Starting phenix.real_space_refine on Wed Sep 17 03:39:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h5j_51886/09_2025/9h5j_51886.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h5j_51886/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9h5j_51886/09_2025/9h5j_51886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h5j_51886/09_2025/9h5j_51886.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9h5j_51886/09_2025/9h5j_51886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h5j_51886/09_2025/9h5j_51886.map" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 0.85, per 1000 atoms: 0.26 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: 0.15 Conformation dependent library (CDL) restraints added in 96.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.17 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: 0.42 Time building geometry restraints manager: 0.23 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: 4.940 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.490 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.400 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.002 ARG E 349 TYR 0.123 0.038 TYR F 310 PHE 0.044 0.016 PHE D 378 HIS 0.014 0.005 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.01168 ( 3354) covalent geometry : angle 1.95868 ( 4488) hydrogen bonds : bond 0.13908 ( 61) hydrogen bonds : angle 6.74091 ( 183) *********************** 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 : 0.141 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: 0.6397 time to fit residues: 82.9473 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 : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 E 336 GLN E 374 HIS F 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.156780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.126535 restraints weight = 3441.344| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.77 r_work: 0.3656 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3354 Z= 0.156 Angle : 0.735 7.480 4488 Z= 0.370 Chirality : 0.048 0.122 504 Planarity : 0.004 0.029 570 Dihedral : 6.094 20.528 438 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 5.56 % Allowed : 14.81 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.54 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.012 0.002 TYR D 310 PHE 0.005 0.001 PHE A 346 HIS 0.005 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 3354) covalent geometry : angle 0.73547 ( 4488) hydrogen bonds : bond 0.02954 ( 61) hydrogen bonds : angle 4.83211 ( 183) *********************** 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 145 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.169 Fit side-chains REVERT: A 321 LYS cc_start: 0.8627 (mttp) cc_final: 0.8351 (mppt) REVERT: A 343 LYS cc_start: 0.8603 (mttt) cc_final: 0.8235 (mtpp) REVERT: B 338 GLU cc_start: 0.8656 (tt0) cc_final: 0.8373 (tm-30) REVERT: B 370 LYS cc_start: 0.8784 (tttm) cc_final: 0.8564 (tmtt) REVERT: B 375 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7889 (tttm) REVERT: C 338 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8001 (tm-30) REVERT: C 343 LYS cc_start: 0.8567 (mttt) cc_final: 0.8250 (mtpp) REVERT: C 345 ASP cc_start: 0.8532 (t0) cc_final: 0.8098 (m-30) REVERT: D 338 GLU cc_start: 0.8551 (tt0) cc_final: 0.8247 (tm-30) REVERT: D 370 LYS cc_start: 0.8474 (tttm) cc_final: 0.8203 (tmtt) REVERT: D 375 LYS cc_start: 0.8217 (ttmt) cc_final: 0.7839 (tttm) REVERT: E 338 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8079 (tm-30) REVERT: E 340 LYS cc_start: 0.8532 (mttt) cc_final: 0.8198 (mttt) REVERT: F 338 GLU cc_start: 0.8487 (tt0) cc_final: 0.8216 (tm-30) REVERT: F 343 LYS cc_start: 0.8726 (mttt) cc_final: 0.8375 (mtpp) REVERT: F 345 ASP cc_start: 0.8484 (t0) cc_final: 0.7939 (m-30) REVERT: F 370 LYS cc_start: 