Starting phenix.real_space_refine on Fri Dec 27 07:01:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h5j_51886/12_2024/9h5j_51886.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h5j_51886/12_2024/9h5j_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_51886/12_2024/9h5j_51886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h5j_51886/12_2024/9h5j_51886.map" model { file = "/net/cci-nas-00/data/ceres_data/9h5j_51886/12_2024/9h5j_51886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h5j_51886/12_2024/9h5j_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-5532/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: 3.64, per 1000 atoms: 1.10 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: 0.74 Conformation dependent library (CDL) restraints added in 404.7 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: 0.58 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: 0.73 Time building geometry restraints manager: 0.88 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: 0.00 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.530 Find NCS groups from input model: 0.110 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:13.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.050 ------------------------------------------------------------------------------- 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= 0.780 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 *********************** 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 : 0.404 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: 1.4329 time to fit residues: 185.9061 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 : 0.429 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 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= 0.192 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 *********************** 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 : 0.422 Fit side-chains REVERT: A 321 LYS cc_start: 0.8393 (mttp) cc_final: 0.8169 (mppt) REVERT: A 338 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7243 (tm-30) REVERT: B 370 LYS cc_start: 0.8501 (tttm) cc_final: 0.8240 (tmtt) REVERT: B 375 LYS cc_start: 0.7938 (ttmt) cc_final: 0.7639 (tttm) REVERT: C 338 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7213 (tm-30) REVERT: C 345 ASP cc_start: 0.7968 (t0) cc_final: 0.7672 (m-30) REVERT: C 349 ARG cc_start: 0.7970 (mtp180) cc_final: 0.7676 (mtp180) REVERT: D 311 LYS cc_start: 0.8119 (tmtt) cc_final: 0.7903 (tmtt) REVERT: D 331 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8728 (mtpm) REVERT: D 370 LYS cc_start: 0.8171 (tttm) cc_final: 0.7881 (tmtt) REVERT: D 375 LYS cc_start: 0.7894 (ttmt) cc_final: 0.7549 (tttm) REVERT: E 338 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7086 (tm-30) REVERT: E 340 LYS cc_start: 0.8283 (mttt) cc_final: 0.7892 (mttt) REVERT: F 345 ASP cc_start: 0.7973 (t0) cc_final: 0.7577 (m-30) REVERT: F 370 LYS cc_start: 0.8492 (tttm) cc_final: 0.8200 (tmtt) outliers start: 20 outliers final: 5 residues processed: 129 average time/residue: 1.4855 time to fit residues: 195.6862 Evaluate side-chains 117 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 D residue 331 LYS 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 31 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN E 368 ASN E 374 HIS ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3976 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= 0.192 Angle : 0.624 6.221 4488 Z= 0.313 Chirality : 0.048 0.128 504 Planarity : 0.004 0.047 570 Dihedral : 5.454 17.347 438 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 5.56 % Allowed : 18.52 % Favored : 75.93 % 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: -2.66 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 362 PHE 0.005 0.001 PHE A 346 TYR 0.009 0.002 