: 0.7401 (pp30) REVERT: A 238 GLN cc_start: 0.8527 (tp40) cc_final: 0.8271 (tp40) REVERT: A 241 GLN cc_start: 0.7843 (tp-100) cc_final: 0.7358 (tp-100) REVERT: A 274 ARG cc_start: 0.8116 (ptm160) cc_final: 0.7794 (ptm160) REVERT: A 351 ARG cc_start: 0.7239 (ttm-80) cc_final: 0.6739 (ttm-80) REVERT: A 364 GLU cc_start: 0.7569 (tp30) cc_final: 0.7179 (tp30) REVERT: A 399 LEU cc_start: 0.8187 (pt) cc_final: 0.7950 (pt) REVERT: A 433 MET cc_start: 0.6516 (tpt) cc_final: 0.6241 (tpt) REVERT: B 236 ILE cc_start: 0.8641 (tp) cc_final: 0.8369 (tp) REVERT: B 241 GLN cc_start: 0.7786 (tp-100) cc_final: 0.7157 (tp-100) REVERT: B 274 ARG cc_start: 0.8167 (ptm160) cc_final: 0.7442 (ptm160) REVERT: B 386 GLN cc_start: 0.7919 (tp40) cc_final: 0.7614 (tp40) REVERT: B 414 GLN cc_start: 0.6916 (OUTLIER) cc_final: 0.6465 (pm20) REVERT: C 236 ILE cc_start: 0.8550 (tp) cc_final: 0.8291 (tp) REVERT: C 237 GLN cc_start: 0.7539 (pp30) cc_final: 0.7218 (pp30) REVERT: C 241 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7511 (mm-40) REVERT: C 343 LYS cc_start: 0.8308 (tptm) cc_final: 0.8070 (tptt) REVERT: C 344 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7468 (tm-30) REVERT: C 370 GLN cc_start: 0.7446 (mm-40) cc_final: 0.7175 (mm-40) REVERT: D 236 ILE cc_start: 0.8605 (tp) cc_final: 0.8332 (tp) REVERT: D 251 LEU cc_start: 0.8288 (tp) cc_final: 0.7989 (tp) REVERT: D 281 TYR cc_start: 0.8437 (t80) cc_final: 0.8225 (t80) REVERT: D 305 GLN cc_start: 0.7847 (tp-100) cc_final: 0.7204 (tp-100) REVERT: D 337 ARG cc_start: 0.7671 (mpt180) cc_final: 0.6919 (mpt180) REVERT: D 385 SER cc_start: 0.8299 (m) cc_final: 0.7595 (t) REVERT: D 386 GLN cc_start: 0.7996 (tp40) cc_final: 0.7754 (tp40) REVERT: D 396 GLU cc_start: 0.7446 (tm-30) cc_final: 0.6984 (tm-30) REVERT: D 433 MET cc_start: 0.6657 (mmp) cc_final: 0.6313 (mmp) REVERT: E 236 ILE cc_start: 0.8708 (tp) cc_final: 0.8453 (tp) REVERT: E 237 GLN cc_start: 0.7565 (pp30) cc_final: 0.7249 (pp30) REVERT: E 241 GLN cc_start: 0.8018 (mm110) cc_final: 0.7310 (tp40) REVERT: E 269 GLN cc_start: 0.7543 (mt0) cc_final: 0.7269 (mt0) REVERT: E 274 ARG cc_start: 0.8340 (ptm160) cc_final: 0.7907 (ptm160) REVERT: E 304 TYR cc_start: 0.7776 (m-80) cc_final: 0.7254 (m-80) REVERT: E 343 LYS cc_start: 0.8061 (tptm) cc_final: 0.7765 (tptp) REVERT: E 410 ARG cc_start: 0.6845 (tmm160) cc_final: 0.6365 (tmm160) REVERT: E 433 MET cc_start: 0.5887 (ttm) cc_final: 0.5412 (ttm) REVERT: F 236 ILE cc_start: 0.8703 (tp) cc_final: 0.8399 (tp) REVERT: F 241 GLN cc_start: 0.7568 (mm-40) cc_final: 0.7311 (mm-40) REVERT: F 251 LEU cc_start: 0.8281 (mp) cc_final: 0.8000 (mm) REVERT: F 343 LYS cc_start: 0.8035 (tptp) cc_final: 0.7754 (tptt) REVERT: G 237 GLN cc_start: 0.7632 (pp30) cc_final: 0.7365 (pp30) REVERT: G 287 HIS cc_start: 0.7001 (t-170) cc_final: 0.6593 (t-170) REVERT: G 321 ARG cc_start: 0.7481 (ttt90) cc_final: 0.7006 (ttt90) REVERT: G 323 LEU cc_start: 0.8329 (tp) cc_final: 0.7998 (tt) REVERT: G 385 SER cc_start: 0.8094 (m) cc_final: 0.7446 (p) REVERT: G 386 GLN cc_start: 0.7855 (tp40) cc_final: 0.7468 (tp40) REVERT: G 426 ARG cc_start: 0.7646 (tmt170) cc_final: 0.7125 (tmt170) REVERT: H 237 GLN cc_start: 0.7611 (pp30) cc_final: 0.7267 (pp30) REVERT: H 250 PHE cc_start: 0.8712 (t80) cc_final: 0.8481 (t80) REVERT: H 281 TYR cc_start: 0.8535 (t80) cc_final: 0.8313 (t80) REVERT: H 343 LYS cc_start: 0.8054 (tptm) cc_final: 0.7827 (tptp) REVERT: H 386 GLN cc_start: 0.8207 (tp40) cc_final: 0.7856 (tp-100) REVERT: H 396 GLU cc_start: 0.6936 (tm-30) cc_final: 0.6596 (tm-30) REVERT: H 433 MET cc_start: 0.6484 (ttm) cc_final: 0.6083 (ttm) outliers start: 50 outliers final: 34 residues processed: 489 average time/residue: 0.3337 time to fit residues: 217.3873 Evaluate side-chains 506 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 471 time to evaluate : 1.436 ------------------------------------------------------------------------------- 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 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 288 GLU Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain E residue 288 GLU Chi-restraints excluded: chain E residue 305 GLN Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 305 GLN Chi-restraints excluded: chain F residue 344 GLN Chi-restraints excluded: chain G residue 244 VAL Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 415 SER Chi-restraints excluded: chain H residue 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: 0.9990 chunk 14 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 30 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- 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 354 GLN ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 GLN ** G 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 HIS H 310 GLN ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.149504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.128182 restraints weight = 21348.