Starting phenix.real_space_refine on Fri Aug 22 13:42:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qjy_14026/08_2025/7qjy_14026.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qjy_14026/08_2025/7qjy_14026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qjy_14026/08_2025/7qjy_14026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qjy_14026/08_2025/7qjy_14026.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qjy_14026/08_2025/7qjy_14026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qjy_14026/08_2025/7qjy_14026.map" } resolution = 3.14 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= 0.004 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 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3444 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 1.01, per 1000 atoms: 0.29 Number of scatterers: 3444 At special positions: 0 Unit cell: (98.1, 132.98, 45.78, 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 642 8.00 N 636 7.00 C 2160 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: 0.16 Conformation dependent library (CDL) restraints added in 91.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 48.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.853A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 325 removed outlier: 6.733A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY B 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 342 removed outlier: 6.594A pdb=" N VAL A 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LYS D 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL A 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N GLU D 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER A 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLU B 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N SER D 341 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS B 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 345 through 346 removed outlier: 6.621A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 354 Processing sheet with id=AA7, first strand: chain 'A' and resid 350 through 354 removed outlier: 9.075A pdb=" N VAL B 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 10.402A pdb=" N LYS D 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N SER B 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 10.297A pdb=" N GLY D 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N ILE B 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N LEU D 357 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N SER B 356 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASN D 359 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ASP B 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N THR D 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE B 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 377 removed outlier: 6.435A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 306 through 310 Processing sheet with id=AB1, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.820A pdb=" N VAL C 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 317 through 325 removed outlier: 6.014A pdb=" N LYS C 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N SER E 320 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR C 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N CYS E 322 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS C 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N SER E 324 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLY C 323 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL C 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LYS F 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER C 320 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLY F 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N CYS C 322 " --> pdb=" O GLY F 323 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU F 325 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER C 324 " --> pdb=" O LEU F 325 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 337 through 342 Processing sheet with id=AB4, first strand: chain 