Starting phenix.real_space_refine on Sun Apr 5 06:33:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u6r_63920/04_2026/9u6r_63920.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u6r_63920/04_2026/9u6r_63920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u6r_63920/04_2026/9u6r_63920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u6r_63920/04_2026/9u6r_63920.map" model { file = "/net/cci-nas-00/data/ceres_data/9u6r_63920/04_2026/9u6r_63920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u6r_63920/04_2026/9u6r_63920.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.029 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 19 5.16 5 C 5698 2.51 5 N 1457 2.21 5 O 1466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8640 Number of models: 1 Model: "" Number of chains: 13 Chain: "N" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2530 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 15, 'TRANS': 305} Chain: "O" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 509 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "P" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 509 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "Q" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 515 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "R" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 509 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "S" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 509 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "T" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 509 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "U" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 509 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "V" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 509 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "W" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 509 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "X" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 505 Classifications: {'peptide': 72} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 509 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "Z" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 509 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 71} Time building chain proxies: 1.99, per 1000 atoms: 0.23 Number of scatterers: 8640 At special positions: 0 Unit cell: (93.24, 102.06, 80.64, 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 19 16.00 O 1466 8.00 N 1457 7.00 C 5698 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: 0.76 Conformation dependent library (CDL) restraints added in 326.7 milliseconds 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1982 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 1 sheets defined 87.6% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'N' and resid 329 through 334 removed outlier: 3.754A pdb=" N LEU N 333 " --> pdb=" O PRO N 329 " (cutoff:3.500A) Processing helix chain 'N' and resid 349 through 363 removed outlier: 4.116A pdb=" N VAL N 353 " --> pdb=" O PRO N 349 " (cutoff:3.500A) Proline residue: N 356 - end of helix Processing helix chain 'N' and resid 365 through 385 Processing helix chain 'N' and resid 399 through 422 Processing helix chain 'N' and resid 458 through 489 removed outlier: 4.607A pdb=" N LEU N 462 " --> pdb=" O LYS N 458 " (cutoff:3.500A) Processing helix chain 'N' and resid 491 through 516 removed outlier: 4.044A pdb=" N PHE N 495 " --> pdb=" O HIS N 491 " (cutoff:3.500A) Processing helix chain 'N' and resid 522 through 543 removed outlier: 4.145A pdb=" N GLY N 526 " --> pdb=" O GLY N 522 " (cutoff:3.500A) Processing helix chain 'N' and resid 549 through 559 removed outlier: 3.755A pdb=" N THR N 553 " --> pdb=" O PRO N 549 " (cutoff:3.500A) Processing helix chain 'N' and resid 562 through 589 Processing helix chain 'N' and resid 589 through 613 removed outlier: 3.625A pdb=" N VAL N 594 " --> pdb=" O GLY N 590 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU N 595 " --> pdb=" O LEU N 591 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU N 596 " --> pdb=" O LEU N 592 " (cutoff:3.500A) Processing helix chain 'N' and resid 614 through 633 Proline residue: N 620 - end of helix removed outlier: 4.963A pdb=" N GLU N 627 " --> pdb=" O LEU N 623 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR N 630 " --> pdb=" O VAL N 626 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE N 632 " --> pdb=" O PHE N 628 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 48 removed outlier: 3.906A pdb=" N ARG O 36 " --> pdb=" O VAL O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 61 Processing helix chain 'O' and resid 63 through 80 Processing helix chain 'P' and resid 9 through 48 removed outlier: 4.032A pdb=" N ARG P 36 " --> pdb=" O VAL P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 61 Processing helix chain 'P' and resid 63 through 80 removed outlier: 3.745A pdb=" N ILE P 67 " --> pdb=" O GLU P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 46 removed outlier: 4.099A pdb=" N ARG Q 12 " --> pdb=" O GLY Q 8 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY Q 13 " --> pdb=" O GLY Q 9 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG Q 36 " --> pdb=" O VAL Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 61 Processing helix chain 'Q' and resid 63 through 80 removed outlier: 3.581A pdb=" N LEU Q 80 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 48 removed outlier: 4.085A pdb=" N GLY R 13 " --> pdb=" O GLY R 9 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ARG R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE R 37 " --> pdb=" O ALA R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 61 Processing helix chain 'R' and resid 63 through 80 Processing helix chain 'S' and resid 10 through 48 removed outlier: 3.902A pdb=" N LEU S 14 " --> pdb=" O LEU S 10 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG S 36 " --> pdb=" O VAL S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 61 Processing helix chain 'S' and resid 63 through 80 Processing helix chain 'T' and resid 9 through 48 removed outlier: 3.981A pdb=" N GLY T 13 " --> pdb=" O GLY T 9 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG T 36 " --> pdb=" O VAL T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 61 Processing helix chain 'T' and resid 63 through 80 Processing helix chain 'U' and resid 9 through 48 removed outlier: 3.684A pdb=" N GLY U 13 " --> pdb=" O GLY U 9 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG U 36 " --> pdb=" O VAL U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 60 Processing helix chain 'U' and resid 63 through 80 Processing helix chain 'V' and resid 9 through 48 removed outlier: 3.965A pdb=" N GLY V 13 " --> pdb=" O GLY V 9 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG V 36 " --> pdb=" O VAL V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 60 Processing helix chain 'V' and resid 63 through 79 Processing helix chain 'W' and resid 10 through 48 removed outlier: 4.001A pdb=" N ARG W 36 " --> pdb=" O VAL W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 51 through 61 Processing helix chain 'W' and resid 63 through 80 Processing helix chain 'X' and resid 10 through 48 removed outlier: 3.854A pdb=" N LEU X 14 " --> pdb=" O LEU X 10 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE X 15 " --> pdb=" O ASP X 11 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA X 16 " --> pdb=" O ARG X 12 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG X 36 " --> pdb=" O VAL X 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 61 Processing helix chain 'X' and resid 63 through 80 Processing helix chain 'Y' and resid 10 through 48 removed outlier: 3.981A pdb=" N ARG Y 36 " --> pdb=" O VAL Y 32 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU Y 47 " --> pdb=" O GLY Y 43 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 61 Processing helix chain 'Y' and resid 63 through 79 Processing helix chain 'Z' and resid 9 through 49 removed outlier: 4.042A pdb=" N ARG Z 36 " --> pdb=" O VAL Z 32 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 60 Processing helix chain 'Z' and resid 63 through 79 Processing sheet with id=AA1, first strand: chain 'N' and resid 389 through 391 820 hydrogen bonds defined for protein. 