0.8771 (tttm) cc_final: 0.8472 (tmtt) outliers start: 21 outliers final: 5 residues processed: 134 average time/residue: 0.7030 time to fit residues: 96.0861 Evaluate side-chains 121 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 338 GLU 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 11 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN D 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.148137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.118228 restraints weight = 3481.366| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.82 r_work: 0.3530 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 3354 Z= 0.295 Angle : 0.839 7.651 4488 Z= 0.424 Chirality : 0.051 0.128 504 Planarity : 0.006 0.056 570 Dihedral : 6.705 22.911 438 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 6.08 % Allowed : 19.58 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.07 (0.29), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.22), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 349 TYR 0.016 0.004 TYR C 310 PHE 0.008 0.002 PHE F 346 HIS 0.006 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00732 ( 3354) covalent geometry : angle 0.83855 ( 4488) hydrogen bonds : bond 0.03841 ( 61) hydrogen bonds : angle 4.93693 ( 183) *********************** 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 149 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.153 Fit side-chains REVERT: A 321 LYS cc_start: 0.8678 (mttp) cc_final: 0.8461 (mppt) REVERT: A 331 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8726 (mtpp) REVERT: A 343 LYS cc_start: 0.8456 (mttt) cc_final: 0.8101 (mtpp) REVERT: A 370 LYS cc_start: 0.8929 (tttp) cc_final: 0.8654 (tmtt) REVERT: B 338 GLU cc_start: 0.8689 (tt0) cc_final: 0.8444 (tm-30) REVERT: B 370 LYS cc_start: 0.8728 (tttm) cc_final: 0.8511 (tmtt) REVERT: B 375 LYS cc_start: 0.8354 (ttmt) cc_final: 0.7952 (tttm) REVERT: C 338 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8017 (tm-30) REVERT: C 343 LYS cc_start: 0.8698 (mttt) cc_final: 0.8279 (mtpp) REVERT: C 345 ASP cc_start: 0.8616 (t0) cc_final: 0.8156 (OUTLIER) REVERT: C 375 LYS cc_start: 0.8325 (ttmt) cc_final: 0.7963 (tttm) REVERT: D 338 GLU cc_start: 0.8658 (tt0) cc_final: 0.8319 (tm-30) REVERT: D 375 LYS cc_start: 0.8334 (ttmt) cc_final: 0.7938 (tttm) REVERT: E 338 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8131 (tm-30) REVERT: E 343 LYS cc_start: 0.8659 (mttt) cc_final: 0.8127 (mtpp) REVERT: E 347 LYS cc_start: 0.8686 (mtpp) cc_final: 0.8294 (mtpt) REVERT: F 321 LYS cc_start: 0.8591 (mttp) cc_final: 0.8269 (mppt) REVERT: F 336 GLN cc_start: 0.9154 (tt0) cc_final: 0.8896 (tt0) REVERT: F 338 GLU cc_start: 0.8572 (tt0) cc_final: 0.8269 (tm-30) REVERT: F 340 LYS cc_start: 0.8787 (mttt) cc_final: 0.8563 (mptt) REVERT: F 343 LYS cc_start: 0.8714 (mttt) cc_final: 0.8318 (mtpp) REVERT: F 347 LYS cc_start: 0.8832 (mtpp) cc_final: 0.8567 (mtpt) outliers start: 23 outliers final: 8 residues processed: 137 average time/residue: 0.7280 time to fit residues: 101.6098 Evaluate side-chains 132 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS 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 5 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.4075 r_free = 0.4075 target = 0.151098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.121177 restraints weight = 3384.719| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.78 r_work: 0.3547 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3354 Z= 0.201 Angle : 0.716 6.716 4488 Z= 0.359 Chirality : 0.049 0.125 504 Planarity : 0.006 0.060 570 Dihedral : 6.211 21.455 438 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 6.08 % Allowed : 21.