'E' and resid 345 through 346 removed outlier: 6.573A pdb=" N ASP C 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 350 through 351 removed outlier: 6.234A pdb=" N VAL C 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 357 through 358 removed outlier: 6.748A pdb=" N LEU C 357 " --> pdb=" O ASP F 358 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 368 through 377 removed outlier: 6.525A pdb=" N LYS C 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLU E 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE C 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N HIS E 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N THR C 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU E 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS C 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) 73 hydrogen bonds defined for protein. 216 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: 0.44 Time building geometry restraints manager: 0.21 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: 988 1.33 - 1.45: 430 1.45 - 1.57: 2074 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3498 Sorted by residual: bond pdb=" CZ ARG E 349 " pdb=" NH2 ARG E 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.08e+00 bond pdb=" CZ ARG C 349 " pdb=" NH2 ARG C 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.54e+00 bond pdb=" C GLY D 323 " pdb=" O GLY D 323 " ideal model delta sigma weight residual 1.236 1.222 0.014 5.30e-03 3.56e+04 6.52e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.33e+00 bond pdb=" CZ ARG D 379 " pdb=" NH2 ARG D 379 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.20e+00 ... (remaining 3493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 3030 1.69 - 3.39: 1328 3.39 - 5.08: 282 5.08 - 6.77: 35 6.77 - 8.46: 5 Bond angle restraints: 4680 Sorted by residual: angle pdb=" OD1 ASN D 327 " pdb=" CG ASN D 327 " pdb=" ND2 ASN D 327 " ideal model delta sigma weight residual 122.60 117.87 4.73 1.00e+00 1.00e+00 2.24e+01 angle pdb=" N GLY A 367 " pdb=" CA GLY A 367 " pdb=" C GLY A 367 " ideal model delta sigma weight residual 114.61 121.51 -6.90 1.49e+00 4.50e-01 2.14e+01 angle pdb=" C ASP B 348 " pdb=" N ARG B 349 " pdb=" CA ARG B 349 " ideal model delta sigma weight residual 121.56 128.34 -6.78 1.56e+00 4.11e-01 1.89e+01 angle pdb=" C ASP F 348 " pdb=" N ARG F 349 " pdb=" CA ARG F 349 " ideal model delta sigma weight residual 121.05 127.23 -6.18 1.43e+00 4.89e-01 1.87e+01 angle pdb=" OD1 ASN A 327 " pdb=" CG ASN A 327 " pdb=" ND2 ASN A 327 " ideal model delta sigma weight residual 122.60 118.30 4.30 1.00e+00 1.00e+00 1.85e+01 ... (remaining 4675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 1967 16.44 - 32.88: 143 32.88 - 49.32: 18 49.32 - 65.75: 3 65.75 - 82.19: 5 Dihedral angle restraints: 2136 sinusoidal: 894 harmonic: 1242 Sorted by residual: dihedral pdb=" CA GLY B 366 " pdb=" C GLY B 366 " pdb=" N GLY B 367 " pdb=" CA GLY B 367 " ideal model delta harmonic sigma weight residual 180.00 150.55 29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA GLY A 366 " pdb=" C GLY A 366 " pdb=" N GLY A 367 " pdb=" CA GLY A 367 " ideal model delta harmonic sigma weight residual 180.00 150.88 29.12 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA GLY D 366 " pdb=" C GLY D 366 " pdb=" N GLY D 367 " pdb=" CA GLY D 367 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 2133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 314 0.070 - 0.140: 174 0.140 - 0.211: 33 0.211 - 0.281: 4 0.281 - 0.351: 3 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA HIS C 329 " pdb=" N HIS C 329 " pdb=" C HIS C 329 " pdb=" CB HIS C 329 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA HIS D 329 " pdb=" N HIS D 329 " pdb=" C HIS D 329 " pdb=" CB HIS D 329 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA HIS A 329 " pdb=" N HIS A 329 " pdb=" C HIS A 329 " pdb=" CB HIS A 329 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 525 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.139 2.00e-02 2.50e+03 7.57e-02 1.15e+02 pdb=" CG TYR F 310 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " -0.070 