2454 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: 1.41 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2744 1.34 - 1.46: 1839 1.46 - 1.58: 4149 1.58 - 1.70: 0 1.70 - 1.83: 38 Bond restraints: 8770 Sorted by residual: bond pdb=" C LEU V 61 " pdb=" N PRO V 62 " ideal model delta sigma weight residual 1.331 1.371 -0.039 7.90e-03 1.60e+04 2.46e+01 bond pdb=" CG1 ILE V 67 " pdb=" CD1 ILE V 67 " ideal model delta sigma weight residual 1.513 1.418 0.095 3.90e-02 6.57e+02 5.97e+00 bond pdb=" C LYS N 399 " pdb=" N PRO N 400 " ideal model delta sigma weight residual 1.335 1.363 -0.028 1.28e-02 6.10e+03 4.93e+00 bond pdb=" CA VAL N 351 " pdb=" CB VAL N 351 " ideal model delta sigma weight residual 1.534 1.549 -0.015 6.80e-03 2.16e+04 4.78e+00 bond pdb=" CG1 ILE Y 67 " pdb=" CD1 ILE Y 67 " ideal model delta sigma weight residual 1.513 1.440 0.073 3.90e-02 6.57e+02 3.48e+00 ... (remaining 8765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.11: 11512 4.11 - 8.22: 273 8.22 - 12.33: 76 12.33 - 16.44: 23 16.44 - 20.55: 12 Bond angle restraints: 11896 Sorted by residual: angle pdb=" CA TRP N 625 " pdb=" CB TRP N 625 " pdb=" CG TRP N 625 " ideal model delta sigma weight residual 113.60 126.48 -12.88 1.90e+00 2.77e-01 4.60e+01 angle pdb=" CA ARG Q 49 " pdb=" CB ARG Q 49 " pdb=" CG ARG Q 49 " ideal model delta sigma weight residual 114.10 126.30 -12.20 2.00e+00 2.50e-01 3.72e+01 angle pdb=" C VAL O 66 " pdb=" N ILE O 67 " pdb=" CA ILE O 67 " ideal model delta sigma weight residual 120.64 110.79 9.85 1.64e+00 3.72e-01 3.60e+01 angle pdb=" C PHE W 58 " pdb=" N LEU W 59 " pdb=" CA LEU W 59 " ideal model delta sigma weight residual 122.26 111.89 10.37 1.73e+00 3.34e-01 3.60e+01 angle pdb=" CA ARG W 49 " pdb=" CB ARG W 49 " pdb=" CG ARG W 49 " ideal model delta sigma weight residual 114.10 125.87 -11.77 2.00e+00 2.50e-01 3.46e+01 ... (remaining 11891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 4298 16.62 - 33.24: 533 33.24 - 49.86: 119 49.86 - 66.49: 9 66.49 - 83.11: 7 Dihedral angle restraints: 4966 sinusoidal: 1789 harmonic: 3177 Sorted by residual: dihedral pdb=" CA TRP N 625 " pdb=" C TRP N 625 " pdb=" N VAL N 626 " pdb=" CA VAL N 626 " ideal model delta harmonic sigma weight residual -180.00 -151.55 -28.45 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA LEU Y 61 " pdb=" C LEU Y 61 " pdb=" N PRO Y 62 " pdb=" CA PRO Y 62 " ideal model delta harmonic sigma weight residual -180.00 -152.54 -27.46 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA GLU T 47 " pdb=" C GLU T 47 " pdb=" N ASP T 48 " pdb=" CA ASP T 48 " ideal model delta harmonic sigma weight residual 180.00 -155.85 -24.15 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 4963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 1282 0.115 - 0.231: 161 0.231 - 0.346: 13 0.346 - 0.461: 8 0.461 - 0.577: 2 Chirality restraints: 1466 Sorted by residual: chirality pdb=" CG LEU W 56 " pdb=" CB LEU W 56 " pdb=" CD1 LEU W 56 " pdb=" CD2 LEU W 56 " both_signs ideal model delta sigma weight residual False -2.59 -2.01 -0.58 2.00e-01 2.50e+01 8.31e+00 chirality pdb=" CG LEU O 60 " pdb=" CB LEU O 60 " pdb=" CD1 LEU O 60 " pdb=" CD2 LEU O 60 " both_signs ideal model delta sigma weight residual False -2.59 -2.12 -0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" CG LEU S 71 " pdb=" CB LEU S 71 " pdb=" CD1 LEU S 71 " pdb=" CD2 LEU S 71 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.84e+00 ... (remaining 1463 not shown) Planarity restraints: 1499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP N 625 " 0.056 2.00e-02 2.50e+03 4.29e-02 4.61e+01 pdb=" CG TRP N 625 " -0.116 2.00e-02 2.50e+03 pdb=" CD1 TRP N 625 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP N 625 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP N 625 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP N 625 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP N 625 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP N 625 " 0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP N 625 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP N 625 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Q 68 " -0.025 2.00e-02 2.50e+03 2.99e-02 1.57e+01 pdb=" CG PHE Q 68 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 68 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 68 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE Q 68 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE Q 68 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE Q 68 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Z 68 " 0.024 2.00e-02 2.50e+03 2.17e-02 8.22e+00 pdb=" CG PHE Z 68 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE Z 68 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE Z 68 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE Z 68 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE Z 68 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE Z 68 " 0.005 2.00e-02 2.50e+03 ... (remaining 1496 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1232 2.75 - 3.28: 9638 3.28 - 3.82: 15472 3.82 - 4.36: 17541 4.36 - 4.90: 27987 Nonbonded interactions: 71870 Sorted by model distance: nonbonded pdb=" O ILE N 608 " pdb=" OG1 THR N 612 " model vdw 2.207 3.040 nonbonded pdb=" NE2 GLN R 34 " pdb=" OE2 GLU R 63 " model vdw 2.260 3.120 nonbonded pdb=" O ASN Q 51 " pdb=" OG1 THR Q 54 " model vdw 2.297 3.040 nonbonded pdb=" O HIS N 557 " pdb=" OG SER N 560 " model vdw 2.300 3.040 nonbonded pdb=" N GLU Z 63 " pdb=" OE1 GLU Z 63 " model vdw 2.305 3.120 ... (remaining 71865 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 'O' and resid 9 through 80) selection = (chain 'P' and resid 9 through 80) selection = (chain 'Q' and resid 9 through 80) selection = (chain 'R' and resid 9 through 80) selection = (chain 'S' and resid 9 through 80) selection = (chain 'T' and resid 9 through 80) selection = (chain 'U' and resid 9 through 80) selection = (chain 'V' and resid 9 through 80) selection = (chain 'W' and resid 9 through 80) selection = chain 'X' selection = (chain 'Y' and resid 9 through 80) selection = (chain 'Z' and resid 9 through 80) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.340 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 : 0.006 0.095 8770 Z= 0.295 Angle : 1.732 20.546 11896 Z= 0.802 Chirality : 0.081 0.577 1466 Planarity : 0.007 0.063 1499 Dihedral : 15.009 83.107 2984 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.09 % Allowed : 46.30 % Favored : 52.