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.11 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 349 TYR 0.012 0.003 TYR D 310 PHE 0.005 0.001 PHE A 346 HIS 0.004 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 3354) covalent geometry : angle 0.71578 ( 4488) hydrogen bonds : bond 0.03115 ( 61) hydrogen bonds : angle 4.69159 ( 183) *********************** 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 149 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.142 Fit side-chains REVERT: A 321 LYS cc_start: 0.8616 (mttp) cc_final: 0.8382 (mppt) REVERT: A 338 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8070 (tm-30) REVERT: A 343 LYS cc_start: 0.8552 (mttt) cc_final: 0.8162 (mtpp) REVERT: A 370 LYS cc_start: 0.8870 (tttp) cc_final: 0.8626 (tmtt) REVERT: B 311 LYS cc_start: 0.8556 (tptm) cc_final: 0.8338 (tptp) REVERT: B 338 GLU cc_start: 0.8608 (tt0) cc_final: 0.8402 (tm-30) REVERT: B 375 LYS cc_start: 0.8324 (ttmt) cc_final: 0.7933 (tttm) REVERT: C 338 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8007 (tm-30) REVERT: C 343 LYS cc_start: 0.8606 (mttt) cc_final: 0.8257 (mtpp) REVERT: C 345 ASP cc_start: 0.8577 (t0) cc_final: 0.8174 (OUTLIER) REVERT: C 375 LYS cc_start: 0.8292 (ttmt) cc_final: 0.7940 (tttm) REVERT: D 321 LYS cc_start: 0.8709 (mttp) cc_final: 0.8383 (mppt) REVERT: D 338 GLU cc_start: 0.8566 (tt0) cc_final: 0.8124 (tm-30) REVERT: D 375 LYS cc_start: 0.8361 (ttmt) cc_final: 0.7961 (tttm) REVERT: E 311 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8227 (tmtt) REVERT: E 331 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8889 (mtpm) REVERT: E 338 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8111 (tm-30) REVERT: E 343 LYS cc_start: 0.8687 (mttt) cc_final: 0.8196 (mtpp) REVERT: E 347 LYS cc_start: 0.8636 (mtpp) cc_final: 0.8352 (mtpt) REVERT: E 375 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7821 (tttm) REVERT: F 321 LYS cc_start: 0.8511 (mttp) cc_final: 0.8187 (mppt) REVERT: F 338 GLU cc_start: 0.8509 (tt0) cc_final: 0.8240 (tm-30) REVERT: F 340 LYS cc_start: 0.8723 (mttt) cc_final: 0.8513 (mptt) REVERT: F 343 LYS cc_start: 0.8714 (mttt) cc_final: 0.8350 (mtpp) REVERT: F 345 ASP cc_start: 0.8580 (t0) cc_final: 0.7980 (OUTLIER) REVERT: F 347 LYS cc_start: 0.8812 (mtpp) cc_final: 0.8568 (mtpt) outliers start: 23 outliers final: 13 residues processed: 135 average time/residue: 0.7289 time to fit residues: 100.2512 Evaluate side-chains 137 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.126 ------------------------------------------------------------------------------- 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 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 331 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.153241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.123404 restraints weight = 3377.669| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.79 r_work: 0.3580 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3354 Z= 0.144 Angle : 0.636 6.848 4488 Z= 0.316 Chirality : 0.048 0.126 504 Planarity : 0.006 0.061 570 Dihedral : 5.792 19.330 438 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 5.56 % Allowed : 23.28 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.03 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.010 0.002 TYR D 310 PHE 0.004 0.001 PHE A 346 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 3354) covalent geometry : angle 0.63635 ( 4488) hydrogen bonds : bond 0.02515 ( 61) hydrogen bonds : angle 4.45821 ( 183) *********************** 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 145 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.102 Fit side-chains REVERT: A 343 LYS cc_start: 0.8577 (mttt) cc_final: 0.8162 (mtpp) REVERT: A 370 LYS cc_start: 0.8843 (tttp) cc_final: 0.8583 (tmtt) REVERT: B 345 ASP cc_start: 0.8584 (t0) cc_final: 0.8230 (m-30) REVERT: B 375 LYS cc_start: 0.8324 (ttmt) cc_final: 0.7931 (tttm) REVERT: C 338 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8002 (tm-30) REVERT: C 343 LYS cc_start: 0.8513 (mttt) cc_final: 0.8193 (mtpp) REVERT: C 345 ASP cc_start: 0.8545 (t0) cc_final: 0.8201 (OUTLIER) REVERT: C 375 LYS cc_start: 0.8302 (ttmt) cc_final: 0.7946 (tttm) REVERT: D 321 LYS cc_start: 0.8666 (mttp) cc_final: 0.8320 (mppt) REVERT: D 338 GLU cc_start: 0.8542 (tt0) cc_final: 0.8291 (tm-30) REVERT: D 345 ASP cc_start: 0.8656 (t0) cc_final: 0.8007 (m-30) REVERT: D 375 LYS cc_start: 0.8352 (ttmt) cc_final: 0.7953 (tttm) REVERT: E 311 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8241 (tmtt) REVERT: E 331 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8875 (mtpm) REVERT: E 338 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7989 (tm-30) REVERT: E 343 LYS cc_start: 0.8699 (mttt) cc_final: 0.8190 (mtpp) REVERT: E 345 ASP cc_start: 0.8447 (t70) cc_final: 0.7996 (m-30) REVERT: E 375 LYS cc_start: 0.8239 (ttmt) cc_final: 0.7811 (tttm) REVERT: F 311 LYS cc_start: 0.8523 (tmtt) cc_final: 0.8289 (tmtt) REVERT: F 321 LYS cc_start: 0.8473 (mttp) cc_final: 0.8137 (mppt) REVERT: F 338 GLU cc_start: 0.8484 (tt0) cc_final: 0.8213 (tm-30) REVERT: F 340 LYS cc_start: 0.8674 (mttt) cc_final: 0.8464 (mttt) REVERT: F 343 LYS cc_start: 0.8736 (mttt) cc_final: 0.8379 (mtpp) REVERT: F 345 ASP cc_start: 0.8553 (t0) cc_final: 0.7978 (OUTLIER) REVERT: F 347 LYS cc_start: 0.8731 (mtpp) cc_final: 0.8517 (mtpt) outliers start: 21 outliers final: 13 residues processed: 135 average time/residue: 0.7005 time to fit residues: 96.3282 Evaluate side-chains 134 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.150 ------------------------------------------------------------------------------- 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 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 331 LYS 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 25 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 13 optimal weight: 0.0370 chunk 29 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 overall best weight: 3.9464 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.151009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.121138 restraints weight = 3367.070| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.80 r_work: 0.3543 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 3354 Z= 0.199 Angle : 0.704 8.166 4488 Z= 0.346 Chirality : 0.049 0.126 504 Planarity : 0.006 0.053 570 Dihedral : 6.033 20.309 438 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 5.56 % Allowed : 23.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.11 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 349 TYR 0.011 0.003 TYR F 310 PHE 0.005 0.002 PHE D 346 HIS 0.003 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 3354) covalent geometry : angle 0.70356 ( 4488) hydrogen bonds : bond 0.02973 ( 61) hydrogen bonds : angle 4.55768 ( 183) *********************** 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 143 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.208 Fit side-chains REVERT: A 343 LYS cc_start: 0.8568 (mttt) cc_final: 0.8139 (mtpp) REVERT: A 370 LYS cc_start: 0.8885 (tttp) cc_final: 0.8653 (tmtt) REVERT: B 345 ASP cc_start: 0.8603 (t0) cc_final: 0.8191 (m-30) REVERT: B 370 LYS cc_start: 0.8723 (tttm) cc_final: 0.8495 (tmtt) REVERT: B 375 LYS cc_start: 0.8333 (ttmt) cc_final: 0.7939 (tttm) REVERT: C 338 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7999 (tm-30) REVERT: C 343 LYS cc_start: 0.8606 (mttt) cc_final: 0.8217 (mtpp) REVERT: C 345 ASP cc_start: 0.8529 (t0) cc_final: 0.8184 (OUTLIER) REVERT: C 375 LYS cc_start: 0.8310 (ttmt) cc_final: 0.7953 (tttm) REVERT: D 321 LYS cc_start: 0.8640 (mttp) cc_final: 0.8314 (mppt) REVERT: D 338 GLU cc_start: 0.8503 (tt0) cc_final: 0.8268 (tm-30) REVERT: D 345 ASP cc_start: 0.8636 (t0) cc_final: 0.7999 (m-30) REVERT: D 375 LYS cc_start: 0.8364 (ttmt) cc_final: 0.7968 (tttm) REVERT: E 311 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8270 (tmtt) REVERT: E 331 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8865 (mtpm) REVERT: E 338 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8076 (tm-30) REVERT: E 343 LYS cc_start: 0.8710 (mttt) cc_final: 0.8190 (mtpp) REVERT: E 345 ASP cc_start: 0.8445 (t70) cc_final: 0.7994 (m-30) REVERT: E 375 LYS cc_start: 0.8253 (ttmt) cc_final: 0.7815 (tttm) REVERT: F 311 LYS cc_start: 0.8493 (tmtt) cc_final: 0.8250 (tmtt) REVERT: F 321 LYS cc_start: 0.8463 (mttp) cc_final: 0.8146 (mppt) REVERT: F 338 GLU cc_start: 0.8492 (tt0) cc_final: 0.8230 (tm-30) REVERT: F 340 LYS cc_start: 0.8713 (mttt) cc_final: 0.8493 (mttt) REVERT: F 343 LYS cc_start: 0.8758 (mttt) cc_final: 0.8392 (mtpp) REVERT: F 345 ASP cc_start: 0.8528 (t0) cc_final: 0.7971 (m-30) REVERT: F 347 LYS cc_start: 0.8766 (mtpp) cc_final: 0.8535 (mtpt) outliers start: 21 outliers final: 13 residues processed: 133 average time/residue: 0.7065 time to fit residues: 95.8239 Evaluate side-chains 136 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.139 ------------------------------------------------------------------------------- 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 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 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 35 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 9 optimal weight: 0.0470 overall best weight: 3.8086 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.150827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.121120 restraints weight = 3398.962| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.79 r_work: 0.3546 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 3354 Z= 0.194 Angle : 0.703 9.195 4488 Z= 0.344 Chirality : 0.049 0.124 504 Planarity : 0.006 0.054 570 Dihedral : 6.013 20.256 438 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 6.35 % Allowed : 23.81 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.11 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 349 TYR 0.011 0.003 TYR D 310 PHE 0.005 0.002 PHE D 346 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 3354) covalent geometry : angle 0.70309 ( 4488) hydrogen bonds : bond 0.02894 ( 61) hydrogen bonds : angle 4.56374 ( 183) *********************** 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 145 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.104 Fit side-chains REVERT: A 343 LYS cc_start: 0.8579 (mttt) cc_final: 0.8140 (mtpp) REVERT: A 370 LYS cc_start: 0.8889 (tttp) cc_final: 0.8651 (tmtt) REVERT: B 345 ASP cc_start: 0.8604 (t0) cc_final: 0.8188 (m-30) REVERT: B 370 LYS cc_start: 0.8738 (tttm) cc_final: 0.8508 (tmtt) REVERT: B 375 LYS cc_start: 0.8338 (ttmt) cc_final: 0.7944 (tttm) REVERT: C 338 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8025 (tm-30) REVERT: C 343 LYS cc_start: 0.8605 (mttt) cc_final: 0.8252 (mtpp) REVERT: C 345 ASP cc_start: 0.8564 (t0) cc_final: 0.8198 (OUTLIER) REVERT: C 375 LYS cc_start: 0.8330 (ttmt) cc_final: 0.7958 (tttm) REVERT: D 321 LYS cc_start: 0.8631 (mttp) cc_final: 0.8315 (mppt) REVERT: D 338 GLU cc_start: 0.8484 (tt0) cc_final: 0.8278 (tm-30) REVERT: D 345 ASP cc_start: 0.8630 (t0) cc_final: 0.7991 (m-30) REVERT: D 375 LYS cc_start: 0.8372 (ttmt) cc_final: 0.7974 (tttm) REVERT: E 331 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8911 (mtpm) REVERT: E 338 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8052 (tm-30) REVERT: E 343 LYS cc_start: 0.8661 (mttt) cc_final: 0.8137 (mtpp) REVERT: E 345 ASP cc_start: 0.8454 (t70) cc_final: 0.8012 (m-30) REVERT: E 375 LYS cc_start: 0.8268 (ttmt) cc_final: 0.7842 (tttm) REVERT: F 311 LYS cc_start: 