Starting phenix.real_space_refine on Wed Sep 17 08:18:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hbb_52014/09_2025/9hbb_52014.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hbb_52014/09_2025/9hbb_52014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hbb_52014/09_2025/9hbb_52014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hbb_52014/09_2025/9hbb_52014.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hbb_52014/09_2025/9hbb_52014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hbb_52014/09_2025/9hbb_52014.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2172 2.51 5 N 642 2.21 5 O 648 1.98 5 H 3606 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s 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: 7074 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "D" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "F" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 1.65, per 1000 atoms: 0.23 Number of scatterers: 7074 At special positions: 0 Unit cell: (129.368, 111.24, 39.552, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 648 8.00 N 642 7.00 C 2172 6.00 H 3606 1.00 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: 0.57 Conformation dependent library (CDL) restraints added in 247.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 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 18 sheets defined 0.0% alpha, 46.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.439A pdb=" N VAL B 306 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N VAL D 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.499A 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: 6.717A 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 318 removed outlier: 6.329A pdb=" N LYS A 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N SER D 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 330 removed outlier: 7.010A pdb=" N GLY D 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN A 327 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLY B 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N HIS D 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 removed outlier: 6.617A pdb=" N GLN A 336 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N VAL D 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.617A 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 344 removed outlier: 6.377A pdb=" N LYS A 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N PHE D 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 350 through 354 Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362 removed outlier: 6.623A pdb=" N ASN B 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.974A 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 378 removed outlier: 6.548A pdb=" N LYS A 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLU D 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE A 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N HIS D 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N THR A 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU D 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYS A 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N PHE D 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR A 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.463A pdb=" N VAL C 306 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL E 309 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE C 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL E 306 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N VAL F 309 " --> pdb=" O VAL E 306 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE E 308 " --> pdb=" O VAL F 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 314 Processing sheet with id=AB3, first strand: chain 'C' and resid 317 through 321 Processing sheet with id=AB4, first strand: chain 'C' and resid 325 through 330 removed outlier: 5.865A pdb=" N GLY C 326 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N HIS E 329 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE C 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLY E 326 " --> pdb=" O ASN F 327 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N HIS F 329 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE E 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 336 through 340 removed outlier: 6.568A pdb=" N VAL E 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N LYS F 340 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL E 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 