Starting phenix.real_space_refine on Sat Dec 28 00:03:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hbb_52014/12_2024/9hbb_52014.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hbb_52014/12_2024/9hbb_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9hbb_52014/12_2024/9hbb_52014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hbb_52014/12_2024/9hbb_52014.map" model { file = "/net/cci-nas-00/data/ceres_data/9hbb_52014/12_2024/9hbb_52014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hbb_52014/12_2024/9hbb_52014.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 5.03, per 1000 atoms: 0.71 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: 1.50 Conformation dependent library (CDL) restraints added in 654.0 milliseconds 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: 0.74 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: 2.82 Time building geometry restraints manager: 1.84 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: 7.950 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: 0.460 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 19.600 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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:15.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.570 ------------------------------------------------------------------------------- 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= 0.741 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.015 0.005 HIS F 362 PHE 0.041 0.010 PHE B 378 TYR 0.099 0.032 TYR A 310 ARG 0.002 0.001 ARG D 379 *********************** 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 : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8512 (tttt) cc_final: 0.7820 (mmtm) REVERT: B 375 LYS cc_start: 0.7563 (ttmt) cc_final: 0.7327 (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: 2.6776 time to fit residues: 343.2666 Evaluate side-chains 67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3522 Z= 0.207 Angle : 0.653 4.206 4710 Z= 0.339 Chirality : 0.051 0.146 528 Planarity : 0.004 0.034 600 Dihedral : 6.679 19.219 468 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.29 % Allowed : 13.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.29), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 362 PHE 0.006 0.001 PHE A 346 TYR 0.014 0.003 TYR D 310 ARG 0.003 0.001 ARG A 349 *********************** 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 85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: B 340 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8028 (mmmm) REVERT: B 342 GLU cc_start: 0.4679 (OUTLIER) cc_final: 0.2435 (mp0) REVERT: B 343 LYS cc_start: 0.7951 (mttt) cc_final: 0.7745 (mtpp) REVERT: B 375 LYS cc_start: 0.7397 (ttmt) cc_final: 0.7162 (ttmm) REVERT: C 342 GLU cc_start: 0.4782 (OUTLIER) cc_final: 0.2519 (mp0) outliers start: 17 outliers final: 9 residues processed: 77 average time/residue: 2.4099 time to fit residues: 191.4442 Evaluate side-chains 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 340 LYS 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3522 Z= 0.197 Angle : 0.562 4.232 4710 Z= 0.284 Chirality : 0.050 0.134 528 Planarity : 0.003 0.026 600 Dihedral : 5.411 14.289 468 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.28 % Allowed : 15.40 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 362 PHE 0.008 0.002 PHE A 346 TYR 0.013 0.003 TYR D 310 ARG 0.002 0.000 ARG B 379 *********************** 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 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: B 342 GLU cc_start: 0.5243 (OUTLIER) cc_final: 0.2721 (mp0) REVERT: B 375 LYS cc_start: 0.7487 (ttmt) cc_final: 0.7252 (ttmm) REVERT: D 324 SER cc_start: 0.8795 (m) cc_final: 0.8548 (t) REVERT: D 375 LYS cc_start: 0.6985 (ttmt) cc_final: 0.6772 (tttt) outliers start: 13 outliers final: 5 residues processed: 70 average time/residue: 2.1342 time to fit residues: 154.7711 Evaluate side-chains 59 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN C 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3522 Z= 0.221 Angle : 0.552 5.600 4710 Z= 0.277 Chirality : 0.050 0.129 528 Planarity : 0.003 0.026 600 Dihedral : 5.154 14.729 468 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.78 % Allowed : 18.18 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 362 PHE 0.007 0.002 PHE B 346 TYR 0.014 0.003 TYR D 310 ARG 0.002 0.000 ARG B 379 *********************** 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 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 342 GLU cc_start: 0.5281 (OUTLIER) cc_final: 0.2755 (mp0) REVERT: B 375 LYS cc_start: 0.7609 (ttmt) cc_final: 0.7345 (ttmm) REVERT: C 342 GLU cc_start: 0.5365 (OUTLIER) cc_final: 0.5020 (mp0) REVERT: D 324 SER cc_start: 0.8817 (m) cc_final: 0.8576 (t) REVERT: D 375 LYS cc_start: 0.7052 (ttmt) cc_final: 0.6846 (tttt) outliers start: 11 outliers final: 5 residues processed: 67 average time/residue: 2.1823 time to fit residues: 151.3465 Evaluate side-chains 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3522 Z= 0.237 Angle : 0.530 4.066 4710 Z= 0.267 Chirality : 0.049 0.127 528 Planarity : 0.003 0.026 600 Dihedral : 4.975 14.754 468 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.28 % Allowed : 18.69 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 362 PHE 0.008 0.001 PHE A 378 TYR 0.013 0.003 TYR D 310 ARG 0.002 0.000 ARG B 379 *********************** 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 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 338 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7551 (tm-30) REVERT: B 342 GLU cc_start: 0.5310 (OUTLIER) cc_final: 0.2877 (mp0) REVERT: B 375 LYS cc_start: 0.7659 (ttmt) cc_final: 0.7376 (ttmm) REVERT: C 342 GLU cc_start: 0.5656 (OUTLIER) cc_final: 0.3176 (mp0) REVERT: D 324 SER cc_start: 0.8770 (m) cc_final: 0.8543 (t) REVERT: D 375 LYS cc_start: 0.7064 (ttmt) cc_final: 0.6855 (tttt) outliers start: 13 outliers final: 7 residues processed: 67 average