Starting phenix.real_space_refine on Sun Mar 10 17:03:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjz_14027/03_2024/7qjz_14027.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjz_14027/03_2024/7qjz_14027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjz_14027/03_2024/7qjz_14027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjz_14027/03_2024/7qjz_14027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjz_14027/03_2024/7qjz_14027.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qjz_14027/03_2024/7qjz_14027.pdb" } resolution = 3.4 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2124 2.51 5 N 612 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 349": "NH1" <-> "NH2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "E ARG 349": "NH1" <-> "NH2" Residue "F ASP 345": "OD1" <-> "OD2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 349": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3378 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "B" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "C" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "D" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "E" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "F" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 563 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Time building chain proxies: 2.23, per 1000 atoms: 0.66 Number of scatterers: 3378 At special positions: 0 Unit cell: (122.08, 116.63, 39.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 636 8.00 N 612 7.00 C 2124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 1.17 Conformation dependent library (CDL) restraints added in 700.9 milliseconds 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 40.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 7.040A pdb=" N VAL A 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N VAL C 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.816A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 326 through 330 removed outlier: 7.938A pdb=" N HIS C 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N HIS A 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 342 Processing sheet with id=AA5, first strand: chain 'B' and resid 354 through 362 removed outlier: 9.046A pdb=" N ILE A 354 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N LEU B 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER A 356 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ASN B 359 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP A 358 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N THR B 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE A 360 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY A 355 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER C 356 " --> pdb=" O GLY A 355 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 370 through 371 removed outlier: 6.479A pdb=" N LYS A 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 306 through 310 removed outlier: 6.461A pdb=" N GLN D 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N TYR E 310 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL D 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 313 through 316 removed outlier: 7.341A pdb=" N SER E 320 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N THR D 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N CYS E 322 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS D 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 313 through 316 Processing sheet with id=AB1, first strand: chain 'E' and resid 327 through 330 removed outlier: 6.377A pdb=" N ASN D 327 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N HIS F 330 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N HIS D 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 337 through 340 removed outlier: 6.984A pdb=" N GLU D 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL D 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N LYS F 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL D 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 350 through 362 removed outlier: 8.960A pdb=" N VAL D 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N LYS E 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N SER D 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 10.417A pdb=" N GLY E 355 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N ILE D 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N LEU E 357 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER D 356 