0.8486 (tmtt) cc_final: 0.8221 (tmtt) REVERT: F 321 LYS cc_start: 0.8473 (mttp) cc_final: 0.8156 (mppt) REVERT: F 338 GLU cc_start: 0.8488 (tt0) cc_final: 0.8218 (tm-30) REVERT: F 340 LYS cc_start: 0.8735 (mttt) cc_final: 0.8530 (mttt) REVERT: F 343 LYS cc_start: 0.8826 (mttt) cc_final: 0.8426 (mtpp) REVERT: F 345 ASP cc_start: 0.8584 (t0) cc_final: 0.8011 (OUTLIER) REVERT: F 347 LYS cc_start: 0.8723 (mtpp) cc_final: 0.8502 (mtpt) outliers start: 24 outliers final: 15 residues processed: 134 average time/residue: 0.7572 time to fit residues: 103.3440 Evaluate side-chains 134 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.108 ------------------------------------------------------------------------------- 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 320 SER Chi-restraints excluded: chain E residue 331 LYS 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 8 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.150572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.120884 restraints weight = 3424.896| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.78 r_work: 0.3542 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3354 Z= 0.211 Angle : 0.741 10.196 4488 Z= 0.360 Chirality : 0.049 0.124 504 Planarity : 0.006 0.054 570 Dihedral : 6.108 20.495 438 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 5.82 % Allowed : 25.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.17 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 349 TYR 0.012 0.003 TYR F 310 PHE 0.005 0.002 PHE D 346 HIS 0.003 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00524 ( 3354) covalent geometry : angle 0.74142 ( 4488) hydrogen bonds : bond 0.03040 ( 61) hydrogen bonds : angle 4.61667 ( 183) *********************** 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 140 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.102 Fit side-chains REVERT: A 343 LYS cc_start: 0.8581 (mttt) cc_final: 0.8167 (mtpp) REVERT: A 370 LYS cc_start: 0.8897 (tttp) cc_final: 0.8647 (tmtt) REVERT: B 345 ASP cc_start: 0.8601 (t0) cc_final: 0.8186 (m-30) REVERT: B 370 LYS cc_start: 0.8751 (tttm) cc_final: 0.8520 (tmtt) REVERT: B 375 LYS cc_start: 0.8338 (ttmt) cc_final: 0.7963 (tttm) REVERT: C 338 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7970 (tm-30) REVERT: C 343 LYS cc_start: 0.8619 (mttt) cc_final: 0.8279 (mtpp) REVERT: C 345 ASP cc_start: 0.8541 (t0) cc_final: 0.8202 (OUTLIER) REVERT: C 375 LYS cc_start: 0.8310 (ttmt) cc_final: 0.7958 (tttm) REVERT: D 321 LYS cc_start: 0.8621 (mttp) cc_final: 0.8268 (mppt) REVERT: D 338 GLU cc_start: 0.8495 (tt0) cc_final: 0.8286 (tm-30) REVERT: D 345 ASP cc_start: 0.8625 (t0) cc_final: 0.7986 (m-30) REVERT: D 375 LYS cc_start: 0.8364 (ttmt) cc_final: 0.7982 (tttm) REVERT: E 331 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8902 (mtpm) REVERT: E 338 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8084 (tm-30) REVERT: E 343 LYS cc_start: 0.8696 (mttt) cc_final: 0.8191 (mtpp) REVERT: E 345 ASP cc_start: 0.8451 (t70) cc_final: 0.8015 (m-30) REVERT: E 375 LYS cc_start: 0.8267 (ttmt) cc_final: 0.7860 (tttm) REVERT: F 311 LYS cc_start: 0.8485 (tmtt) cc_final: 0.8181 (tmtt) REVERT: F 321 LYS cc_start: 0.8491 (mttp) cc_final: 0.8189 (mppt) REVERT: F 338 GLU cc_start: 0.8468 (tt0) cc_final: 0.8200 (tm-30) REVERT: F 340 LYS cc_start: 0.8735 (mttt) cc_final: 0.8522 (mttt) REVERT: F 343 LYS cc_start: 0.8812 (mttt) cc_final: 0.8451 (mtpp) REVERT: F 345 ASP cc_start: 0.8568 (t0) cc_final: 0.8025 (OUTLIER) REVERT: F 347 LYS cc_start: 0.8756 (mtpp) cc_final: 0.8546 (mtpt) outliers start: 22 outliers final: 16 residues processed: 132 average time/residue: 0.6989 time to fit residues: 93.9576 Evaluate side-chains 137 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 373 THR 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 