Starting phenix.real_space_refine on Wed Jun 26 16:42:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bbl_44421/06_2024/9bbl_44421_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bbl_44421/06_2024/9bbl_44421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bbl_44421/06_2024/9bbl_44421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bbl_44421/06_2024/9bbl_44421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bbl_44421/06_2024/9bbl_44421_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bbl_44421/06_2024/9bbl_44421_neut.pdb" } resolution = 2.5 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 9 5.16 5 C 3198 2.51 5 N 936 2.21 5 O 951 1.98 5 H 5301 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 10395 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1121 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "B" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1121 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "E" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "G" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1121 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "H" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "I" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 6.32, per 1000 atoms: 0.61 Number of scatterers: 10395 At special positions: 0 Unit cell: (151.58, 134.62, 41.34, 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 9 16.00 O 951 8.00 N 936 7.00 C 3198 6.00 H 5301 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: 7.92 Conformation dependent library (CDL) restraints added in 1.1 seconds 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1170 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 25 sheets defined 0.0% alpha, 42.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.823A pdb=" N VAL A 313 " --> pdb=" O ASP G 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 317 through 321 removed outlier: 6.359A pdb=" N LYS A 317 " --> pdb=" O VAL G 318 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N SER G 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR A 319 " --> pdb=" O SER G 320 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 330 removed outlier: 6.561A pdb=" N HIS A 329 " --> pdb=" O HIS G 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 339 removed outlier: 6.437A pdb=" N GLN A 336 " --> pdb=" O VAL G 337 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL G 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLU A 338 " --> pdb=" O VAL G 339 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 345 through 347 removed outlier: 6.431A pdb=" N PHE D 346 " --> pdb=" O LYS G 347 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 356 removed outlier: 6.836A pdb=" N SER G 356 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER D 352 " --> pdb=" O LYS G 353 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N GLY G 355 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ILE D 354 " --> pdb=" O GLY G 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 359 through 362 removed outlier: 6.252A pdb=" N ILE A 360 " --> pdb=" O THR G 361 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN D 359 " --> pdb=" O ILE G 360 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N HIS G 362 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR D 361 " --> pdb=" O HIS G 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 372 removed outlier: 6.737A pdb=" N LYS A 369 " --> pdb=" O LYS G 370 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N GLU G 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE A 371 " --> pdb=" O GLU G 372 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 306 through 308 Processing sheet with id=AB1, first strand: chain 'B' and resid 317 through 