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.23), residues: 1171 helix: -0.40 (0.15), residues: 1020 sheet: -1.28 (1.98), residues: 10 loop : -2.61 (0.45), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 49 TYR 0.015 0.002 TYR N 501 PHE 0.069 0.004 PHE Q 68 TRP 0.116 0.004 TRP N 625 HIS 0.005 0.001 HIS N 491 Details of bonding type rmsd covalent geometry : bond 0.00640 ( 8770) covalent geometry : angle 1.73222 (11896) hydrogen bonds : bond 0.09878 ( 820) hydrogen bonds : angle 5.79273 ( 2454) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 335 time to evaluate : 0.298 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: N 344 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8680 (p) REVERT: O 45 ILE cc_start: 0.8856 (mm) cc_final: 0.8599 (mm) REVERT: O 47 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8179 (pm20) REVERT: P 34 GLN cc_start: 0.9343 (mt0) cc_final: 0.9097 (mt0) REVERT: Q 19 MET cc_start: 0.9107 (mtt) cc_final: 0.8884 (mmt) REVERT: Q 28 LEU cc_start: 0.9648 (mm) cc_final: 0.9323 (mm) REVERT: R 34 GLN cc_start: 0.9359 (mt0) cc_final: 0.8786 (mm-40) REVERT: T 19 MET cc_start: 0.8688 (mtm) cc_final: 0.8312 (ptp) REVERT: T 63 GLU cc_start: 0.9142 (tp30) cc_final: 0.8941 (tp30) REVERT: U 74 PHE cc_start: 0.8880 (m-80) cc_final: 0.8575 (m-80) REVERT: Z 19 MET cc_start: 0.9278 (mtm) cc_final: 0.8979 (mtm) outliers start: 9 outliers final: 5 residues processed: 340 average time/residue: 0.0686 time to fit residues: 35.3694 Evaluate side-chains 338 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 331 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 344 THR Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain P residue 14 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain X residue 34 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 GLN Q 34 GLN ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.059672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.049365 restraints weight = 48188.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.050475 restraints weight = 32952.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.051176 restraints weight = 24944.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.051565 restraints weight = 20484.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.052066 restraints weight = 17987.203| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 8770 Z= 0.187 Angle : 1.016 13.473 11896 Z= 0.485 Chirality : 0.052 0.333 1466 Planarity : 0.006 0.058 1499 Dihedral : 6.005 46.934 1278 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.85 % Allowed : 31.52 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.24), residues: 1171 helix: 0.41 (0.16), residues: 1027 sheet: None (None), residues: 0 loop : -2.36 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 49 TYR 0.008 0.001 TYR N 565 PHE 0.045 0.003 PHE O 68 TRP 0.071 0.002 TRP N 625 HIS 0.005 0.001 HIS N 491 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8770) covalent geometry : angle 1.01606 (11896) hydrogen bonds : bond 0.06150 ( 820) hydrogen bonds : angle 4.70722 ( 2454) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 323 time to evaluate : 0.267 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: N 536 LEU cc_start: 0.9600 (tp) cc_final: 0.9371 (pp) REVERT: N 547 MET cc_start: 0.8938 (pmm) cc_final: 0.8524 (pmm) REVERT: N 577 LEU cc_start: 0.9446 (tt) cc_final: 0.9188 (pp) REVERT: N 617 MET cc_start: 0.9321 (tmm) cc_final: 0.8861 (tmm) REVERT: N 618 LEU cc_start: 0.9506 (mm) cc_final: 0.9113 (mm) REVERT: N 622 ARG cc_start: 0.9722 (OUTLIER) cc_final: 0.9453 (ptm-80) REVERT: N 625 TRP cc_start: 0.9383 (m-90) cc_final: 0.8893 (m-90) REVERT: P 34 GLN cc_start: 0.9408 (mt0) cc_final: 0.8511 (mp10) REVERT: P 68 PHE cc_start: 0.9371 (m-80) cc_final: 0.9050 (m-80) REVERT: Q 19 MET cc_start: 0.8907 (mtt) cc_final: 0.8669 (mtt) REVERT: Q 28 LEU cc_start: 0.9610 (mm) cc_final: 0.9207 (mm) REVERT: R 19 MET cc_start: 0.9407 (mpp) cc_final: 0.9111 (mpp) REVERT: R 34 GLN cc_start: 0.9623 (mt0) cc_final: 0.9096 (mm-40) REVERT: S 47 GLU cc_start: 0.9208 (tp30) cc_final: 0.8885 (tp30) REVERT: T 56 LEU cc_start: 0.9581 (mp) cc_final: 0.9334 (mp) REVERT: U 70 LEU cc_start: 0.9372 (mp) cc_final: 0.9160 (mp) REVERT: U 74 PHE cc_start: 0.8687 (m-80) cc_final: 0.8253 (m-80) REVERT: V 34 GLN cc_start: 0.9612 (OUTLIER) cc_final: 0.9391 (mt0) REVERT: V 68 PHE cc_start: 0.9243 (m-80) cc_final: 0.8979 (m-80) REVERT: W 47 GLU cc_start: 0.9241 (tm-30) cc_final: 0.8986 (tm-30) REVERT: W 58 PHE cc_start: 0.9474 (m-80) cc_final: 0.9051 (m-10) REVERT: W 76 LEU cc_start: 0.9449 (tt) cc_final: 0.8681 (tt) REVERT: Y 48 ASP cc_start: 0.8618 (t0) cc_final: 0.8400 (t70) REVERT: Z 19 MET cc_start: 0.9376 (mtm) cc_final: 0.9167 (mtm) REVERT: Z 58 PHE cc_start: 0.9425 (OUTLIER) cc_final: 0.8577 (t80) REVERT: Z 74 PHE cc_start: 0.8749 (m-80) cc_final: 0.8338 (m-80) outliers start: 40 outliers final: 17 residues processed: 338 average time/residue: 0.0647 time to fit residues: 33.0677 Evaluate side-chains 319 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 299 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 545 TRP Chi-restraints excluded: chain N residue 622 ARG Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain Q residue 49 ARG Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 21 LEU Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 34 GLN Chi-restraints excluded: chain V residue 56 LEU Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain Z residue 58 PHE Chi-restraints excluded: chain Z residue 65 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 619 GLN S 34 GLN V 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.059910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.049315 restraints weight = 48476.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.050098 restraints weight = 33657.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.050991 restraints weight = 26960.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.051573 restraints weight = 21805.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.051989 restraints weight = 18637.676| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 8770 Z= 0.178 Angle : 0.997 13.452 11896 Z= 0.472 Chirality : 0.051 0.319 1466 Planarity : 0.005 0.054 1499 Dihedral : 5.523 45.068 1267 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 6.18 % Allowed : 31.27 % Favored : 62.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.24), residues: 1171 helix: 0.57 (0.15), residues: 1027 sheet: None (None), residues: 0 loop : -2.34 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 49 TYR 0.006 0.001 TYR N 501 PHE 0.036 0.002 PHE Y 52 TRP 0.058 0.002 TRP N 625 HIS 0.005 0.001 HIS N 491 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 8770) covalent geometry : angle 0.99659 (11896) hydrogen bonds : bond 0.05877 ( 820) hydrogen bonds : angle 4.60536 ( 2454) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 329 time to evaluate : 0.303 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: N 547 MET cc_start: 0.8894 (pmm) cc_final: 0.8505 (pmm) REVERT: N 577 LEU cc_start: 0.9456 (tt) cc_final: 0.9214 (pp) REVERT: N 617 MET cc_start: 0.9283 (tmm) cc_final: 0.8829 (tmm) REVERT: N 618 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9028 (mm) REVERT: N 622 ARG cc_start: 0.9736 (OUTLIER) cc_final: 0.9423 (ptm-80) REVERT: N 625 TRP cc_start: 0.9371 (m-90) cc_final: 0.8927 (m-90) REVERT: P 19 MET cc_start: 0.8954 (mmt) cc_final: 0.8281 (mmm) REVERT: P 68 PHE cc_start: 0.9352 (m-80) cc_final: 0.8969 (m-80) REVERT: P 76 LEU cc_start: 0.9552 (tp) cc_final: 0.9157 (tt) REVERT: Q 19 MET cc_start: 0.8892 (mtt) cc_final: 0.8667 (mtt) REVERT: Q 28 LEU cc_start: 0.9614 (mm) cc_final: 0.9182 (mm) REVERT: R 34 GLN cc_start: 0.9616 (mt0) cc_final: 0.9094 (mm-40) REVERT: S 47 GLU cc_start: 0.9265 (tp30) cc_final: 0.8903 (tp30) REVERT: U 70 LEU cc_start: 0.9382 (mp) cc_final: 0.9162 (mp) REVERT: U 74 PHE cc_start: 0.8706 (m-80) cc_final: 0.8285 (m-80) REVERT: V 34 GLN cc_start: 0.9620 (OUTLIER) cc_final: 