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ASN E 359 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP D 358 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR E 361 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE D 360 " --> pdb=" O THR E 361 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 350 through 362 removed outlier: 8.960A pdb=" N VAL D 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N LYS E 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N SER D 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 10.417A pdb=" N GLY E 355 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N ILE D 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N LEU E 357 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER D 356 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ASN E 359 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP D 358 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR E 361 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE D 360 " --> pdb=" O THR E 361 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE F 354 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY D 355 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER F 356 " --> pdb=" O GLY D 355 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 369 through 371 removed outlier: 6.438A pdb=" N LYS D 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) 51 hydrogen bonds defined for protein. 153 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.70 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 881 1.33 - 1.45: 493 1.45 - 1.57: 2052 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3432 Sorted by residual: bond pdb=" CZ ARG F 349 " pdb=" NH2 ARG F 349 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.03e+00 bond pdb=" CA LYS D 311 " pdb=" CB LYS D 311 " ideal model delta sigma weight residual 1.526 1.553 -0.026 9.30e-03 1.16e+04 8.02e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.69e+00 bond pdb=" CZ ARG B 349 " pdb=" NH2 ARG B 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.45e+00 bond pdb=" CZ ARG E 349 " pdb=" NH2 ARG E 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.31e+00 ... (remaining 3427 not shown) Histogram of bond angle deviations from ideal: 100.66 - 106.37: 133 106.37 - 112.07: 1417 112.07 - 117.78: 1021 117.78 - 123.48: 1663 123.48 - 129.19: 362 Bond angle restraints: 4596 Sorted by residual: angle pdb=" CA ASN C 327 " pdb=" CB ASN C 327 " pdb=" CG ASN C 327 " ideal model delta sigma weight residual 112.60 119.73 -7.13 1.00e+00 1.00e+00 5.09e+01 angle pdb=" CA LYS C 331 " pdb=" C LYS C 331 " pdb=" N PRO C 332 " ideal model delta sigma weight residual 118.16 122.99 -4.83 7.00e-01 2.04e+00 4.75e+01 angle pdb=" CA ASN A 327 " pdb=" CB ASN A 327 " pdb=" CG ASN A 327 " ideal model delta sigma weight residual 112.60 119.09 -6.49 1.00e+00 1.00e+00 4.22e+01 angle pdb=" CA LYS B 331 " pdb=" C LYS B 331 " pdb=" N PRO B 332 " ideal model delta sigma weight residual 118.16 122.34 -4.18 7.00e-01 2.04e+00 3.56e+01 angle pdb=" CA ASN B 327 " pdb=" CB ASN B 327 " pdb=" CG ASN B 327 " ideal model delta sigma weight residual 112.60 118.20 -5.60 1.00e+00 1.00e+00 3.13e+01 ... (remaining 4591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.24: 1888 16.24 - 32.48: 156 32.48 - 48.72: 29 48.72 - 64.96: 5 64.96 - 81.19: 10 Dihedral angle restraints: 2088 sinusoidal: 864 harmonic: 1224 Sorted by residual: dihedral pdb=" CA THR A 319 " pdb=" C THR A 319 " pdb=" N SER A 320 " pdb=" CA SER A 320 " ideal model delta harmonic sigma weight residual 180.00 152.94 27.06 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA GLY F 365 " pdb=" C GLY F 365 " pdb=" N GLY F 366 " pdb=" CA GLY F 366 " ideal model delta harmonic sigma weight residual 180.00 -153.00 -27.00 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA ASP E 314 " pdb=" C ASP E 314 " pdb=" N LEU E 315 " pdb=" CA LEU E 315 " ideal model delta harmonic sigma weight residual 180.00 153.52 26.48 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 2085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 258 0.062 - 0.124: 161 0.124 - 0.185: 73 0.185 - 0.247: 23 0.247 - 0.309: 7 Chirality restraints: 522 Sorted by residual: chirality pdb=" CA LYS C 343 " pdb=" N LYS C 343 " pdb=" C LYS C 343 " pdb=" CB LYS C 343 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA SER A 324 " pdb=" N SER A 324 " pdb=" C SER A 324 " pdb=" CB SER A 324 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ASP D 345 " pdb=" N ASP D 345 " pdb=" C ASP D 345 " pdb=" CB