Starting phenix.real_space_refine on Sat Apr 26 20:13:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h5j_51886/04_2025/9h5j_51886.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h5j_51886/04_2025/9h5j_51886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9h5j_51886/04_2025/9h5j_51886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h5j_51886/04_2025/9h5j_51886.map" model { file = "/net/cci-nas-00/data/ceres_data/9h5j_51886/04_2025/9h5j_51886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h5j_51886/04_2025/9h5j_51886.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 6 5.16 5 C 2076 2.51 5 N 600 2.21 5 O 618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3300 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "B" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "C" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "D" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "E" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "F" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Time building chain proxies: 3.16, per 1000 atoms: 0.96 Number of scatterers: 3300 At special positions: 0 Unit cell: (146.568, 75.144, 34.968, 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 6 16.00 O 618 8.00 N 600 7.00 C 2076 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: 0.70 Conformation dependent library (CDL) restraints added in 384.9 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 20 sheets defined 0.0% alpha, 48.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 310 removed outlier: 6.889A pdb=" N ILE B 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.892A pdb=" N VAL A 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 322 removed outlier: 6.625A pdb=" N VAL B 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N LYS D 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 330 removed outlier: 7.024A pdb=" N GLY D 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN A 327 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLY B 326 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASN D 327 " --> pdb=" O GLY B 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 removed outlier: 6.658A pdb=" N GLN A 336 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N VAL D 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU A 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 347 removed outlier: 6.670A pdb=" N LEU B 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LYS D 347 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE B 346 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 350 through 356 removed outlier: 6.778A pdb=" N SER D 356 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL B 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LYS D 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER B 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N GLY D 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ILE B 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362 removed outlier: 6.662A pdb=" N ASN B 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N HIS D 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 371 removed outlier: 6.607A pdb=" N LYS B 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 377 removed outlier: 6.578A pdb=" N HIS B 374 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N THR D 377 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU B 376 " --> pdb=" O THR D 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 308 through 310 removed outlier: 6.949A pdb=" N ILE C 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE E 308 " --> pdb=" O VAL F 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 313 through 314 Processing sheet with id=AB4, first strand: chain 'C' and resid 317 through 322 Processing sheet with id=AB5, first strand: chain 'C' and resid 325 through 330 removed outlier: 6.969A pdb=" N GLY C 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN E 327 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLY E 326 " --> pdb=" O LEU F 325 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN F 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 336 through 340 Processing sheet with id=AB7, first strand: chain 'C' and resid 343 through 347 removed outlier: 6.658A pdb=" N LEU C 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LYS E 347 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE C 346 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU E 344 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LYS F 347 