0.9290 (mt0) REVERT: V 64 THR cc_start: 0.9205 (p) cc_final: 0.8797 (m) REVERT: V 68 PHE cc_start: 0.9248 (m-80) cc_final: 0.8769 (m-80) REVERT: W 47 GLU cc_start: 0.9251 (tm-30) cc_final: 0.8866 (tm-30) REVERT: X 50 SER cc_start: 0.9017 (t) cc_final: 0.8807 (p) REVERT: Y 48 ASP cc_start: 0.8534 (t0) cc_final: 0.8186 (t0) REVERT: Z 19 MET cc_start: 0.9317 (mtm) cc_final: 0.9070 (mtm) REVERT: Z 58 PHE cc_start: 0.9391 (OUTLIER) cc_final: 0.8568 (t80) REVERT: Z 60 LEU cc_start: 0.9364 (mm) cc_final: 0.8972 (mm) REVERT: Z 74 PHE cc_start: 0.8723 (m-80) cc_final: 0.8173 (m-80) outliers start: 51 outliers final: 24 residues processed: 353 average time/residue: 0.0689 time to fit residues: 36.8740 Evaluate side-chains 337 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 309 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 399 LYS Chi-restraints excluded: chain N residue 545 TRP Chi-restraints excluded: chain N residue 562 ILE Chi-restraints excluded: chain N residue 618 LEU Chi-restraints excluded: chain N residue 622 ARG Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 77 ASN Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 34 GLN Chi-restraints excluded: chain V residue 56 LEU Chi-restraints excluded: chain V residue 58 PHE Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 58 PHE Chi-restraints excluded: chain Z residue 58 PHE Chi-restraints excluded: chain Z residue 64 THR Chi-restraints excluded: chain Z residue 65 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.059920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.049514 restraints weight = 49332.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.050620 restraints weight = 33267.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.051387 restraints weight = 25033.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.051979 restraints weight = 20254.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.052306 restraints weight = 17205.919| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 8770 Z= 0.180 Angle : 1.012 12.931 11896 Z= 0.477 Chirality : 0.051 0.351 1466 Planarity : 0.005 0.059 1499 Dihedral : 5.658 55.559 1267 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 6.30 % Allowed : 32.73 % Favored : 60.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.24), residues: 1171 helix: 0.60 (0.15), residues: 1027 sheet: None (None), residues: 0 loop : -2.28 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 622 TYR 0.007 0.001 TYR N 565 PHE 0.043 0.002 PHE S 68 TRP 0.048 0.002 TRP N 625 HIS 0.005 0.001 HIS N 491 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 8770) covalent geometry : angle 1.01195 (11896) hydrogen bonds : bond 0.05749 ( 820) hydrogen bonds : angle 4.63549 ( 2454) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 327 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 361 MET cc_start: 0.9208 (mpp) cc_final: 0.8948 (mpp) REVERT: N 547 MET cc_start: 0.8841 (pmm) cc_final: 0.8494 (pmm) REVERT: N 617 MET cc_start: 0.9299 (tmm) cc_final: 0.8772 (tmm) REVERT: N 618 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9085 (mm) REVERT: N 619 GLN cc_start: 0.9485 (mm-40) cc_final: 0.8800 (mm-40) REVERT: N 622 ARG cc_start: 0.9740 (OUTLIER) cc_final: 0.9020 (ttp80) REVERT: N 625 TRP cc_start: 0.9366 (m-10) cc_final: 0.9011 (m-90) REVERT: N 629 PHE cc_start: 0.9530 (m-10) cc_final: 0.9264 (m-80) REVERT: O 47 GLU cc_start: 0.6478 (mt-10) cc_final: 0.5625 (mp0) REVERT: P 19 MET cc_start: 0.9027 (mmt) cc_final: 0.7963 (mmm) REVERT: P 68 PHE cc_start: 0.9434 (m-80) cc_final: 0.8814 (m-80) REVERT: Q 19 MET cc_start: 0.8859 (mtt) cc_final: 0.8609 (mtt) REVERT: Q 28 LEU cc_start: 0.9663 (mm) cc_final: 0.9450 (mm) REVERT: R 34 GLN cc_start: 0.9624 (mt0) cc_final: 0.9033 (mm-40) REVERT: S 19 MET cc_start: 0.9188 (mtt) cc_final: 0.8937 (mtt) REVERT: T 56 LEU cc_start: 0.9583 (mp) cc_final: 0.9359 (mp) REVERT: U 70 LEU cc_start: 0.9444 (mp) cc_final: 0.9204 (mp) REVERT: U 74 PHE cc_start: 0.8740 (m-80) cc_final: 0.8311 (m-80) REVERT: V 64 THR cc_start: 0.9131 (p) cc_final: 0.8895 (m) REVERT: V 68 PHE cc_start: 0.9234 (m-80) cc_final: 0.8894 (m-10) REVERT: W 47 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8927 (tm-30) REVERT: W 58 PHE cc_start: 0.9427 (m-80) cc_final: 0.9155 (m-10) REVERT: W 74 PHE cc_start: 0.7989 (t80) cc_final: 0.7732 (t80) REVERT: X 34 GLN cc_start: 0.9563 (mt0) cc_final: 0.9206 (mt0) REVERT: X 47 GLU cc_start: 0.9361 (mm-30) cc_final: 0.9017 (pp20) REVERT: X 50 SER cc_start: 0.9034 (t) cc_final: 0.8806 (p) REVERT: X 63 GLU cc_start: 0.9414 (mp0) cc_final: 0.9062 (mp0) REVERT: Y 48 ASP cc_start: 0.8582 (t0) cc_final: 0.8179 (t0) REVERT: Z 58 PHE cc_start: 0.9371 (OUTLIER) cc_final: 0.8565 (t80) REVERT: Z 70 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9198 (pt) REVERT: Z 74 PHE cc_start: 0.8728 (m-80) cc_final: 0.8175 (m-80) outliers start: 52 outliers final: 31 residues processed: 353 average time/residue: 0.0712 time to fit residues: 37.9525 Evaluate side-chains 335 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 300 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 322 ASP Chi-restraints excluded: chain N residue 399 LYS Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain N residue 545 TRP Chi-restraints excluded: chain N residue 558 ILE Chi-restraints excluded: chain N residue 562 ILE Chi-restraints excluded: chain N residue 606 LEU Chi-restraints excluded: chain N residue 618 LEU Chi-restraints excluded: chain N residue 622 ARG Chi-restraints excluded: chain O residue 19 MET Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 60 LEU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain Q residue 50 SER Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 77 ASN Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 21 LEU Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain Z residue 17 VAL Chi-restraints excluded: chain Z residue 58 PHE Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain Z residue 70 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.059364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.049164 restraints weight = 49732.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.050297 restraints weight = 33256.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.051079 restraints weight = 24837.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.051700 restraints weight = 19947.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.052082 restraints weight = 16832.448| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 8770 Z= 0.187 Angle : 1.069 15.371 11896 Z= 0.498 Chirality : 0.053 0.331 1466 Planarity : 0.005 0.060 1499 Dihedral : 5.680 53.948 1267 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 6.91 % Allowed : 33.82 % Favored : 59.