ASP D 345 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 519 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.075 2.00e-02 2.50e+03 5.14e-02 5.29e+01 pdb=" CG TYR E 310 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.046 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.044 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.022 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " 0.084 2.00e-02 2.50e+03 5.11e-02 5.22e+01 pdb=" CG TYR D 310 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 329 " -0.076 2.00e-02 2.50e+03 5.66e-02 4.81e+01 pdb=" CG HIS F 329 " 0.077 2.00e-02 2.50e+03 pdb=" ND1 HIS F 329 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS F 329 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 HIS F 329 " -0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS F 329 " -0.050 2.00e-02 2.50e+03 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 1511 2.97 - 3.45: 2933 3.45 - 3.94: 5105 3.94 - 4.42: 5246 4.42 - 4.90: 10498 Nonbonded interactions: 25293 Sorted by model distance: nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.490 2.440 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.509 2.440 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.539 2.440 nonbonded pdb=" N GLY A 366 " pdb=" O GLY A 366 " model vdw 2.640 2.496 nonbonded pdb=" OD2 ASP A 314 " pdb=" NZ LYS A 370 " model vdw 2.643 2.520 ... (remaining 25288 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.730 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: 3.510 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.350 Find NCS groups from input model: 0.240 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 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 0.037 3432 Z= 0.762 Angle : 2.094 10.065 4596 Z= 1.374 Chirality : 0.097 0.309 522 Planarity : 0.013 0.062 582 Dihedral : 13.722 81.195 1308 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 0.44 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.32 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % 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: -3.28 (0.30), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.004 HIS B 362 PHE 0.072 0.018 PHE E 346 TYR 0.097 0.028 TYR E 310 ARG 0.004 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 341 SER cc_start: 0.7637 (p) cc_final: 0.7416 (t) REVERT: A 347 LYS cc_start: 0.8093 (mttt) cc_final: 0.7784 (tptm) REVERT: B 341 SER cc_start: 0.7599 (p) cc_final: 0.7306 (t) REVERT: C 341 SER cc_start: 0.8039 (p) cc_final: 0.7824 (t) REVERT: C 345 ASP cc_start: 0.8747 (t0) cc_final: 0.8365 (t0) REVERT: C 347 LYS cc_start: 0.8144 (mttt) cc_final: 0.7858 (tttt) REVERT: C 353 LYS cc_start: 0.8249 (tttm) cc_final: 0.7741 (mtpt) REVERT: E 321 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7755 (tptp) REVERT: E 347 LYS cc_start: 0.7176 (mmtm) cc_final: 0.5849 (mtmm) REVERT: F 343 LYS cc_start: 0.8540 (mtmt) cc_final: 0.6804 (tptt) REVERT: F 349 ARG cc_start: 0.8927 (ttp80) cc_final: 0.7725 (tpm170) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2208 time to fit residues: 23.2690 Evaluate side-chains 57 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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: 5.9990 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN A 362 HIS C 327 ASN D 307 GLN D 336 GLN E 307 GLN E 336 GLN E 362 HIS F 307 GLN F 336 GLN F 362 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3432 Z= 0.334 Angle : 0.853 6.426 4596 Z= 0.442 Chirality : 0.056 0.176 522 Planarity : 0.004 0.035 582 Dihedral : 7.984 19.486 450 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.82 % Allowed : 8.72 % Favored : 88.46 % 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: -3.06 (0.31), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS C 362 PHE 0.010 0.002 PHE D 346 TYR 0.020 0.004 TYR A 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.402 Fit side-chains REVERT: A 347 LYS cc_start: 0.8156 (mttt) cc_final: 0.7936 (tptm) REVERT: A 353 LYS cc_start: 0.8326 (tttm) cc_final: 0.7853 (mtpt) REVERT: C 345 ASP cc_start: 0.8888 (t0) cc_final: 0.8477 (t0) REVERT: C 347 LYS cc_start: 0.8054 (mttt) cc_final: 0.7787 (tttt) REVERT: C 353 LYS cc_start: 0.8339 (tttm) cc_final: 0.7755 (mtpt) REVERT: C 372 GLU cc_start: 0.6581 (mp0) cc_final: 0.6364 (mt-10) REVERT: D 348 ASP cc_start: 0.7837 (t0) cc_final: 0.7636 (t0) outliers start: 11 outliers final: 9 residues processed: 68 average time/residue: 0.1681 time to fit residues: 13.8373 Evaluate side-chains 61 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 