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE E 346 " --> pdb=" O LYS F 347 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 350 through 356 removed outlier: 6.295A pdb=" N VAL C 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N LYS E 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N SER C 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N GLY E 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ILE C 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL E 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N LYS F 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER E 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N GLY F 355 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ILE E 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.624A pdb=" N ASN C 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N HIS E 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR C 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN E 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N HIS F 362 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR E 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 369 through 371 removed outlier: 6.592A pdb=" N LYS C 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS E 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 374 through 377 removed outlier: 6.532A pdb=" N HIS C 374 " --> pdb=" O LYS E 375 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N THR E 377 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU C 376 " --> pdb=" O THR E 377 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N HIS E 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N THR F 377 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU E 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 61 hydrogen bonds defined for protein. 183 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: 0.78 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 690 1.33 - 1.45: 638 1.45 - 1.57: 2020 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3354 Sorted by residual: bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.34e+00 bond pdb=" CZ ARG E 349 " pdb=" NH2 ARG E 349 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.09e+00 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.71e+00 bond pdb=" CZ ARG F 349 " pdb=" NH2 ARG F 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.30e+00 bond pdb=" CZ ARG B 349 " pdb=" NH2 ARG B 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.26e+00 ... (remaining 3349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 2212 1.26 - 2.53: 1398 2.53 - 3.79: 618 3.79 - 5.05: 210 5.05 - 6.32: 50 Bond angle restraints: 4488 Sorted by residual: angle pdb=" CA PHE B 346 " pdb=" CB PHE B 346 " pdb=" CG PHE B 346 " ideal model delta sigma weight residual 113.80 119.06 -5.26 1.00e+00 1.00e+00 2.76e+01 angle pdb=" CA PHE E 346 " pdb=" CB PHE E 346 " pdb=" CG PHE E 346 " ideal model delta sigma weight residual 113.80 118.84 -5.04 1.00e+00 1.00e+00 2.54e+01 angle pdb=" CB HIS F 362 " pdb=" CG HIS F 362 " pdb=" CD2 HIS F 362 " ideal model delta sigma weight residual 131.20 124.99 6.21 1.30e+00 5.92e-01 2.28e+01 angle pdb=" N GLY E 326 " pdb=" CA GLY E 326 " pdb=" C GLY E 326 " ideal model delta sigma weight residual 110.69 117.00 -6.31 1.33e+00 5.65e-01 2.25e+01 angle pdb=" CB HIS D 329 " pdb=" CG HIS D 329 " pdb=" CD2 HIS D 329 " ideal model delta sigma weight residual 131.20 125.21 5.99 1.30e+00 5.92e-01 2.12e+01 ... (remaining 4483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 1906 16.56 - 33.13: 115 33.13 - 49.69: 12 49.69 - 66.25: 2 66.25 - 82.81: 5 Dihedral angle restraints: 2040 sinusoidal: 852 harmonic: 1188 Sorted by residual: dihedral pdb=" CA SER D 341 " pdb=" C SER D 341 " pdb=" N GLU D 342 " pdb=" CA GLU D 342 " ideal model delta harmonic sigma weight residual 180.00 160.50 19.50 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LYS C 347 " pdb=" C LYS C 347 " pdb=" N ASP C 348 " pdb=" CA ASP C 348 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA SER E 341 " pdb=" C SER E 341 " pdb=" N GLU E 342 " pdb=" CA GLU E 342 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 2037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 223 0.050 - 0.100: 158 0.100 - 0.150: 86 0.150 - 0.200: 29 0.200 - 0.250: 8 Chirality restraints: 504 Sorted by residual: chirality pdb=" CA PRO D 332 " pdb=" N PRO D 332 " pdb=" C PRO D 332 " pdb=" CB PRO D 332 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA PRO E 332 " pdb=" N PRO E 332 " pdb=" C PRO E 332 " pdb=" CB PRO E 332 