322 removed outlier: 6.377A pdb=" N LYS B 317 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N SER H 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR B 319 " --> pdb=" O SER H 320 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N CYS H 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS B 321 " --> pdb=" O CYS H 322 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 325 through 330 removed outlier: 8.725A pdb=" N LEU B 325 " --> pdb=" O GLY H 326 " (cutoff:3.500A) removed outlier: 9.780A pdb=" N ILE H 328 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASN B 327 " --> pdb=" O ILE H 328 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N HIS H 330 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N HIS B 329 " --> pdb=" O HIS H 330 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY E 326 " --> pdb=" O LEU H 325 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN H 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.338A pdb=" N VAL E 337 " --> pdb=" O GLU H 338 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LYS H 340 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL E 339 " --> pdb=" O LYS H 340 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 344 through 347 removed outlier: 6.695A pdb=" N LEU E 344 " --> pdb=" O ASP H 345 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LYS H 347 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE E 346 " --> pdb=" O LYS H 347 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 351 through 354 removed outlier: 6.448A pdb=" N GLN B 351 " --> pdb=" O SER H 352 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ILE H 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS B 353 " --> pdb=" O ILE H 354 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 357 through 362 removed outlier: 6.501A pdb=" N ASP B 358 " --> pdb=" O ASN H 359 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N THR H 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE B 360 " --> pdb=" O THR H 361 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 369 through 374 removed outlier: 6.634A pdb=" N LYS B 369 " --> pdb=" O LYS H 370 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N GLU H 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 371 " --> pdb=" O GLU H 372 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N HIS H 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N THR B 373 " --> pdb=" O HIS H 374 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 377 through 378 removed outlier: 6.394A pdb=" N THR B 377 " --> pdb=" O PHE H 378 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.567A pdb=" N GLN C 307 " --> pdb=" O ILE I 308 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR I 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL C 309 " --> pdb=" O TYR I 310 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL F 306 " --> pdb=" O GLN I 307 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N VAL I 309 " --> pdb=" O VAL F 306 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE F 308 " --> pdb=" O VAL I 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.399A pdb=" N LYS C 317 " --> pdb=" O VAL I 318 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N SER I 320 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR C 319 " --> pdb=" O SER I 320 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N CYS I 322 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LYS C 321 " --> pdb=" O CYS I 322 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 325 through 330 removed outlier: 8.706A pdb=" N LEU C 325 " --> pdb=" O GLY I 326 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N ILE I 328 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN C 327 " --> pdb=" O ILE I 328 