368 ASN Chi-restraints excluded: chain F residue 376 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 chunk 13 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3432 Z= 0.280 Angle : 0.759 6.346 4596 Z= 0.388 Chirality : 0.052 0.137 522 Planarity : 0.004 0.028 582 Dihedral : 6.963 18.980 450 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.33 % Allowed : 10.00 % Favored : 86.67 % 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: -3.01 (0.32), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 362 PHE 0.013 0.002 PHE A 346 TYR 0.007 0.002 TYR E 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.419 Fit side-chains REVERT: A 342 GLU cc_start: 0.6297 (tt0) cc_final: 0.6039 (tt0) REVERT: A 345 ASP cc_start: 0.8499 (t0) cc_final: 0.8272 (t0) REVERT: A 347 LYS cc_start: 0.8174 (mttt) cc_final: 0.7912 (tttt) REVERT: A 353 LYS cc_start: 0.8355 (tttm) cc_final: 0.7871 (mtpt) REVERT: B 307 GLN cc_start: 0.7481 (tm-30) cc_final: 0.6834 (mp-120) REVERT: B 347 LYS cc_start: 0.8123 (mttt) cc_final: 0.7499 (pttm) REVERT: C 347 LYS cc_start: 0.8099 (mttt) cc_final: 0.7832 (tttt) REVERT: C 353 LYS cc_start: 0.8257 (tttm) cc_final: 0.7734 (mtpt) REVERT: F 349 ARG cc_start: 0.9040 (ttp80) cc_final: 0.8085 (mmp80) outliers start: 13 outliers final: 12 residues processed: 66 average time/residue: 0.1793 time to fit residues: 14.1806 Evaluate side-chains 64 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 376 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 overall best weight: 6.1388 ------------------------------------------------------------------------------- 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: 0.7390 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 3432 Z= 0.408 Angle : 0.814 8.051 4596 Z= 0.419 Chirality : 0.052 0.138 522 Planarity : 0.004 0.030 582 Dihedral : 6.929 19.116 450 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 5.38 % Allowed : 10.77 % Favored : 83.85 % 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: -3.35 (0.31), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 374 PHE 0.009 0.002 PHE D 346 TYR 0.010 0.002 TYR E 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 65 time to evaluate : 0.426 Fit side-chains REVERT: A 345 ASP cc_start: 0.8617 (t0) cc_final: 0.8379 (t0) REVERT: A 347 LYS cc_start: 0.8206 (mttt) cc_final: 0.7943 (tttt) REVERT: A 353 LYS cc_start: 0.8330 (tttm) cc_final: 0.7807 (mtpt) REVERT: B 347 LYS cc_start: 0.8325 (mttt) cc_final: 0.7706 (pttm) REVERT: B 372 GLU cc_start: 0.6812 (mp0) cc_final: 0.6592 (mt-10) REVERT: C 347 LYS cc_start: 0.8109 (mttt) cc_final: 0.7855 (tttt) REVERT: C 353 LYS cc_start: 0.8342 (tttm) cc_final: 0.7745 (mtpt) REVERT: F 349 ARG cc_start: 0.9076 (ttp80) cc_final: 0.8049 (mmp80) outliers start: 21 outliers final: 16 residues processed: 77 average time/residue: 0.1826 time to fit residues: 16.8113 Evaluate side-chains 78 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 368 ASN Chi-restraints excluded: chain F residue 376 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 0.0970 chunk 10 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3432 Z= 0.281 Angle : 0.749 8.038 4596 Z= 0.375 Chirality : 0.051 0.137 522 Planarity : 0.003 0.032 582 Dihedral : 6.411 17.798 450 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.85 % Allowed : 13.59 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.21 (0.32), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 362 PHE 0.008 0.002 PHE D 346 TYR 0.006 0.002 TYR E 310 ARG 0.002 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 0.414 Fit side-chains REVERT: A 347 LYS cc_start: 0.8133 (mttt) cc_final: 0.7933 (tttt) REVERT: A 353 LYS cc_start: 0.8314 (tttm) cc_final: 0.7858 (mtpt) REVERT: A 363 VAL cc_start: 0.8964 (t) cc_final: 0.8763 (t) REVERT: B 307 GLN cc_start: 0.7596 (tm-30) cc_final: 0.6984 (mp-120) REVERT: B 345 ASP cc_start: 0.8779 (t0) cc_final: 0.8560 (t0) REVERT: B 347 LYS cc_start: 0.8388 (mttt) cc_final: 0.7706 (pttm) REVERT: C 347 LYS cc_start: 0.8231 (mttt) cc_final: 0.7933 (tttt) REVERT: C 353 LYS cc_start: 0.8210 (tttm) cc_final: 0.7706 (mtpt) REVERT: D 338 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7918 (tm-30) REVERT: F 349 ARG cc_start: 0.9025 (ttp80) cc_final: 0.7975 (mmp80) outliers start: 15 outliers final: 13 residues processed: 72 average time/residue: 0.1877 time to fit residues: 16.1034 Evaluate side-chains 75 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 368 ASN Chi-restraints excluded: chain F residue 376 