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " -0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " -0.115 2.00e-02 2.50e+03 6.66e-02 8.88e+01 pdb=" CG TYR D 310 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " 0.058 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " 0.038 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.106 2.00e-02 2.50e+03 6.04e-02 7.29e+01 pdb=" CG TYR C 310 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.052 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.100 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 1660 3.00 - 3.47: 2701 3.47 - 3.95: 5423 3.95 - 4.42: 5462 4.42 - 4.90: 10569 Nonbonded interactions: 25815 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.519 3.040 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.525 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.536 3.040 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.543 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.548 3.040 ... (remaining 25810 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: 1.480 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.710 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 : 0.011 0.039 3498 Z= 0.706 Angle : 1.870 8.465 4680 Z= 1.233 Chirality : 0.085 0.351 528 Planarity : 0.013 0.095 594 Dihedral : 12.320 82.193 1344 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.25 % Allowed : 2.53 % Favored : 97.22 % 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: -2.50 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 379 TYR 0.139 0.043 TYR F 310 PHE 0.055 0.013 PHE F 346 HIS 0.014 0.005 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.01096 ( 3498) covalent geometry : angle 1.86969 ( 4680) hydrogen bonds : bond 0.07429 ( 68) hydrogen bonds : angle 7.99598 ( 216) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.108 Fit side-chains REVERT: A 311 LYS cc_start: 0.8249 (mttt) cc_final: 0.8028 (mttm) REVERT: A 340 LYS cc_start: 0.7560 (mmmm) cc_final: 0.6774 (mtmm) REVERT: A 347 LYS cc_start: 0.8276 (mttt) cc_final: 0.8005 (mmmt) REVERT: B 311 LYS cc_start: 0.8084 (mttt) cc_final: 0.7603 (mmtt) REVERT: B 321 LYS cc_start: 0.7909 (mttt) cc_final: 0.7456 (mtpt) REVERT: B 347 LYS cc_start: 0.7604 (mttt) cc_final: 0.7164 (mmtt) REVERT: B 373 THR cc_start: 0.9195 (m) cc_final: 0.8945 (m) REVERT: C 343 LYS cc_start: 0.8288 (tttt) cc_final: 0.7702 (tptt) REVERT: C 347 LYS cc_start: 0.8331 (mttt) cc_final: 0.8078 (mmtt) REVERT: C 349 ARG cc_start: 0.8234 (ttm170) cc_final: 0.7959 (ttm110) REVERT: C 375 LYS cc_start: 0.8260 (tttt) cc_final: 0.7919 (mttt) REVERT: E 343 LYS cc_start: 0.8336 (tttt) cc_final: 0.7998 (pttp) REVERT: E 347 LYS cc_start: 0.8601 (mttt) cc_final: 0.7805 (pttm) REVERT: E 375 LYS cc_start: 0.8279 (tttt) cc_final: 0.7995 (mttt) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.1098 time to fit residues: 18.7716 Evaluate side-chains 119 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.084 ------------------------------------------------------------------------------- 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: 7.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 374 HIS B 307 GLN B 374 HIS C 359 ASN C 374 HIS D 307 GLN D 374 HIS E 329 HIS E 359 ASN E 374 HIS F 374 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.115608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.105869 restraints weight = 5108.030| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.82 r_work: 0.3478 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3498 Z= 0.227 Angle : 0.763 7.965 4680 Z= 0.389 Chirality : 0.050 0.144 528 Planarity : 0.005 0.049 594 Dihedral : 6.606 23.591 462 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.02 % Allowed : 11.62 % Favored : 86.36 % 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: -2.45 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 379 TYR 0.014 0.003 TYR F 310 PHE 0.012 0.002 PHE C 346 HIS 0.006 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 3498) covalent geometry : angle 0.76346 ( 4680) hydrogen bonds : bond 0.02326 ( 68) hydrogen