Starting phenix.real_space_refine on Sat Aug 3 05:15:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcp_18331/08_2024/8qcp_18331.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcp_18331/08_2024/8qcp_18331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcp_18331/08_2024/8qcp_18331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcp_18331/08_2024/8qcp_18331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcp_18331/08_2024/8qcp_18331.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcp_18331/08_2024/8qcp_18331.cif" } resolution = 3.21 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 2154 2.51 5 N 630 2.21 5 O 645 1.98 5 H 3567 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 358": "OD1" <-> "OD2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 358": "OD1" <-> "OD2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 358": "OD1" <-> "OD2" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7002 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} 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: "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: "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} Time building chain proxies: 4.50, per 1000 atoms: 0.64 Number of scatterers: 7002 At special positions: 0 Unit cell: (138.13, 109.05, 47.255, 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 645 8.00 N 630 7.00 C 2154 6.00 H 3567 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 - 3.50 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: 5.29 Conformation dependent library (CDL) restraints added in 849.3 milliseconds 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 17 sheets defined 0.0% alpha, 38.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 306 through 310 Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.783A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 319 through 324 removed outlier: 6.316A pdb=" N SER B 320 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N GLY F 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N CYS B 322 " --> pdb=" O GLY F 323 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 337 through 341 Processing sheet with id=AA5, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.599A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 353 through 354 removed outlier: 6.393A pdb=" N LYS B 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.412A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 368 through 371 removed outlier: 6.409A pdb=" N ASN B 368 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE F 371 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS B 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 374 through 377 removed outlier: 6.629A pdb=" N HIS B 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N THR F 377 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU B 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 306 through 310 Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.791A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.625A pdb=" N VAL A 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N LYS E 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER A 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 327 through 330 removed outlier: 6.870A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 336 through 340 removed outlier: 6.548A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 343 through 346 removed outlier: 6.151A pdb=" N LYS A 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N PHE C 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 357 through 362 Processing sheet with id=AB8, first strand: chain 'C' and resid 369 through 378 removed outlier: 6.512A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N PHE C 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) 75 hydrogen bonds defined for protein. 