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.2980 chunk 40 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3432 Z= 0.242 Angle : 0.710 7.138 4596 Z= 0.353 Chirality : 0.051 0.164 522 Planarity : 0.003 0.034 582 Dihedral : 6.115 16.509 450 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.85 % Allowed : 14.62 % Favored : 81.54 % 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: -3.18 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 362 PHE 0.007 0.001 PHE A 346 TYR 0.004 0.001 TYR E 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 58 time to evaluate : 0.425 Fit side-chains REVERT: A 347 LYS cc_start: 0.8248 (mttt) cc_final: 0.7972 (tttt) REVERT: A 353 LYS cc_start: 0.8333 (tttm) cc_final: 0.7838 (mtpt) REVERT: B 307 GLN cc_start: 0.7460 (tm-30) cc_final: 0.6946 (mp10) REVERT: B 347 LYS cc_start: 0.8399 (mttt) cc_final: 0.7724 (pttm) REVERT: C 347 LYS cc_start: 0.8299 (mttt) cc_final: 0.8001 (tttt) REVERT: C 353 LYS cc_start: 0.8185 (tttm) cc_final: 0.7702 (mtpt) REVERT: D 338 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7907 (tm-30) REVERT: E 376 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7694 (tt) REVERT: F 349 ARG cc_start: 0.9035 (ttp80) cc_final: 0.7951 (mmp80) outliers start: 15 outliers final: 12 residues processed: 67 average time/residue: 0.1933 time to fit residues: 15.3791 Evaluate side-chains 69 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 368 ASN Chi-restraints excluded: chain F residue 376 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 0.0770 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 27 optimal weight: 0.0470 chunk 20 optimal weight: 3.9990 overall best weight: 4.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3432 Z= 0.320 Angle : 0.758 7.048 4596 Z= 0.383 Chirality : 0.052 0.167 522 Planarity : 0.004 0.036 582 Dihedral : 6.235 16.699 450 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 4.36 % Allowed : 14.36 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.35 (0.33), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS A 362 PHE 0.008 0.002 PHE D 346 TYR 0.006 0.002 TYR E 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 0.411 Fit side-chains REVERT: A 342 GLU cc_start: 0.6677 (tt0) cc_final: 0.6361 (tt0) REVERT: A 347 LYS cc_start: 0.8337 (mttt) cc_final: 0.8032 (tttt) REVERT: A 353 LYS cc_start: 0.8325 (tttm) cc_final: 0.7724 (mtpt) REVERT: B 307 GLN cc_start: 0.7427 (tm-30) cc_final: 0.6970 (mp10) REVERT: B 347 LYS cc_start: 0.8526 (mttt) cc_final: 0.7823 (pttm) REVERT: B 353 LYS cc_start: 0.8113 (tttm) cc_final: 0.7482 (mtpt) REVERT: C 347 LYS cc_start: 0.8373 (mttt) cc_final: 0.8090 (tttt) REVERT: C 353 LYS cc_start: 0.8205 (tttm) cc_final: 0.7735 (mtpt) REVERT: D 338 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7946 (tm-30) REVERT: E 376 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7719 (tt) REVERT: F 349 ARG cc_start: 0.9105 (ttp80) cc_final: 0.7823 (mmp80) outliers start: 17 outliers final: 14 residues processed: 71 average time/residue: 0.1861 time to fit residues: 15.7680 Evaluate side-chains 74 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 59 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 368 ASN Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 376 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 0.0370 chunk 38 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3432 Z= 0.196 Angle : 0.695 7.384 4596 Z= 0.345 Chirality : 0.051 0.166 522 Planarity : 0.003 0.038 582 Dihedral : 5.875 15.417 450 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.85 % Allowed : 14.62 % Favored : 81.54 % 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: -3.20 (0.34), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.009 0.001 PHE A 378 TYR 0.004 0.001 TYR A 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 59 time to evaluate : 0.406 Fit side-chains REVERT: A 342 GLU cc_start: 0.6682 (tt0) cc_final: 0.6410 (tt0) REVERT: A 347 LYS cc_start: 0.8355 (mttt) cc_final: 0.8048 (tttt) REVERT: A 353 LYS cc_start: 0.8305 (tttm) cc_final: 0.7727 (mtpt) REVERT: B 347 LYS cc_start: 0.8467 (mttt) cc_final: 0.7790 (pttm) REVERT: B 353 LYS cc_start: 0.8032 (tttm) cc_final: 0.7500 (mtpt) REVERT: B 375 LYS cc_start: 0.5474 (pttm) cc_final: 0.4985 (tptm) REVERT: C 347 LYS cc_start: 0.8410 (mttt) cc_final: 0.8124 (tttt) REVERT: C 353 LYS cc_start: 0.8191 (tttm) cc_final: 0.7736 (mtpt) REVERT: D 338 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7944 (tm-30) REVERT: E 358 ASP cc_start: 0.6598 (OUTLIER) cc_final: 0.6225 (m-30) REVERT: E 376 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7667 (tt) REVERT: F 349 ARG cc_start: 0.9059 (ttp80) cc_final: 0.7748 (mmp80) outliers start: 15 outliers final: 11 residues processed: 68 average time/residue: 0.1995 time to fit residues: 15.9920 Evaluate side-chains 71 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 368 ASN Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 376 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 0.0970 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 0.2980 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3432 Z= 0.147 Angle : 0.653 7.273 4596 Z= 0.322 Chirality : 0.050 0.163 522 Planarity : 0.004 0.040 582 Dihedral : 5.475 14.411 450 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.08 % Allowed : 15.64 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.00 (0.35), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.009 0.001 PHE A 346 TYR 0.005 0.001 TYR B 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.347 Fit side-chains REVERT: A 347 LYS cc_start: 0.8320 (mttt) cc_final: 0.8017 (tttt) REVERT: A 353 LYS cc_start: 0.8295 (tttm) cc_final: 0.7736 (mtpt) REVERT: B 347 LYS cc_start: 0.8425 (mttt) cc_final: 0.7751 (pttm) REVERT: B 353 LYS cc_start: 0.8023 (tttm) cc_final: 0.7507 (mtpt) REVERT: B 375 LYS cc_start: 0.5325 (pttm) cc_final: 0.4903 (tptm) REVERT: C 321 LYS cc_start: 0.7662 (mttt) cc_final: 0.7287 (mttp) REVERT: C 347 LYS cc_start: 0.8489 (mttt) cc_final: 0.8254 (tttt) REVERT: C 353 LYS cc_start: 0.8115 (tttm) cc_final: 0.7703 (mtpt) REVERT: E 358 ASP cc_start: 0.6458 (OUTLIER) cc_final: 0.6087 (m-30) REVERT: F 349 ARG cc_start: 0.8998 (ttp80) cc_final: 0.7770 (mmp80) outliers start: 12 outliers final: 10 residues processed: 69 average time/residue: 0.2084 time to fit residues: 16.7956 Evaluate side-chains 68 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 368 ASN Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 376 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3432 Z= 0.268 Angle : 0.695 6.803 4596 Z= 0.347 Chirality : 0.050 0.164 522 Planarity : 0.004 0.040 582 Dihedral : 5.682 14.433 450 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.85 % Allowed : 15.38 % Favored : 80.77 % 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: -3.21 (0.34), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 362 PHE 0.007 0.002 PHE D 346 TYR 0.005 0.002 TYR D 310 ARG 0.002 0.000 ARG D 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.454 Fit side-chains REVERT: A 342 GLU cc_start: 0.6706 (tt0) cc_final: 0.6462 (tt0) REVERT: A 353 LYS cc_start: 0.8366 (tttm) cc_final: 0.7724 (mtpt) REVERT: B 347 LYS cc_start: 0.8506 (mttt) cc_final: 0.7913 (mtmm) REVERT: B 353 LYS cc_start: 0.8025 (tttm) cc_final: 0.7483 (mtpt) REVERT: B 375 LYS cc_start: 0.5423 (pttm) cc_final: 0.4934 (tptm) REVERT: C 321 LYS cc_start: 0.7855 (mttt) cc_final: 0.7508 (mttp) REVERT: C 347 LYS cc_start: 0.8489 (mttt) cc_final: 0.8284 (tttt) REVERT: C 353 LYS cc_start: 0.8063 (tttm) cc_final: 0.7633 (mtpt) REVERT: E 358 ASP cc_start: 0.6651 (OUTLIER) cc_final: 0.6275 (m-30) REVERT: E 376 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7651 (tt) REVERT: F 342 GLU cc_start: 0.8397 (tt0) cc_final: 0.8132 (tt0) REVERT: F 349 ARG cc_start: 0.9092 (ttp80) cc_final: 0.7814 (mmp80) outliers start: 15 outliers final: 10 residues processed: 72 average time/residue: 0.1878 time to fit residues: 16.1395 Evaluate side-chains 73 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 368 ASN Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 376 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 28 optimal weight: 0.2980 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.132117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.114635 restraints weight = 5060.413| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.25 r_work: 0.3877 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3775 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3432 Z= 0.240 Angle : 0.677 6.574 4596 Z= 0.337 Chirality : 0.050 0.135 522 Planarity : 0.004 0.040 582 Dihedral : 5.656 14.271 450 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 3.33 % Allowed : 15.64 % Favored : 81.03 % 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: -3.19 (0.34), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.007 0.001 PHE D 346 TYR 0.004 0.001 TYR B 310 ARG 0.001 0.000 ARG D 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1160.05 seconds wall clock time: 21 minutes 55.92 seconds (1315.92 seconds total)