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.132455 restraints weight = 12929.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.135374 restraints weight = 8857.804| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2245 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= 0.212 Angle : 0.566 7.671 17451 Z= 0.296 Chirality : 0.037 0.160 1878 Planarity : 0.004 0.041 2311 Dihedral : 4.149 20.379 1863 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 5.19 % Allowed : 23.72 % Favored : 71.09 % 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: 0.71 (0.14), residues: 1400 sheet: None (None), residues: 0 loop : -1.69 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP F 377 HIS 0.003 0.001 HIS E 390 PHE 0.015 0.001 PHE H 250 TYR 0.020 0.002 TYR G 281 ARG 0.005 0.000 ARG F 388 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 474 time to evaluate : 1.525 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: 0.7758 (pp30) cc_final: 0.7362 (pp30) REVERT: A 241 GLN cc_start: 0.7792 (tp-100) cc_final: 0.7522 (tp-100) REVERT: A 274 ARG cc_start: 0.8093 (ptm160) cc_final: 0.7742 (ptp-170) REVERT: A 343 LYS cc_start: 0.8271 (tptp) cc_final: 0.7685 (tptp) REVERT: A 351 ARG cc_start: 0.7325 (ttm-80) cc_final: 0.6823 (ttm-80) REVERT: A 385 SER cc_start: 0.8085 (m) cc_final: 0.7665 (p) REVERT: A 396 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7291 (tm-30) REVERT: A 399 LEU cc_start: 0.8129 (pt) cc_final: 0.7858 (pt) REVERT: A 433 MET cc_start: 0.6577 (tpt) cc_final: 0.6331 (tpt) REVERT: B 236 ILE cc_start: 0.8596 (tp) cc_final: 0.8314 (tp) REVERT: B 241 GLN cc_start: 0.7824 (tp-100) cc_final: 0.7028 (tp-100) REVERT: B 274 ARG cc_start: 0.8134 (ptm160) cc_final: 0.7376 (ptm160) REVERT: B 386 GLN cc_start: 0.7972 (tp40) cc_final: 0.7530 (tp40) REVERT: C 236 ILE cc_start: 0.8454 (tp) cc_final: 0.8221 (tp) REVERT: C 241 GLN cc_start: 0.7765 (mm-40) cc_final: 0.7463 (mm-40) REVERT: C 324 LEU cc_start: 0.8158 (tp) cc_final: 0.7879 (tt) REVERT: C 337 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7313 (mpt180) REVERT: C 344 GLN cc_start: 0.7844 (tm-30) cc_final: 0.7509 (tm-30) REVERT: C 370 GLN cc_start: 0.7467 (mm-40) cc_final: 0.7189 (mm-40) REVERT: D 236 ILE cc_start: 0.8594 (tp) cc_final: 0.8326 (tp) REVERT: D 251 LEU cc_start: 0.8325 (tp) cc_final: 0.8023 (tp) REVERT: D 274 ARG cc_start: 0.8007 (ptm160) cc_final: 0.7727 (mtp85) REVERT: D 281 TYR cc_start: 0.8545 (t80) cc_final: 0.8338 (t80) REVERT: D 337 ARG cc_start: 0.7679 (mpt180) cc_final: 0.6938 (mpt180) REVERT: D 344 GLN cc_start: 0.7961 (pp30) cc_final: 0.7511 (pp30) REVERT: D 385 SER cc_start: 0.8295 (m) cc_final: 0.7584 (t) REVERT: D 396 GLU cc_start: 0.7421 (tm-30) cc_final: 0.6980 (tm-30) REVERT: D 433 MET cc_start: 0.6796 (mmp) cc_final: 0.6503 (mmp) REVERT: E 236 ILE cc_start: 0.8696 (tp) cc_final: 0.8434 (tp) REVERT: E 237 GLN cc_start: 0.7589 (pp30) cc_final: 0.7181 (pp30) REVERT: E 269 GLN cc_start: 0.7531 (mt0) cc_final: 0.7268 (mt0) REVERT: E 304 TYR cc_start: 0.7840 (m-80) cc_final: 0.7377 (m-80) REVERT: E 343 LYS cc_start: 0.8057 (tptm) cc_final: 0.7753 (tptp) REVERT: E 410 ARG cc_start: 0.6932 (tmm160) cc_final: 0.6415 (tmm160) REVERT: E 433 MET cc_start: 0.6115 (ttm) cc_final: 0.5524 (ttm) REVERT: F 236 ILE cc_start: 0.8698 (tp) cc_final: 0.8403 (tp) REVERT: F 241 GLN cc_start: 0.7550 (mm-40) cc_final: 0.7287 (mm-40) REVERT: F 251 LEU cc_start: 0.8267 (mp) cc_final: 0.8018 (mm) REVERT: F 321 ARG cc_start: 0.7440 (tmt-80) cc_final: 0.6687 (tmt-80) REVERT: F 343 LYS cc_start: 0.8077 (tptp) cc_final: 0.7715 (tptp) REVERT: G 237 GLN cc_start: 0.7677 (pp30) cc_final: 0.7359 (pp30) REVERT: G 321 ARG cc_start: 0.7593 (ttt90) cc_final: 0.7099 (ttt90) REVERT: G 323 LEU cc_start: 0.8351 (tp) cc_final: 0.7994 (tt) REVERT: G 385 SER cc_start: 0.8172 (m) cc_final: 0.7539 (p) REVERT: G 386 GLN cc_start: 0.7915 (tp40) cc_final: 0.7529 (tp40) REVERT: G 426 ARG cc_start: 0.7653 (tmt170) cc_final: 0.7126 (tmt170) REVERT: H 237 GLN cc_start: 0.7659 (pp30) cc_final: 0.7325 (pp30) REVERT: H 250 PHE cc_start: 0.8759 (t80) cc_final: 0.8420 (t80) REVERT: H 281 TYR cc_start: 0.8538 (t80) cc_final: 0.8288 (t80) REVERT: H 321 ARG cc_start: 0.7379 (tmt-80) cc_final: 0.6582 (tmt-80) REVERT: H 343 LYS cc_start: 0.8161 (tptm) cc_final: 0.7845 (tptp) REVERT: H 396 GLU cc_start: 0.6967 (tm-30) cc_final: 0.6671 (tm-30) REVERT: H 433 MET cc_start: 0.6655 (ttm) cc_final: 0.6309 (ttm) outliers start: 63 outliers final: 44 residues processed: 488 average time/residue: 0.3258 time to fit residues: 209.6816 Evaluate side-chains 517 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 471 time to evaluate : 1.505 ------------------------------------------------------------------------------- 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 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 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 D residue 244 VAL 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 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: 0.6980 chunk 110 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 0.0980 chunk 79 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** 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 414 GLN F 289 HIS ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 HIS ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.149960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.128606 restraints weight = 21523.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.133040 restraints weight = 12826.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.136181 restraints weight = 8683.369| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2424 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= 0.196 Angle : 0.553 7.350 17451 Z= 0.290 Chirality : 0.036 0.161 1878 Planarity : 0.004 0.041 2311 Dihedral : 4.129 20.145 1863 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.27 % Allowed : 24.63 % Favored : 70.10 % 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: 0.53 (0.20), residues: 1664 helix: 0.79 (0.14), residues: 1400 sheet: None (None), residues: 0 loop : -1.68 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 377 HIS 0.004 0.001 HIS C 289 PHE 0.015 0.001 PHE D 356 TYR 0.024 0.002 TYR G 281 ARG 0.004 0.000 ARG F 388 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 463 time to evaluate : 1.288 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: 0.7768 (pp30) cc_final: 0.7345 (pp30) REVERT: A 241 GLN cc_start: 0.7785 (tp-100) cc_final: 0.7462 (tp-100) REVERT: A 244 VAL cc_start: 0.8787 (p) cc_final: 0.8542 (p) REVERT: A 274 ARG cc_start: 0.8083 (ptm160) cc_final: 0.7759 (ptp-170) REVERT: A 343 LYS cc_start: 0.8280 (tptp) cc_final: 0.7701 (tptp) REVERT: A 378 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8088 (tp) REVERT: A 385 SER cc_start: 0.8095 (m) cc_final: 0.7658 (p) REVERT: A 396 GLU cc_start: 0.7586 (pp20) cc_final: 0.7314 (tm-30) REVERT: A 399 LEU cc_start: 0.8127 (pt) cc_final: 0.7850 (pt) REVERT: A 433 MET cc_start: 0.6569 (tpt) cc_final: 0.6333 (tpt) REVERT: B 236 ILE cc_start: 0.8570 (tp) cc_final: 0.8296 (tp) REVERT: B 241 GLN cc_start: 0.7848 (tp-100) cc_final: 0.6925 (tp-100) REVERT: B 274 ARG cc_start: 0.8168 (ptm160) cc_final: 0.7424 (ptm160) REVERT: B 386 GLN cc_start: 0.7970 (tp40) cc_final: 0.7733 (tp40) REVERT: C 236 ILE cc_start: 0.8452 (tp) cc_final: 0.8217 (tp) REVERT: C 241 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7468 (mm-40) REVERT: C 324 LEU cc_start: 0.8145 (tp) cc_final: 0.7866 (tt) REVERT: C 337 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7251 (mpt180) REVERT: C 343 LYS cc_start: 0.8465 (tptt) cc_final: 0.8247 (tptt) REVERT: C 344 GLN cc_start: 0.7855 (tm-30) cc_final: 0.7554 (tm-30) REVERT: C 370 GLN cc_start: 0.7492 (mm-40) cc_final: 0.7184 (mm-40) REVERT: C 385 SER cc_start: 0.8124 (m) cc_final: 0.7552 (p) REVERT: D 236 ILE cc_start: 0.8560 (tp) cc_final: 0.8288 (tp) REVERT: D 244 VAL cc_start: 0.8813 (OUTLIER) cc_final: 0.8347 (p) REVERT: D 251 LEU cc_start: 0.8378 (tp) cc_final: 0.8089 (tp) REVERT: D 274 ARG cc_start: 0.8019 (ptm160) cc_final: 0.7810 (mtp85) REVERT: D 281 TYR cc_start: 0.8514 (t80) cc_final: 0.8285 (t80) REVERT: D 337 ARG cc_start: 0.7689 (mpt180) cc_final: 0.6935 (mpt180) REVERT: D 344 GLN cc_start: 0.8015 (pp30) cc_final: 0.7441 (pp30) REVERT: D 385 SER cc_start: 0.8271 (m) cc_final: 0.7545 (t) REVERT: D 386 GLN cc_start: 0.8104 (tp40) cc_final: 0.7825 (tp-100) REVERT: D 396 GLU cc_start: 0.7406 (tm-30) cc_final: 0.6975 (tm-30) REVERT: D 433 MET cc_start: 0.6814 (mmp) cc_final: 0.6538 (mmp) REVERT: E 236 ILE cc_start: 0.8701 (tp) cc_final: 0.8441 (tp) REVERT: E 237 GLN cc_start: 0.7595 (pp30) cc_final: 0.7228 (pp30) REVERT: E 241 GLN cc_start: 0.8014 (mm110) cc_final: 0.7455 (tp40) REVERT: E 269 GLN cc_start: 0.7532 (mt0) cc_final: 0.7177 (mt0) REVERT: E 274 ARG cc_start: 0.8295 (ptm160) cc_final: 0.7765 (ptp-170) REVERT: E 343 LYS cc_start: 0.8086 (tptm) cc_final: 0.7732 (tptp) REVERT: E 387 SER cc_start: 0.8468 (m) cc_final: 0.8067 (p) REVERT: E 410 ARG cc_start: 0.7024 (tmm160) cc_final: 0.6489 (tmm160) REVERT: E 433 MET cc_start: 0.6150 (ttm) cc_final: 0.5574 (ttm) REVERT: F 236 ILE cc_start: 0.8684 (tp) cc_final: 0.8383 (tp) REVERT: F 241 GLN cc_start: 0.7570 (mm-40) cc_final: 0.7284 (mm-40) REVERT: F 321 ARG cc_start: 0.7450 (tmt-80) cc_final: 0.6723 (tmt-80) REVERT: F 343 LYS cc_start: 0.8065 (tptp) cc_final: 0.7667 (tptp) REVERT: G 237 GLN cc_start: 0.7681 (pp30) cc_final: 0.7341 (pp30) REVERT: G 278 LYS cc_start: 0.8188 (mttt) cc_final: 0.7738 (mtmm) REVERT: G 293 THR cc_start: 0.7920 (m) cc_final: 0.7435 (p) REVERT: G 321 ARG cc_start: 0.7677 (ttt90) cc_final: 0.7204 (ttt90) REVERT: G 323 LEU cc_start: 0.8353 (tp) cc_final: 0.7979 (tt) REVERT: G 385 SER cc_start: 0.8181 (m) cc_final: 0.7527 (p) REVERT: G 426 ARG cc_start: 0.7592 (tmt170) cc_final: 0.7147 (tmt170) REVERT: H 237 GLN cc_start: 0.7641 (pp30) cc_final: 0.7303 (pp30) REVERT: H 250 PHE cc_start: 0.8767 (t80) cc_final: 0.8358 (t80) REVERT: H 281 TYR cc_start: 0.8461 (t80) cc_final: 0.8224 (t80) REVERT: H 304 TYR cc_start: 0.7798 (m-80) cc_final: 0.7268 (m-80) REVERT: H 321 ARG cc_start: 0.7395 (tmt-80) cc_final: 0.6557 (tmt-80) REVERT: H 343 LYS cc_start: 0.8176 (tptm) cc_final: 0.7847 (tptp) REVERT: H 396 GLU cc_start: 0.6980 (tm-30) cc_final: 0.6678 (tm-30) REVERT: H 433 MET cc_start: 0.6687 (ttm) cc_final: 0.6357 (ttm) outliers start: 64 outliers final: 50 residues processed: 477 average time/residue: 0.3276 time to fit residues: 205.0029 Evaluate side-chains 514 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 461 time to evaluate : 1.374 ------------------------------------------------------------------------------- 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 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 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 D residue 244 VAL Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 426 ARG Chi-restraints excluded: chain E residue 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 414 GLN Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 266 SER Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 122 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 167 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 164 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS E 310 GLN ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 GLN 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 289 HIS ** G 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 HIS ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.150028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.128843 restraints weight = 21899.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.133196 restraints weight = 12907.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.136336 restraints weight = 8675.972| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2593 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= 0.205 Angle : 0.557 7.508 17451 Z= 0.293 Chirality : 0.036 0.156 1878 Planarity : 0.004 0.043 2311 Dihedral : 4.125 20.140 1863 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.68 % Allowed : 25.95 % Favored : 68.37 % 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 : -1.73 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 377 HIS 0.006 0.001 HIS B 287 PHE 0.012 0.001 PHE D 356 TYR 0.025 0.002 TYR G 281 ARG 0.004 0.000 ARG F 388 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 473 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.7783 (pp30) cc_final: 0.7379 (pp30) REVERT: A 241 GLN cc_start: 0.7756 (tp-100) cc_final: 0.7516 (tp-100) REVERT: A 244 VAL cc_start: 0.8792 (p) cc_final: 0.8533 (p) REVERT: A 274 ARG cc_start: 0.8079 (ptm160) cc_final: 0.7760 (ptp-170) REVERT: A 343 LYS cc_start: 0.8266 (tptp) cc_final: 0.7653 (tptp) REVERT: A 364 GLU cc_start: 0.7728 (tp30) cc_final: 0.7338 (tp30) REVERT: A 378 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8047 (tp) REVERT: A 385 SER cc_start: 0.8128 (m) cc_final: 0.7688 (p) REVERT: A 396 GLU cc_start: 0.7595 (pp20) cc_final: 0.7329 (tm-30) REVERT: A 399 LEU cc_start: 0.8140 (pt) cc_final: 0.7868 (pt) REVERT: A 410 ARG cc_start: 0.7330 (ptt180) cc_final: 0.6947 (pmt170) REVERT: A 433 MET cc_start: 0.6462 (tpt) cc_final: 0.6247 (tpt) REVERT: B 236 ILE cc_start: 0.8577 (tp) cc_final: 0.8307 (tp) REVERT: B 241 GLN cc_start: 0.7846 (tp-100) cc_final: 0.6875 (tp-100) REVERT: B 274 ARG cc_start: 0.8118 (ptm160) cc_final: 0.7206 (ptm160) REVERT: B 378 LEU cc_start: 0.8482 (tt) cc_final: 0.8155 (pp) REVERT: B 386 GLN cc_start: 0.7992 (tp40) cc_final: 0.7711 (tp40) REVERT: C 236 ILE cc_start: 0.8470 (tp) cc_final: 0.8230 (tp) REVERT: C 237 GLN cc_start: 0.7621 (pp30) cc_final: 0.7259 (pp30) REVERT: C 241 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7590 (mm-40) REVERT: C 312 HIS cc_start: 0.8256 (t-90) cc_final: 0.8044 (t70) REVERT: C 337 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7067 (mpt180) REVERT: C 343 LYS cc_start: 0.8487 (tptt) cc_final: 0.8238 (tptt) REVERT: C 344 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7625 (tm-30) REVERT: C 370 GLN cc_start: 0.7507 (mm-40) cc_final: 0.7177 (mm-40) REVERT: C 385 SER cc_start: 0.8138 (m) cc_final: 0.7552 (p) REVERT: D 236 ILE cc_start: 0.8545 (tp) cc_final: 0.8278 (tp) REVERT: D 244 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8271 (p) REVERT: D 251 LEU cc_start: 0.8403 (tp) cc_final: 0.8115 (tp) REVERT: D 281 TYR cc_start: 0.8522 (t80) cc_final: 0.8316 (t80) REVERT: D 337 ARG cc_start: 0.7711 (mpt180) cc_final: 0.6923 (mpt180) REVERT: D 344 GLN cc_start: 0.8032 (pp30) cc_final: 0.7522 (pp30) REVERT: D 385 SER cc_start: 0.8237 (m) cc_final: 0.7486 (t) REVERT: D 386 GLN cc_start: 0.8099 (tp40) cc_final: 0.7810 (tp-100) REVERT: D 396 GLU cc_start: 0.7396 (tm-30) cc_final: 0.6959 (tm-30) REVERT: D 433 MET cc_start: 0.6875 (mmp) cc_final: 0.6599 (mmp) REVERT: E 236 ILE cc_start: 0.8687 (tp) cc_final: 0.8432 (tp) REVERT: E 237 GLN cc_start: 0.7612 (pp30) cc_final: 0.7223 (pp30) REVERT: E 241 GLN cc_start: 0.8016 (mm110) cc_final: 0.7432 (tp40) REVERT: E 269 GLN cc_start: 0.7553 (mt0) cc_final: 0.7188 (mt0) REVERT: E 274 ARG cc_start: 0.8286 (ptm160) cc_final: 0.7675 (ptp-170) REVERT: E 343 LYS cc_start: 0.8092 (tptm) cc_final: 0.7769 (tptp) REVERT: E 387 SER cc_start: 0.8454 (m) cc_final: 0.8044 (p) REVERT: E 396 GLU cc_start: 0.7739 (tt0) cc_final: 0.7441 (tt0) REVERT: E 410 ARG cc_start: 0.7025 (tmm160) cc_final: 0.6537 (tmm160) REVERT: E 433 MET cc_start: 0.6161 (ttm) cc_final: 0.5564 (ttm) REVERT: F 236 ILE cc_start: 0.8705 (tp) cc_final: 0.8396 (tp) REVERT: F 241 GLN cc_start: 0.7557 (mm-40) cc_final: 0.7246 (mm-40) REVERT: F 280 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7512 (mt0) REVERT: F 321 ARG cc_start: 0.7468 (tmt-80) cc_final: 0.6700 (tmt-80) REVERT: F 343 LYS cc_start: 0.8061 (tptp) cc_final: 0.7705 (tptp) REVERT: F 433 MET cc_start: 0.7028 (mtm) cc_final: 0.6459 (mtm) REVERT: G 237 GLN cc_start: 0.7691 (pp30) cc_final: 0.7358 (pp30) REVERT: G 278 LYS cc_start: 0.8210 (mttt) cc_final: 0.7700 (mtmm) REVERT: G 287 HIS cc_start: 0.6848 (OUTLIER) cc_final: 0.6508 (m170) REVERT: G 321 ARG cc_start: 0.7695 (ttt90) cc_final: 0.7224 (ttt90) REVERT: G 323 LEU cc_start: 0.8375 (tp) cc_final: 0.8005 (tt) REVERT: G 385 SER cc_start: 0.8175 (m) cc_final: 0.7509 (p) REVERT: G 426 ARG cc_start: 0.7614 (tmt170) cc_final: 0.7159 (tmt170) REVERT: H 237 GLN cc_start: 0.7657 (pp30) cc_final: 0.7304 (pp30) REVERT: H 250 PHE cc_start: 0.8766 (t80) cc_final: 0.8319 (t80) REVERT: H 321 ARG cc_start: 0.7393 (tmt-80) cc_final: 0.6518 (tmt-80) REVERT: H 343 LYS cc_start: 0.8182 (tptm) cc_final: 0.7831 (tptp) REVERT: H 396 GLU cc_start: 0.6990 (tm-30) cc_final: 0.6709 (tm-30) REVERT: H 433 MET cc_start: 0.6756 (ttm) cc_final: 0.6437 (ttm) outliers start: 69 outliers final: 50 residues processed: 488 average time/residue: 0.3298 time to fit residues: 211.8330 Evaluate side-chains 527 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 472 time to evaluate : 1.433 ------------------------------------------------------------------------------- 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 278 LYS Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 305 GLN Chi-restraints excluded: chain B residue 344 GLN Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 337 ARG Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 305 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 414 GLN 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 G residue 246 ILE Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 287 HIS Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 289 HIS Chi-restraints excluded: chain G residue 305 GLN Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain 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: 1.9990 chunk 145 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 90 optimal weight: 0.0060 chunk 61 optimal weight: 0.8980 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 GLN 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 289 HIS ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 HIS H 310 GLN ** H 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 = 0.3874 r_free = 0.3874 target = 0.147935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.126630 restraints weight = 21618.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.130994 restraints weight = 12919.