225 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: 2.23 Time building geometry restraints manager: 5.59 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: 3561 1.11 - 1.29: 573 1.29 - 1.46: 950 1.46 - 1.64: 1966 1.64 - 1.81: 6 Bond restraints: 7056 Sorted by residual: bond pdb=" N GLY E 367 " pdb=" H GLY E 367 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N HIS E 362 " pdb=" H HIS E 362 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N HIS B 362 " pdb=" H HIS B 362 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" NE2 GLN C 336 " pdb="HE21 GLN C 336 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N GLY A 334 " pdb=" H GLY A 334 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 7051 not shown) Histogram of bond angle deviations from ideal: 96.04 - 102.65: 19 102.65 - 109.27: 4639 109.27 - 115.89: 4540 115.89 - 122.50: 2970 122.50 - 129.12: 690 Bond angle restraints: 12858 Sorted by residual: angle pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " pdb=" CD2 HIS C 374 " ideal model delta sigma weight residual 131.20 124.41 6.79 1.30e+00 5.92e-01 2.73e+01 angle pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " pdb=" CD2 HIS A 374 " ideal model delta sigma weight residual 131.20 124.70 6.50 1.30e+00 5.92e-01 2.50e+01 angle pdb=" N LYS F 317 " pdb=" CA LYS F 317 " pdb=" C LYS F 317 " ideal model delta sigma weight residual 110.44 116.25 -5.81 1.20e+00 6.94e-01 2.35e+01 angle pdb=" CA ASP E 358 " pdb=" CB ASP E 358 " pdb=" CG ASP E 358 " ideal model delta sigma weight residual 112.60 117.36 -4.76 1.00e+00 1.00e+00 2.26e+01 angle pdb=" C ASP B 348 " pdb=" N ARG B 349 " pdb=" CA ARG B 349 " ideal model delta sigma weight residual 120.90 127.48 -6.58 1.41e+00 5.03e-01 2.18e+01 ... (remaining 12853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.23: 2813 14.23 - 28.45: 228 28.45 - 42.68: 81 42.68 - 56.91: 66 56.91 - 71.13: 64 Dihedral angle restraints: 3252 sinusoidal: 1857 harmonic: 1395 Sorted by residual: dihedral pdb=" CA LYS E 343 " pdb=" C LYS E 343 " pdb=" N LEU E 344 " pdb=" CA LEU E 344 " ideal model delta harmonic sigma weight residual 180.00 150.51 29.49 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA LYS C 343 " pdb=" C LYS C 343 " pdb=" N LEU C 344 " pdb=" CA LEU C 344 " ideal model delta harmonic sigma weight residual 180.00 151.60 28.40 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA LYS A 343 " pdb=" C LYS A 343 " pdb=" N LEU A 344 " pdb=" CA LEU A 344 " ideal model delta harmonic sigma weight residual 180.00 151.67 28.33 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 3249 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.080: 344 0.080 - 0.159: 141 0.159 - 0.238: 33 0.238 - 0.317: 4 0.317 - 0.397: 3 Chirality restraints: 525 Sorted by residual: chirality pdb=" CA LYS F 317 " pdb=" N LYS F 317 " pdb=" C LYS F 317 " pdb=" CB LYS F 317 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" CA LEU B 325 " pdb=" N LEU B 325 " pdb=" C LEU B 325 " pdb=" CB LEU B 325 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA LEU C 325 " pdb=" N LEU C 325 " pdb=" C LEU C 325 " pdb=" CB LEU C 325 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 522 not shown) Planarity restraints: 1023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 374 " 0.069 2.00e-02 2.50e+03 3.94e-02 3.50e+01 pdb=" CG HIS C 374 " -0.032 2.00e-02 2.50e+03 pdb=" ND1 HIS C 374 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 HIS C 374 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 HIS C 374 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 HIS C 374 " -0.022 2.00e-02 2.50e+03 pdb=" HD2 HIS C 374 " -0.013 2.00e-02 2.50e+03 pdb=" HE1 HIS C 374 " 0.019 2.00e-02 2.50e+03 pdb=" HE2 HIS C 374 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 346 " -0.081 2.00e-02 2.50e+03 3.37e-02 3.41e+01 pdb=" CG PHE C 346 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 PHE C 346 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 346 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE C 346 