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA LYS C 317 " pdb=" N LYS C 317 " pdb=" C LYS C 317 " pdb=" CB LYS C 317 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 501 not shown) Planarity restraints: 570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.123 2.00e-02 2.50e+03 6.81e-02 9.28e+01 pdb=" CG TYR F 310 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " -0.062 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " -0.044 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.113 2.00e-02 2.50e+03 6.62e-02 8.77e+01 pdb=" CG TYR A 310 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.055 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.044 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.092 2.00e-02 2.50e+03 5.10e-02 5.21e+01 pdb=" CG TYR E 310 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.024 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.079 2.00e-02 2.50e+03 ... (remaining 567 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.02: 1613 3.02 - 3.49: 2756 3.49 - 3.96: 5062 3.96 - 4.43: 5166 4.43 - 4.90: 10090 Nonbonded interactions: 24687 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.556 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.557 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.562 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.564 3.040 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.575 3.040 ... (remaining 24682 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 individual isotropic 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: 2.680 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.120 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:12.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 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 : 0.012 0.040 3354 Z= 0.743 Angle : 1.959 6.317 4488 Z= 1.294 Chirality : 0.083 0.250 504 Planarity : 0.016 0.141 570 Dihedral : 11.324 82.812 1284 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 1.67 % Allowed : 6.19 % Favored : 92.14 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.005 HIS D 374 PHE 0.044 0.016 PHE D 378 TYR 0.123 0.038 TYR F 310 ARG 0.007 0.002 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.13908 ( 61) hydrogen bonds : angle 6.74091 ( 183) covalent geometry : bond 0.01168 ( 3354) covalent geometry : angle 1.95868 ( 4488) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: C 343 LYS cc_start: 0.8412 (mttt) cc_final: 0.8208 (mtpp) REVERT: E 343 LYS cc_start: 0.8233 (mttt) cc_final: 0.7997 (mtpp) REVERT: F 338 GLU cc_start: 0.7477 (tt0) cc_final: 0.7183 (tt0) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 1.4000 time to fit residues: 181.7053 Evaluate side-chains 111 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN C 368 ASN D 368 ASN E 336 GLN F 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.159445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.129773 restraints weight = 3383.922| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.70 r_work: 0.3703 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3354 Z= 0.133 Angle : 0.693 7.496 4488 Z= 0.348 Chirality : 0.048 0.122 504 Planarity : 0.003 0.028 570 Dihedral : 5.887 19.302 438 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 5.29 % Allowed : 14.29 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 362 PHE 0.004 0.001 PHE D 346 TYR 0.010 0.002 TYR D 310 ARG 0.001 0.000 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.02527 ( 61) hydrogen bonds : angle 4.73771 ( 183) covalent geometry : bond 0.00287 ( 3354) covalent geometry : angle 0.69307 ( 4488) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.435 Fit side-chains REVERT: A 321 LYS cc_start: 0.8654 (mttp) cc_final: 0.8422 (mppt) REVERT: A 338 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8009 (tm-30) REVERT: A 343 LYS cc_start: 0.8630 (mttt) cc_final: 0.8278 (mtpp) REVERT: B 338 GLU cc_start: 0.8590 (tt0) cc_final: 0.8331 (tm-30) REVERT: B 370 LYS cc_start: 0.8716 (tttm) cc_final: 0.8470 (tmtt) REVERT: B 375 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7894 (tttm) REVERT: C 338 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7904 (tm-30) REVERT: C 343 LYS cc_start: 0.8541 (mttt) cc_final: 0.8206 (mtpp) REVERT: C 345 ASP cc_start: 0.8502 (t0) cc_final: 0.8085 (m-30) REVERT: C 349 ARG cc_start: 0.8360 (mtp180) cc_final: 0.8097 (mtp180) REVERT: D 311 LYS cc_start: 0.8262 (tmtt) cc_final: 0.8024 (tmtt) REVERT: D 338 GLU cc_start: 0.8500 (tt0) cc_final: 0.8115 (tm-30) REVERT: D 370 LYS cc_start: 0.8423 (tttm) cc_final: 0.8179 (tmtt) REVERT: D 375 LYS cc_start: 0.8175 (ttmt) cc_final: 0.7788 (tttm) REVERT: E 338 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7863 (tm-30) REVERT: E 340 LYS cc_start: 0.8508 (mttt) cc_final: 0.8173 (mttt) REVERT: F 338 GLU cc_start: 0.8448 (tt0) cc_final: 0.8156 (tm-30) REVERT: F 343 LYS cc_start: 0.8734 (mttt) cc_final: 0.8406 (mtpp) REVERT: F 345 ASP cc_start: 0.8439 (t0) cc_final: 0.7945 (m-30) REVERT: F 370 LYS cc_start: 0.8767 (tttm) cc_final: 0.8503 (tmtt) outliers start: 20 outliers final: 5 residues processed: 129 average time/residue: 1.4953 time to fit residues: 196.9393 Evaluate side-chains 118 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 overall best weight: 5.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN E 374 HIS ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.150719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.120505 restraints weight = 3350.256| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.77 r_work: 0.3556 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 3354 Z= 0.268 Angle : 0.807 7.154 4488 Z= 0.408 Chirality : 0.051 0.130 504 Planarity : 0.006 0.055 570 Dihedral : 6.511 22.085 438 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 5.56 % Allowed : 18.78 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 362 PHE 0.008 0.002 PHE F 346 TYR 0.014 0.004 TYR C 310 ARG 0.002 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 61) hydrogen bonds : angle 4.87441 ( 183) covalent geometry : bond 0.00665 ( 3354) covalent geometry : angle 0.80688 ( 4488) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.743 Fit side-chains REVERT: A 321 LYS cc_start: 0.8612 (mttp) cc_final: 0.8403 (mppt) REVERT: A 331 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8673 (mtpp) REVERT: A 338 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8063 (tm-30) REVERT: A 343 LYS cc_start: 0.8494 (mttt) cc_final: 0.8139 (mtpp) REVERT: B 338 GLU cc_start: 0.8674 (tt0) cc_final: 0.8424 (tm-30) REVERT: B 375 LYS cc_start: 0.8322 (ttmt) cc_final: 0.7951 (tttm) REVERT: C 311 LYS cc_start: 0.8634 (tptm) cc_final: 0.8426 (tptp) REVERT: C 338 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8020 (tm-30) REVERT: C 343 LYS cc_start: 0.8630 (mttt) cc_final: 0.8253 (mtpp) REVERT: C 345 ASP cc_start: 0.8606 (t0) cc_final: 0.8162 (m-30) REVERT: C 375 LYS cc_start: 0.8366 (ttmt) cc_final: 0.8007 (tttm) REVERT: D 338 GLU cc_start: 0.8603 (tt0) cc_final: 0.8118 (tm-30) REVERT: D 347 LYS cc_start: 0.8823 (mtpp) cc_final: 0.8541 (mtpt) REVERT: D 375 LYS cc_start: 0.8319 (ttmt) cc_final: 0.7924 (tttm) REVERT: E 338 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8083 (tm-30) REVERT: E 340 LYS cc_start: 0.8546 (mttt) cc_final: 0.8190 (mttt) REVERT: E 343 LYS cc_start: 0.8643 (mttt) cc_final: 0.8102 (mtpp) REVERT: E 347 LYS cc_start: 0.8665 (mtpp) cc_final: 0.8289 (mtpt) REVERT: F 321 LYS cc_start: 0.8549 (mttp) cc_final: 0.8221 (mppt) REVERT: F 336 GLN cc_start: 0.9133 (tt0) cc_final: 0.8849 (tt0) REVERT: F 338 GLU cc_start: 0.8520 (tt0) cc_final: 0.8246 (tm-30) REVERT: F 340 LYS cc_start: 0.8761 (mttt) cc_final: 0.8508 (mptt) REVERT: F 343 LYS cc_start: 0.8709 (mttt) cc_final: 0.8322 (mtpp) outliers start: 21 outliers final: 7 residues processed: 139 average time/residue: 1.6868 time to fit residues: 239.1747 Evaluate side-chains 132 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 336 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 = 0.4097 r_free = 0.4097 target = 0.152951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.122880 restraints weight = 3415.283| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.78 r_work: 0.3571 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3354 Z= 0.163 Angle : 0.665 5.769 4488 Z= 0.334 Chirality : 0.048 0.127 504 Planarity : 0.006 0.059 570 Dihedral : 5.904 19.900 438 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.76 % Allowed : 22.75 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.005 0.001 PHE A 346 TYR 0.011 0.003 TYR F 310 ARG 0.002 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.02808 ( 61) hydrogen bonds : angle 4.56953 ( 183) covalent geometry : bond 0.00399 ( 3354) covalent geometry : angle 0.66450 ( 4488) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.383 Fit side-chains REVERT: A 321 LYS cc_start: 0.8603 (mttp) cc_final: 0.8388 (mppt) REVERT: A 338 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8097 (tm-30) REVERT: A 343 LYS cc_start: 0.8553 (mttt) cc_final: 0.8158 (mtpp) REVERT: B 311 LYS cc_start: 0.8530 (tptm) cc_final: 0.8305 (tptp) REVERT: B 375 LYS cc_start: 0.8320 (ttmt) cc_final: 0.7934 (tttm) REVERT: C 343 LYS cc_start: 0.8513 (mttt) cc_final: 0.8184 (mtpp) REVERT: C 345 ASP cc_start: 0.8565 (t0) cc_final: 0.8181 (OUTLIER) REVERT: C 375 LYS cc_start: 0.8327 (ttmt) cc_final: 0.7971 (tttm) REVERT: D 315 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7756 (tt) REVERT: D 321 LYS cc_start: 0.8685 (mttp) cc_final: 0.8339 (mppt) REVERT: D 338 GLU cc_start: 0.8555 (tt0) cc_final: 0.8228 (tm-30) REVERT: D 347 LYS cc_start: 0.8731 (mtpp) cc_final: 0.8471 (mtpt) REVERT: D 375 LYS cc_start: 0.8319 (ttmt) cc_final: 0.7941 (tttm) REVERT: E 311 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8159 (tmtt) REVERT: E 338 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7990 (tm-30) REVERT: E 343 LYS cc_start: 0.8681 (mttt) cc_final: 0.8213 (mtpp) REVERT: E 347 LYS cc_start: 0.8616 (mtpp) cc_final: 0.8340 (mtpt) REVERT: E 375 LYS cc_start: 0.8209 (ttmt) cc_final: 0.7785 (tttm) REVERT: F 311 LYS cc_start: 0.8501 (tptm) cc_final: 0.8275 (tptp) REVERT: F 321 LYS cc_start: 0.8502 (mttp) cc_final: 0.8179 (mppt) REVERT: F 338 GLU cc_start: 0.8500 (tt0) cc_final: 0.8239 (tm-30) REVERT: F 340 LYS cc_start: 0.8708 (mttt) cc_final: 0.8497 (mptt) REVERT: F 343 LYS cc_start: 0.8719 (mttt) cc_final: 0.8363 (mtpp) REVERT: F 345 ASP cc_start: 0.8528 (t0) cc_final: 0.7931 (OUTLIER) outliers start: 18 outliers final: 11 residues processed: 130 average time/residue: 1.6491 time to fit residues: 218.4092 Evaluate side-chains 130 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 336 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 = 0.4087 r_free = 0.4087 target = 0.151933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.121959 restraints weight = 3396.248| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.78 r_work: 0.3577 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3354 Z= 0.169 Angle : 0.666 6.447 4488 Z= 0.332 Chirality : 0.049 0.127 504 Planarity : 0.006 0.059 570 Dihedral : 5.865 19.550 438 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 5.29 % Allowed : 23.28 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.005 0.001 PHE A 346 TYR 0.010 0.002 TYR D 310 ARG 0.001 0.000 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.02807 ( 61) hydrogen bonds : angle 4.50973 ( 183) covalent geometry : bond 0.00416 ( 3354) covalent geometry : angle 0.66631 ( 4488) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.384 Fit side-chains REVERT: A 338 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7974 (tm-30) REVERT: A 343 LYS cc_start: 0.8579 (mttt) cc_final: 0.8136 (mtpp) REVERT: B 345 ASP cc_start: 0.8594 (t0) cc_final: 0.8173 (m-30) REVERT: B 370 LYS cc_start: 0.8714 (tttp) cc_final: 0.8471 (tmtt) REVERT: B 375 LYS cc_start: 0.8337 (ttmt) cc_final: 0.7932 (tttm) REVERT: C 338 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8053 (tm-30) REVERT: C 343 LYS cc_start: 0.8543 (mttt) cc_final: 0.8165 (mtpp) REVERT: C 345 ASP cc_start: 0.8500 (t0) cc_final: 0.8176 (OUTLIER) REVERT: C 375 LYS cc_start: 0.8301 (ttmt) cc_final: 0.7938 (tttm) REVERT: D 311 LYS cc_start: 0.8367 (tmtt) cc_final: 0.8139 (tmtt) REVERT: D 315 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7806 (tt) REVERT: D 321 LYS cc_start: 0.8670 (mttp) cc_final: 0.8337 (mppt) REVERT: D 338 GLU cc_start: 0.8512 (tt0) cc_final: 0.8113 (tm-30) REVERT: D 347 LYS cc_start: 0.8720 (mtpp) cc_final: 0.8484 (mtpt) REVERT: D 375 LYS cc_start: 0.8358 (ttmt) cc_final: 0.7955 (tttm) REVERT: E 311 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8142 (tmtp) REVERT: E 338 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7999 (tm-30) REVERT: E 343 LYS cc_start: 0.8710 (mttt) cc_final: 0.8190 (mtpp) REVERT: E 345 ASP cc_start: 0.8466 (t70) cc_final: 0.7999 (m-30) REVERT: E 375 LYS cc_start: 0.8246 (ttmt) cc_final: 0.7821 (tttm) REVERT: F 321 LYS cc_start: 0.8489 (mttp) cc_final: 0.8174 (mppt) REVERT: F 338 GLU cc_start: 0.8487 (tt0) cc_final: 0.8209 (tm-30) REVERT: F 340 LYS cc_start: 0.8724 (mttt) cc_final: 0.8516 (mttt) REVERT: F 343 LYS cc_start: 0.8750 (mttt) cc_final: 0.8358 (mtpp) REVERT: F 345 ASP cc_start: 0.8575 (t0) cc_final: 0.7982 (OUTLIER) outliers start: 20 outliers final: 13 residues processed: 133 average time/residue: 1.6499 time to fit residues: 223.4829 Evaluate side-chains 130 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 36 optimal weight: 0.2980 chunk 20 optimal weight: 9.9990 overall best weight: 5.