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.24), residues: 1171 helix: 0.67 (0.16), residues: 1021 sheet: -1.28 (2.05), residues: 10 loop : -2.39 (0.47), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 622 TYR 0.013 0.001 TYR N 424 PHE 0.036 0.002 PHE Q 68 TRP 0.043 0.002 TRP N 625 HIS 0.004 0.001 HIS N 491 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 8770) covalent geometry : angle 1.06900 (11896) hydrogen bonds : bond 0.05674 ( 820) hydrogen bonds : angle 4.62749 ( 2454) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 325 time to evaluate : 0.311 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: N 413 MET cc_start: 0.9432 (mmm) cc_final: 0.9216 (mmm) REVERT: N 547 MET cc_start: 0.8845 (pmm) cc_final: 0.8625 (pmm) REVERT: N 617 MET cc_start: 0.9328 (tmm) cc_final: 0.8757 (tmm) REVERT: N 618 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9003 (mm) REVERT: N 622 ARG cc_start: 0.9746 (OUTLIER) cc_final: 0.8952 (ttp80) REVERT: N 625 TRP cc_start: 0.9449 (m-10) cc_final: 0.8824 (m-90) REVERT: P 19 MET cc_start: 0.9086 (mmt) cc_final: 0.8794 (mmt) REVERT: P 68 PHE cc_start: 0.9417 (m-80) cc_final: 0.8769 (m-80) REVERT: Q 19 MET cc_start: 0.8944 (mtt) cc_final: 0.8674 (mtt) REVERT: Q 28 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9468 (mm) REVERT: Q 49 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8095 (tpp-160) REVERT: Q 76 LEU cc_start: 0.9377 (mm) cc_final: 0.9177 (mt) REVERT: R 19 MET cc_start: 0.9438 (mtt) cc_final: 0.8795 (mpp) REVERT: R 34 GLN cc_start: 0.9612 (mt0) cc_final: 0.8957 (mm-40) REVERT: R 60 LEU cc_start: 0.9284 (tp) cc_final: 0.9063 (pp) REVERT: S 47 GLU cc_start: 0.9238 (tp30) cc_final: 0.8909 (tp30) REVERT: U 70 LEU cc_start: 0.9487 (mp) cc_final: 0.9251 (mp) REVERT: U 74 PHE cc_start: 0.8743 (m-10) cc_final: 0.8283 (m-80) REVERT: V 68 PHE cc_start: 0.9238 (m-10) cc_final: 0.8951 (m-10) REVERT: W 47 GLU cc_start: 0.9139 (tm-30) cc_final: 0.8869 (tm-30) REVERT: W 58 PHE cc_start: 0.9463 (m-80) cc_final: 0.8923 (m-10) REVERT: W 68 PHE cc_start: 0.9061 (m-80) cc_final: 0.8748 (m-80) REVERT: W 74 PHE cc_start: 0.8027 (t80) cc_final: 0.7691 (t80) REVERT: X 28 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9259 (mm) REVERT: X 34 GLN cc_start: 0.9551 (mt0) cc_final: 0.9151 (mt0) REVERT: X 47 GLU cc_start: 0.9426 (mm-30) cc_final: 0.9017 (pp20) REVERT: X 50 SER cc_start: 0.9017 (t) cc_final: 0.8776 (p) REVERT: X 63 GLU cc_start: 0.9408 (mp0) cc_final: 0.9041 (mp0) REVERT: Y 30 THR cc_start: 0.9692 (OUTLIER) cc_final: 0.9393 (p) REVERT: Y 48 ASP cc_start: 0.8613 (t0) cc_final: 0.8219 (t0) REVERT: Y 61 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9298 (mm) REVERT: Z 19 MET cc_start: 0.9299 (mtm) cc_final: 0.8758 (mtm) REVERT: Z 70 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9132 (pt) REVERT: Z 74 PHE cc_start: 0.8737 (m-80) cc_final: 0.8294 (m-80) outliers start: 57 outliers final: 36 residues processed: 353 average time/residue: 0.0673 time to fit residues: 36.3402 Evaluate side-chains 352 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 308 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 322 ASP Chi-restraints excluded: chain N residue 399 LYS Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain N residue 430 THR Chi-restraints excluded: chain N residue 545 TRP Chi-restraints excluded: chain N residue 558 ILE Chi-restraints excluded: chain N residue 559 LEU Chi-restraints excluded: chain N residue 562 ILE Chi-restraints excluded: chain N residue 606 LEU Chi-restraints excluded: chain N residue 618 LEU Chi-restraints excluded: chain N residue 622 ARG Chi-restraints excluded: chain O residue 19 MET Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain Q residue 28 LEU Chi-restraints excluded: chain Q residue 49 ARG Chi-restraints excluded: chain Q residue 50 SER Chi-restraints excluded: chain Q residue 63 GLU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 77 ASN Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain T residue 21 LEU Chi-restraints excluded: chain T residue 59 LEU Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Z residue 17 VAL Chi-restraints excluded: chain Z residue 64 THR Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain Z residue 70 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 34 GLN V 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.060665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.050154 restraints weight = 48605.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.051259 restraints weight = 33380.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.052063 restraints weight = 25230.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.052610 restraints weight = 20435.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.052984 restraints weight = 17579.452| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 8770 Z= 0.183 Angle : 1.111 14.822 11896 Z= 0.510 Chirality : 0.055 0.403 1466 Planarity : 0.005 0.061 1499 Dihedral : 5.648 55.179 1267 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 5.94 % Allowed : 37.21 % Favored : 56.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.23), residues: 1171 helix: 0.56 (0.15), residues: 1027 sheet: -1.07 (2.07), residues: 10 loop : -2.48 (0.48), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 622 TYR 0.008 0.001 TYR N 424 PHE 0.053 0.002 PHE N 476 TRP 0.038 0.002 TRP N 625 HIS 0.004 0.001 HIS N 491 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 8770) covalent geometry : angle 1.11130 (11896) hydrogen bonds : bond 0.05515 ( 820) hydrogen bonds : angle 4.57066 ( 2454) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 335 time to evaluate : 0.293 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: N 361 MET cc_start: 0.9384 (mpp) cc_final: 0.8347 (mpp) REVERT: N 420 TRP cc_start: 0.9449 (t-100) cc_final: 0.9079 (t60) REVERT: N 528 MET cc_start: 0.8783 (mpp) cc_final: 0.8455 (mpp) REVERT: N 547 MET cc_start: 0.8844 (pmm) cc_final: 0.8605 (pmm) REVERT: N 617 MET cc_start: 0.9298 (tmm) cc_final: 0.8689 (tmm) REVERT: N 618 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.8868 (mm) REVERT: N 622 ARG cc_start: 0.9714 (OUTLIER) cc_final: 0.8986 (ttp80) REVERT: N 625 TRP cc_start: 0.9440 (m-10) cc_final: 0.8947 (m-90) REVERT: N 627 GLU cc_start: 0.8987 (mp0) cc_final: 0.8695 (mp0) REVERT: O 45 ILE cc_start: 0.8732 (mm) cc_final: 0.8460 (mm) REVERT: P 19 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8527 (mmt) REVERT: P 34 GLN cc_start: 0.9637 (mt0) cc_final: 0.9169 (mt0) REVERT: P 68 PHE cc_start: 0.9408 (m-80) cc_final: 0.8828 (m-80) REVERT: Q 19 MET cc_start: 0.8933 (mtt) cc_final: 0.8648 (mtt) REVERT: Q 28 LEU cc_start: 0.9674 (OUTLIER) cc_final: 0.9185 (mm) REVERT: Q 76 LEU cc_start: 0.9317 (mm) cc_final: 0.9115 (mt) REVERT: R 34 GLN cc_start: 0.9592 (mt0) cc_final: 0.8961 (mm-40) REVERT: R 59 LEU cc_start: 0.9811 (tp) cc_final: 0.9379 (tp) REVERT: R 60 LEU cc_start: 0.9290 (tp) cc_final: 0.9024 (pp) REVERT: U 34 GLN cc_start: 0.9446 (mt0) cc_final: 0.9119 (mm-40) REVERT: U 70 LEU cc_start: 0.9421 (mp) cc_final: 0.9102 (mp) REVERT: U 74 PHE cc_start: 0.8790 (m-10) cc_final: 0.8399 (m-80) REVERT: V 68 PHE cc_start: 0.9304 (m-10) cc_final: 0.8885 (m-10) REVERT: W 19 MET cc_start: 0.8686 (mtt) cc_final: 0.8344 (mmm) REVERT: W 47 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8847 (tm-30) REVERT: W 58 PHE cc_start: 0.9424 (m-80) cc_final: 0.8988 (m-10) REVERT: W 74 PHE cc_start: 0.7993 (t80) cc_final: 0.7673 (t80) REVERT: X 47 GLU cc_start: 0.9400 (mm-30) cc_final: 0.8980 (pp20) REVERT: X 50 SER cc_start: 0.8950 (t) cc_final: 0.8713 (p) REVERT: X 63 GLU cc_start: 0.9450 (mp0) cc_final: 0.9113 (mp0) REVERT: Y 30 THR cc_start: 0.9695 (OUTLIER) cc_final: 0.9404 (p) REVERT: Y 48 ASP cc_start: 0.8493 (t0) cc_final: 0.8106 (t0) REVERT: Y 61 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9105 (mt) REVERT: Z 60 LEU cc_start: 0.9244 (mm) cc_final: 0.8957 (mm) REVERT: Z 70 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9064 (pt) REVERT: Z 74 PHE cc_start: 0.8713 (m-80) cc_final: 0.8230 (m-80) outliers start: 49 outliers final: 27 residues processed: 354 average time/residue: 0.0636 time to fit residues: 34.7803 Evaluate side-chains 349 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 315 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 399 LYS Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain N residue 545 TRP Chi-restraints excluded: chain N residue 558 ILE Chi-restraints excluded: chain N residue 559 LEU Chi-restraints excluded: chain N residue 562 ILE Chi-restraints excluded: chain N residue 606 LEU Chi-restraints excluded: chain N residue 618 LEU Chi-restraints excluded: chain N residue 622 ARG Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain P residue 19 MET Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain Q residue 28 LEU Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain T residue 59 LEU Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 59 LEU Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Z residue 64 THR Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain Z residue 70 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 16 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 12 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.060848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.050128 restraints weight = 49028.