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE C 346 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE C 346 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE C 346 " 0.030 2.00e-02 2.50e+03 pdb=" HD2 PHE C 346 " 0.042 2.00e-02 2.50e+03 pdb=" HE1 PHE C 346 " 0.008 2.00e-02 2.50e+03 pdb=" HE2 PHE C 346 " -0.021 2.00e-02 2.50e+03 pdb=" HZ PHE C 346 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.081 2.00e-02 2.50e+03 3.28e-02 3.22e+01 pdb=" CG TYR A 310 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.058 2.00e-02 2.50e+03 pdb=" HD1 TYR A 310 " 0.008 2.00e-02 2.50e+03 pdb=" HD2 TYR A 310 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 TYR A 310 " 0.009 2.00e-02 2.50e+03 pdb=" HE2 TYR A 310 " 0.004 2.00e-02 2.50e+03 ... (remaining 1020 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 585 2.19 - 2.79: 12518 2.79 - 3.39: 18047 3.39 - 4.00: 24454 4.00 - 4.60: 34817 Nonbonded interactions: 90421 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.587 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.603 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.610 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.620 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.638 2.450 ... (remaining 90416 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' and resid 304 through 378) selection = chain 'B' selection = (chain 'C' and resid 304 through 378) selection = chain 'D' selection = (chain 'E' and resid 304 through 378) 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: 2.570 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: 0.110 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 27.010 Find NCS groups from input model: 0.220 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 3489 Z= 0.750 Angle : 1.859 7.579 4668 Z= 1.233 Chirality : 0.092 0.397 525 Planarity : 0.009 0.038 594 Dihedral : 11.524 58.039 1332 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.25 % 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: -2.03 (0.35), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.004 HIS A 330 PHE 0.040 0.010 PHE C 346 TYR 0.071 0.020 TYR A 310 ARG 0.003 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.7915 (mttt) cc_final: 0.7644 (tttm) REVERT: B 340 LYS cc_start: 0.7699 (mttt) cc_final: 0.7187 (mtpt) REVERT: B 347 LYS cc_start: 0.8228 (tttt) cc_final: 0.8009 (mmmt) REVERT: D 318 VAL cc_start: 0.7290 (m) cc_final: 0.6957 (m) REVERT: D 331 LYS cc_start: 0.8007 (mttt) cc_final: 0.7713 (tttm) REVERT: D 338 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7469 (pm20) REVERT: D 340 LYS cc_start: 0.8560 (mttt) cc_final: 0.8023 (mtpt) REVERT: D 347 LYS cc_start: 0.8028 (tttt) cc_final: 0.7820 (mtmt) REVERT: D 369 LYS cc_start: 0.8730 (mttt) cc_final: 0.8426 (mtmm) REVERT: F 311 LYS cc_start: 0.8168 (mttm) cc_final: 0.7618 (mmtt) REVERT: F 338 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7309 (mt-10) REVERT: F 340 LYS cc_start: 0.7723 (mttt) cc_final: 0.7192 (mtpt) REVERT: F 343 LYS cc_start: 0.8349 (mtmt) cc_final: 0.8114 (mtmm) REVERT: F 353 LYS cc_start: 0.7707 (tttt) cc_final: 0.7424 (tppt) REVERT: A 321 LYS cc_start: 0.7804 (mttt) cc_final: 0.7516 (mttm) REVERT: A 351 GLN cc_start: 0.7859 (mt0) cc_final: 0.7596 (tt0) REVERT: C 307 GLN cc_start: 0.7493 (mt0) cc_final: 0.6801 (pm20) REVERT: C 321 LYS cc_start: 0.8383 (mttt) cc_final: 0.8122 (mttp) REVERT: C 342 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7003 (pm20) REVERT: C 351 GLN cc_start: 0.8012 (mt0) cc_final: 0.7780 (tt0) REVERT: E 311 LYS cc_start: 0.8089 (mttt) cc_final: 0.6783 (mmtt) REVERT: E 321 LYS cc_start: 0.7921 (mttt) cc_final: 0.7618 (mttp) REVERT: E 338 GLU cc_start: 0.7582 (tt0) cc_final: 0.7382 (tt0) REVERT: E 340 LYS cc_start: 0.7724 (mttt) cc_final: 0.7325 (tttt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.4904 time to fit residues: 78.9644 Evaluate side-chains 93 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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: 5.