343 through 346 Processing sheet with id=AB7, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.138A pdb=" N VAL E 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N LYS F 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N SER E 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.626A pdb=" N ASN C 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N HIS E 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR C 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN E 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N HIS F 362 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR E 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 369 through 378 77 hydrogen bonds defined for protein. 231 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 3600 1.11 - 1.29: 576 1.29 - 1.46: 925 1.46 - 1.63: 2021 1.63 - 1.81: 6 Bond restraints: 7128 Sorted by residual: bond pdb=" N GLY D 333 " pdb=" H GLY D 333 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CD2 HIS D 362 " pdb=" HD2 HIS D 362 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N ILE E 371 " pdb=" H ILE E 371 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N LEU C 357 " pdb=" H LEU C 357 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N SER E 324 " pdb=" H SER E 324 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 7123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 10869 2.47 - 4.94: 1596 4.94 - 7.41: 494 7.41 - 9.88: 19 9.88 - 12.36: 6 Bond angle restraints: 12984 Sorted by residual: angle pdb=" CB HIS E 362 " pdb=" CG HIS E 362 " pdb=" CD2 HIS E 362 " ideal model delta sigma weight residual 131.20 124.50 6.70 1.30e+00 5.92e-01 2.66e+01 angle pdb=" CB HIS D 362 " pdb=" CG HIS D 362 " pdb=" CD2 HIS D 362 " ideal model delta sigma weight residual 131.20 124.69 6.51 1.30e+00 5.92e-01 2.51e+01 angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 117.60 -5.00 1.00e+00 1.00e+00 2.50e+01 angle pdb=" CB HIS A 362 " pdb=" CG HIS A 362 " pdb=" CD2 HIS A 362 " ideal model delta sigma weight residual 131.20 124.79 6.41 1.30e+00 5.92e-01 2.43e+01 angle pdb=" CA PHE F 346 " pdb=" CB PHE F 346 " pdb=" CG PHE F 346 " ideal model delta sigma weight residual 113.80 118.71 -4.91 1.00e+00 1.00e+00 2.42e+01 ... (remaining 12979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.96: 2835 13.96 - 27.92: 221 27.92 - 41.87: 101 41.87 - 55.83: 52 55.83 - 69.78: 73 Dihedral angle restraints: 3282 sinusoidal: 1878 harmonic: 1404 Sorted by residual: dihedral pdb=" CA PHE B 378 " pdb=" C PHE B 378 " pdb=" N ARG B 379 " pdb=" CA ARG B 379 " ideal model delta harmonic sigma weight residual -180.00 -154.55 -25.45 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA VAL A 350 " pdb=" C VAL A 350 " pdb=" N GLN A 351 " pdb=" CA GLN A 351 " ideal model delta harmonic sigma weight residual 180.00 156.52 23.48 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA LEU F 357 " pdb=" C LEU F 357 " pdb=" N ASP F 358 " pdb=" CA ASP F 358 " ideal model delta harmonic sigma weight residual -180.00 -157.67 -22.33 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 3279 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.056: 258 0.056 - 0.112: 172 0.112 - 0.167: 68 0.167 - 0.223: 24 0.223 - 0.279: 6 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS E 317 " pdb=" N LYS E 317 " pdb=" C LYS E 317 " pdb=" CB LYS E 317 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA LYS D 317 " pdb=" N LYS D 317 " pdb=" C LYS D 317 " pdb=" CB LYS D 317 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CG LEU B 344 " pdb=" CB LEU B 344 " pdb=" CD1 LEU B 344 " pdb=" CD2 LEU B 344 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 525 not shown) Planarity restraints: 1032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN C 336 " -0.065 2.00e-02 2.50e+03 6.21e-02 5.79e+01 pdb=" CD GLN C 336 " 0.012 2.00e-02 2.50e+03 pdb=" OE1 GLN C 336 " 0.056 2.00e-02 2.50e+03 pdb=" NE2 GLN C 336 " 0.039 2.00e-02 2.50e+03 pdb="HE21 GLN C 336 " 0.061 2.00e-02 2.50e+03 pdb="HE22 GLN C 336 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.107 2.00e-02 2.50e+03 4.33e-02 5.62e+01 pdb=" CG TYR A 310 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.044 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.055 2.00e-02 2.50e+03 pdb=" HD1 TYR A 310 " -0.006 2.00e-02 2.50e+03 pdb=" HD2 TYR A 310 " 0.030 2.00e-02 2.50e+03 pdb=" HE1 TYR A 310 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR A 310 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 336 " 0.063 2.00e-02 2.50e+03 5.97e-02 5.35e+01 pdb=" CD GLN B 336 " -0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN B 336 " -0.055 2.00e-02 2.50e+03 pdb=" NE2 GLN B 336 " -0.033 2.00e-02 2.50e+03 pdb="HE21 GLN B 336 " -0.062 2.00e-02 2.50e+03 pdb="HE22 GLN B 336 " 0.097 2.00e-02 2.50e+03 ... (remaining 1029 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 421 2.15 - 2.76: 11699 2.76 - 3.37: 19008 3.37 - 3.99: 24864 3.99 - 4.60: 36206 Nonbonded interactions: 92198 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.537 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.542 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.554 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.574 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.578 2.450 ... (remaining 92193 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: 3.920 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: 0.040 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.560 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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 0.036 3522 Z= 0.695 Angle : 1.881 7.312 4710 Z= 1.228 Chirality : 0.087 0.279 528 Planarity : 0.012 0.063 600 Dihedral : 10.827 47.714 1350 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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: -1.24 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 379 TYR 0.099 0.032 TYR A 310 PHE 0.041 0.010 PHE B 378 HIS 0.015 0.005 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.01103 ( 3522) covalent geometry : angle 1.88121 ( 4710) hydrogen bonds : bond 0.09030 ( 77) hydrogen bonds : angle 6.30318 ( 231) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8512 (tttt) cc_final: 0.7821 (mmtm) REVERT: B 375 LYS cc_start: 0.7563 (ttmt) cc_final: 0.7326 (ttmm) REVERT: D 375 LYS cc_start: 0.6968 (ttmt) cc_final: 0.6754 (tttt) REVERT: F 311 LYS cc_start: 0.8433 (tttt) cc_final: 0.7758 (mmtm) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 1.4255 time to fit residues: 182.4804 Evaluate side-chains 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.141431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.125022 restraints weight = 13725.110| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 1.91 r_work: 0.4026 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3939 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3522 Z= 0.127 Angle : 0.635 4.148 4710 Z= 0.330 Chirality : 0.051 0.145 528 Planarity : 0.004 0.032 600 Dihedral : 6.593 18.894 468 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.79 % Allowed : 13.38 % Favored : 82.83 % 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: -1.38 (0.29), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 349 TYR 0.012 0.003 TYR D 310 PHE 0.005 0.001 PHE A 346 HIS 0.005 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3522) covalent geometry : angle 0.63468 ( 4710) hydrogen bonds : bond 0.02492 ( 77) hydrogen bonds : angle 4.70776 ( 231) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.183 Fit side-chains REVERT: B 342 GLU cc_start: 0.4240 (OUTLIER) cc_final: 0.2091 (mp0) REVERT: B 343 LYS cc_start: 0.8175 (mttt) cc_final: 0.7789 (mtpp) REVERT: C 342 GLU cc_start: 0.4515 (OUTLIER) cc_final: 0.2184 (mp0) REVERT: C 343 LYS cc_start: 0.8192 (mttt) cc_final: 0.7862 (mtpm) REVERT: D 324 SER cc_start: 0.8980 (m) cc_final: 0.8530 (t) REVERT: D 340 LYS cc_start: 0.7704 (ttmt) cc_final: 0.7464 (mmmm) REVERT: F 370 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8072 (tttp) outliers start: 15 outliers final: 9 residues processed: 83 average time/residue: 1.3033 time to fit residues: 111.0814 Evaluate side-chains 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 370 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.146380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.130865 restraints weight = 14006.765| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 1.88 r_work: 0.4094 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.4007 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3522 Z= 0.096 Angle : 0.534 4.742 4710 Z= 0.267 Chirality : 0.050 0.142 528 Planarity : 0.003 0.024 600 Dihedral : 5.238 14.039 468 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.02 % Allowed : 17.93 % Favored : 80.05 % 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: -1.29 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 379 TYR 0.007 0.002 TYR B 310 PHE 0.007 0.001 PHE A 346 HIS 0.004 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 3522) covalent geometry : angle 0.53445 ( 4710) hydrogen bonds : bond 0.02014 ( 77) hydrogen bonds : angle 4.40647 ( 231) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.173 Fit side-chains REVERT: B 343 LYS cc_start: 0.8215 (mttt) cc_final: 0.7859 (mtpm) REVERT: C 342 GLU cc_start: 0.4436 (OUTLIER) cc_final: 0.1975 (mp0) REVERT: D 324 SER cc_start: 0.8978 (OUTLIER) cc_final: 0.8530 (t) REVERT: D 340 LYS cc_start: 0.7702 (ttmt) cc_final: 0.7479 (mmmm) outliers start: 8 outliers final: 3 residues processed: 68 average time/residue: 0.9723 time to fit residues: 68.4588 Evaluate side-chains 59 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 358 ASP 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 30 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN C 359 ASN C 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.138470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.121992 restraints weight = 14109.700| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 1.90 r_work: 0.3982 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3892 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3522 Z= 0.145 Angle : 0.549 4.659 4710 Z= 0.276 Chirality : 0.050 0.131 528 Planarity : 0.003 0.025 600 Dihedral : 5.043 13.969 468 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.29 % Allowed : 17.42 % Favored : 78.28 % 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: -1.32 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 379 TYR 0.015 0.003 TYR D 310 PHE 0.008 0.002 PHE B 346 HIS 0.004 0.001 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 3522) covalent geometry : angle 0.54871 ( 4710) hydrogen bonds : bond 0.01880 ( 77) hydrogen bonds : angle 4.06656 ( 231) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.253 Fit side-chains REVERT: B 340 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8351 (mmmm) REVERT: B 342 GLU cc_start: 0.5329 (OUTLIER) cc_final: 0.3018 (mp0) REVERT: B 343 LYS cc_start: 0.8170 (mttt) cc_final: 0.7833 (mtpp) REVERT: B 375 LYS cc_start: 0.7830 (ttmt) cc_final: 0.7555 (ttmm) REVERT: C 342 GLU cc_start: 0.4746 (OUTLIER) cc_final: 0.4312 (mp0) REVERT: D 324 SER cc_start: 0.9057 (m) cc_final: 0.8620 (t) REVERT: D 340 LYS cc_start: 0.7794 (ttmt) cc_final: 0.7496 (mmmm) REVERT: D 375 LYS cc_start: 0.7334 (ttmt) cc_final: 0.7056 (tttt) outliers start: 17 outliers final: 8 residues processed: 70 average time/residue: 1.1179 time to fit residues: 80.5727 Evaluate side-chains 67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 13 optimal weight: 0.0030 chunk 24 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.4294 r_free = 0.4294 target = 0.141540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.125923 restraints weight = 14063.338| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 1.84 r_work: 0.4032 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3946 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3522 Z= 0.096 Angle : 0.483 4.276 4710 Z= 0.240 Chirality : 0.049 0.127 528 Planarity : 0.003 0.025 600 Dihedral : 4.651 14.269 468 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.04 % Allowed : 18.18 % Favored : 77.78 % 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: -1.31 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.99 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 379 TYR 0.008 0.002 TYR D 310 PHE 0.004 0.001 PHE A 378 HIS 0.003 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 3522) covalent geometry : angle 0.48267 ( 4710) hydrogen bonds : bond 0.01559 ( 77) hydrogen bonds : angle 3.81659 ( 231) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.210 Fit side-chains REVERT: B 342 GLU cc_start: 0.5401 (OUTLIER) cc_final: 0.3064 (mp0) REVERT: B 343 LYS cc_start: 0.8112 (mttt) cc_final: 0.7788 (mtpp) REVERT: B 352 SER cc_start: 0.8805 (t) cc_final: 0.8580 (m) REVERT: B 375 LYS cc_start: 0.7752 (ttmt) cc_final: 0.7484 (ttmm) REVERT: C 342 GLU cc_start: 0.4850 (OUTLIER) cc_final: 0.4492 (mp0) REVERT: D 324 SER cc_start: 0.9049 (m) cc_final: 0.8636 (t) REVERT: D 340 LYS cc_start: 0.7709 (ttmt) cc_final: 0.7435 (mmmm) REVERT: D 375 LYS cc_start: 0.7263 (ttmt) cc_final: 0.7017 (tttt) outliers start: 16 outliers final: 6 residues processed: 65 average time/residue: 1.2043 time to fit residues: 80.5846 Evaluate side-chains 58 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 0.0010 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.4297 r_free = 0.4297 target = 0.141016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.125669 restraints weight = 14137.581| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 1.85 r_work: 0.4039 