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.051279 restraints weight = 33505.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.052080 restraints weight = 25355.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.052707 restraints weight = 20457.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.053105 restraints weight = 17392.125| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 8770 Z= 0.186 Angle : 1.173 16.809 11896 Z= 0.532 Chirality : 0.057 0.444 1466 Planarity : 0.005 0.060 1499 Dihedral : 5.642 50.744 1267 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.33 % Allowed : 39.64 % Favored : 55.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.23), residues: 1171 helix: 0.49 (0.15), residues: 1020 sheet: -0.91 (2.08), residues: 10 loop : -2.31 (0.47), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 49 TYR 0.008 0.001 TYR N 424 PHE 0.058 0.002 PHE W 68 TRP 0.033 0.002 TRP N 625 HIS 0.002 0.001 HIS N 408 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 8770) covalent geometry : angle 1.17281 (11896) hydrogen bonds : bond 0.05492 ( 820) hydrogen bonds : angle 4.59714 ( 2454) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 321 time to evaluate : 0.353 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: N 361 MET cc_start: 0.9297 (mpp) cc_final: 0.8271 (mpp) REVERT: N 362 ILE cc_start: 0.9558 (OUTLIER) cc_final: 0.9333 (mm) REVERT: N 413 MET cc_start: 0.9441 (mmm) cc_final: 0.8726 (tmm) REVERT: N 420 TRP cc_start: 0.9482 (t-100) cc_final: 0.9208 (t60) REVERT: N 547 MET cc_start: 0.8799 (pmm) cc_final: 0.8546 (pmm) REVERT: N 617 MET cc_start: 0.9324 (tmm) cc_final: 0.8656 (tmm) REVERT: N 618 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.8850 (mm) REVERT: N 622 ARG cc_start: 0.9731 (OUTLIER) cc_final: 0.8995 (ttp80) REVERT: N 625 TRP cc_start: 0.9448 (m-10) cc_final: 0.9068 (m-90) REVERT: N 627 GLU cc_start: 0.9100 (mp0) cc_final: 0.8895 (mp0) REVERT: N 629 PHE cc_start: 0.9473 (m-10) cc_final: 0.9212 (m-80) REVERT: O 45 ILE cc_start: 0.8880 (mm) cc_final: 0.8529 (mm) REVERT: P 19 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8542 (mmt) REVERT: P 68 PHE cc_start: 0.9358 (m-80) cc_final: 0.8923 (m-80) REVERT: Q 19 MET cc_start: 0.8887 (mtt) cc_final: 0.8580 (mtt) REVERT: Q 28 LEU cc_start: 0.9668 (OUTLIER) cc_final: 0.9177 (mm) REVERT: Q 76 LEU cc_start: 0.9337 (mm) cc_final: 0.9137 (mt) REVERT: R 34 GLN cc_start: 0.9613 (mt0) cc_final: 0.8925 (mm-40) REVERT: R 59 LEU cc_start: 0.9828 (tp) cc_final: 0.9407 (tp) REVERT: T 19 MET cc_start: 0.9417 (ptp) cc_final: 0.9207 (ptp) REVERT: U 34 GLN cc_start: 0.9463 (mt0) cc_final: 0.9106 (mm-40) REVERT: U 70 LEU cc_start: 0.9445 (mp) cc_final: 0.9132 (mp) REVERT: U 74 PHE cc_start: 0.8733 (m-10) cc_final: 0.8334 (m-80) REVERT: V 68 PHE cc_start: 0.9260 (m-10) cc_final: 0.8854 (m-80) REVERT: W 47 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8815 (tm-30) REVERT: W 58 PHE cc_start: 0.9433 (m-80) cc_final: 0.9148 (m-80) REVERT: W 74 PHE cc_start: 0.8041 (t80) cc_final: 0.7682 (t80) REVERT: X 34 GLN cc_start: 0.9557 (mt0) cc_final: 0.8945 (mm-40) REVERT: X 47 GLU cc_start: 0.9423 (mm-30) cc_final: 0.8956 (pp20) REVERT: X 48 ASP cc_start: 0.9256 (t0) cc_final: 0.8953 (t70) REVERT: X 63 GLU cc_start: 0.9464 (mp0) cc_final: 0.8870 (mp0) REVERT: Y 30 THR cc_start: 0.9701 (OUTLIER) cc_final: 0.9409 (p) REVERT: Y 48 ASP cc_start: 0.8493 (t0) cc_final: 0.8108 (t0) REVERT: Y 61 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9120 (mt) REVERT: Z 60 LEU cc_start: 0.9250 (mm) cc_final: 0.8925 (mm) REVERT: Z 70 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9051 (pt) REVERT: Z 74 PHE cc_start: 0.8821 (m-80) cc_final: 0.8274 (m-80) outliers start: 44 outliers final: 30 residues processed: 341 average time/residue: 0.0638 time to fit residues: 33.5708 Evaluate side-chains 351 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 313 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 362 ILE Chi-restraints excluded: chain N residue 399 LYS Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain N residue 430 THR Chi-restraints excluded: chain N residue 545 TRP Chi-restraints excluded: chain N residue 559 LEU Chi-restraints excluded: chain N residue 562 ILE Chi-restraints excluded: chain N residue 606 LEU Chi-restraints excluded: chain N residue 618 LEU Chi-restraints excluded: chain N residue 622 ARG Chi-restraints excluded: chain O residue 19 MET Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain P residue 19 MET Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain Q residue 28 LEU Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 59 LEU Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Z residue 17 VAL Chi-restraints excluded: chain Z residue 64 THR Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain Z residue 70 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 112 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 22 optimal weight: 0.0270 chunk 12 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 overall best weight: 1.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.060736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.050319 restraints weight = 48944.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.051445 restraints weight = 33858.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.052203 restraints weight = 25357.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.052799 restraints weight = 20681.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.053234 restraints weight = 17655.718| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 8770 Z= 0.191 Angle : 1.184 16.037 11896 Z= 0.542 Chirality : 0.059 0.454 1466 Planarity : 0.005 0.061 1499 Dihedral : 5.579 47.805 1267 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.09 % Allowed : 40.97 % Favored : 53.