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 3489 Z= 0.391 Angle : 0.724 7.501 4668 Z= 0.379 Chirality : 0.051 0.156 525 Planarity : 0.004 0.025 594 Dihedral : 7.124 27.268 462 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.78 % Allowed : 7.63 % Favored : 90.59 % 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: -1.95 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS D 330 PHE 0.009 0.001 PHE E 346 TYR 0.014 0.002 TYR C 310 ARG 0.003 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 331 LYS cc_start: 0.7791 (mttt) cc_final: 0.7294 (tttm) REVERT: B 338 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7463 (mt-10) REVERT: B 340 LYS cc_start: 0.7776 (mttt) cc_final: 0.7273 (mtpt) REVERT: B 345 ASP cc_start: 0.7771 (t0) cc_final: 0.7471 (t0) REVERT: B 370 LYS cc_start: 0.8113 (tttm) cc_final: 0.7783 (tttp) REVERT: D 331 LYS cc_start: 0.7871 (mttt) cc_final: 0.7614 (tttm) REVERT: D 338 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7492 (pm20) REVERT: D 340 LYS cc_start: 0.8596 (mttt) cc_final: 0.8054 (mtpt) REVERT: D 347 LYS cc_start: 0.8210 (tttt) cc_final: 0.7560 (pttm) REVERT: D 372 GLU cc_start: 0.5058 (tp30) cc_final: 0.4844 (tp30) REVERT: F 311 LYS cc_start: 0.8113 (mttm) cc_final: 0.7662 (mmtt) REVERT: F 338 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7179 (mt-10) REVERT: F 340 LYS cc_start: 0.7870 (mttt) cc_final: 0.7357 (mtpt) REVERT: F 343 LYS cc_start: 0.8300 (mtmt) cc_final: 0.8100 (mtmm) REVERT: C 307 GLN cc_start: 0.7528 (mt0) cc_final: 0.6767 (pm20) REVERT: E 311 LYS cc_start: 0.8185 (mttt) cc_final: 0.6895 (mmtt) REVERT: E 321 LYS cc_start: 0.8013 (mttt) cc_final: 0.7738 (mttm) REVERT: E 338 GLU cc_start: 0.7793 (tt0) cc_final: 0.7544 (tt0) REVERT: E 340 LYS cc_start: 0.7789 (mttt) cc_final: 0.7437 (tttp) REVERT: E 351 GLN cc_start: 0.8669 (tm-30) cc_final: 0.8092 (tm-30) outliers start: 7 outliers final: 6 residues processed: 101 average time/residue: 0.4563 time to fit residues: 53.2894 Evaluate side-chains 91 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain E residue 305 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: 10.0000 chunk 10 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS F 330 HIS C 336 GLN ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3489 Z= 0.173 Angle : 0.559 5.283 4668 Z= 0.288 Chirality : 0.051 0.132 525 Planarity : 0.003 0.026 594 Dihedral : 6.203 24.190 462 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.02 % Allowed : 11.45 % Favored : 87.53 % 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: -2.07 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 330 PHE 0.005 0.001 PHE C 346 TYR 0.009 0.002 TYR C 310 ARG 0.002 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 358 ASP cc_start: 0.8064 (t70) cc_final: 0.7820 (m-30) REVERT: B 370 LYS cc_start: 0.8113 (tttm) cc_final: 0.7857 (tttp) REVERT: D 331 LYS cc_start: 0.7813 (mttt) cc_final: 0.7554 (tttm) REVERT: D 338 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7919 (mt-10) REVERT: D 340 LYS cc_start: 0.8585 (mttt) cc_final: 0.8047 (mtpt) REVERT: D 347 LYS cc_start: 0.8115 (tttt) cc_final: 0.7495 (pttm) REVERT: F 311 LYS cc_start: 0.8142 (mttm) cc_final: 0.7648 (mmtt) REVERT: F 338 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7168 (mt-10) REVERT: F 340 LYS cc_start: 0.7888 (mttt) cc_final: 0.7374 (mtpt) REVERT: F 343 LYS cc_start: 0.8328 (mtmt) cc_final: 0.8114 (mtmm) REVERT: F 353 LYS cc_start: 0.8020 (ttmt) cc_final: 0.7229 (tppt) REVERT: C 321 LYS cc_start: 0.8288 (mttt) cc_final: 0.8013 (mttp) REVERT: E 311 LYS cc_start: 0.8138 (mttt) cc_final: 0.6827 (mmtt) REVERT: E 321 LYS cc_start: 0.7949 (mttt) cc_final: 0.7668 (mttm) REVERT: E 338 GLU cc_start: 0.7760 (tt0) cc_final: 0.7535 (tt0) REVERT: E 340 LYS cc_start: 0.7864 (mttt) cc_final: 0.7601 (tttp) REVERT: E 351 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8053 (tm-30) outliers start: 4 outliers final: 2 residues processed: 93 average time/residue: 0.5001 time to fit residues: 53.6597 Evaluate side-chains 84 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 324 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: 7.