bonds : angle 6.15545 ( 216) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.082 Fit side-chains REVERT: A 311 LYS cc_start: 0.8752 (mttt) cc_final: 0.8405 (mttt) REVERT: A 347 LYS cc_start: 0.8208 (mttt) cc_final: 0.7915 (mmmt) REVERT: B 311 LYS cc_start: 0.8667 (mttt) cc_final: 0.7773 (mmtt) REVERT: B 347 LYS cc_start: 0.7563 (mttt) cc_final: 0.7296 (mmtt) REVERT: B 375 LYS cc_start: 0.8488 (tttm) cc_final: 0.8039 (ttmt) REVERT: C 343 LYS cc_start: 0.8078 (tttt) cc_final: 0.7369 (tptt) REVERT: C 347 LYS cc_start: 0.8280 (mttt) cc_final: 0.8049 (mmtt) REVERT: C 349 ARG cc_start: 0.7830 (ttm170) cc_final: 0.7528 (ttm110) REVERT: C 375 LYS cc_start: 0.8603 (tttt) cc_final: 0.8347 (tttm) REVERT: D 347 LYS cc_start: 0.8265 (mmmt) cc_final: 0.8016 (mmmt) REVERT: E 343 LYS cc_start: 0.8112 (tttt) cc_final: 0.7421 (ttpt) REVERT: E 349 ARG cc_start: 0.8075 (ttm170) cc_final: 0.6275 (ptt-90) REVERT: F 340 LYS cc_start: 0.8343 (mmtt) cc_final: 0.7860 (mtpp) outliers start: 8 outliers final: 6 residues processed: 106 average time/residue: 0.0957 time to fit residues: 11.2442 Evaluate side-chains 97 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 359 ASN Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 2 optimal weight: 0.0870 chunk 32 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 359 ASN E 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.120244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.111024 restraints weight = 4885.454| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.68 r_work: 0.3568 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3498 Z= 0.104 Angle : 0.592 6.607 4680 Z= 0.300 Chirality : 0.049 0.128 528 Planarity : 0.005 0.051 594 Dihedral : 5.639 20.555 462 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.52 % Allowed : 13.13 % Favored : 85.35 % 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: -2.11 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 379 TYR 0.018 0.003 TYR D 310 PHE 0.006 0.001 PHE F 378 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 3498) covalent geometry : angle 0.59154 ( 4680) hydrogen bonds : bond 0.01776 ( 68) hydrogen bonds : angle 5.60534 ( 216) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8855 (mttt) cc_final: 0.8595 (mttt) REVERT: A 343 LYS cc_start: 0.8471 (mtmt) cc_final: 0.8265 (mtmt) REVERT: A 347 LYS cc_start: 0.8228 (mttt) cc_final: 0.7897 (mmmt) REVERT: A 349 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7840 (ttm170) REVERT: A 372 GLU cc_start: 0.7605 (tp30) cc_final: 0.7221 (tt0) REVERT: B 311 LYS cc_start: 0.8670 (mttt) cc_final: 0.7806 (mmtt) REVERT: B 347 LYS cc_start: 0.7584 (mttt) cc_final: 0.7381 (mmtt) REVERT: B 375 LYS cc_start: 0.8459 (tttm) cc_final: 0.7984 (ttmt) REVERT: C 349 ARG cc_start: 0.7745 (ttm170) cc_final: 0.7419 (ttm110) REVERT: C 351 GLN cc_start: 0.7476 (tm-30) cc_final: 0.7037 (mp10) REVERT: C 375 LYS cc_start: 0.8528 (tttt) cc_final: 0.8312 (tttm) REVERT: D 347 LYS cc_start: 0.8262 (mmmt) cc_final: 0.7958 (mmmt) REVERT: E 343 LYS cc_start: 0.8089 (tttt) cc_final: 0.7418 (ttpt) REVERT: E 349 ARG cc_start: 0.8017 (ttm170) cc_final: 0.6209 (ptt-90) REVERT: E 369 LYS cc_start: 0.8309 (mtpp) cc_final: 0.7863 (tttt) REVERT: F 340 LYS cc_start: 0.8476 (mmtt) cc_final: 0.8234 (mptt) REVERT: F 369 LYS cc_start: 0.8279 (mttm) cc_final: 0.7734 (mtpt) outliers start: 6 outliers final: 3 residues processed: 105 average time/residue: 0.1173 time to fit residues: 13.6611 Evaluate side-chains 91 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 360 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN C 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.113731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.104013 restraints weight = 4867.320| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.69 r_work: 0.3428 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 3498 Z= 0.343 Angle : 0.770 8.329 4680 Z= 0.389 Chirality : 0.050 0.160 528 Planarity : 0.005 0.049 594 Dihedral : 6.183 24.535 462 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.54 % Allowed : 11.36 % Favored : 85.10 % 