TYR D 310 ARG 0.001 0.000 ARG A 349 *********************** 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 144 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.430 Fit side-chains REVERT: A 331 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8691 (mtpp) REVERT: A 338 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: B 370 LYS cc_start: 0.8548 (tttm) cc_final: 0.8239 (tmtt) REVERT: C 345 ASP cc_start: 0.7980 (t0) cc_final: 0.7712 (m-30) REVERT: C 375 LYS cc_start: 0.7937 (ttmt) cc_final: 0.7665 (tttm) REVERT: D 311 LYS cc_start: 0.8187 (tmtt) cc_final: 0.7915 (tptp) REVERT: D 331 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8645 (mtmm) REVERT: D 338 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7075 (tm-30) REVERT: D 375 LYS cc_start: 0.8028 (ttmt) cc_final: 0.7685 (tttm) REVERT: E 311 LYS cc_start: 0.8181 (tmtt) cc_final: 0.7886 (tmtp) REVERT: E 338 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7179 (tm-30) REVERT: E 343 LYS cc_start: 0.8330 (mttt) cc_final: 0.8126 (mtpp) REVERT: E 347 LYS cc_start: 0.8450 (mtpp) cc_final: 0.8192 (mtpt) REVERT: F 321 LYS cc_start: 0.8218 (mttp) cc_final: 0.7892 (mppt) REVERT: F 345 ASP cc_start: 0.8057 (t0) cc_final: 0.7596 (m-30) REVERT: F 370 LYS cc_start: 0.8471 (tttm) cc_final: 0.8138 (tmtt) outliers start: 21 outliers final: 7 residues processed: 130 average time/residue: 1.6922 time to fit residues: 224.0890 Evaluate side-chains 126 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER 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 D residue 320 SER Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 338 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.0170 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN E 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3354 Z= 0.285 Angle : 0.703 6.177 4488 Z= 0.347 Chirality : 0.049 0.128 504 Planarity : 0.005 0.058 570 Dihedral : 5.844 19.260 438 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 6.88 % Allowed : 21.69 % 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: -2.78 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.007 0.001 PHE F 346 TYR 0.014 0.003 TYR F 310 ARG 0.001 0.000 ARG E 349 *********************** 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 143 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.375 Fit side-chains REVERT: A 321 LYS cc_start: 0.8389 (mttp) cc_final: 0.8149 (mppt) REVERT: A 331 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8678 (mtpp) REVERT: A 338 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: B 370 LYS cc_start: 0.8497 (tttm) cc_final: 0.8286 (tmtt) REVERT: C 321 LYS cc_start: 0.8403 (mttp) cc_final: 0.8138 (mppt) REVERT: C 338 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7169 (tm-30) REVERT: C 345 ASP cc_start: 0.7966 (t0) cc_final: 0.7717 (m-30) REVERT: C 347 LYS cc_start: 0.8762 (mtpp) cc_final: 0.8516 (mtpt) REVERT: C 375 LYS cc_start: 0.7999 (ttmt) cc_final: 0.7717 (tttm) REVERT: D 311 LYS cc_start: 0.8244 (tmtt) cc_final: 0.7978 (tptp) REVERT: D 321 LYS cc_start: 0.8448 (mttp) cc_final: 0.8140 (mppt) REVERT: D 338 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7018 (tt0) REVERT: D 347 LYS cc_start: 0.8698 (mtpp) cc_final: 0.8436 (mtpt) REVERT: D 375 LYS cc_start: 0.8083 (ttmt) cc_final: 0.7756 (tttm) REVERT: E 338 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7014 (tm-30) REVERT: E 343 LYS cc_start: 0.8369 (mttt) cc_final: 0.8119 (mtpp) REVERT: E 345 ASP cc_start: 0.8022 (t0) cc_final: 0.7598 (m-30) REVERT: E 347 LYS cc_start: 0.8565 (mtpp) cc_final: 0.8270 (mtpt) REVERT: E 375 LYS cc_start: 0.7938 (ttmt) cc_final: 0.7614 (tttm) REVERT: F 321 LYS cc_start: 0.8271 (mttp) cc_final: 0.7891 (mptt) REVERT: F 338 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7186 (tm-30) REVERT: F 344 LEU cc_start: 0.9127 (mt) cc_final: 