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.149181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.119195 restraints weight = 3514.046| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.81 r_work: 0.3525 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 3354 Z= 0.275 Angle : 0.793 7.895 4488 Z= 0.392 Chirality : 0.050 0.124 504 Planarity : 0.007 0.061 570 Dihedral : 6.390 22.051 438 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 6.35 % Allowed : 23.02 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 362 PHE 0.007 0.002 PHE D 346 TYR 0.014 0.003 TYR F 310 ARG 0.002 0.001 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 61) hydrogen bonds : angle 4.67157 ( 183) covalent geometry : bond 0.00686 ( 3354) covalent geometry : angle 0.79341 ( 4488) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.426 Fit side-chains REVERT: A 338 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8010 (tm-30) REVERT: A 343 LYS cc_start: 0.8603 (mttt) cc_final: 0.8152 (mtpp) REVERT: B 321 LYS cc_start: 0.8706 (mttp) cc_final: 0.8437 (mppt) REVERT: B 331 LYS cc_start: 0.8972 (mtmm) cc_final: 0.8751 (mtpm) REVERT: B 370 LYS cc_start: 0.8722 (tttp) cc_final: 0.8464 (tmtt) REVERT: B 375 LYS cc_start: 0.8347 (ttmt) cc_final: 0.7947 (tttm) REVERT: C 338 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8079 (tm-30) REVERT: C 343 LYS cc_start: 0.8687 (mttt) cc_final: 0.8304 (mtpp) REVERT: C 345 ASP cc_start: 0.8616 (t0) cc_final: 0.8221 (OUTLIER) REVERT: C 375 LYS cc_start: 0.8336 (ttmt) cc_final: 0.7974 (tttm) REVERT: D 311 LYS cc_start: 0.8380 (tmtt) cc_final: 0.8167 (tmtt) REVERT: D 321 LYS cc_start: 0.8667 (mttp) cc_final: 0.8338 (mppt) REVERT: D 338 GLU cc_start: 0.8531 (tt0) cc_final: 0.8120 (tm-30) REVERT: D 347 LYS cc_start: 0.8800 (mtpp) cc_final: 0.8497 (mtpt) REVERT: D 375 LYS cc_start: 0.8370 (ttmt) cc_final: 0.7965 (tttm) REVERT: E 311 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8182 (tmtt) REVERT: E 338 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8099 (tm-30) REVERT: E 343 LYS cc_start: 0.8731 (mttt) cc_final: 0.8214 (mtpp) REVERT: E 375 LYS cc_start: 0.8284 (ttmt) cc_final: 0.7851 (tttm) REVERT: F 321 LYS cc_start: 0.8525 (mttp) cc_final: 0.8179 (mppt) REVERT: F 338 GLU cc_start: 0.8515 (tt0) cc_final: 0.8233 (tm-30) REVERT: F 340 LYS cc_start: 0.8777 (mttt) cc_final: 0.8551 (mttt) REVERT: F 343 LYS cc_start: 0.8750 (mttt) cc_final: 0.8371 (mtpp) outliers start: 24 outliers final: 11 residues processed: 139 average time/residue: 1.5344 time to fit residues: 217.5617 Evaluate side-chains 128 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.150395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.120701 restraints weight = 3371.455| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.79 r_work: 0.3531 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3354 Z= 0.210 Angle : 0.735 8.805 4488 Z= 0.361 Chirality : 0.049 0.126 504 Planarity : 0.007 0.060 570 Dihedral : 6.192 20.779 438 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 5.29 % Allowed : 24.07 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.005 0.002 PHE D 346 TYR 0.011 0.003 TYR D 310 ARG 0.002 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.03048 ( 61) hydrogen bonds : angle 4.59564 ( 183) covalent geometry : bond 0.00525 ( 3354) covalent geometry : angle 0.73531 ( 4488) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.440 Fit side-chains REVERT: A 343 LYS cc_start: 0.8576 (mttt) cc_final: 0.8144 (mtpp) REVERT: B 375 LYS cc_start: 0.8334 (ttmt) cc_final: 0.7938 (tttm) REVERT: C 338 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: C 343 LYS cc_start: 0.8586 (mttt) cc_final: 0.8244 (mtpp) REVERT: C 345 ASP cc_start: 0.8545 (t0) cc_final: 0.8181 (OUTLIER) REVERT: C 375 LYS cc_start: 0.8329 (ttmt) cc_final: 0.7959 (tttm) REVERT: D 311 LYS cc_start: 0.8354 (tmtt) cc_final: 0.8099 (tmtt) REVERT: D 321 LYS cc_start: 0.8633 (mttp) cc_final: 0.8303 (mppt) REVERT: D 338 GLU cc_start: 0.8487 (tt0) cc_final: 0.8256 (tm-30) REVERT: D 347 LYS cc_start: 0.8752 (mtpp) cc_final: 0.8457 (mtpt) REVERT: D 375 LYS cc_start: 0.8356 (ttmt) cc_final: 0.7952 (tttm) REVERT: E 311 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8217 (tmtt) REVERT: E 338 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8074 (tm-30) REVERT: E 343 LYS cc_start: 0.8738 (mttt) cc_final: 0.8224 (mtpp) REVERT: E 345 ASP cc_start: 0.8436 (t70) cc_final: 0.7956 (m-30) REVERT: E 375 LYS cc_start: 0.8264 (ttmt) cc_final: 0.7835 (tttm) REVERT: F 311 LYS cc_start: 0.8742 (tptp) cc_final: 0.7792 (tptt) REVERT: F 321 LYS cc_start: 0.8492 (mttp) cc_final: 0.8190 (mppt) REVERT: F 338 GLU cc_start: 