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N HIS I 330 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N HIS C 329 " --> pdb=" O HIS I 330 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLY F 326 " --> pdb=" O LEU I 325 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN I 327 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 336 through 340 removed outlier: 6.430A pdb=" N VAL F 337 " --> pdb=" O GLU I 338 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N LYS I 340 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL F 339 " --> pdb=" O LYS I 340 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 344 through 347 removed outlier: 6.483A pdb=" N LEU F 344 " --> pdb=" O ASP I 345 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LYS I 347 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE F 346 " --> pdb=" O LYS I 347 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 350 through 356 removed outlier: 6.829A pdb=" N SER I 356 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL F 350 " --> pdb=" O GLN I 351 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LYS I 353 " --> pdb=" O VAL F 350 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER F 352 " --> pdb=" O LYS I 353 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N GLY I 355 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N ILE F 354 " --> pdb=" O GLY I 355 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.553A pdb=" N ASN F 359 " --> pdb=" O ILE I 360 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N HIS I 362 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR F 361 " --> pdb=" O HIS I 362 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 369 through 377 91 hydrogen bonds defined for protein. 273 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: 2.78 Time building geometry restraints manager: 8.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.09: 5292 1.09 - 1.27: 846 1.27 - 1.45: 1242 1.45 - 1.63: 3087 1.63 - 1.81: 9 Bond restraints: 10476 Sorted by residual: bond pdb=" N THR G 361 " pdb=" H THR G 361 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" ND1 HIS D 330 " pdb=" HD1 HIS D 330 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CE2 PHE D 378 " pdb=" HE2 PHE D 378 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" CD1 PHE D 378 " pdb=" HD1 PHE D 378 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N SER D 324 " pdb=" H SER D 324 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 10471 not shown) Histogram of bond angle deviations from ideal: 96.68 - 103.28: 48 103.28 - 109.88: 9141 109.88 - 116.47: 4651 116.47 - 123.07: 4460 123.07 - 129.67: 795 Bond angle restraints: 19095 Sorted by residual: angle pdb=" CA ASP D 358 " pdb=" CB ASP D 358 " pdb=" CG ASP D 358 " ideal model delta sigma weight residual 112.60 118.26 -5.66 1.00e+00 1.00e+00 3.20e+01 angle pdb=" C GLU C 342 " pdb=" CA GLU C 342 " pdb=" CB GLU C 342 " ideal model delta sigma weight residual 110.42 121.14 -10.72 1.99e+00 2.53e-01 2.90e+01 angle pdb=" CA PHE D 346 " pdb=" CB PHE D 346 " pdb=" CG PHE D 346 " ideal model delta sigma weight residual 113.80 119.17 -5.37 1.00e+00 1.00e+00 2.89e+01 angle pdb=" CA ASP G 358 " pdb=" CB ASP G 358 " pdb=" CG ASP G 358 " ideal model delta sigma weight residual 112.60 117.77 -5.17 1.00e+00 1.00e+00 2.67e+01 angle pdb=" CB HIS G 329 " pdb=" CG HIS G 329 " pdb=" CD2 HIS G 329 " ideal model delta sigma weight residual 131.20 124.51 6.69 1.30e+00 5.92e-01 2.65e+01 ... (remaining 19090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 4344 17.30 - 34.61: 233 34.61 - 51.91: 101 51.91 - 69.22: 143 69.22 - 86.52: 6 Dihedral angle restraints: 4827 sinusoidal: 2757 harmonic: 2070 Sorted by residual: dihedral pdb=" C GLU C 342 " pdb=" N