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: -2.27 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 379 TYR 0.019 0.003 TYR F 310 PHE 0.015 0.003 PHE F 346 HIS 0.007 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00787 ( 3498) covalent geometry : angle 0.76984 ( 4680) hydrogen bonds : bond 0.02331 ( 68) hydrogen bonds : angle 5.42606 ( 216) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8813 (mttt) cc_final: 0.8542 (mttt) REVERT: A 321 LYS cc_start: 0.8483 (mttt) cc_final: 0.8020 (mtpt) REVERT: A 347 LYS cc_start: 0.8200 (mttt) cc_final: 0.7920 (mmtt) REVERT: A 349 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7910 (ttm170) REVERT: B 311 LYS cc_start: 0.8768 (mttt) cc_final: 0.7841 (mmtt) REVERT: B 347 LYS cc_start: 0.7549 (mttt) cc_final: 0.7254 (mmtt) REVERT: B 375 LYS cc_start: 0.8471 (tttm) cc_final: 0.8001 (ttmt) REVERT: C 317 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8430 (mttp) REVERT: C 343 LYS cc_start: 0.8541 (mttp) cc_final: 0.8241 (mttm) REVERT: C 349 ARG cc_start: 0.7864 (ttm170) cc_final: 0.7286 (ttm110) REVERT: C 351 GLN cc_start: 0.7578 (tm-30) cc_final: 0.7314 (mp10) REVERT: C 375 LYS cc_start: 0.8598 (tttt) cc_final: 0.8366 (tttm) REVERT: D 347 LYS cc_start: 0.8250 (mmmt) cc_final: 0.7778 (mmmt) REVERT: D 372 GLU cc_start: 0.7986 (tp30) cc_final: 0.7695 (tt0) REVERT: D 378 PHE cc_start: 0.8878 (t80) cc_final: 0.8635 (t80) REVERT: E 343 LYS cc_start: 0.8169 (tttt) cc_final: 0.7505 (ttpt) REVERT: F 311 LYS cc_start: 0.6359 (mmtm) cc_final: 0.4413 (ptpt) REVERT: F 340 LYS cc_start: 0.8379 (mmtt) cc_final: 0.7865 (mmmt) REVERT: F 349 ARG cc_start: 0.7719 (ttm170) cc_final: 0.7326 (mtp180) REVERT: F 369 LYS cc_start: 0.8354 (mttm) cc_final: 0.7771 (mtpt) outliers start: 14 outliers final: 9 residues processed: 99 average time/residue: 0.1099 time to fit residues: 12.0910 Evaluate side-chains 96 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 359 ASN F 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.116862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.107439 restraints weight = 4876.588| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.73 r_work: 0.3491 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3498 Z= 0.160 Angle : 0.614 6.915 4680 Z= 0.307 Chirality : 0.048 0.127 528 Planarity : 0.004 0.048 594 Dihedral : 5.667 21.653 462 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.53 % Allowed : 13.64 % Favored : 83.84 % 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: -2.17 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 379 TYR 0.014 0.002 TYR F 310 PHE 0.010 0.002 PHE C 346 HIS 0.003 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 3498) covalent geometry : angle 0.61413 ( 4680) hydrogen bonds : bond 0.01804 ( 68) hydrogen bonds : angle 5.17504 ( 216) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8686 (mttt) cc_final: 0.8413 (mttt) REVERT: A 347 LYS cc_start: 0.8190 (mttt) cc_final: 0.7908 (mmtt) REVERT: A 349 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7866 (ttm170) REVERT: B 311 LYS cc_start: 0.8702 (mttt) cc_final: 0.7746 (mmtt) REVERT: B 347 LYS cc_start: 0.7559 (mttt) cc_final: 0.7319 (mmtt) REVERT: B 375 LYS cc_start: 0.8446 (tttm) cc_final: 0.7988 (ttmt) REVERT: C 347 LYS cc_start: 0.7980 (mmtt) cc_final: 0.7747 (mmtt) REVERT: C 349 ARG cc_start: 0.7866 (ttm170) cc_final: 0.7249 (ttm110) REVERT: C 351 GLN cc_start: 0.7538 (tm-30) cc_final: 0.7233 (mp10) REVERT: C 375 LYS cc_start: 0.8551 (tttt) cc_final: 0.7481 (mttt) REVERT: D 347 LYS cc_start: 0.8288 (mmmt) cc_final: 0.7895 (mmmt) REVERT: D 378 PHE cc_start: 0.8870 (t80) cc_final: 0.8657 (t80) REVERT: E 343 LYS cc_start: 0.8185 (tttt) cc_final: 0.7478 (ttpt) REVERT: F 311 LYS cc_start: 0.6273 (mmtm) cc_final: 0.4280 (ptpt) REVERT: F 340 LYS cc_start: 0.8485 (mmtt) cc_final: 0.8178 (mptt) REVERT: F 349 ARG cc_start: 0.7698 (ttm170) cc_final: 0.7329 (mtp180) REVERT: F 369 LYS cc_start: 0.8385 (mttm) cc_final: 0.7813 (mtpt) outliers start: 10 outliers final: 7 residues processed: 96 average time/residue: 0.1161 time to fit residues: 12.3455 Evaluate side-chains 84 