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.134103 restraints weight = 8781.513| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2741 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= 0.239 Angle : 0.583 7.722 17451 Z= 0.306 Chirality : 0.037 0.158 1878 Planarity : 0.004 0.040 2311 Dihedral : 4.197 20.518 1863 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 5.68 % Allowed : 26.77 % Favored : 67.55 % 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: 0.51 (0.20), residues: 1664 helix: 0.82 (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 D 377 HIS 0.005 0.001 HIS F 289 PHE 0.011 0.001 PHE C 265 TYR 0.025 0.002 TYR G 281 ARG 0.004 0.000 ARG F 388 *********************** 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 542 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 473 time to evaluate : 1.483 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: 0.7807 (pp30) cc_final: 0.7394 (pp30) REVERT: A 244 VAL cc_start: 0.8809 (p) cc_final: 0.8516 (p) REVERT: A 274 ARG cc_start: 0.8138 (ptm160) cc_final: 0.7854 (ptp-170) REVERT: A 343 LYS cc_start: 0.8293 (tptp) cc_final: 0.7688 (tptp) REVERT: A 364 GLU cc_start: 0.7742 (tp30) cc_final: 0.7307 (tp30) REVERT: A 378 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8080 (tp) REVERT: A 385 SER cc_start: 0.8151 (m) cc_final: 0.7699 (p) REVERT: A 396 GLU cc_start: 0.7789 (pp20) cc_final: 0.7497 (tm-30) REVERT: A 399 LEU cc_start: 0.8111 (pt) cc_final: 0.7824 (pt) REVERT: A 410 ARG cc_start: 0.7360 (ptt180) cc_final: 0.7105 (pmt170) REVERT: A 433 MET cc_start: 0.6481 (tpt) cc_final: 0.6259 (tpt) REVERT: B 236 ILE cc_start: 0.8607 (tp) cc_final: 0.8324 (tp) REVERT: B 241 GLN cc_start: 0.7835 (tp-100) cc_final: 0.6854 (tp-100) REVERT: B 274 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7260 (ptm160) REVERT: C 236 ILE cc_start: 0.8474 (tp) cc_final: 0.8228 (tp) REVERT: C 237 GLN cc_start: 0.7630 (pp30) cc_final: 0.7271 (pp30) REVERT: C 241 GLN cc_start: 0.7745 (mm-40) cc_final: 0.7508 (mm-40) REVERT: C 337 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7066 (mpt180) REVERT: C 343 LYS cc_start: 0.8482 (tptt) cc_final: 0.8217 (tptt) REVERT: C 344 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7533 (tm-30) REVERT: C 385 SER cc_start: 0.8154 (m) cc_final: 0.7544 (p) REVERT: D 236 ILE cc_start: 0.8557 (tp) cc_final: 0.8289 (tp) REVERT: D 281 TYR cc_start: 0.8550 (t80) cc_final: 0.8327 (t80) REVERT: D 337 ARG cc_start: 0.7704 (mpt180) cc_final: 0.6930 (mpt180) REVERT: D 385 SER cc_start: 0.8230 (m) cc_final: 0.7487 (t) REVERT: D 386 GLN cc_start: 0.8104 (tp40) cc_final: 0.7832 (tp-100) REVERT: D 396 GLU cc_start: 0.7403 (tm-30) cc_final: 0.6961 (tm-30) REVERT: D 433 MET cc_start: 0.6889 (mmp) cc_final: 0.6646 (mmp) REVERT: E 236 ILE cc_start: 0.8679 (tp) cc_final: 0.8435 (tp) REVERT: E 237 GLN cc_start: 0.7627 (pp30) cc_final: 0.7204 (pp30) REVERT: E 241 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7417 (tp40) REVERT: E 269 GLN cc_start: 0.7553 (mt0) cc_final: 0.7193 (mt0) REVERT: E 274 ARG cc_start: 0.8274 (ptm160) cc_final: 0.7641 (ptp-170) REVERT: E 319 TYR cc_start: 0.7945 (t80) cc_final: 0.7716 (t80) REVERT: E 343 LYS cc_start: 0.8136 (tptm) cc_final: 0.7799 (tptp) REVERT: E 363 LYS cc_start: 0.8142 (tmtt) cc_final: 0.7716 (tmtt) REVERT: E 387 SER cc_start: 0.8577 (m) cc_final: 0.8205 (p) REVERT: E 396 GLU cc_start: 0.7750 (tt0) cc_final: 0.7392 (tt0) REVERT: E 433 MET cc_start: 0.6186 (ttm) cc_final: 0.5602 (ttm) REVERT: F 236 ILE cc_start: 0.8733 (tp) cc_final: 0.8412 (tp) REVERT: F 241 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7222 (mm-40) REVERT: F 280 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7502 (mt0) REVERT: F 297 ILE cc_start: 0.8525 (mm) cc_final: 0.8262 (mm) REVERT: F 321 ARG cc_start: 0.7493 (tmt-80) cc_final: 0.6727 (tmt-80) REVERT: F 343 LYS cc_start: 0.8183 (tptp) cc_final: 0.7824 (tptp) REVERT: F 357 LEU cc_start: 0.7706 (tp) cc_final: 0.7505 (tp) REVERT: F 433 MET cc_start: 0.7043 (mtm) cc_final: 0.6469 (mtm) REVERT: G 237 GLN cc_start: 0.7703 (pp30) cc_final: 0.7345 (pp30) REVERT: G 278 LYS cc_start: 0.8232 (mttt) cc_final: 0.7742 (mtmm) REVERT: G 287 HIS cc_start: 0.6895 (OUTLIER) cc_final: 0.6645 (m170) REVERT: G 321 ARG cc_start: 0.7686 (ttt90) cc_final: 0.7198 (ttt180) REVERT: G 323 LEU cc_start: 0.8357 (tp) cc_final: 0.7963 (tt) REVERT: G 363 LYS cc_start: 0.8229 (tmtt) cc_final: 0.7593 (tmtt) REVERT: G 385 SER cc_start: 0.8156 (m) cc_final: 0.7488 (p) REVERT: G 426 ARG cc_start: 0.7615 (tmt170) cc_final: 0.7173 (tmt170) REVERT: H 237 GLN cc_start: 0.7653 (pp30) cc_final: 0.7300 (pp30) REVERT: H 250 PHE cc_start: 0.8793 (t80) cc_final: 0.8307 (t80) REVERT: H 321 ARG cc_start: 0.7397 (tmt-80) cc_final: 0.6555 (tmt-80) REVERT: H 343 LYS cc_start: 0.8235 (tptm) cc_final: 0.7824 (tptp) REVERT: H 363 LYS cc_start: 0.8091 (tmtt) cc_final: 0.7727 (tmtt) REVERT: H 388 ARG cc_start: 0.7042 (ttt90) cc_final: 0.6807 (ttt90) REVERT: H 433 MET cc_start: 0.6858 (ttm) cc_final: 0.6524 (ttm) outliers start: 69 outliers final: 52 residues processed: 486 average time/residue: 0.3287 time to fit residues: 211.0980 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 : 1.334 ------------------------------------------------------------------------------- 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 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 289 HIS Chi-restraints excluded: chain