time/residue: 2.4999 time to fit residues: 172.5655 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 : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 305 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 E residue 356 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 10 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3522 Z= 0.267 Angle : 0.538 4.265 4710 Z= 0.271 Chirality : 0.049 0.125 528 Planarity : 0.003 0.028 600 Dihedral : 4.995 15.199 468 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.04 % Allowed : 19.19 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.008 0.002 PHE E 378 TYR 0.015 0.004 TYR D 310 ARG 0.002 0.000 ARG B 379 *********************** 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 72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.685 Fit side-chains REVERT: B 338 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7615 (tm-30) REVERT: B 340 LYS cc_start: 0.8309 (mmtp) cc_final: 0.8101 (mmtm) REVERT: B 375 LYS cc_start: 0.7686 (ttmt) cc_final: 0.7401 (ttmm) REVERT: D 324 SER cc_start: 0.8774 (m) cc_final: 0.8551 (t) REVERT: D 375 LYS cc_start: 0.7124 (ttmt) cc_final: 0.6912 (tttt) REVERT: E 379 ARG cc_start: 0.6327 (mtm110) cc_final: 0.6082 (mtm110) outliers start: 16 outliers final: 11 residues processed: 67 average time/residue: 2.2739 time to fit residues: 157.6299 Evaluate side-chains 66 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 40 optimal weight: 0.0270 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.6038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3522 Z= 0.252 Angle : 0.523 4.333 4710 Z= 0.263 Chirality : 0.049 0.126 528 Planarity : 0.003 0.027 600 Dihedral : 4.900 15.724 468 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.79 % Allowed : 19.44 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.007 0.001 PHE E 378 TYR 0.014 0.003 TYR D 310 ARG 0.002 0.000 ARG B 379 *********************** 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 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 324 SER cc_start: 0.8750 (m) cc_final: 0.8523 (t) REVERT: E 379 ARG cc_start: 0.6288 (mtm110) cc_final: 0.6045 (mtm110) outliers start: 15 outliers final: 12 residues processed: 66 average time/residue: 2.6054 time to fit residues: 177.0985 Evaluate side-chains 58 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.6241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3522 Z= 0.134 Angle : 0.461 3.588 4710 Z= 0.229 Chirality : 0.049 0.127 528 Planarity : 0.003 0.025 600 Dihedral : 4.509 15.185 468 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.26 % Allowed : 22.47 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 362 PHE 0.003 0.000 PHE E 378 TYR 0.007 0.002 TYR D 310 ARG 0.002 0.000 ARG B 379 *********************** 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 58 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.654 Fit side-chains REVERT: B 338 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7590 (tm-30) REVERT: D 324 SER cc_start: 0.8705 (m) cc_final: 0.8487 (t) outliers start: 5 outliers final: 5 residues processed: 56 average time/residue: 2.4973 time to fit residues: 144.9627 Evaluate side-chains 53 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 358 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.6319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3522 Z= 0.237 Angle : 0.499 3.561 4710 Z= 0.251 Chirality : 0.049 0.126 528 Planarity : 0.003 0.026 600 Dihedral : 4.608 15.008 468 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.77 % Allowed : 23.48 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.008 0.001 PHE E 378 TYR 0.014 0.003 TYR D 310 ARG 0.002 0.000 ARG E 379 *********************** 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 57 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: D 324 SER cc_start: 0.8724 (m) cc_final: 0.8494 (t) outliers start: 7 outliers final: 6 residues processed: 54 average time/residue: 2.3677 time to fit residues: 132.4322 Evaluate side-chains 54 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.6436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3522 Z= 0.129 Angle : 0.452 3.607 4710 Z= 0.223 Chirality : 0.049 0.126 528 Planarity : 0.003 0.025 600 Dihedral : 4.356 14.859 468 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.52 % Allowed : 23.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 362 PHE 0.004 0.000 PHE E 378 TYR 0.006 0.002 TYR D 310 ARG 0.001 0.000 ARG E 379 ********************** 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 60 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: B 338 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7586 (tm-30) REVERT: D 324 SER cc_start: 0.8673 (m) cc_final: 0.8459 (t) REVERT: F 338 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7340 (tt0) outliers start: 6 outliers final: 6 residues processed: 57 average time/residue: 2.4502 time to fit residues: 144.3210 Evaluate side-chains 56 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 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 E residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 8.9990 chunk 1 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.139968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.125165 restraints weight = 14019.918| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 1.80 r_work: 0.4023 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3938 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.6488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3522 Z= 0.142 Angle : 0.452 3.479 4710 Z= 0.224 Chirality : 0.049 0.128 528 Planarity : 0.003 0.026 600 Dihedral : 4.229 14.269 468 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.77 % Allowed : 23.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.003 0.001 PHE E 378 TYR 0.009 0.002 TYR D 310 ARG 0.001 0.000 ARG B 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4374.39 seconds wall clock time: 79 minutes 22.70 seconds (4762.70 seconds total)