0.8867 (mt) REVERT: F 345 ASP cc_start: 0.8051 (t0) cc_final: 0.7571 (OUTLIER) outliers start: 26 outliers final: 9 residues processed: 127 average time/residue: 1.6441 time to fit residues: 212.7389 Evaluate side-chains 130 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 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 D residue 338 GLU 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 Chi-restraints excluded: chain F residue 338 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 0.0970 chunk 23 optimal weight: 3.9990 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3354 Z= 0.268 Angle : 0.670 6.425 4488 Z= 0.329 Chirality : 0.048 0.127 504 Planarity : 0.005 0.057 570 Dihedral : 5.709 18.636 438 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 5.03 % Allowed : 26.19 % Favored : 68.78 % 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: -2.86 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.005 0.001 PHE A 346 TYR 0.012 0.002 TYR F 310 ARG 0.002 0.000 ARG E 349 *********************** 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 129 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.408 Fit side-chains REVERT: B 370 LYS cc_start: 0.8493 (tttm) cc_final: 0.8256 (tmtt) REVERT: C 338 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: C 345 ASP cc_start: 0.7948 (t0) cc_final: 0.7740 (OUTLIER) REVERT: C 375 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7694 (tttm) REVERT: D 311 LYS cc_start: 0.8236 (tmtt) cc_final: 0.7995 (tptp) REVERT: D 321 LYS cc_start: 0.8436 (mttp) cc_final: 0.8113 (mppt) REVERT: D 331 LYS cc_start: 0.8935 (mtpm) cc_final: 0.8594 (mtmm) REVERT: D 338 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7135 (tm-30) REVERT: D 347 LYS cc_start: 0.8650 (mtpp) cc_final: 0.8438 (mtpt) REVERT: D 375 LYS cc_start: 0.8094 (ttmt) cc_final: 0.7774 (tttm) REVERT: E 331 LYS cc_start: 0.9008 (mtpm) cc_final: 0.8639 (mtmm) REVERT: E 338 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.6958 (tm-30) REVERT: E 343 LYS cc_start: 0.8387 (mttt) cc_final: 0.8163 (mtpp) REVERT: E 344 LEU cc_start: 0.9258 (mt) cc_final: 0.9036 (mt) REVERT: E 345 ASP cc_start: 0.8013 (t0) cc_final: 0.7621 (m-30) REVERT: E 375 LYS cc_start: 0.7940 (ttmt) cc_final: 0.7621 (tttm) REVERT: F 311 LYS cc_start: 0.5982 (mmpt) cc_final: 0.5275 (tmtt) REVERT: F 321 LYS cc_start: 0.8252 (mttp) cc_final: 0.7908 (mppt) REVERT: F 338 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7089 (tm-30) REVERT: F 345 ASP cc_start: 0.8053 (t0) cc_final: 0.7571 (OUTLIER) REVERT: F 347 LYS cc_start: 0.8658 (mtpp) cc_final: 0.8390 (mtpt) outliers start: 19 outliers final: 11 residues processed: 117 average time/residue: 1.5304 time to fit residues: 182.7229 Evaluate side-chains 119 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 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 D residue 338 GLU 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 Chi-restraints excluded: chain F residue 338 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 13 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 0.0980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3354 Z= 0.154 Angle : 0.582 7.739 4488 Z= 0.280 Chirality : 0.047 0.125 504 Planarity : 0.005 0.047 570 Dihedral : 5.103 15.442 438 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.70 % Allowed : 26.98 % 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: -2.70 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 362 PHE 0.003 0.001 PHE A 346 TYR 0.007 0.001 TYR F 310 ARG 0.001 0.000 ARG E 349 *********************** 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 130 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.552 Fit side-chains REVERT: A 321 LYS cc_start: 0.8402 (mttp) cc_final: 0.8154 (mppt) REVERT: A 331 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8699 (mtmm) REVERT: B 370 LYS cc_start: 0.8488 (tttm) cc_final: 0.8262 (tmtt) REVERT: C 375 LYS cc_start: 0.7961 (ttmt) cc_final: 0.7684 (tttm) REVERT: D 311 LYS cc_start: 0.8238 (tmtt) cc_final: 0.7940 (tptp) REVERT: D 321 LYS cc_start: 0.8337 (mttp) cc_final: 0.8102 (mppt) REVERT: D 338 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7221 (tm-30) REVERT: D 345 ASP cc_start: 0.8034 (t0) cc_final: 0.7728 (m-30) REVERT: D 375 LYS cc_start: 0.8077 (ttmt) cc_final: 0.7767 (tttm) REVERT: E 331 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8613 (mtmm) REVERT: E 338 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7391 (tm-30) REVERT: E 343 LYS cc_start: 0.8437 (mttt) cc_final: 0.8234 (mtpp) REVERT: E 344 LEU cc_start: 0.9143 (mt) cc_final: 0.8921 (mt) REVERT: E 345 ASP cc_start: 0.7989 (t0) cc_final: 0.7640 (m-30) REVERT: E 375 LYS cc_start: 0.7952 (ttmt) cc_final: 0.7634 (tttm) REVERT: F 311 LYS cc_start: 0.6091 (mmpt) cc_final: 0.5371 (tmtt) REVERT: F 321 LYS cc_start: 0.8226 (mttp) cc_final: 0.7854 (mppt) REVERT: F 338 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7062 (tt0) REVERT: F 345 ASP cc_start: 0.8006 (t0) cc_final: 0.7554 (OUTLIER) REVERT: F 375 LYS cc_start: 0.7921 (ttmt) cc_final: 0.7562 (tttm) outliers start: 14 outliers final: 7 residues processed: 121 average time/residue: 1.6683 time to fit residues: 205.6391 Evaluate side-chains 125 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 315 LEU 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 D residue 338 GLU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain F residue 338 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN F 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3354 Z= 0.233 Angle : 0.664 8.873 4488 Z= 0.318 Chirality : 0.048 0.127 504 Planarity : 0.005 0.051 570 Dihedral : 5.422 16.992 438 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 5.82 % Allowed : 26.19 % 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: -2.72 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.005 0.001 PHE A 346 TYR 0.011 0.002 TYR F 310 ARG 0.001 0.000 ARG D 349 *********************** 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: 22 poor density : 112 time to evaluate : 0.410 Fit side-chains REVERT: A 331 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8541 (mtpp) REVERT: B 370 LYS cc_start: 0.8471 (tttm) cc_final: 0.8252 (tmtt) REVERT: C 375 LYS cc_start: 0.7960 (ttmt) cc_final: 0.7679 (tttm) REVERT: D 311 LYS cc_start: 0.8226 (tmtt) cc_final: 0.7913 (tptp) REVERT: D 321 LYS cc_start: 0.8378 (mttp) cc_final: 0.8137 (mppt) REVERT: D 331 LYS cc_start: 0.8884 (mtpm) cc_final: 0.8548 (mtmm) REVERT: D 338 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7120 (tm-30) REVERT: D 345 ASP cc_start: 0.8089 (t0) cc_final: 0.7737 (m-30) REVERT: D 347 LYS cc_start: 0.8642 (mtpp) cc_final: 0.8316 (mtpt) REVERT: D 375 LYS cc_start: 0.8119 (ttmt) cc_final: 0.7793 (tttm) REVERT: E 343 LYS cc_start: 0.8441 (mttt) cc_final: 0.8201 (mtpp) REVERT: E 344 LEU cc_start: 0.9167 (mt) cc_final: 0.8919 (mt) REVERT: E 345 ASP cc_start: 0.8033 (t0) cc_final: 0.7657 (m-30) REVERT: E 375 LYS cc_start: 0.7972 (ttmt) cc_final: 0.7650 (tttm) REVERT: F 311 LYS cc_start: 0.6106 (mmpt) cc_final: 0.5225 (tmtt) REVERT: F 321 LYS cc_start: 0.8226 (mttp) cc_final: 0.7872 (mppt) REVERT: F 338 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7003 (tm-30) REVERT: F 345 ASP cc_start: 0.8041 (t0) cc_final: 0.7574 (OUTLIER) outliers start: 22 outliers final: 11 residues processed: 121 average time/residue: 1.5596 time to fit residues: 192.4723 Evaluate side-chains 123 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 331 LYS 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 D residue 338 GLU Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 338 