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.24), residues: 1171 helix: 0.48 (0.16), residues: 1027 sheet: -0.87 (2.07), residues: 10 loop : -2.42 (0.49), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 622 TYR 0.007 0.001 TYR N 424 PHE 0.036 0.002 PHE Y 52 TRP 0.052 0.003 TRP N 496 HIS 0.002 0.001 HIS N 494 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 8770) covalent geometry : angle 1.18353 (11896) hydrogen bonds : bond 0.05524 ( 820) hydrogen bonds : angle 4.65114 ( 2454) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 320 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 361 MET cc_start: 0.9242 (mpp) cc_final: 0.8285 (mpp) REVERT: N 362 ILE cc_start: 0.9572 (OUTLIER) cc_final: 0.9342 (mm) REVERT: N 413 MET cc_start: 0.9463 (mmm) cc_final: 0.8698 (tmm) REVERT: N 420 TRP cc_start: 0.9471 (t-100) cc_final: 0.9240 (t60) REVERT: N 547 MET cc_start: 0.8739 (pmm) cc_final: 0.8480 (pmm) REVERT: N 617 MET cc_start: 0.9355 (tmm) cc_final: 0.8674 (tmm) REVERT: N 618 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.8799 (mm) REVERT: N 622 ARG cc_start: 0.9714 (OUTLIER) cc_final: 0.8926 (ttp80) REVERT: N 625 TRP cc_start: 0.9450 (m-10) cc_final: 0.8864 (m-90) REVERT: P 19 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8521 (mmt) REVERT: P 34 GLN cc_start: 0.9687 (mt0) cc_final: 0.8973 (mp10) REVERT: P 68 PHE cc_start: 0.9365 (m-80) cc_final: 0.8986 (m-80) REVERT: Q 28 LEU cc_start: 0.9703 (OUTLIER) cc_final: 0.9219 (mm) REVERT: Q 51 ASN cc_start: 0.7904 (m110) cc_final: 0.7435 (m-40) REVERT: R 34 GLN cc_start: 0.9591 (mt0) cc_final: 0.8880 (mm-40) REVERT: S 19 MET cc_start: 0.8875 (mtt) cc_final: 0.8478 (mpp) REVERT: U 34 GLN cc_start: 0.9466 (mt0) cc_final: 0.9116 (mm-40) REVERT: U 70 LEU cc_start: 0.9511 (mp) cc_final: 0.9239 (mp) REVERT: U 74 PHE cc_start: 0.8769 (m-10) cc_final: 0.8357 (m-80) REVERT: V 68 PHE cc_start: 0.9263 (m-10) cc_final: 0.8837 (m-80) REVERT: W 47 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8774 (tm-30) REVERT: W 58 PHE cc_start: 0.9465 (m-80) cc_final: 0.8915 (m-10) REVERT: W 74 PHE cc_start: 0.8087 (t80) cc_final: 0.7722 (t80) REVERT: X 34 GLN cc_start: 0.9530 (mt0) cc_final: 0.9043 (mt0) REVERT: X 47 GLU cc_start: 0.9390 (mm-30) cc_final: 0.8974 (pp20) REVERT: X 63 GLU cc_start: 0.9446 (mp0) cc_final: 0.8961 (mp0) REVERT: Y 30 THR cc_start: 0.9710 (OUTLIER) cc_final: 0.9422 (p) REVERT: Y 48 ASP cc_start: 0.8525 (t0) cc_final: 0.8135 (t0) REVERT: Y 61 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9140 (mt) REVERT: Z 58 PHE cc_start: 0.9362 (OUTLIER) cc_final: 0.8765 (t80) REVERT: Z 60 LEU cc_start: 0.9251 (mm) cc_final: 0.8931 (mm) REVERT: Z 70 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9056 (pt) REVERT: Z 74 PHE cc_start: 0.8812 (m-80) cc_final: 0.8277 (m-80) outliers start: 42 outliers final: 27 residues processed: 340 average time/residue: 0.0636 time to fit residues: 33.5725 Evaluate side-chains 348 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 312 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 362 ILE Chi-restraints excluded: chain N residue 399 LYS Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain N residue 430 THR Chi-restraints excluded: chain N residue 545 TRP Chi-restraints excluded: chain N residue 559 LEU Chi-restraints excluded: chain N residue 606 LEU Chi-restraints excluded: chain N residue 618 LEU Chi-restraints excluded: chain N residue 622 ARG Chi-restraints excluded: chain O residue 19 MET Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain P residue 19 MET Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain Q residue 28 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 59 LEU Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Z residue 58 PHE Chi-restraints excluded: chain Z residue 64 THR Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain Z residue 70 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 14 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 0.1980 chunk 16 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 27 optimal weight: 30.0000 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.060123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.049824 restraints weight = 49869.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.050929 restraints weight = 33963.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.051735 restraints weight = 25586.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.052163 restraints weight = 20669.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.052695 restraints weight = 17973.609| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 8770 Z= 0.200 Angle : 1.214 19.696 11896 Z= 0.558 Chirality : 0.060 0.452 1466 Planarity : 0.005 0.062 1499 Dihedral : 5.617 48.797 1267 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 22.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.45 % Allowed : 41.45 % Favored : 53.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.24), residues: 1171 helix: 0.45 (0.16), residues: 1026 sheet: -0.78 (2.05), residues: 10 loop : -2.45 (0.49), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 622 TYR 0.006 0.001 TYR N 424 PHE 0.037 0.002 PHE Y 52 TRP 0.031 0.002 TRP N 625 HIS 0.003 0.001 HIS N 561 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 8770) covalent geometry : angle 1.21364 (11896) hydrogen bonds : bond 0.05600 ( 820) hydrogen bonds : angle 4.77682 ( 2454) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 320 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 361 MET cc_start: 0.9222 (mpp) cc_final: 0.8233 (mpp) REVERT: N 362 ILE cc_start: 0.9586 (OUTLIER) cc_final: 0.9355 (mm) REVERT: N 413 MET cc_start: 0.9464 (mmm) cc_final: 0.8668 (tmm) REVERT: N 420 TRP cc_start: 0.9481 (t-100) cc_final: 0.9262 (t60) REVERT: N 617 MET cc_start: 0.9389 (tmm) cc_final: 0.8683 (tmm) REVERT: N 618 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.8841 (mm) REVERT: N 619 GLN cc_start: 0.9567 (mm110) cc_final: 0.8912 (mm-40) REVERT: N 622 ARG cc_start: 0.9733 (OUTLIER) cc_final: 0.8834 (ttp80) REVERT: N 625 TRP cc_start: 0.9434 (m-10) cc_final: 0.8981 (m-90) REVERT: P 19 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8565 (mmt) REVERT: P 34 GLN cc_start: 0.9695 (mt0) cc_final: 0.8987 (mp10) REVERT: P 68 PHE cc_start: 0.9378 (m-80) cc_final: 0.9008 (m-80) REVERT: Q 19 MET cc_start: 0.8844 (mtt) cc_final: 0.8553 (mtt) REVERT: Q 28 LEU cc_start: 0.9731 (OUTLIER) cc_final: 0.9419 (mm) REVERT: Q 51 ASN cc_start: 0.7948 (m110) cc_final: 0.7607 (m-40) REVERT: R 34 GLN cc_start: 0.9612 (mt0) cc_final: 0.8883 (mm-40) REVERT: S 19 MET cc_start: 0.8914 (mtt) cc_final: 0.8521 (mpp) REVERT: U 34 GLN cc_start: 0.9495 (mt0) cc_final: 0.9173 (mm-40) REVERT: U 70 LEU cc_start: 0.9523 (mp) cc_final: 0.9246 (mp) REVERT: U 74 PHE cc_start: 0.8791 (m-10) cc_final: 0.8341 (m-80) REVERT: V 58 PHE cc_start: 0.9372 (t80) cc_final: 0.9154 (t80) REVERT: V 64 THR cc_start: 0.9144 (p) cc_final: 0.8598 (m) REVERT: V 68 PHE cc_start: 0.9261 (m-10) cc_final: 0.8707 (m-80) REVERT: W 19 MET cc_start: 0.8834 (mmm) cc_final: 0.8339 (mmm) REVERT: W 47 GLU cc_start: 0.9106 (tm-30) cc_final: 0.8782 (tm-30) REVERT: W 58 PHE cc_start: 0.9535 (m-80) cc_final: 0.8899 (m-10) REVERT: W 74 PHE cc_start: 0.8098 (t80) cc_final: 0.7703 (t80) REVERT: X 19 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.9029 (tpp) REVERT: X 34 GLN cc_start: 0.9524 (mt0) cc_final: 0.9040 (mt0) REVERT: X 47 GLU cc_start: 0.9401 (mm-30) cc_final: 0.8958 (pp20) REVERT: X 63 GLU cc_start: 0.9423 (mp0) cc_final: 0.8931 (mp0) REVERT: Y 48 ASP cc_start: 0.8514 (t0) cc_final: 0.8099 (t0) REVERT: Y 61 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9143 (mt) REVERT: Z 58 PHE cc_start: 0.9423 (OUTLIER) cc_final: 0.8755 (t80) REVERT: Z 60 LEU cc_start: 0.9153 (mm) cc_final: 0.8935 (mm) REVERT: Z 70 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9056 (pt) REVERT: Z 74 PHE cc_start: 0.8917 (m-80) cc_final: 0.8342 (m-80) outliers start: 45 outliers final: 28 residues processed: 337 average time/residue: 0.0642 time to fit residues: 33.4947 Evaluate side-chains 346 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 309 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 362 ILE Chi-restraints excluded: chain N residue 379 LEU Chi-restraints excluded: chain N residue 399 LYS Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain N residue 430 THR Chi-restraints excluded: chain N residue 545 TRP Chi-restraints excluded: chain N residue 606 LEU Chi-restraints excluded: chain N residue 618 LEU Chi-restraints excluded: chain N residue 622 ARG Chi-restraints excluded: chain O residue 19 MET Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain P residue 19 MET Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain Q residue 28 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain W residue 67 ILE Chi-restraints excluded: chain X residue 19 MET Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 48 ASP Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Z residue 58 PHE Chi-restraints excluded: chain Z residue 64 THR Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain Z residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 27 optimal weight: 30.0000 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 114 optimal weight: 0.0060 chunk 109 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.061316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.050863 restraints weight = 49043.