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 359 ASN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 359 ASN F 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.115251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.106047 restraints weight = 4912.202| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.65 r_work: 0.3439 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 3498 Z= 0.335 Angle : 0.731 7.802 4680 Z= 0.372 Chirality : 0.050 0.140 528 Planarity : 0.005 0.047 594 Dihedral : 6.009 23.710 462 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.28 % Allowed : 13.64 % Favored : 83.08 % 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: -2.39 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 379 TYR 0.020 0.004 TYR F 310 PHE 0.015 0.002 PHE C 346 HIS 0.006 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00766 ( 3498) covalent geometry : angle 0.73145 ( 4680) hydrogen bonds : bond 0.02177 ( 68) hydrogen bonds : angle 5.29645 ( 216) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.148 Fit side-chains REVERT: A 311 LYS cc_start: 0.8683 (mttt) cc_final: 0.8409 (mttt) REVERT: A 340 LYS cc_start: 0.8144 (mmmm) cc_final: 0.7926 (mptt) REVERT: A 347 LYS cc_start: 0.8183 (mttt) cc_final: 0.7951 (mmtt) REVERT: A 349 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7980 (ttm170) REVERT: B 311 LYS cc_start: 0.8752 (mttt) cc_final: 0.7817 (mmtt) REVERT: B 347 LYS cc_start: 0.7485 (mttt) cc_final: 0.7262 (mmtt) REVERT: B 375 LYS cc_start: 0.8422 (tttm) cc_final: 0.7950 (ttmt) REVERT: C 317 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8376 (mttp) REVERT: C 349 ARG cc_start: 0.7888 (ttm170) cc_final: 0.7251 (ttm110) REVERT: C 351 GLN cc_start: 0.7521 (tm-30) cc_final: 0.7244 (mp10) REVERT: D 343 LYS cc_start: 0.8504 (tttp) cc_final: 0.8196 (mttt) REVERT: D 347 LYS cc_start: 0.8204 (mmmt) cc_final: 0.7714 (mmtt) REVERT: E 340 LYS cc_start: 0.8581 (mmmm) cc_final: 0.8239 (mmmt) REVERT: E 343 LYS cc_start: 0.8191 (tttt) cc_final: 0.7470 (ttpt) REVERT: F 311 LYS cc_start: 0.6287 (mmtm) cc_final: 0.4296 (ptpt) REVERT: F 340 LYS cc_start: 0.8464 (mmtt) cc_final: 0.7900 (mmmt) REVERT: F 349 ARG cc_start: 0.7726 (ttm170) cc_final: 0.7375 (mtp180) REVERT: F 369 LYS cc_start: 0.8354 (mttm) cc_final: 0.7762 (mtpt) outliers start: 13 outliers final: 8 residues processed: 89 average time/residue: 0.1290 time to fit residues: 12.7869 Evaluate side-chains 90 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 359 ASN Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 359 ASN F 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.119784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.110471 restraints weight = 4880.443| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.72 r_work: 0.3541 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3498 Z= 0.113 Angle : 0.569 6.163 4680 Z= 0.287 Chirality : 0.048 0.130 528 Planarity : 0.004 0.048 594 Dihedral : 5.352 20.486 462 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.52 % Allowed : 16.41 % Favored : 82.07 % 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: -2.20 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 379 TYR 0.013 0.002 TYR A 310 PHE 0.006 0.001 PHE F 346 HIS 0.003 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3498) covalent geometry : angle 0.56928 ( 4680) hydrogen bonds : bond 0.01581 ( 68) hydrogen bonds : angle 4.98069 ( 216) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8799 (mttt) cc_final: 0.8576 (mttt) REVERT: A 321 LYS cc_start: 0.8404 (mttt) cc_final: 0.7928 (mtpt) REVERT: A 347 LYS cc_start: 0.8140 (mttt) cc_final: 0.7916 (mmtt) REVERT: B 311 LYS cc_start: 0.8708 (mttt) cc_final: 0.7783 (mmtt) REVERT: B 347 LYS cc_start: 0.7496 (mttt) cc_final: 0.7281 (mmtt) REVERT: B 375 LYS cc_start: 0.8442 (tttm) cc_final: 0.8011 (ttmt) REVERT: C 349 ARG cc_start: 0.7891 (ttm170) cc_final: 0.7249 (ttm110) REVERT: C 351 GLN cc_start: 0.7512 (tm-30) cc_final: 0.7264 (mp10) REVERT: D 347 LYS cc_start: 0.8292 (mmmt) cc_final: 0.7961 (mmtt) REVERT: E 340 LYS cc_start: 0.8572 (mmmm) cc_final: 0.8251 (mmmt) REVERT: E 343 LYS cc_start: 0.8250 (tttt) cc_final: 0.7574 (ttpt) REVERT: F 311 LYS cc_start: 0.6206 (mmtm) cc_final: 0.4258 (ptpt) REVERT: F 340 LYS cc_start: 0.8528 (mmtt) cc_final: 0.8009 (mmmt) REVERT: F 349 ARG cc_start: 0.7728 (ttm170) cc_final: 0.7022 (mtp-110) REVERT: F 351 GLN cc_start: 0.7901 (tt0) cc_final: 0.7574 (mt0) REVERT: F 369 LYS cc_start: 0.8429 (mttm) cc_final: 0.7881 (mtpt) outliers start: 6 outliers final: 3 residues processed: 92 average time/residue: 0.1264 time to fit residues: 13.0703 Evaluate side-chains 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 360 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 359 ASN F 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.114967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.105488 restraints weight = 4986.739| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.75 r_work: 0.3417 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.050 3498 Z= 0.376 Angle : 0.762 7.913 4680 Z= 0.389 Chirality : 0.051 0.138 528 Planarity : 0.005 0.045 594 Dihedral : 6.027 24.776 462 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.02 % Allowed : 16.41 % Favored : 81.57 % 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: -2.50 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 379 TYR 0.022 0.003 TYR F 310 PHE 0.016 0.003 PHE C 346 HIS 0.006 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00860 ( 3498) covalent geometry : angle 0.76178 ( 4680) hydrogen bonds : bond 0.02261 ( 68) hydrogen bonds : angle 5.28220 ( 216) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.143 Fit side-chains REVERT: A 311 LYS cc_start: 0.8718 (mttt) cc_final: 0.8455 (mtpp) REVERT: A 340 LYS cc_start: 0.8286 (mmmm) cc_final: 0.8046 (mptt) REVERT: A 347 LYS cc_start: 0.8134 (mttt) cc_final: 0.7906 (mmtt) REVERT: B 311 LYS cc_start: 0.8808 (mttt) cc_final: 0.7875 (mmtt) REVERT: B 375 LYS cc_start: 0.8413 (tttm) cc_final: 0.7934 (ttmt) REVERT: C 349 ARG cc_start: 0.7882 (ttm170) cc_final: 0.7244 (ttm110) REVERT: C 351 GLN cc_start: 0.7565 (tm-30) cc_final: 0.7295 (mp10) REVERT: D 343 LYS cc_start: 0.8480 (tttp) cc_final: 0.8194 (mttt) REVERT: D 347 LYS cc_start: 0.8223 (mmmt) cc_final: 0.8001 (mmmt) REVERT: E 340 LYS cc_start: 0.8579 (mmmm) cc_final: 0.8101 (mmmt) REVERT: E 343 LYS cc_start: 0.8256 (tttt) cc_final: 0.7519 (ttpt) REVERT: F 320 SER cc_start: 0.8914 (t) cc_final: 0.8698 (p) REVERT: F 340 LYS cc_start: 0.8490 (mmtt) cc_final: 0.7944 (mmmt) REVERT: F 349 ARG cc_start: 0.7746 (ttm170) cc_final: 0.7408 (mtp180) REVERT: F 369 LYS cc_start: 0.8371 (mttm) cc_final: 0.7785 (mtpt) outliers start: 8 outliers final: 5 residues processed: 89 average time/residue: 0.1398 time to fit residues: 13.8376 Evaluate side-chains 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 359 ASN Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.117722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.108542 restraints weight = 4822.580| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.65 r_work: 0.3476 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3498 Z= 0.192 Angle : 0.639 6.453 4680 Z= 0.323 Chirality : 0.048 0.128 528 Planarity : 0.004 0.046 594 Dihedral : 5.661 22.397 462 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.52 % Allowed : 16.92 % Favored : 81.57 % 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: -2.38 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 379 TYR 0.017 0.003 TYR A 310 PHE 0.009 0.002 PHE D 378 HIS 0.005 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 3498) covalent geometry : angle 0.63862 ( 4680) hydrogen bonds : bond 0.01815 ( 68) hydrogen bonds : angle 5.05206 ( 216) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.165 Fit side-chains REVERT: A 311 LYS cc_start: 0.8757 (mttt) cc_final: 0.8529 (mttt) REVERT: A 340 LYS cc_start: 0.8217 (mmmm) cc_final: 0.7975 (mptt) REVERT: A 347 LYS cc_start: 0.8091 (mttt) cc_final: 0.7859 (mmtt) REVERT: A 379 ARG cc_start: 0.8485 (ttt180) cc_final: 0.7239 (pmt-80) REVERT: B 311 LYS cc_start: 0.8743 (mttt) cc_final: 0.7798 (mmtt) REVERT: C 349 ARG cc_start: 0.7866 (ttm170) cc_final: 