GLU C 342 " pdb=" CA GLU C 342 " pdb=" CB GLU C 342 " ideal model delta harmonic sigma weight residual -122.60 -134.00 11.40 0 2.50e+00 1.60e-01 2.08e+01 dihedral pdb=" C GLU I 342 " pdb=" N GLU I 342 " pdb=" CA GLU I 342 " pdb=" CB GLU I 342 " ideal model delta harmonic sigma weight residual -122.60 -132.42 9.82 0 2.50e+00 1.60e-01 1.54e+01 dihedral pdb=" C ARG B 349 " pdb=" N ARG B 349 " pdb=" CA ARG B 349 " pdb=" CB ARG B 349 " ideal model delta harmonic sigma weight residual -122.60 -131.72 9.12 0 2.50e+00 1.60e-01 1.33e+01 ... (remaining 4824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 463 0.081 - 0.161: 238 0.161 - 0.242: 63 0.242 - 0.323: 11 0.323 - 0.403: 5 Chirality restraints: 780 Sorted by residual: chirality pdb=" CA PRO I 332 " pdb=" N PRO I 332 " pdb=" C PRO I 332 " pdb=" CB PRO I 332 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CA LEU A 325 " pdb=" N LEU A 325 " pdb=" C LEU A 325 " pdb=" CB LEU A 325 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CG LEU C 357 " pdb=" CB LEU C 357 " pdb=" CD1 LEU C 357 " pdb=" CD2 LEU C 357 " both_signs ideal model delta sigma weight residual False -2.59 -2.93 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 777 not shown) Planarity restraints: 1509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 329 " 0.040 2.00e-02 2.50e+03 6.00e-02 8.11e+01 pdb=" CG HIS B 329 " -0.118 2.00e-02 2.50e+03 pdb=" ND1 HIS B 329 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 HIS B 329 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 HIS B 329 " -0.013 2.00e-02 2.50e+03 pdb=" NE2 HIS B 329 " -0.022 2.00e-02 2.50e+03 pdb=" HD1 HIS B 329 " 0.058 2.00e-02 2.50e+03 pdb=" HD2 HIS B 329 " 0.091 2.00e-02 2.50e+03 pdb=" HE1 HIS B 329 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 329 " 0.045 2.00e-02 2.50e+03 5.67e-02 7.23e+01 pdb=" CG HIS H 329 " -0.131 2.00e-02 2.50e+03 pdb=" ND1 HIS H 329 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS H 329 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 HIS H 329 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS H 329 " -0.015 2.00e-02 2.50e+03 pdb=" HD1 HIS H 329 " 0.032 2.00e-02 2.50e+03 pdb=" HD2 HIS H 329 " 0.077 2.00e-02 2.50e+03 pdb=" HE1 HIS H 329 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 329 " -0.058 2.00e-02 2.50e+03 5.00e-02 5.62e+01 pdb=" CG HIS C 329 " 0.101 2.00e-02 2.50e+03 pdb=" ND1 HIS C 329 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 HIS C 329 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 HIS C 329 " 0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS C 329 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 HIS C 329 " -0.032 2.00e-02 2.50e+03 pdb=" HD2 HIS C 329 " -0.054 2.00e-02 2.50e+03 pdb=" HE1 HIS C 329 " -0.045 2.00e-02 2.50e+03 ... (remaining 1506 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 542 2.15 - 2.76: 17211 2.76 - 3.37: 28116 3.37 - 3.99: 36273 3.99 - 4.60: 52416 Nonbonded interactions: 134558 Sorted by model distance: nonbonded pdb=" OD1 ASP G 314 " pdb=" HG SER G 316 " model vdw 1.532 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.539 1.850 nonbonded pdb=" OD1 ASP I 314 " pdb=" HG SER I 316 " model vdw 1.543 1.850 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.548 1.850 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.552 1.850 ... (remaining 134553 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' and resid 307 through 378) selection = (chain 'C' and resid 307 through 378) selection = chain 'D' selection = (chain 'E' and resid 307 through 378) selection = (chain 'F' and resid 307 through 378) selection = chain 'G' selection = (chain 'H' and resid 307 through 378) selection = (chain 'I' and resid 307 through 378) } 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: 6.200 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: 0.170 Extract box with map and model: 11.870 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 34.510 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.030 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:10.