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 0.2980 chunk 37 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN E 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3354 Z= 0.218 Angle : 0.675 10.550 4488 Z= 0.319 Chirality : 0.048 0.126 504 Planarity : 0.005 0.047 570 Dihedral : 5.421 17.176 438 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.76 % Allowed : 27.25 % 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: -2.75 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.004 0.001 PHE A 346 TYR 0.010 0.002 TYR F 310 ARG 0.001 0.000 ARG B 349 *********************** 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 130 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.435 Fit side-chains REVERT: A 321 LYS cc_start: 0.8395 (mttp) cc_final: 0.8119 (mppt) REVERT: B 370 LYS cc_start: 0.8461 (tttm) cc_final: 0.8242 (tmtt) REVERT: C 375 LYS cc_start: 0.7958 (ttmt) cc_final: 0.7683 (tttm) REVERT: D 311 LYS cc_start: 0.8249 (tmtt) cc_final: 0.8006 (tptp) REVERT: D 331 LYS cc_start: 0.8891 (mtpm) cc_final: 0.8552 (mtmm) REVERT: D 338 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7103 (tm-30) REVERT: D 345 ASP cc_start: 0.8081 (t0) cc_final: 0.7735 (m-30) REVERT: D 347 LYS cc_start: 0.8648 (mtpp) cc_final: 0.8352 (mtpt) REVERT: D 375 LYS cc_start: 0.8118 (ttmt) cc_final: 0.7800 (tttm) REVERT: E 331 LYS cc_start: 0.8988 (mtpm) cc_final: 0.8649 (mtmm) REVERT: E 343 LYS cc_start: 0.8444 (mttt) cc_final: 0.8209 (mtpp) REVERT: E 344 LEU cc_start: 0.9147 (mt) cc_final: 0.8913 (mt) REVERT: E 345 ASP cc_start: 0.8052 (t0) cc_final: 0.7690 (m-30) REVERT: E 375 LYS cc_start: 0.7975 (ttmt) cc_final: 0.7650 (tttm) REVERT: F 311 LYS cc_start: 0.5791 (mmpt) cc_final: 0.4935 (tmtt) REVERT: F 321 LYS cc_start: 0.8204 (mttp) cc_final: 0.7843 (mppt) REVERT: F 338 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7140 (tm-30) REVERT: F 345 ASP cc_start: 0.8029 (t0) cc_final: 0.7560 (OUTLIER) outliers start: 18 outliers final: 10 residues processed: 121 average time/residue: 1.5624 time to fit residues: 192.9667 Evaluate side-chains 123 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 C residue 315 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 338 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 0.0040 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN E 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3354 Z= 0.226 Angle : 0.700 11.262 4488 Z= 0.326 Chirality : 0.048 0.126 504 Planarity : 0.005 0.049 570 Dihedral : 5.439 17.323 438 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 5.03 % Allowed : 27.25 % Favored : 67.72 % 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: -2.78 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.24), 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 F 310 ARG 0.001 0.000 ARG A 349 *********************** 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 127 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.408 Fit side-chains REVERT: A 321 LYS cc_start: 0.8382 (mttp) cc_final: 0.8160 (mppt) REVERT: A 349 ARG cc_start: 0.7925 (mtp180) cc_final: 0.7709 (mtp180) REVERT: B 370 LYS cc_start: 0.8457 (tttm) cc_final: 0.8243 (tmtt) REVERT: C 375 LYS cc_start: 0.7948 (ttmt) cc_final: 0.7683 (tttm) REVERT: D 311 LYS cc_start: 0.8255 (tmtt) cc_final: 0.8018 (tptp) REVERT: D 321 LYS cc_start: 0.8405 (mppt) cc_final: 0.8095 (mttp) REVERT: D 331 LYS cc_start: 0.8899 (mtpm) cc_final: 0.8567 (mtmm) REVERT: D 338 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7138 (tm-30) REVERT: D 345 ASP cc_start: 0.8071 (t0) cc_final: 0.7729 (m-30) REVERT: D 347 LYS cc_start: 0.8658 (mtpp) cc_final: 0.8367 (mtpt) REVERT: D 375 LYS cc_start: 0.8117 (ttmt) cc_final: 0.7800 (tttm) REVERT: E 343 LYS cc_start: 0.8427 (mttt) cc_final: 0.8192 (mtpp) REVERT: E 344 LEU cc_start: 0.9183 (mt) cc_final: 0.8941 (mt) REVERT: E 345 ASP cc_start: 0.8033 (t0) cc_final: 0.7662 (m-30) REVERT: E 375 LYS cc_start: 0.7970 (ttmt) cc_final: 0.7643 (tttm) REVERT: F 311 LYS cc_start: 0.5802 (mmpt) cc_final: 0.4853 (tmtt) REVERT: F 321 LYS cc_start: 0.8203 (mttp) cc_final: 0.7852 (mppt) REVERT: F 338 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7069 (tm-30) REVERT: F 345 ASP cc_start: 0.8050 (t0) cc_final: 0.7591 (OUTLIER) outliers start: 19 outliers final: 10 residues processed: 117 average time/residue: 1.6483 time to fit residues: 196.9090 Evaluate side-chains 122 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 C residue 315 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 338 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 0.0050 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN E 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.4640 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= 0.204 Angle : 0.709 13.058 4488 Z= 0.324 Chirality : 0.048 0.125 504 Planarity : 0.005 0.055 570 Dihedral : 5.349 16.776 438 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.23 % Allowed : 27.78 % 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: -2.78 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.004 0.001 PHE A 346 TYR 0.009 0.002 TYR F 310 ARG 0.001 0.000 ARG A 349 ********************** 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 126 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.493 Fit side-chains REVERT: A 349 ARG cc_start: 0.7921 (mtp180) cc_final: 0.7696 (mtp180) REVERT: B 370 LYS cc_start: 0.8469 (tttm) cc_final: 0.8255 (tmtt) REVERT: C 375 LYS cc_start: 0.7938 (ttmt) cc_final: 0.7672 (tttm) REVERT: D 311 LYS cc_start: 0.8259 (tmtt) cc_final: 0.8031 (tptp) REVERT: D 321 LYS cc_start: 0.8376 (mppt) cc_final: 0.8087 (mttp) REVERT: D 331 LYS cc_start: 0.8884 (mtpm) cc_final: 0.8564 (mtmm) REVERT: D 338 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7127 (tm-30) REVERT: D 345 ASP cc_start: 0.8077 (t0) cc_final: 0.7740 (m-30) REVERT: D 347 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8329 (mtpt) REVERT: D 375 LYS cc_start: 0.8113 (ttmt) cc_final: 0.7799 (tttm) REVERT: E 343 LYS cc_start: 0.8436 (mttt) cc_final: 0.8204 (mtpp) REVERT: E 344 LEU cc_start: 0.9157 (mt) cc_final: 0.8909 (mt) REVERT: E 345 ASP cc_start: 0.8017 (t0) cc_final: 0.7678 (m-30) REVERT: E 375 LYS cc_start: 0.7965 (ttmt) cc_final: 0.7639 (tttm) REVERT: F 311 LYS cc_start: 0.5828 (mmpt) cc_final: 0.4839 (tmtt) REVERT: F 321 LYS cc_start: 0.8217 (mttp) cc_final: 0.7851 (mppt) REVERT: F 338 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7037 (tm-30) REVERT: F 345 ASP cc_start: 0.8022 (t0) cc_final: 0.7577 (OUTLIER) outliers start: 16 outliers final: 12 residues processed: 119 average time/residue: 1.5813 time to fit residues: 192.4035 Evaluate side-chains 122 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 C residue 315 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 338 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN E 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.145643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.117299 restraints weight = 3535.208| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.78 r_work: 0.3518 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 3354 Z= 0.385 Angle : 0.815 13.144 4488 Z= 0.382 Chirality : 0.050 0.123 504 Planarity : 0.006 0.061 570 Dihedral : 5.957 19.877 438 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 4.50 % Allowed : 27.78 % Favored : 67.72 % 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: -2.97 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.008 0.002 PHE D 346 TYR 0.016 0.003 TYR F 310 ARG 0.002 0.001 ARG D 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3047.18 seconds wall clock time: 56 minutes 10.96 seconds (3370.96 seconds total)