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.051979 restraints weight = 33498.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.052816 restraints weight = 25168.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.053252 restraints weight = 20287.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.053815 restraints weight = 17619.837| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 8770 Z= 0.195 Angle : 1.278 20.540 11896 Z= 0.577 Chirality : 0.062 0.465 1466 Planarity : 0.005 0.063 1499 Dihedral : 5.348 44.056 1265 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 23.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.61 % Allowed : 42.91 % Favored : 52.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.23), residues: 1171 helix: 0.33 (0.15), residues: 1020 sheet: -0.82 (2.04), residues: 10 loop : -2.26 (0.48), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 49 TYR 0.005 0.001 TYR N 424 PHE 0.036 0.002 PHE Y 52 TRP 0.033 0.002 TRP N 625 HIS 0.002 0.001 HIS N 491 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 8770) covalent geometry : angle 1.27783 (11896) hydrogen bonds : bond 0.05579 ( 820) hydrogen bonds : angle 4.76726 ( 2454) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 319 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 361 MET cc_start: 0.9190 (mpp) cc_final: 0.8203 (mpp) REVERT: N 362 ILE cc_start: 0.9556 (OUTLIER) cc_final: 0.9326 (mm) REVERT: N 384 LYS cc_start: 0.9730 (ttmm) cc_final: 0.9513 (ptpt) REVERT: N 547 MET cc_start: 0.8861 (pmm) cc_final: 0.8571 (pmm) REVERT: N 617 MET cc_start: 0.9389 (tmm) cc_final: 0.8631 (tmm) REVERT: N 618 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.8870 (mm) REVERT: N 619 GLN cc_start: 0.9589 (mm110) cc_final: 0.8977 (mm-40) REVERT: N 622 ARG cc_start: 0.9721 (OUTLIER) cc_final: 0.8953 (ptm-80) REVERT: N 625 TRP cc_start: 0.9452 (m-10) cc_final: 0.8852 (m-90) REVERT: P 19 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.7869 (mmm) REVERT: P 34 GLN cc_start: 0.9688 (mt0) cc_final: 0.8993 (mp10) REVERT: P 68 PHE cc_start: 0.9379 (m-80) cc_final: 0.9002 (m-80) REVERT: Q 19 MET cc_start: 0.8911 (mtt) cc_final: 0.8602 (mtt) REVERT: Q 28 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9413 (mm) REVERT: Q 51 ASN cc_start: 0.7917 (m110) cc_final: 0.7462 (m-40) REVERT: R 19 MET cc_start: 0.9237 (mtt) cc_final: 0.8986 (mmm) REVERT: R 34 GLN cc_start: 0.9592 (mt0) cc_final: 0.8830 (mm-40) REVERT: S 19 MET cc_start: 0.8862 (mtt) cc_final: 0.8508 (mpp) REVERT: U 34 GLN cc_start: 0.9501 (mt0) cc_final: 0.9187 (mm-40) REVERT: U 70 LEU cc_start: 0.9532 (mp) cc_final: 0.9252 (mp) REVERT: U 74 PHE cc_start: 0.8824 (m-10) cc_final: 0.8417 (m-80) REVERT: V 68 PHE cc_start: 0.9277 (m-10) cc_final: 0.8837 (m-80) REVERT: W 19 MET cc_start: 0.8809 (mmm) cc_final: 0.8394 (mmm) REVERT: W 47 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8787 (tm-30) REVERT: W 58 PHE cc_start: 0.9488 (m-80) cc_final: 0.8980 (m-10) REVERT: W 74 PHE cc_start: 0.8079 (t80) cc_final: 0.7683 (t80) REVERT: X 19 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.9028 (tpp) REVERT: X 34 GLN cc_start: 0.9554 (mt0) cc_final: 0.9054 (mt0) REVERT: X 47 GLU cc_start: 0.9398 (mm-30) cc_final: 0.8922 (pp20) REVERT: X 63 GLU cc_start: 0.9439 (mp0) cc_final: 0.8993 (mp0) REVERT: Y 30 THR cc_start: 0.9693 (OUTLIER) cc_final: 0.9433 (p) REVERT: Y 48 ASP cc_start: 0.8440 (t0) cc_final: 0.8067 (t0) REVERT: Y 61 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9120 (mt) REVERT: Z 58 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.8761 (t80) REVERT: Z 60 LEU cc_start: 0.9178 (mm) cc_final: 0.8956 (mm) REVERT: Z 70 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9056 (pt) REVERT: Z 74 PHE cc_start: 0.8972 (m-80) cc_final: 0.8460 (m-80) outliers start: 38 outliers final: 26 residues processed: 337 average time/residue: 0.0646 time to fit residues: 33.5876 Evaluate side-chains 347 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 311 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 362 ILE Chi-restraints excluded: chain N residue 379 LEU Chi-restraints excluded: chain N residue 399 LYS Chi-restraints excluded: chain N residue 422 VAL Chi-restraints excluded: chain N residue 430 THR Chi-restraints excluded: chain N residue 545 TRP Chi-restraints excluded: chain N residue 606 LEU Chi-restraints excluded: chain N residue 618 LEU Chi-restraints excluded: chain N residue 622 ARG Chi-restraints excluded: chain O residue 19 MET Chi-restraints excluded: chain P residue 19 MET Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain Q residue 28 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 77 ASN Chi-restraints excluded: chain T residue 17 VAL Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain V residue 34 GLN Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 59 LEU Chi-restraints excluded: chain X residue 19 MET Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Z residue 58 PHE Chi-restraints excluded: chain Z residue 64 THR Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain Z residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 22 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 78 optimal weight: 0.0470 chunk 38 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.062091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.051079 restraints weight = 49026.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.052272 restraints weight = 33999.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.053062 restraints weight = 25974.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.053691 restraints weight = 21213.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.054165 restraints weight = 18116.975| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 8770 Z= 0.197 Angle : 1.283 18.839 11896 Z= 0.582 Chirality : 0.063 0.458 1466 Planarity : 0.005 0.063 1499 Dihedral : 5.422 44.056 1265 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.36 % Allowed : 44.36 % Favored : 51.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.23), residues: 1171 helix: 0.23 (0.15), residues: 1023 sheet: -0.84 (2.03), residues: 10 loop : -2.19 (0.49), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 622 TYR 0.004 0.001 TYR N 529 PHE 0.036 0.002 PHE X 74 TRP 0.046 0.003 TRP N 420 HIS 0.003 0.001 HIS N 491 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 8770) covalent geometry : angle 1.28329 (11896) hydrogen bonds : bond 0.05505 ( 820) hydrogen bonds : angle 4.82452 ( 2454) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1522.94 seconds wall clock time: 27 minutes 0.73 seconds (1620.73 seconds total)