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3949 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.5790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3522 Z= 0.085 Angle : 0.465 4.096 4710 Z= 0.228 Chirality : 0.049 0.127 528 Planarity : 0.003 0.026 600 Dihedral : 4.344 13.550 468 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.03 % Allowed : 20.96 % Favored : 76.01 % 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: -1.23 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.93 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 379 TYR 0.009 0.002 TYR D 310 PHE 0.004 0.001 PHE A 378 HIS 0.003 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 3522) covalent geometry : angle 0.46459 ( 4710) hydrogen bonds : bond 0.01435 ( 77) hydrogen bonds : angle 3.69447 ( 231) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.279 Fit side-chains REVERT: B 342 GLU cc_start: 0.5468 (OUTLIER) cc_final: 0.3091 (mp0) REVERT: B 343 LYS cc_start: 0.8048 (mttt) cc_final: 0.7776 (mtpp) REVERT: B 375 LYS cc_start: 0.7717 (ttmt) cc_final: 0.7461 (ttmm) REVERT: C 342 GLU cc_start: 0.5020 (OUTLIER) cc_final: 0.4651 (mp0) REVERT: D 324 SER cc_start: 0.9043 (m) cc_final: 0.8647 (t) REVERT: D 340 LYS cc_start: 0.7693 (ttmt) cc_final: 0.7443 (mmmm) REVERT: D 375 LYS cc_start: 0.7270 (ttmt) cc_final: 0.7033 (tttt) outliers start: 12 outliers final: 7 residues processed: 65 average time/residue: 1.1411 time to fit residues: 76.5154 Evaluate side-chains 59 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.4262 r_free = 0.4262 target = 0.139127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.123585 restraints weight = 14118.466| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 1.80 r_work: 0.3994 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3904 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.5908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3522 Z= 0.120 Angle : 0.485 4.442 4710 Z= 0.241 Chirality : 0.049 0.125 528 Planarity : 0.003 0.026 600 Dihedral : 4.393 13.614 468 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.04 % Allowed : 21.46 % Favored : 74.49 % 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: -1.32 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 379 TYR 0.013 0.003 TYR D 310 PHE 0.005 0.001 PHE E 378 HIS 0.003 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 3522) covalent geometry : angle 0.48509 ( 4710) hydrogen bonds : bond 0.01483 ( 77) hydrogen bonds : angle 3.56886 ( 231) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.167 Fit side-chains REVERT: B 342 GLU cc_start: 0.5654 (OUTLIER) cc_final: 0.5440 (mp0) REVERT: B 343 LYS cc_start: 0.8047 (mttt) cc_final: 0.7806 (mtpp) REVERT: B 375 LYS cc_start: 0.7863 (ttmt) cc_final: 0.7590 (ttmm) REVERT: C 342 GLU cc_start: 0.5094 (OUTLIER) cc_final: 0.2623 (mp0) REVERT: D 324 SER cc_start: 0.9044 (m) cc_final: 0.8673 (t) REVERT: D 340 LYS cc_start: 0.7712 (ttmt) cc_final: 0.7490 (mmmm) REVERT: D 375 LYS cc_start: 0.7360 (ttmt) cc_final: 0.7124 (tttt) outliers start: 16 outliers final: 7 residues processed: 65 average time/residue: 1.2597 time to fit residues: 84.3021 Evaluate side-chains 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.4259 r_free = 0.4259 target = 0.138427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.123292 restraints weight = 14297.484| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 1.81 r_work: 0.3993 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3905 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.6206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3522 Z= 0.119 Angle : 0.481 4.396 4710 Z= 0.239 Chirality : 0.049 0.126 528 Planarity : 0.003 0.027 600 Dihedral : 4.398 14.141 468 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.28 % Allowed : 22.98 % Favored : 73.74 % 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: -1.43 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 379 TYR 0.012 0.003 TYR D 310 PHE 0.007 0.001 PHE E 378 HIS 0.003 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 3522) covalent geometry : angle 0.48087 ( 4710) hydrogen bonds : bond 0.01448 ( 77) hydrogen bonds : angle 3.56249 ( 231) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.153 Fit side-chains REVERT: B 343 LYS cc_start: 0.8002 (mttt) cc_final: 0.7741 (mtpp) REVERT: B 375 LYS cc_start: 0.7879 (ttmt) cc_final: 0.7598 (ttmm) REVERT: D 324 SER cc_start: 0.9020 (m) cc_final: 0.8649 (t) REVERT: D 340 LYS cc_start: 0.7696 (ttmt) cc_final: 0.7478 (mmmm) REVERT: D 375 LYS cc_start: 0.7360 (ttmt) cc_final: 0.7121 (tttt) REVERT: E 379 ARG cc_start: 0.6503 (mtm110) cc_final: 0.6283 (mtm110) outliers start: 13 outliers final: 9 residues processed: 65 average time/residue: 1.2834 time to fit residues: 85.6629 Evaluate side-chains 62 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.4280 r_free = 0.4280 target = 0.140142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.125149 restraints weight = 14057.507| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 1.81 r_work: 0.4017 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3928 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.6303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3522 Z= 0.101 Angle : 0.464 4.384 4710 Z= 0.230 Chirality : 0.049 0.128 528 Planarity : 0.003 0.027 600 Dihedral : 4.293 14.234 468 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.28 % Allowed : 23.48 % Favored : 73.23 % 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: -1.47 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 379 TYR 0.011 0.002 TYR D 310 PHE 0.005 0.001 PHE E 378 HIS 0.002 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 3522) covalent geometry : angle 0.46413 ( 4710) hydrogen bonds : bond 0.01380 ( 77) hydrogen bonds : angle 3.53386 ( 231) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: B 342 GLU cc_start: 0.5047 (OUTLIER) cc_final: 0.2225 (mp0) REVERT: B 343 LYS cc_start: 0.7982 (mttt) cc_final: 0.7725 (mtpp) REVERT: B 375 LYS cc_start: 0.7849 (ttmt) cc_final: 0.7590 (ttmm) REVERT: D 324 SER cc_start: 0.9025 (m) cc_final: 0.8648 (t) REVERT: D 340 LYS cc_start: 0.7692 (ttmt) cc_final: 0.7461 (mmmm) REVERT: D 375 LYS cc_start: 0.7350 (ttmt) cc_final: 0.7120 (tttt) REVERT: E 379 ARG cc_start: 0.6514 (mtm110) cc_final: 0.6307 (mtm110) outliers start: 13 outliers final: 8 residues processed: 63 average time/residue: 1.2909 time to fit residues: 83.5900 Evaluate side-chains 62 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN C 359 ASN E 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.140852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.125917 restraints weight = 14278.189| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 1.81 r_work: 0.4032 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3945 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.6341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 3522 Z= 0.223 Angle : 1.174 59.195 4710 Z= 0.719 Chirality : 0.049 0.158 528 Planarity : 0.003 0.027 600 Dihedral : 4.290 14.204 468 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.53 % Allowed : 23.99 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 379 TYR 0.011 0.002 TYR D 310 PHE 0.005 0.001 PHE E 378 HIS 0.002 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 3522) covalent geometry : angle 1.17397 ( 4710) hydrogen bonds : bond 0.01380 ( 77) hydrogen bonds : angle 3.53565 ( 231) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: B 342 GLU cc_start: 0.5077 (OUTLIER) cc_final: 0.2244 (mp0) REVERT: B 343 LYS cc_start: 0.7988 (mttt) cc_final: 0.7735 (mtpp) REVERT: B 375 LYS cc_start: 0.7839 (ttmt) cc_final: 0.7582 (ttmm) REVERT: D 324 SER cc_start: 0.9017 (m) cc_final: 0.8641 (t) REVERT: D 340 LYS cc_start: 0.7698 (ttmt) cc_final: 0.7480 (mmmm) REVERT: D 375 LYS cc_start: 0.7360 (ttmt) cc_final: 0.7131 (tttt) REVERT: E 379 ARG cc_start: 0.6495 (mtm110) cc_final: 0.6285 (mtm110) outliers start: 10 outliers final: 8 residues processed: 59 average time/residue: 1.3971 time to fit residues: 84.6044 Evaluate side-chains 62 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4280 r_free = 0.4280 target = 0.140142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.125222 restraints weight = 14187.358| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 1.81 r_work: 0.4020 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3931 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.6327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 3522 Z= 0.223 Angle : 1.174 59.195 4710 Z= 0.719 Chirality : 0.049 0.158 528 Planarity : 0.003 0.027 600 Dihedral : 4.290 14.204 468 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.53 % Allowed : 23.99 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 379 TYR 0.011 0.002 TYR D 310 PHE 0.005 0.001 PHE E 378 HIS 0.002 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 3522) covalent geometry : angle 1.17397 ( 4710) hydrogen bonds : bond 0.01380 ( 77) hydrogen bonds : angle 3.53565 ( 231) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3160.79 seconds wall clock time: 54 minutes 25.07 seconds (3265.07 seconds total)