320 SER Chi-restraints excluded: chain E residue 331 LYS 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 9 optimal weight: 0.0870 chunk 32 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.155029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.125178 restraints weight = 3404.594| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.82 r_work: 0.3618 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.4633 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= 0.109 Angle : 0.631 11.506 4488 Z= 0.302 Chirality : 0.048 0.123 504 Planarity : 0.006 0.050 570 Dihedral : 5.430 17.279 438 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.44 % Allowed : 27.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.94 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.007 0.001 TYR D 310 PHE 0.003 0.001 PHE D 346 HIS 0.002 0.000 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 3354) covalent geometry : angle 0.63062 ( 4488) hydrogen bonds : bond 0.01991 ( 61) hydrogen bonds : angle 4.34764 ( 183) *********************** 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 137 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.098 Fit side-chains REVERT: A 343 LYS cc_start: 0.8568 (mttt) cc_final: 0.8123 (mtpp) REVERT: A 370 LYS cc_start: 0.8857 (tttp) cc_final: 0.8555 (tmtt) REVERT: B 331 LYS cc_start: 0.8936 (mtmm) cc_final: 0.8730 (mtpm) REVERT: B 345 ASP cc_start: 0.8568 (t0) cc_final: 0.8226 (m-30) REVERT: B 370 LYS cc_start: 0.8759 (tttm) cc_final: 0.8527 (tmtt) REVERT: B 375 LYS cc_start: 0.8320 (ttmt) cc_final: 0.7928 (tttm) REVERT: C 321 LYS cc_start: 0.8486 (mttp) cc_final: 0.8252 (mppt) REVERT: C 343 LYS cc_start: 0.8420 (mttt) cc_final: 0.8046 (mtpp) REVERT: C 345 ASP cc_start: 0.8510 (t0) cc_final: 0.8203 (OUTLIER) REVERT: C 375 LYS cc_start: 0.8309 (ttmt) cc_final: 0.7928 (tttm) REVERT: D 311 LYS cc_start: 0.8380 (tmtt) cc_final: 0.7981 (tptp) REVERT: D 321 LYS cc_start: 0.8567 (mttp) cc_final: 0.8236 (mppt) REVERT: D 331 LYS cc_start: 0.9068 (mtpm) cc_final: 0.8671 (mtmm) REVERT: D 345 ASP cc_start: 0.8624 (t0) cc_final: 0.8016 (m-30) REVERT: D 370 LYS cc_start: 0.8273 (tttm) cc_final: 0.7997 (tmtt) REVERT: D 375 LYS cc_start: 0.8356 (ttmt) cc_final: 0.7966 (tttm) REVERT: E 331 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8860 (mtmm) REVERT: E 343 LYS cc_start: 0.8636 (mttt) cc_final: 0.8137 (mtpp) REVERT: E 344 LEU cc_start: 0.9258 (mt) cc_final: 0.8999 (mt) REVERT: E 345 ASP cc_start: 0.8381 (t70) cc_final: 0.8014 (m-30) REVERT: E 375 LYS cc_start: 0.8259 (ttmt) cc_final: 0.7832 (tttm) REVERT: F 311 LYS cc_start: 0.8486 (tmtt) cc_final: 0.8215 (tmtt) REVERT: F 321 LYS cc_start: 0.8493 (mttp) cc_final: 0.8166 (mppt) REVERT: F 338 GLU cc_start: 0.8430 (tt0) cc_final: 0.8175 (tm-30) REVERT: F 340 LYS cc_start: 0.8662 (mttt) cc_final: 0.8457 (mttt) REVERT: F 343 LYS cc_start: 0.8882 (mttt) cc_final: 0.8499 (mtpp) REVERT: F 345 ASP cc_start: 0.8514 (t0) cc_final: 0.7963 (m-30) outliers start: 13 outliers final: 9 residues processed: 131 average time/residue: 0.7364 time to fit residues: 98.2224 Evaluate side-chains 128 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.117 ------------------------------------------------------------------------------- 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 E residue 320 SER Chi-restraints excluded: chain E residue 331 LYS 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 9 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 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 = 0.4061 r_free = 0.4061 target = 0.150779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.120949 restraints weight = 3428.309| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.81 r_work: 0.3542 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3354 