C residue 337 ARG Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 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 426 ARG Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 289 HIS Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 414 GLN Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 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 427 LEU Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 287 HIS Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 289 HIS Chi-restraints excluded: chain G residue 305 GLN Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 375 TYR Chi-restraints excluded: chain G residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 88 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 153 optimal weight: 0.0670 chunk 17 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 135 optimal weight: 0.0570 overall best weight: 0.4236 ------------------------------------------------------------------------------- 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 312 HIS ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 GLN F 289 HIS ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 289 HIS G 310 GLN ** G 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 414 GLN H 289 HIS ** H 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.150146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.128649 restraints weight = 21603.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.133150 restraints weight = 12708.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.136161 restraints weight = 8540.248| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.2825 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= 0.175 Angle : 0.581 8.540 17451 Z= 0.296 Chirality : 0.035 0.161 1878 Planarity : 0.004 0.041 2311 Dihedral : 4.116 19.372 1863 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 5.44 % Allowed : 27.84 % Favored : 66.72 % 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: 0.65 (0.20), residues: 1664 helix: 0.92 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -1.78 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP B 377 HIS 0.007 0.001 HIS F 289 PHE 0.010 0.001 PHE H 250 TYR 0.022 0.002 TYR G 281 ARG 0.004 0.000 ARG C 351 *********************** 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 530 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 464 time to evaluate : 1.606 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: 0.7847 (tp-100) cc_final: 0.7566 (tp-100) REVERT: A 244 VAL cc_start: 0.8779 (p) cc_final: 0.8369 (p) REVERT: A 343 LYS cc_start: 0.8280 (tptp) cc_final: 0.7653 (tptp) REVERT: A 351 ARG cc_start: 0.7260 (ttm-80) cc_final: 0.6697 (ttm-80) REVERT: A 364 GLU cc_start: 0.7714 (tp30) cc_final: 0.7314 (tp30) REVERT: A 378 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8034 (tp) REVERT: A 385 SER cc_start: 0.8191 (m) cc_final: 0.7781 (p) REVERT: A 399 LEU cc_start: 0.8080 (pt) cc_final: 0.7791 (pt) REVERT: A 410 ARG cc_start: 0.7330 (ptt180) cc_final: 0.7060 (pmt170) REVERT: A 433 MET cc_start: 0.6567 (tpt) cc_final: 0.6333 (tpt) REVERT: B 236 ILE cc_start: 0.8552 (tp) cc_final: 0.8289 (tp) REVERT: B 241 GLN cc_start: 0.7864 (tp-100) cc_final: 0.6873 (tp-100) REVERT: B 274 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7364 (ptm160) REVERT: B 377 TRP cc_start: 0.6880 (t60) cc_final: 0.6622 (t60) REVERT: C 236 ILE cc_start: 0.8441 (tp) cc_final: 0.8182 (tp) REVERT: C 237 GLN cc_start: 0.7595 (pp30) cc_final: 0.7233 (pp30) REVERT: C 337 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7058 (mpt180) REVERT: C 343 LYS cc_start: 0.8455 (tptt) cc_final: 0.8139 (tptt) REVERT: C 344 GLN cc_start: 0.7911 (tm-30) cc_final: 0.7521 (tm-30) REVERT: C 385 SER cc_start: 0.8141 (m) cc_final: 0.7508 (p) REVERT: D 236 ILE cc_start: 0.8518 (tp) cc_final: 0.8261 (tp) REVERT: D 319 TYR cc_start: 0.7526 (t80) cc_final: 0.7301 (t80) REVERT: D 337 ARG cc_start: 0.7682 (mpt180) cc_final: 0.6886 (mpt180) REVERT: D 385 SER cc_start: 0.8226 (m) cc_final: 0.7472 (t) REVERT: D 386 GLN cc_start: 0.8102 (tp40) cc_final: 0.7813 (tp-100) REVERT: D 396 GLU cc_start: 0.7381 (tm-30) cc_final: 0.6952 (tm-30) REVERT: D 433 MET cc_start: 0.6913 (mmp) cc_final: 0.6639 (mmp) REVERT: E 236 ILE cc_start: 0.8643 (tp) cc_final: 0.8390 (tp) REVERT: E 237 GLN cc_start: 0.7615 (pp30) cc_final: 0.7225 (pp30) REVERT: E 241 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7440 (tp40) REVERT: E 269 GLN cc_start: 0.7566 (mt0) cc_final: 0.7291 (mt0) REVERT: E 274 ARG cc_start: 0.8243 (ptm160) cc_final: 0.7671 (ptp-170) REVERT: E 343 LYS cc_start: 0.8134 (tptm) cc_final: 0.7750 (tptp) REVERT: E 363 LYS cc_start: 0.8115 (tmtt) cc_final: 0.7658 (tmtt) REVERT: E 387 SER cc_start: 0.8443 (m) cc_final: 0.8056 (p) REVERT: E 396 GLU cc_start: 0.7772 (tt0) cc_final: 0.7449 (tt0) REVERT: E 433 MET cc_start: 0.6238 (ttm) cc_final: 0.5638 (ttm) REVERT: F 236 ILE cc_start: 0.8694 (tp) cc_final: 0.8378 (tp) REVERT: F 241 GLN cc_start: 0.7569 (mm-40) cc_final: 0.7063 (mm-40) REVERT: F 274 ARG cc_start: 0.8296 (ptm160) cc_final: 0.7694 (ptm160) REVERT: F 321 ARG cc_start: 0.7504 (tmt-80) cc_final: 0.6707 (tmt-80) REVERT: F 343 LYS cc_start: 0.8143 (tptp) cc_final: 0.7752 (tptp) REVERT: F 357 LEU cc_start: 0.7701 (tp) cc_final: 0.7498 (tp) REVERT: F 433 MET cc_start: 0.7031 (mtm) cc_final: 0.6462 (mtm) REVERT: G 237 GLN cc_start: 0.7715 (pp30) cc_final: 0.7363 (pp30) REVERT: G 278 LYS cc_start: 0.8145 (mttt) cc_final: 0.7547 (mtmm) REVERT: G 321 ARG cc_start: 0.7695 (ttt90) cc_final: 0.7232 (ttt90) REVERT: G 385 SER cc_start: 0.8157 (m) cc_final: 0.7496 (p) REVERT: G 386 GLN cc_start: 0.7912 (tp40) cc_final: 0.7477 (tp40) REVERT: G 426 ARG cc_start: 0.7602 (tmt170) cc_final: 0.7126 (tmt170) REVERT: H 237 GLN cc_start: 0.7656 (pp30) cc_final: 0.7274 (pp30) REVERT: H 250 PHE cc_start: 0.8762 (t80) cc_final: 0.8317 (t80) REVERT: H 321 ARG cc_start: 0.7444 (tmt-80) cc_final: 0.6652 (tmt-80) REVERT: H 343 LYS cc_start: 0.8200 (tptm) cc_final: 0.7811 (tptp) REVERT: H 363 LYS cc_start: 0.8072 (tmtt) cc_final: 0.7678 (tmtt) REVERT: H 396 GLU cc_start: 0.6931 (tm-30) cc_final: 0.6650 (tm-30) REVERT: H 433 MET cc_start: 0.6902 (ttm) cc_final: 0.6569 (ttm) outliers start: 66 outliers final: 53 residues processed: 477 average time/residue: 0.3311 time to fit residues: 208.3591 Evaluate side-chains 522 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 465 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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 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 251 LEU Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 337 ARG Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain E residue 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 414 GLN Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 305 GLN Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 344 GLN Chi-restraints excluded: chain F residue 427 LEU Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 256 MET Chi-restraints excluded: chain G residue 288 GLU Chi-restraints excluded: chain G residue 289 HIS Chi-restraints excluded: chain G residue 305 GLN Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain H residue 241 GLN Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 289 HIS Chi-restraints excluded: chain H residue 305 GLN Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain H residue 414 GLN Chi-restraints excluded: chain H residue 415 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.4952 > 50: distance: 17 - 33: 26.778 distance: 21 - 43: 22.644 distance: 25 - 52: 27.332 distance: 29 - 33: 29.440 distance: 33 - 34: 8.771 distance: 34 - 35: 40.717 distance: 34 - 37: 11.222 distance: 35 - 36: 41.836 distance: 35 - 43: 8.796 distance: 37 - 38: 17.672 distance: 38 - 39: 20.837 distance: 38 - 40: 11.701 distance: 39 - 41: 5.144 distance: 40 - 42: 12.009 distance: 41 - 42: 4.313 distance: 43 - 44: 8.743 distance: 44 - 45: 31.869 distance: 44 - 47: 21.254 distance: 45 - 46: 31.969 distance: 45 - 52: 11.461 distance: 47 - 48: 13.945 distance: 49 - 50: 19.540 distance: 49 - 51: 26.063 distance: 52 - 53: 17.185 distance: 53 - 54: 42.497 distance: 53 - 56: 25.150 distance: 54 - 55: 32.776 distance: 54 - 62: 24.063 distance: 56 - 57: 22.991 distance: 57 - 58: 39.507 distance: 57 - 59: 30.820 distance: 58 - 60: 13.021 distance: 59 - 61: 10.223 distance: 60 - 61: 41.880 distance: 62 - 63: 4.433 distance: 63 - 64: 29.328 distance: 64 - 65: 35.977 distance: 64 - 66: 36.189 distance: 66 - 67: 16.559 distance: 67 - 68: 14.869 distance: 67 - 70: 34.527 distance: 68 - 69: 34.872 distance: 68 - 71: 21.486 distance: 71 - 72: 49.200 distance: 72 - 73: 33.271 distance: 73 - 74: 24.173 distance: 73 - 75: 15.291 distance: 75 - 76: 27.244 distance: 76 - 77: 31.058 distance: 76 - 79: 20.452 distance: 77 - 78: 28.779 distance: 77 - 82: 30.921 distance: 79 - 80: 7.278 distance: 79 - 81: 35.475 distance: 82 - 83: 10.566 distance: 82 - 88: 29.330 distance: 83 - 84: 18.432 distance: 83 - 86: 21.077 distance: 84 - 85: 42.319 distance: 84 - 89: 18.911 distance: 86 - 87: 23.968 distance: 87 - 88: 21.036 distance: 89 - 90: 7.134 distance: 90 - 91: 16.200 distance: 90 - 93: 6.310 distance: 91 - 92: 13.927 distance: 91 - 100: 11.492 distance: 93 - 94: 17.217 distance: 94 - 95: 17.241 distance: 95 - 96: 26.218 distance: 96 - 97: 10.259 distance: 97 - 98: 9.479 distance: 97 - 99: 11.627 distance: 100 - 101: 11.988 distance: 101 - 102: 12.143 distance: 101 - 104: 20.858 distance: 102 - 108: 30.091 distance: 104 - 105: 4.189 distance: 105 - 106: 19.037 distance: 105 - 107: 18.054