0.7210 (ttm110) REVERT: C 351 GLN cc_start: 0.7529 (tm-30) cc_final: 0.7260 (mp10) REVERT: D 343 LYS cc_start: 0.8499 (tttp) cc_final: 0.8189 (mttt) REVERT: E 340 LYS cc_start: 0.8558 (mmmm) cc_final: 0.8139 (mmmt) REVERT: E 343 LYS cc_start: 0.8262 (tttt) cc_final: 0.7570 (ttpt) REVERT: F 340 LYS cc_start: 0.8462 (mmtt) cc_final: 0.7949 (mmmt) REVERT: F 349 ARG cc_start: 0.7722 (ttm170) cc_final: 0.7017 (mtp-110) REVERT: F 369 LYS cc_start: 0.8350 (mttm) cc_final: 0.7795 (mtpt) outliers start: 6 outliers final: 5 residues processed: 84 average time/residue: 0.1443 time to fit residues: 13.5415 Evaluate side-chains 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 8.9990 chunk 37 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 0.0870 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.121435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.112289 restraints weight = 4821.799| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.72 r_work: 0.3558 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3498 Z= 0.092 Angle : 0.563 6.325 4680 Z= 0.284 Chirality : 0.048 0.130 528 Planarity : 0.005 0.051 594 Dihedral : 5.059 18.519 462 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.01 % Allowed : 18.18 % Favored : 80.81 % 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: -2.14 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 379 TYR 0.015 0.002 TYR A 310 PHE 0.006 0.001 PHE D 378 HIS 0.004 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 3498) covalent geometry : angle 0.56290 ( 4680) hydrogen bonds : bond 0.01516 ( 68) hydrogen bonds : angle 4.77525 ( 216) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.145 Fit side-chains REVERT: A 321 LYS cc_start: 0.8413 (mttt) cc_final: 0.7959 (mtpt) REVERT: A 347 LYS cc_start: 0.8042 (mttt) cc_final: 0.7807 (mmtt) REVERT: A 379 ARG cc_start: 0.8481 (ttt180) cc_final: 0.7254 (pmt-80) REVERT: B 311 LYS cc_start: 0.8701 (mttt) cc_final: 0.7749 (mmtt) REVERT: B 379 ARG cc_start: 0.6130 (mmp-170) cc_final: 0.5730 (mmp-170) REVERT: C 349 ARG cc_start: 0.7859 (ttm170) cc_final: 0.7175 (ttm110) REVERT: C 351 GLN cc_start: 0.7493 (tm-30) cc_final: 0.7261 (mp10) REVERT: D 343 LYS cc_start: 0.8444 (tttp) cc_final: 0.8122 (mttt) REVERT: D 347 LYS cc_start: 0.8223 (mmmt) cc_final: 0.7995 (mmmt) REVERT: D 357 LEU cc_start: 0.8703 (tp) cc_final: 0.8501 (tt) REVERT: E 340 LYS cc_start: 0.8541 (mmmm) cc_final: 0.8123 (mmmt) REVERT: E 343 LYS cc_start: 0.8177 (tttt) cc_final: 0.7542 (ttpt) REVERT: F 340 LYS cc_start: 0.8441 (mmtt) cc_final: 0.7982 (mmmt) REVERT: F 349 ARG cc_start: 0.7687 (ttm170) cc_final: 0.7007 (mtp-110) REVERT: F 369 LYS cc_start: 0.8373 (mttm) cc_final: 0.7813 (mtpt) REVERT: F 375 LYS cc_start: 0.8380 (tttm) cc_final: 0.8121 (tttm) outliers start: 4 outliers final: 3 residues processed: 83 average time/residue: 0.1028 time to fit residues: 9.5767 Evaluate side-chains 77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 359 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 0.2980 chunk 24 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 30 optimal weight: 0.0370 chunk 35 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.123310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.114470 restraints weight = 4821.229| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.64 r_work: 0.3570 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3498 Z= 0.089 Angle : 0.550 6.208 4680 Z= 0.275 Chirality : 0.048 0.128 528 Planarity : 0.005 0.049 594 Dihedral : 4.822 17.503 462 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.01 % Allowed : 18.43 % Favored : 80.56 % 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: -2.04 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 379 TYR 0.018 0.002 TYR A 310 PHE 0.008 0.001 PHE D 378 HIS 0.003 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 3498) covalent geometry : angle 0.54985 ( 4680) hydrogen bonds : bond 0.01492 ( 68) hydrogen bonds : angle 4.69847 ( 216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1001.74 seconds wall clock time: 17 minutes 59.97 seconds (1079.97 seconds total)