Z= 0.206 Angle : 0.765 12.064 4488 Z= 0.363 Chirality : 0.049 0.126 504 Planarity : 0.006 0.053 570 Dihedral : 5.961 19.777 438 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 4.23 % Allowed : 27.25 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.06 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 349 TYR 0.011 0.003 TYR D 310 PHE 0.006 0.002 PHE F 346 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 3354) covalent geometry : angle 0.76462 ( 4488) hydrogen bonds : bond 0.02939 ( 61) hydrogen bonds : angle 4.61586 ( 183) ********************** 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 135 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.141 Fit side-chains REVERT: A 343 LYS cc_start: 0.8575 (mttt) cc_final: 0.8123 (mtpp) REVERT: A 370 LYS cc_start: 0.8898 (tttp) cc_final: 0.8632 (tmtt) REVERT: B 345 ASP cc_start: 0.8587 (t0) cc_final: 0.8179 (m-30) REVERT: B 370 LYS cc_start: 0.8743 (tttm) cc_final: 0.8517 (tmtt) REVERT: B 375 LYS cc_start: 0.8342 (ttmt) cc_final: 0.7949 (tttm) REVERT: C 343 LYS cc_start: 0.8642 (mttt) cc_final: 0.8277 (mtpp) REVERT: C 345 ASP cc_start: 0.8561 (t0) cc_final: 0.8218 (OUTLIER) REVERT: C 375 LYS cc_start: 0.8319 (ttmt) cc_final: 0.7946 (tttm) REVERT: D 311 LYS cc_start: 0.8372 (tmtt) cc_final: 0.7976 (tptp) REVERT: D 321 LYS cc_start: 0.8613 (mttp) cc_final: 0.8267 (mppt) REVERT: D 331 LYS cc_start: 0.9081 (mtpm) cc_final: 0.8764 (mtmm) REVERT: D 338 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8063 (tm-30) REVERT: D 345 ASP cc_start: 0.8631 (t0) cc_final: 0.7991 (m-30) REVERT: D 375 LYS cc_start: 0.8369 (ttmt) cc_final: 0.7973 (tttm) REVERT: E 331 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8910 (mtpm) REVERT: E 343 LYS cc_start: 0.8664 (mttt) cc_final: 0.8122 (mtpp) REVERT: E 345 ASP cc_start: 0.8449 (t70) cc_final: 0.8021 (m-30) REVERT: E 375 LYS cc_start: 0.8269 (ttmt) cc_final: 0.7845 (tttm) REVERT: F 311 LYS cc_start: 0.8516 (tmtt) cc_final: 0.8228 (tmtt) REVERT: F 321 LYS cc_start: 0.8500 (mttp) cc_final: 0.8194 (mppt) REVERT: F 338 GLU cc_start: 0.8476 (tt0) cc_final: 0.8200 (tm-30) REVERT: F 340 LYS cc_start: 0.8731 (mttt) cc_final: 0.8519 (mttt) REVERT: F 343 LYS cc_start: 0.8857 (mttt) cc_final: 0.8428 (mtpp) REVERT: F 345 ASP cc_start: 0.8557 (t0) cc_final: 0.7981 (OUTLIER) REVERT: F 347 LYS cc_start: 0.8747 (mtpp) cc_final: 0.8437 (mtpt) outliers start: 16 outliers final: 12 residues processed: 127 average time/residue: 0.7303 time to fit residues: 94.4703 Evaluate side-chains 128 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.142 ------------------------------------------------------------------------------- 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 320 SER Chi-restraints excluded: chain E residue 331 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.154554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.124634 restraints weight = 3453.069| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.82 r_work: 0.3604 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.4664 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= 0.119 Angle : 0.671 13.138 4488 Z= 0.315 Chirality : 0.048 0.124 504 Planarity : 0.006 0.049 570 Dihedral : 5.427 17.358 438 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.44 % Allowed : 28.31 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.93 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG E 349 TYR 0.007 0.002 TYR D 310 PHE 0.003 0.001 PHE D 346 HIS 0.002 0.000 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 3354) covalent geometry : angle 0.67087 ( 4488) hydrogen bonds : bond 0.02061 ( 61) hydrogen bonds : angle 4.38219 ( 183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2039.72 seconds wall clock time: 35 minutes 30.56 seconds (2130.56 seconds total)