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 HIS F 368 ASN C 351 GLN ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3489 Z= 0.182 Angle : 0.527 4.454 4668 Z= 0.270 Chirality : 0.051 0.129 525 Planarity : 0.003 0.028 594 Dihedral : 5.710 22.152 462 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.29 % Allowed : 10.18 % Favored : 87.53 % 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: -2.10 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 330 PHE 0.004 0.001 PHE B 346 TYR 0.009 0.002 TYR C 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 358 ASP cc_start: 0.8046 (t70) cc_final: 0.7842 (m-30) REVERT: B 369 LYS cc_start: 0.8245 (mttp) cc_final: 0.7903 (ttmm) REVERT: B 370 LYS cc_start: 0.8157 (tttm) cc_final: 0.7910 (tttp) REVERT: D 331 LYS cc_start: 0.7844 (mttt) cc_final: 0.7561 (tttm) REVERT: D 338 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7851 (mt-10) REVERT: D 340 LYS cc_start: 0.8592 (mttt) cc_final: 0.8052 (mtpt) REVERT: D 347 LYS cc_start: 0.8124 (tttt) cc_final: 0.7520 (pttm) REVERT: F 311 LYS cc_start: 0.8164 (mttm) cc_final: 0.7660 (mmtt) REVERT: F 320 SER cc_start: 0.9220 (OUTLIER) cc_final: 0.8983 (t) REVERT: F 338 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7192 (mt-10) REVERT: F 340 LYS cc_start: 0.7854 (mttt) cc_final: 0.7372 (mtpt) REVERT: F 343 LYS cc_start: 0.8337 (mtmt) cc_final: 0.8132 (mtmm) REVERT: F 353 LYS cc_start: 0.7966 (ttmt) cc_final: 0.7615 (tptt) REVERT: A 351 GLN cc_start: 0.7923 (mt0) cc_final: 0.7699 (tt0) REVERT: C 321 LYS cc_start: 0.8305 (mttt) cc_final: 0.8009 (mttp) REVERT: E 311 LYS cc_start: 0.8126 (mttt) cc_final: 0.6864 (mmtt) REVERT: E 321 LYS cc_start: 0.7955 (mttt) cc_final: 0.7673 (mttm) REVERT: E 338 GLU cc_start: 0.7762 (tt0) cc_final: 0.7529 (tt0) REVERT: E 340 LYS cc_start: 0.7929 (mttt) cc_final: 0.7647 (tttp) REVERT: E 351 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8377 (tm-30) outliers start: 9 outliers final: 6 residues processed: 91 average time/residue: 0.4693 time to fit residues: 49.6670 Evaluate side-chains 86 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain C residue 359 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.0020 chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 0.4980 chunk 36 optimal weight: 0.5980 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN C 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3489 Z= 0.125 Angle : 0.470 4.073 4668 Z= 0.240 Chirality : 0.051 0.127 525 Planarity : 0.003 0.029 594 Dihedral : 5.087 21.059 462 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.76 % Allowed : 11.70 % Favored : 87.53 % 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: -2.07 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 362 PHE 0.003 0.001 PHE C 346 TYR 0.005 0.001 TYR E 310 ARG 0.000 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 369 LYS cc_start: 0.8272 (mttp) cc_final: 0.7970 (ttmm) REVERT: B 370 LYS cc_start: 0.8215 (tttm) cc_final: 0.7967 (tttp) REVERT: D 331 LYS cc_start: 0.7816 (mttt) cc_final: 0.7567 (tttm) REVERT: D 338 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7860 (mt-10) REVERT: D 340 LYS cc_start: 0.8579 (mttt) cc_final: 0.8044 (mtpt) REVERT: D 341 SER cc_start: 0.9156 (m) cc_final: 0.8551 (p) REVERT: D 347 LYS cc_start: 0.8086 (tttt) cc_final: 0.7414 (pttm) REVERT: F 311 LYS cc_start: 0.8197 (mttm) cc_final: 0.7698 (mmtt) REVERT: F 340 LYS cc_start: 0.7780 (mttt) cc_final: 0.7481 (mttp) REVERT: F 343 LYS cc_start: 0.8268 (mtmt) cc_final: 0.7940 (mtmm) REVERT: F 353 LYS cc_start: 0.7939 (ttmt) cc_final: 0.7591 (tptt) REVERT: A 351 GLN cc_start: 0.7913 (mt0) cc_final: 0.7704 (tt0) REVERT: C 321 LYS cc_start: 0.8209 (mttt) cc_final: 0.7913 (mttp) REVERT: E 311 LYS cc_start: 0.8144 (mttt) cc_final: 0.6886 (mmtt) REVERT: E 321 LYS cc_start: 0.7959 (mttt) cc_final: 0.7669 (mttm) REVERT: E 338 GLU cc_start: 0.7819 (tt0) cc_final: 0.7593 (tt0) REVERT: E 340 LYS cc_start: 0.7930 (mttt) cc_final: 0.7689 (tttp) REVERT: E 351 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8336 (tm-30) outliers start: 3 outliers final: 2 residues processed: 95 average time/residue: 0.4604 time to fit residues: 50.8544 Evaluate side-chains 86 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain C residue 359 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN D 368 ASN C 351 GLN E 327 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3489 Z= 0.208 Angle : 0.500 4.051 4668 Z= 0.255 Chirality : 0.051 0.126 525 Planarity : 0.003 0.026 594 Dihedral : 5.132 20.203 462 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.53 % Allowed : 11.45 % Favored : 87.02 % 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: -2.08 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 362 PHE 0.004 0.001 PHE E 346 TYR 0.010 0.002 TYR C 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 369 LYS cc_start: 0.8269 (mttp) cc_final: 0.7953 (ttmm) REVERT: D 331 LYS cc_start: 0.7830 (mttt) cc_final: 0.7568 (tttm) REVERT: D 338 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7920 (mt-10) REVERT: D 340 LYS cc_start: 0.8565 (mttt) cc_final: 0.7993 (mtpt) REVERT: D 347 LYS cc_start: 0.8146 (tttt) cc_final: 0.7531 (pttm) REVERT: F 311 LYS cc_start: 0.8177 (mttm) cc_final: 0.7685 (mmtt) REVERT: F 320 SER cc_start: 0.9223 (OUTLIER) cc_final: 0.9015 (t) REVERT: F 340 LYS cc_start: 0.7832 (mttt) cc_final: 0.7524 (mttp) REVERT: F 343 LYS cc_start: 0.8370 (mtmt) cc_final: 0.8049 (mtmm) REVERT: F 353 LYS cc_start: 0.7935 (ttmt) cc_final: 0.7635 (tptt) REVERT: A 338 GLU cc_start: 0.7672 (tt0) cc_final: 0.7440 (tt0) REVERT: A 351 GLN cc_start: 0.7900 (mt0) cc_final: 0.7665 (tt0) REVERT: C 321 LYS cc_start: 0.8242 (mttt) cc_final: 0.7956 (mttp) REVERT: E 311 LYS cc_start: 0.8140 (mttt) cc_final: 0.6868 (mmtt) REVERT: E 321 LYS cc_start: 0.8019 (mttt) cc_final: 0.7693 (mttm) REVERT: E 338 GLU cc_start: 0.7833 (tt0) cc_final: 0.7604 (tt0) REVERT: E 340 LYS cc_start: 0.7943 (mttt) cc_final: 0.7687 (tttp) REVERT: E 351 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8327 (tm-30) outliers start: 6 outliers final: 4 residues processed: 89 average time/residue: 0.4517 time to fit residues: 46.6318 Evaluate side-chains 84 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain C residue 359 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 0.0060 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 0.0470 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.4100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3489 Z= 0.140 Angle : 0.472 3.975 4668 Z= 0.239 Chirality : 0.051 0.126 525 Planarity : 0.003 0.026 594 Dihedral : 4.901 19.839 462 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.04 % Allowed : 11.20 % Favored : 86.77 % 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: -2.06 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 362 PHE 0.003 0.001 PHE A 346 TYR 0.007 0.001 TYR C 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 369 LYS cc_start: 0.8265 (mttp) cc_final: 0.7918 (ttmm) REVERT: D 331 LYS cc_start: 0.7816 (mttt) cc_final: 0.7564 (tttm) REVERT: D 338 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7895 (mt-10) REVERT: D 340 LYS cc_start: 0.8560 (mttt) cc_final: 0.8033 (mtpt) REVERT: D 347 LYS cc_start: 0.8181 (tttt) cc_final: 0.7549 (pttm) REVERT: F 311 LYS cc_start: 0.8182 (mttm) cc_final: 0.7689 (mmtt) REVERT: F 340 LYS cc_start: 0.7811 (mttt) cc_final: 0.7512 (mttp) REVERT: F 353 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7625 (tptt) REVERT: A 338 GLU cc_start: 0.7650 (tt0) cc_final: 0.7428 (tt0) REVERT: A 351 GLN cc_start: 0.7893 (mt0) cc_final: 0.7626 (tt0) REVERT: C 321 LYS cc_start: 0.8200 (mttt) cc_final: 0.7921 (mttp) REVERT: E 311 LYS cc_start: 0.8118 (mttt) cc_final: 0.6864 (mmtt) REVERT: E 321 LYS cc_start: 0.7986 (mttt) cc_final: 0.7671 (mttm) REVERT: E 338 GLU cc_start: 0.7874 (tt0) cc_final: 0.7657 (tt0) REVERT: E 340 LYS cc_start: 0.7966 (mttt) cc_final: 0.7713 (tttp) REVERT: E 351 GLN cc_start: 0.8588 (tm-30) cc_final: 0.8317 (tm-30) REVERT: E 358 ASP cc_start: 0.7966 (m-30) cc_final: 0.7746 (m-30) REVERT: E 370 LYS cc_start: 0.8574 (ttpt) cc_final: 0.8211 (ttpp) outliers start: 8 outliers final: 7 residues processed: 87 average time/residue: 0.4752 time to fit residues: 47.5907 Evaluate side-chains 85 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 324 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain E residue 305 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 329 HIS C 351 GLN ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3489 Z= 0.275 Angle : 0.536 4.374 4668 Z= 0.274 Chirality : 0.051 0.125 525 Planarity : 0.003 0.024 594 Dihedral : 5.264 19.205 462 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.80 % Allowed : 9.67 % Favored : 87.53 % 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: -2.13 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 PHE 0.007 0.001 PHE E 346 TYR 0.013 0.002 TYR E 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: B 369 LYS cc_start: 0.8310 (mttp) cc_final: 0.7965 (ttmm) REVERT: B 372 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6960 (mt-10) REVERT: D 331 LYS cc_start: 0.7809 (mttt) cc_final: 0.7571 (tttm) REVERT: D 340 LYS cc_start: 0.8575 (mttt) cc_final: 0.8046 (mtpt) REVERT: D 347 LYS cc_start: 0.8308 (tttt) cc_final: 0.7613 (pttm) REVERT: F 311 LYS cc_start: 0.8118 (mttm) cc_final: 0.7661 (mmtt) REVERT: F 340 LYS cc_start: 0.7857 (mttt) cc_final: 0.7569 (mttm) REVERT: F 353 LYS cc_start: 0.7948 (ttmt) cc_final: 0.7603 (tptt) REVERT: A 317 LYS cc_start: 0.7180 (mttt) cc_final: 0.6765 (mtmt) REVERT: A 338 GLU cc_start: 0.7710 (tt0) cc_final: 0.7469 (tt0) REVERT: A 351 GLN cc_start: 0.7901 (mt0) cc_final: 0.7593 (tt0) REVERT: C 321 LYS cc_start: 0.8291 (mttt) cc_final: 0.7992 (mttp) REVERT: E 311 LYS cc_start: 0.8063 (mttt) cc_final: 0.6853 (mmtt) REVERT: E 321 LYS cc_start: 0.8074 (mttt) cc_final: 0.7741 (mttp) REVERT: E 338 GLU cc_start: 0.7896 (tt0) cc_final: 0.7668 (tt0) REVERT: E 340 LYS cc_start: 0.7952 (mttt) cc_final: 0.7653 (tttp) REVERT: E 351 GLN cc_start: 0.8583 (tm-30) cc_final: 0.7959 (tm-30) REVERT: E 358 ASP cc_start: 0.8014 (m-30) cc_final: 0.7781 (m-30) REVERT: E 370 LYS cc_start: 0.8596 (ttpt) cc_final: 0.8250 (ttpp) outliers start: 11 outliers final: 10 residues processed: 88 average time/residue: 0.4771 time to fit residues: 48.1672 Evaluate side-chains 86 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 372 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3489 Z= 0.178 Angle : 0.497 4.068 4668 Z= 0.252 Chirality : 0.050 0.126 525 Planarity : 0.002 0.027 594 Dihedral : 5.082 19.496 462 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.54 % Allowed : 10.18 % Favored : 87.28 % 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: -2.14 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 329 PHE 0.004 0.001 PHE E 346 TYR 0.008 0.002 TYR C 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.605 Fit side-chains REVERT: B 369 LYS cc_start: 0.8275 (mttp) cc_final: 0.7938 (ttmm) REVERT: B 372 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6939 (mt-10) REVERT: D 331 LYS cc_start: 0.7819 (mttt) cc_final: 0.7488 (mtpt) REVERT: D 338 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7909 (mt-10) REVERT: D 340 LYS cc_start: 0.8567 (mttt) cc_final: 0.8026 (mtpt) REVERT: D 347 LYS cc_start: 0.8289 (tttt) cc_final: 0.7610 (pttm) REVERT: F 311 LYS cc_start: 0.8126 (mttm) cc_final: 0.7668 (mmtt) REVERT: F 340 LYS cc_start: 0.7818 (mttt) cc_final: 0.7548 (mttm) REVERT: F 353 LYS cc_start: 0.7906 (ttmt) cc_final: 0.7609 (tptt) REVERT: F 358 ASP cc_start: 0.8192 (t70) cc_final: 0.7680 (m-30) REVERT: A 338 GLU cc_start: 0.7676 (tt0) cc_final: 0.7439 (tt0) REVERT: A 351 GLN cc_start: 0.7903 (mt0) cc_final: 0.7584 (tt0) REVERT: E 311 LYS cc_start: 0.8058 (mttt) cc_final: 0.6864 (mmtt) REVERT: E 321 LYS cc_start: 0.8051 (mttt) cc_final: 0.7730 (mttp) REVERT: E 338 GLU cc_start: 0.7893 (tt0) cc_final: 0.7681 (tt0) REVERT: E 340 LYS cc_start: 0.7977 (mttt) cc_final: 0.7686 (tttp) REVERT: E 351 GLN cc_start: 0.8578 (tm-30) cc_final: 0.7973 (tm-30) REVERT: E 358 ASP cc_start: 0.8069 (m-30) cc_final: 0.7790 (m-30) REVERT: E 370 LYS cc_start: 0.8586 (ttpt) cc_final: 0.8237 (ttpp) outliers start: 10 outliers final: 9 residues processed: 84 average time/residue: 0.4288 time to fit residues: 41.9240 Evaluate side-chains 84 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 372 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3489 Z= 0.199 Angle : 0.502 4.683 4668 Z= 0.254 Chirality : 0.051 0.125 525 Planarity : 0.002 0.026 594 Dihedral : 5.047 19.008 462 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.54 % Allowed : 10.94 % Favored : 86.51 % 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: -2.15 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 329 PHE 0.005 0.001 PHE E 346 TYR 0.009 0.002 TYR C 310 ARG 0.001 0.000 ARG F 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.623 Fit side-chains REVERT: B 347 LYS cc_start: 0.8310 (mmmt) cc_final: 0.7962 (mmtp) REVERT: B 369 LYS cc_start: 0.8258 (mttp) cc_final: 0.7936 (ttmm) REVERT: B 372 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6923 (mt-10) REVERT: D 331 LYS cc_start: 0.7827 (mttt) cc_final: 0.7490 (mtpt) REVERT: D 347 LYS cc_start: 0.8304 (tttt) cc_final: 0.7648 (pttm) REVERT: F 311 LYS cc_start: 0.8203 (mttm) cc_final: 0.7671 (mmtt) REVERT: F 340 LYS cc_start: 0.7813 (mttt) cc_final: 0.7549 (mttm) REVERT: F 347 LYS cc_start: 0.8662 (mtpt) cc_final: 0.8398 (mtpp) REVERT: F 353 LYS cc_start: 0.7894 (ttmt) cc_final: 0.7606 (tptt) REVERT: F 358 ASP cc_start: 0.8184 (t70) cc_final: 0.7685 (m-30) REVERT: A 338 GLU cc_start: 0.7703 (tt0) cc_final: 0.7463 (tt0) REVERT: A 351 GLN cc_start: 0.7877 (mt0) cc_final: 0.7553 (tt0) REVERT: E 311 LYS cc_start: 0.8099 (mttt) cc_final: 0.6897 (mmtt) REVERT: E 321 LYS cc_start: 0.8047 (mttt) cc_final: 0.7749 (mttm) REVERT: E 338 GLU cc_start: 0.7921 (tt0) cc_final: 0.7705 (tt0) REVERT: E 340 LYS cc_start: 0.7995 (mttt) cc_final: 0.7665 (tttm) REVERT: E 351 GLN cc_start: 0.8582 (tm-30) cc_final: 0.7975 (tm-30) REVERT: E 358 ASP cc_start: 0.8081 (m-30) cc_final: 0.7798 (m-30) REVERT: E 370 LYS cc_start: 0.8587 (ttpt) cc_final: 0.8241 (ttpp) outliers start: 10 outliers final: 10 residues processed: 83 average time/residue: 0.4302 time to fit residues: 41.5022 Evaluate side-chains 84 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 372 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 0.0270 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.3042 ------------------------------------------------------------------------------- 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 = 0.4030 r_free = 0.4030 target = 0.135629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.123766 restraints weight = 17277.923| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.14 r_work: 0.3826 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3755 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3489 Z= 0.139 Angle : 0.480 4.272 4668 Z= 0.241 Chirality : 0.051 0.136 525 Planarity : 0.002 0.027 594 Dihedral : 4.837 18.760 462 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.78 % Allowed : 12.47 % Favored : 85.75 % 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: -2.11 (0.34), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 329 PHE 0.002 0.000 PHE A 346 TYR 0.007 0.001 TYR C 310 ARG 0.001 0.000 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2854.68 seconds wall clock time: 50 minutes 23.06 seconds (3023.06 seconds total)