0.8487 (tt0) cc_final: 0.8208 (tm-30) REVERT: F 340 LYS cc_start: 0.8740 (mttt) cc_final: 0.8526 (mttt) REVERT: F 343 LYS cc_start: 0.8809 (mttt) cc_final: 0.8420 (mtpp) outliers start: 20 outliers final: 12 residues processed: 123 average time/residue: 1.5632 time to fit residues: 196.2432 Evaluate side-chains 124 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 12 optimal weight: 0.4980 chunk 6 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.152192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.122353 restraints weight = 3339.660| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.79 r_work: 0.3579 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3354 Z= 0.159 Angle : 0.691 10.010 4488 Z= 0.335 Chirality : 0.048 0.125 504 Planarity : 0.006 0.057 570 Dihedral : 5.887 19.260 438 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.44 % Allowed : 27.25 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.004 0.001 PHE F 346 TYR 0.009 0.002 TYR D 310 ARG 0.001 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.02579 ( 61) hydrogen bonds : angle 4.47054 ( 183) covalent geometry : bond 0.00393 ( 3354) covalent geometry : angle 0.69081 ( 4488) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.467 Fit side-chains REVERT: A 343 LYS cc_start: 0.8575 (mttt) cc_final: 0.8125 (mtpp) REVERT: B 345 ASP cc_start: 0.8634 (t0) cc_final: 0.8227 (m-30) REVERT: B 375 LYS cc_start: 0.8343 (ttmt) cc_final: 0.7945 (tttm) REVERT: C 338 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8039 (tm-30) REVERT: C 343 LYS cc_start: 0.8501 (mttt) cc_final: 0.8130 (mtpp) REVERT: C 345 ASP cc_start: 0.8480 (t0) cc_final: 0.8138 (m-30) REVERT: C 375 LYS cc_start: 0.8317 (ttmt) cc_final: 0.7938 (tttm) REVERT: D 311 LYS cc_start: 0.8380 (tmtt) cc_final: 0.7910 (tptp) REVERT: D 321 LYS cc_start: 0.8568 (mttp) cc_final: 0.8210 (mppt) REVERT: D 338 GLU cc_start: 0.8455 (tt0) cc_final: 0.8244 (tm-30) REVERT: D 345 ASP cc_start: 0.8644 (t0) cc_final: 0.8010 (m-30) REVERT: D 347 LYS cc_start: 0.8709 (mtpp) cc_final: 0.8485 (mtpt) REVERT: D 370 LYS cc_start: 0.8340 (tttm) cc_final: 0.8077 (tmtt) REVERT: D 375 LYS cc_start: 0.8347 (ttmt) cc_final: 0.7951 (tttm) REVERT: E 311 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8222 (tmtt) REVERT: E 338 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8004 (tm-30) REVERT: E 343 LYS cc_start: 0.8784 (mttt) cc_final: 0.8257 (mtpp) REVERT: E 345 ASP cc_start: 0.8414 (t70) cc_final: 0.7961 (m-30) REVERT: E 375 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7843 (tttm) REVERT: F 311 LYS cc_start: 0.8723 (tptp) cc_final: 0.7760 (tptt) REVERT: F 321 LYS cc_start: 0.8489 (mttp) cc_final: 0.8182 (mppt) REVERT: F 338 GLU cc_start: 0.8472 (tt0) cc_final: 0.8204 (tm-30) REVERT: F 340 LYS cc_start: 0.8702 (mttt) cc_final: 0.8491 (mttt) REVERT: F 343 LYS cc_start: 0.8812 (mttt) cc_final: 0.8413 (mtpp) outliers start: 13 outliers final: 9 residues processed: 118 average time/residue: 1.5361 time to fit residues: 184.8983 Evaluate side-chains 120 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.150631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.120936 restraints weight = 3385.954| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.79 r_work: 0.3554 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3354 Z= 0.205 Angle : 0.752 10.426 4488 Z= 0.362 Chirality : 0.049 0.128 504 Planarity : 0.006 0.058 570 Dihedral : 6.089 20.511 438 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 5.82 % Allowed : 24.60 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.006 0.002 PHE F 346 TYR 0.011 0.003 TYR D 310 ARG 0.002 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.02973 ( 61) hydrogen bonds : angle 4.57050 ( 183) covalent geometry : bond 0.00509 ( 3354) covalent geometry : angle 0.75151 ( 4488) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.377 Fit side-chains REVERT: A 343 LYS cc_start: 0.8575 (mttt) cc_final: 0.8120 (mtpp) REVERT: B 345 ASP cc_start: 0.8647 (t0) cc_final: 0.8186 (m-30) REVERT: B 375 LYS cc_start: 0.8353 (ttmt) cc_final: 0.7967 (tttm) REVERT: C 338 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8021 (tm-30) REVERT: C 343 LYS cc_start: 0.8595 (mttt) cc_final: 0.8246 (mtpp) REVERT: C 345 ASP cc_start: 0.8512 (t0) cc_final: 0.8175 (m-30) REVERT: C 375 LYS cc_start: 0.8322 (ttmt) cc_final: 0.7950 (tttm) REVERT: D 311 LYS cc_start: 0.8369 (tmtt) cc_final: 0.7905 (tptp) REVERT: D 321 LYS cc_start: 0.8614 (mttp) cc_final: 0.8264 (mppt) REVERT: D 338 GLU cc_start: 0.8502 (tt0) cc_final: 0.8275 (tm-30) REVERT: D 345 ASP cc_start: 0.8652 (t0) cc_final: 0.8016 (m-30) REVERT: D 347 LYS cc_start: 0.8742 (mtpp) cc_final: 0.8457 (mtpt) REVERT: D 375 LYS cc_start: 0.8351 (ttmt) cc_final: 0.7954 (tttm) REVERT: E 311 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8216 (tmtt) REVERT: E 338 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8092 (tm-30) REVERT: E 343 LYS cc_start: 0.8749 (mttt) cc_final: 0.8229 (mtpp) REVERT: E 345 ASP cc_start: 0.8433 (t70) cc_final: 0.7970 (m-30) REVERT: E 375 LYS cc_start: 0.8282 (ttmt) cc_final: 0.7855 (tttm) REVERT: F 311 LYS cc_start: 0.8733 (tptp) cc_final: 0.7776 (tptt) REVERT: F 321 LYS cc_start: 0.8517 (mttp) cc_final: 0.8208 (mppt) REVERT: F 338 GLU cc_start: 0.8490 (tt0) cc_final: 0.8217 (tm-30) REVERT: F 340 LYS cc_start: 0.8734 (mttt) cc_final: 0.8512 (mttt) REVERT: F 343 LYS cc_start: 0.8809 (mttt) cc_final: 0.8422 (mtpp) REVERT: F 345 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.7963 (m-30) outliers start: 22 outliers final: 13 residues processed: 122 average time/residue: 1.4805 time to fit residues: 184.3115 Evaluate side-chains 126 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.153665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.124000 restraints weight = 3333.004| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.78 r_work: 0.3588 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3354 Z= 0.131 Angle : 0.675 11.358 4488 Z= 0.323 Chirality : 0.048 0.124 504 Planarity : 0.006 0.056 570 Dihedral : 5.643 18.085 438 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.97 % Allowed : 26.98 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.003 0.001 PHE D 346 TYR 0.007 0.002 TYR D 310 ARG 0.001 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.02231 ( 61) hydrogen bonds : angle 4.38108 ( 183) covalent geometry : bond 0.00323 ( 3354) covalent geometry : angle 0.67537 ( 4488) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.435 Fit side-chains REVERT: A 343 LYS cc_start: 0.8570 (mttt) cc_final: 0.8129 (mtpp) REVERT: B 345 ASP cc_start: 0.8594 (t0) cc_final: 0.8217 (m-30) REVERT: B 375 LYS cc_start: 0.8330 (ttmt) cc_final: 0.7943 (tttm) REVERT: C 321 LYS cc_start: 0.8530 (mttp) cc_final: 0.8281 (mppt) REVERT: C 343 LYS cc_start: 0.8347 (mttt) cc_final: 0.7993 (mtpp) REVERT: C 345 ASP cc_start: 0.8428 (t0) cc_final: 0.8123 (m-30) REVERT: C 375 LYS cc_start: 0.8306 (ttmt) cc_final: 0.7923 (tttm) REVERT: D 311 LYS cc_start: 0.8378 (tmtt) cc_final: 0.7979 (tptp) REVERT: D 315 LEU cc_start: 0.8094 (mp) cc_final: 0.7802 (tt) REVERT: D 321 LYS cc_start: 0.8555 (mttp) cc_final: 0.8197 (mppt) REVERT: D 345 ASP cc_start: 0.8629 (t0) cc_final: 0.8021 (m-30) REVERT: D 370 LYS cc_start: 0.8264 (tttm) cc_final: 0.7993 (tmtt) REVERT: D 375 LYS cc_start: 0.8338 (ttmt) cc_final: 0.7949 (tttm) REVERT: E 311 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8229 (tmtt) REVERT: E 343 LYS cc_start: 0.8744 (mttt) cc_final: 0.8221 (mtpp) REVERT: E 345 ASP cc_start: 0.8367 (t70) cc_final: 0.7963 (m-30) REVERT: E 375 LYS cc_start: 0.8265 (ttmt) cc_final: 0.7841 (tttm) REVERT: F 311 LYS cc_start: 0.8721 (tptp) cc_final: 0.7762 (tptt) REVERT: F 321 LYS cc_start: 0.8487 (mttp) cc_final: 0.8172 (mppt) REVERT: F 338 GLU cc_start: 0.8447 (tt0) cc_final: 0.8196 (tm-30) REVERT: F 340 LYS cc_start: 0.8659 (mttt) cc_final: 0.8440 (mttt) REVERT: F 343 LYS cc_start: 0.8848 (mttt) cc_final: 0.8385 (mtpp) REVERT: F 345 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.7899 (m-30) outliers start: 15 outliers final: 10 residues processed: 122 average time/residue: 1.4047 time to fit residues: 175.0359 Evaluate side-chains 121 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.154781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.125053 restraints weight = 3362.562| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.81 r_work: 0.3611 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3354 Z= 0.117 Angle : 0.668 11.160 4488 Z= 0.316 Chirality : 0.048 0.124 504 Planarity : 0.006 0.055 570 Dihedral : 5.441 16.836 438 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.97 % Allowed : 28.04 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 362 PHE 0.003 0.001 PHE D 346 TYR 0.007 0.001 TYR D 310 ARG 0.001 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.02013 ( 61) hydrogen bonds : angle 4.29904 ( 183) covalent geometry : bond 0.00287 ( 3354) covalent geometry : angle 0.66798 ( 4488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4363.74 seconds wall clock time: 75 minutes 0.09 seconds (4500.09 seconds total)