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 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 0.045 5175 Z= 0.738 Angle : 2.112 10.719 6924 Z= 1.371 Chirality : 0.102 0.403 780 Planarity : 0.013 0.110 879 Dihedral : 10.019 86.521 1986 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 1.39 % Allowed : 9.72 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.34 % 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: -2.48 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.043 0.008 HIS H 329 PHE 0.027 0.010 PHE I 346 TYR 0.059 0.014 TYR B 310 ARG 0.009 0.002 ARG H 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 0.946 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.8083 (mtmt) cc_final: 0.6036 (tptp) REVERT: A 342 GLU cc_start: 0.7620 (mt-10) cc_final: 0.6624 (mp0) REVERT: A 343 LYS cc_start: 0.8253 (mttt) cc_final: 0.8044 (mtmt) REVERT: A 356 SER cc_start: 0.7966 (p) cc_final: 0.7681 (t) REVERT: A 358 ASP cc_start: 0.7916 (m-30) cc_final: 0.7523 (m-30) REVERT: B 307 GLN cc_start: 0.7736 (pt0) cc_final: 0.7487 (pt0) REVERT: B 311 LYS cc_start: 0.7880 (mttt) cc_final: 0.6900 (mmtm) REVERT: B 317 LYS cc_start: 0.7429 (mtmt) cc_final: 0.6527 (tttp) REVERT: B 321 LYS cc_start: 0.7563 (tttt) cc_final: 0.7139 (tmmm) REVERT: B 336 GLN cc_start: 0.7656 (mt0) cc_final: 0.7398 (mt0) REVERT: B 338 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6766 (mt-10) REVERT: B 340 LYS cc_start: 0.7572 (tttt) cc_final: 0.7152 (mtpp) REVERT: B 345 ASP cc_start: 0.7816 (t0) cc_final: 0.7469 (t0) REVERT: B 347 LYS cc_start: 0.7145 (mttp) cc_final: 0.6716 (mttp) REVERT: B 348 ASP cc_start: 0.7527 (t0) cc_final: 0.7217 (t0) REVERT: C 311 LYS cc_start: 0.7807 (mttt) cc_final: 0.6969 (mmtm) REVERT: C 321 LYS cc_start: 0.7327 (ttmt) cc_final: 0.6426 (tmtm) REVERT: C 331 LYS cc_start: 0.7388 (mttt) cc_final: 0.6965 (mtpt) REVERT: C 338 GLU cc_start: 0.7151 (tt0) cc_final: 0.6913 (tt0) REVERT: C 345 ASP cc_start: 0.8198 (t0) cc_final: 0.7530 (t0) REVERT: C 347 LYS cc_start: 0.7187 (mttt) cc_final: 0.6769 (mtpp) REVERT: C 348 ASP cc_start: 0.7867 (t0) cc_final: 0.7647 (t0) REVERT: C 372 GLU cc_start: 0.8161 (tt0) cc_final: 0.7899 (tt0) REVERT: D 311 LYS cc_start: 0.8118 (tttt) cc_final: 0.7580 (ttmp) REVERT: D 317 LYS cc_start: 0.8165 (mttt) cc_final: 0.7523 (mtpt) REVERT: D 321 LYS cc_start: 0.8220 (mttt) cc_final: 0.7463 (tptp) REVERT: D 331 LYS cc_start: 0.8116 (mtmt) cc_final: 0.7851 (mtpt) REVERT: D 340 LYS cc_start: 0.8093 (mttt) cc_final: 0.7431 (mttm) REVERT: D 341 SER cc_start: 0.8729 (m) cc_final: 0.8525 (m) REVERT: D 342 GLU cc_start: 0.7791 (mt-10) cc_final: 0.6985 (mp0) REVERT: D 343 LYS cc_start: 0.8306 (mttt) cc_final: 0.7838 (mttm) REVERT: D 347 LYS cc_start: 0.7821 (mttt) cc_final: 0.7319 (mtmm) REVERT: D 356 SER cc_start: 0.8138 (p) cc_final: 0.7878 (t) REVERT: D 358 ASP cc_start: 0.7682 (m-30) cc_final: 0.7250 (m-30) REVERT: D 369 LYS cc_start: 0.8145 (mttt) cc_final: 0.7845 (mttp) REVERT: D 372 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7603 (mt-10) REVERT: D 375 LYS cc_start: 0.8076 (ttpt) cc_final: 0.7831 (ttmt) REVERT: E 317 LYS cc_start: 0.7738 (mtmt) cc_final: 0.7509 (mtpm) REVERT: E 320 SER cc_start: 0.7993 (t) cc_final: 0.7773 (p) REVERT: E 321 LYS cc_start: 0.7950 (tttt) cc_final: 0.7587 (tmmt) REVERT: E 331 LYS cc_start: 0.8589 (mttt) cc_final: 0.8358 (mttp) REVERT: E 336 GLN cc_start: 0.8036 (mt0) cc_final: 0.7421 (mt0) REVERT: E 338 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7235 (tt0) REVERT: E 340 LYS cc_start: 0.7734 (tttt) cc_final: 0.7431 (tptp) REVERT: E 341 SER cc_start: 0.8173 (m) cc_final: 0.7835 (t) REVERT: E 342 GLU cc_start: 0.7662 (mt-10) cc_final: 0.6370 (mp0) REVERT: E 347 LYS cc_start: 0.7662 (mttp) cc_final: 0.7173 (mmtm) REVERT: E 369 LYS cc_start: 0.8492 (mttt) cc_final: 0.8172 (mttp) REVERT: F 311 LYS cc_start: 0.8344 (mttt) cc_final: 0.7480 (ttpp) REVERT: F 317 LYS cc_start: 0.7870 (pttt) cc_final: 0.7669 (ptmt) REVERT: F 342 GLU cc_start: 0.7678 (mt-10) cc_final: 0.6057 (mp0) REVERT: F 345 ASP cc_start: 0.8372 (t0) cc_final: 0.7979 (t0) REVERT: F 347 LYS cc_start: 0.7694 (mttt) cc_final: 0.6913 (mtmm) REVERT: F 349 ARG cc_start: 0.7266 (mtt180) cc_final: 0.6836 (mtp180) REVERT: F 353 LYS cc_start: 0.8380 (tttt) cc_final: 0.8022 (tttp) REVERT: F 369 LYS cc_start: 0.7983 (mttt) cc_final: 0.7404 (mtpp) REVERT: F 375 LYS cc_start: 0.8054 (tttt) cc_final: 0.7849 (ttmt) REVERT: G 311 LYS cc_start: 0.7831 (tttt) cc_final: 0.7403 (tppp) REVERT: G 317 LYS cc_start: 0.7457 (mttt) cc_final: 0.7166 (mtpm) REVERT: G 321 LYS cc_start: 0.7936 (mttt) cc_final: 0.7362 (mptt) REVERT: G 340 LYS cc_start: 0.7876 (mttt) cc_final: 0.6960 (mtpp) REVERT: G 342 GLU cc_start: 0.7607 (mt-10) cc_final: 0.6768 (mp0) REVERT: G 343 LYS cc_start: 0.8061 (mttt) cc_final: 0.7729 (mttp) REVERT: G 345 ASP cc_start: 0.7417 (m-30) cc_final: 0.7113 (m-30) REVERT: G 353 LYS cc_start: 0.7471 (mttt) cc_final: 0.7243 (mtmt) REVERT: G 356 SER cc_start: 0.8045 (p) cc_final: 0.7759 (p) REVERT: G 358 ASP cc_start: 0.7738 (m-30) cc_final: 0.7379 (m-30) REVERT: G 369 LYS cc_start: 0.7434 (mttt) cc_final: 0.7052 (mttp) REVERT: G 371 ILE cc_start: 0.8054 (mt) cc_final: 0.7747 (mp) REVERT: H 317 LYS cc_start: 0.7620 (mtmt) cc_final: 0.7378 (ttmm) REVERT: H 321 LYS cc_start: 0.7702 (tttt) cc_final: 0.7142 (mttp) REVERT: H 331 LYS cc_start: 0.8066 (mttt) cc_final: 0.7774 (mttp) REVERT: H 336 GLN cc_start: 0.7517 (mt0) cc_final: 0.6995 (mt0) REVERT: H 347 LYS cc_start: 0.7097 (mttp) cc_final: 0.6517 (mmtm) REVERT: H 356 SER cc_start: 0.8112 (m) cc_final: 0.7533 (p) REVERT: H 375 LYS cc_start: 0.7688 (tttt) cc_final: 0.7232 (tttm) REVERT: I 317 LYS cc_start: 0.7575 (pttt) cc_final: 0.7242 (pttt) REVERT: I 321 LYS cc_start: 0.7401 (ttmt) cc_final: 0.6922 (ttmm) REVERT: I 331 LYS cc_start: 0.7229 (mttt) cc_final: 0.6750 (mtpt) REVERT: I 338 GLU cc_start: 0.7508 (tt0) cc_final: 0.6791 (tt0) REVERT: I 347 LYS cc_start: 0.7326 (mttt) cc_final: 0.6226 (mmtm) REVERT: I 349 ARG cc_start: 0.7024 (mtt180) cc_final: 0.6545 (mtm180) REVERT: I 369 LYS cc_start: 0.7510 (mttt) cc_final: 0.6963 (mtpm) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 2.7115 time to fit residues: 728.9068 Evaluate side-chains 206 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN I 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5175 Z= 0.208 Angle : 0.701 5.682 6924 Z= 0.359 Chirality : 0.051 0.152 780 Planarity : 0.004 0.039 879 Dihedral : 6.495 19.433 681 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.34 % Allowed : 11.79 % Favored : 87.86 % 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: -2.65 (0.25), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.19), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS B 362 PHE 0.017 0.002 PHE E 378 TYR 0.008 0.002 TYR F 310 ARG 0.004 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 207 time to evaluate : 0.923 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: symmetry clash REVERT: A 342 GLU cc_start: 0.7662 (mt-10) cc_final: 0.6553 (mp0) REVERT: A 345 ASP cc_start: 0.7194 (t0) cc_final: 0.6565 (m-30) REVERT: A 356 SER cc_start: 0.7969 (p) cc_final: 0.7653 (t) REVERT: B 311 LYS cc_start: 0.7893 (mttt) cc_final: 0.6912 (mmtm) REVERT: B 321 LYS cc_start: 0.7797 (tttt) cc_final: 0.7242 (tmmm) REVERT: B 336 GLN cc_start: 0.7652 (mt0) cc_final: 0.7404 (mt0) REVERT: B 338 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6521 (tt0) REVERT: B 340 LYS cc_start: 0.7503 (tttt) cc_final: 0.7206 (mtpp) REVERT: B 345 ASP cc_start: 0.7756 (t0) cc_final: 0.7551 (t0) REVERT: B 348 ASP cc_start: 0.7963 (t0) cc_final: 0.7465 (t0) REVERT: B 358 ASP cc_start: 0.7289 (m-30) cc_final: 0.7087 (m-30) REVERT: B 375 LYS cc_start: 0.7536 (tttt) cc_final: 0.7315 (ttpp) REVERT: C 311 LYS cc_start: 0.7924 (mttt) cc_final: 0.7079 (mmtm) REVERT: C 321 LYS cc_start: 0.7525 (ttmt) cc_final: 0.6614 (tmtm) REVERT: C 331 LYS cc_start: 0.7227 (mttt) cc_final: 0.6831 (mtpt) REVERT: C 338 GLU cc_start: 0.7115 (tt0) cc_final: 0.6829 (tt0) REVERT: C 345 ASP cc_start: 0.7711 (t0) cc_final: 0.6863 (t0) REVERT: C 347 LYS cc_start: 0.7031 (mttt) cc_final: 0.6617 (mtpp) REVERT: C 348 ASP cc_start: 0.7765 (t0) cc_final: 0.7534 (t0) REVERT: C 369 LYS cc_start: 0.7688 (mttt) cc_final: 0.7317 (ttmm) REVERT: D 311 LYS cc_start: 0.8235 (tttt) cc_final: 0.7694 (ttmp) REVERT: D 317 LYS cc_start: 0.8043 (mttt) cc_final: 0.7369 (mtpt) REVERT: D 321 LYS cc_start: 0.8127 (mttt) cc_final: 0.7391 (tptp) REVERT: D 340 LYS cc_start: 0.8327 (mttt) cc_final: 0.7960 (mttm) REVERT: D 341 SER cc_start: 0.8691 (m) cc_final: 0.8471 (m) REVERT: D 342 GLU cc_start: 0.7714 (mt-10) cc_final: 0.6856 (mp0) REVERT: D 343 LYS cc_start: 0.8192 (mttt) cc_final: 0.7818 (mttm) REVERT: D 369 LYS cc_start: 0.8177 (mttt) cc_final: 0.7869 (mttp) REVERT: E 317 LYS cc_start: 0.7645 (mtmt) cc_final: 0.7381 (mtpm) REVERT: E 320 SER cc_start: 0.7848 (t) cc_final: 0.7461 (p) REVERT: E 321 LYS cc_start: 0.7978 (tttt) cc_final: 0.7657 (tmmt) REVERT: E 336 GLN cc_start: 0.8002 (mt0) cc_final: 0.7393 (mt0) REVERT: E 340 LYS cc_start: 0.7854 (tttt) cc_final: 0.7515 (tptp) REVERT: E 341 SER cc_start: 0.7650 (m) cc_final: 0.7448 (t) REVERT: E 347 LYS cc_start: 0.7670 (mttp) cc_final: 0.7125 (mmtm) REVERT: E 356 SER cc_start: 0.8238 (m) cc_final: 0.7917 (p) REVERT: E 369 LYS cc_start: 0.8531 (mttt) cc_final: 0.8220 (mttp) REVERT: F 311 LYS cc_start: 0.8379 (mttt) cc_final: 0.6620 (pmtt) REVERT: F 338 GLU cc_start: 0.7597 (tt0) cc_final: 0.7333 (tt0) REVERT: F 345 ASP cc_start: 0.8033 (t0) cc_final: 0.7704 (t0) REVERT: F 349 ARG cc_start: 0.7173 (mtt180) cc_final: 0.6842 (mtp180) REVERT: F 353 LYS cc_start: 0.8304 (tttt) cc_final: 0.7921 (tttt) REVERT: F 369 LYS cc_start: 0.7981 (mttt) cc_final: 0.7422 (mtpp) REVERT: F 373 THR cc_start: 0.8356 (m) cc_final: 0.8009 (p) REVERT: G 311 LYS cc_start: 0.7730 (tttt) cc_final: 0.7431 (tttm) REVERT: G 317 LYS cc_start: 0.7398 (mttt) cc_final: 0.7109 (mtpm) REVERT: G 321 LYS cc_start: 0.7807 (mttt) cc_final: 0.7477 (mttm) REVERT: G 340 LYS cc_start: 0.7898 (mttt) cc_final: 0.7155 (mttm) REVERT: G 342 GLU cc_start: 0.7654 (mt-10) cc_final: 0.6682 (mp0) REVERT: G 343 LYS cc_start: 0.7814 (mttt) cc_final: 0.7601 (mttp) REVERT: G 345 ASP cc_start: 0.7447 (m-30) cc_final: 0.7234 (m-30) REVERT: G 353 LYS cc_start: 0.7449 (mttt) cc_final: 0.7239 (mtmt) REVERT: G 356 SER cc_start: 0.8131 (p) cc_final: 0.7868 (t) REVERT: G 369 LYS cc_start: 0.7382 (mttt) cc_final: 0.6964 (mttp) REVERT: G 371 ILE cc_start: 0.7897 (mt) cc_final: 0.7589 (mp) REVERT: H 317 LYS cc_start: 0.7594 (mtmt) cc_final: 0.7320 (mtpm) REVERT: H 321 LYS cc_start: 0.7748 (tttt) cc_final: 0.7058 (mptp) REVERT: H 331 LYS cc_start: 0.8012 (mttt) cc_final: 0.7721 (mttp) REVERT: H 336 GLN cc_start: 0.7529 (mt0) cc_final: 0.7012 (mt0) REVERT: H 347 LYS cc_start: 0.7073 (mttp) cc_final: 0.6428 (mmtm) REVERT: H 356 SER cc_start: 0.7936 (m) cc_final: 0.7500 (t) REVERT: H 358 ASP cc_start: 0.6859 (m-30) cc_final: 0.6534 (m-30) REVERT: H 375 LYS cc_start: 0.7858 (tttt) cc_final: 0.7416 (tttm) REVERT: I 311 LYS cc_start: 0.7531 (mtpt) cc_final: 0.6684 (tttp) REVERT: I 317 LYS cc_start: 0.7625 (pttt) cc_final: 0.7313 (ptpp) REVERT: I 321 LYS cc_start: 0.7327 (ttmt) cc_final: 0.6827 (ttmm) REVERT: I 331 LYS cc_start: 0.6998 (mttt) cc_final: 0.6451 (mtpt) REVERT: I 341 SER cc_start: 0.7598 (p) cc_final: 0.7249 (t) REVERT: I 347 LYS cc_start: 0.7324 (mttt) cc_final: 0.6203 (mmtm) REVERT: I 349 ARG cc_start: 0.6832 (mtt180) cc_final: 0.6400 (mtm180) REVERT: I 369 LYS cc_start: 0.7456 (mttt) cc_final: 0.7161 (ttmm) outliers start: 2 outliers final: 1 residues processed: 208 average time/residue: 2.8552 time to fit residues: 613.4004 Evaluate side-chains 190 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 315 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN C 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5175 Z= 0.209 Angle : 0.570 4.281 6924 Z= 0.293 Chirality : 0.050 0.134 780 Planarity : 0.003 0.031 879 Dihedral : 6.111 17.666 681 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.68 % Allowed : 13.50 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.63 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS H 329 PHE 0.016 0.001 PHE E 378 TYR 0.008 0.001 TYR F 310 ARG 0.003 0.001 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 191 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8455 (mp) cc_final: 0.8250 (mp) REVERT: A 342 GLU cc_start: 0.7675 (mt-10) cc_final: 0.6519 (mp0) REVERT: A 345 ASP cc_start: 0.6910 (t0) cc_final: 0.6547 (m-30) REVERT: B 311 LYS cc_start: 0.8057 (mttt) cc_final: 0.7045 (mmtm) REVERT: B 321 LYS cc_start: 0.7788 (tttt) cc_final: 0.7199 (tmmm) REVERT: B 336 GLN cc_start: 0.7639 (mt0) cc_final: 0.7401 (mt0) REVERT: B 338 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6529 (tt0) REVERT: B 340 LYS cc_start: 0.7487 (tttt) cc_final: 0.7177 (mtpp) REVERT: B 345 ASP cc_start: 0.7776 (t0) cc_final: 0.7386 (t0) REVERT: B 347 LYS cc_start: 0.6921 (mttp) cc_final: 0.6487 (mttm) REVERT: B 348 ASP cc_start: 0.7588 (t0) cc_final: 0.7371 (t70) REVERT: B 356 SER cc_start: 0.8472 (m) cc_final: 0.8028 (t) REVERT: B 358 ASP cc_start: 0.7273 (m-30) cc_final: 0.6830 (m-30) REVERT: B 375 LYS cc_start: 0.7657 (tttt) cc_final: 0.7366 (ttpp) REVERT: B 379 ARG cc_start: 0.6312 (ttp-110) cc_final: 0.5939 (mtt90) REVERT: C 311 LYS cc_start: 0.7934 (mttt) cc_final: 0.7083 (mmtm) REVERT: C 321 LYS cc_start: 0.7329 (ttmt) cc_final: 0.6428 (tmtm) REVERT: C 331 LYS cc_start: 0.7154 (mttt) cc_final: 0.6732 (mtpt) REVERT: C 338 GLU cc_start: 0.7124 (tt0) cc_final: 0.6829 (tt0) REVERT: C 345 ASP cc_start: 0.7608 (t0) cc_final: 0.6719 (t0) REVERT: C 347 LYS cc_start: 0.6958 (mttt) cc_final: 0.6596 (mtpp) REVERT: C 369 LYS cc_start: 0.7656 (mttt) cc_final: 0.7268 (ttmm) REVERT: D 311 LYS cc_start: 0.8283 (tttt) cc_final: 0.7795 (ttmp) REVERT: D 314 ASP cc_start: 0.8425 (t0) cc_final: 0.8155 (t70) REVERT: D 317 LYS cc_start: 0.8025 (mttt) cc_final: 0.7407 (mtpt) REVERT: D 321 LYS cc_start: 0.8169 (mttt) cc_final: 0.7525 (mmmt) REVERT: D 340 LYS cc_start: 0.8282 (mttt) cc_final: 0.7900 (mttm) REVERT: D 341 SER cc_start: 0.8687 (m) cc_final: 0.8438 (m) REVERT: D 342 GLU cc_start: 0.7748 (mt-10) cc_final: 0.6872 (mp0) REVERT: D 343 LYS cc_start: 0.8195 (mttt) cc_final: 0.7847 (mttm) REVERT: D 347 LYS cc_start: 0.8005 (mtpt) cc_final: 0.7725 (mtpt) REVERT: D 369 LYS cc_start: 0.8098 (mttt) cc_final: 0.7757 (mttp) REVERT: E 317 LYS cc_start: 0.7727 (mtmt) cc_final: 0.7505 (mtpm) REVERT: E 320 SER cc_start: 0.7857 (t) cc_final: 0.7461 (p) REVERT: E 321 LYS cc_start: 0.8066 (tttt) cc_final: 0.7645 (tmmt) REVERT: E 336 GLN cc_start: 0.8031 (mt0) cc_final: 0.7439 (mt0) REVERT: E 338 GLU cc_start: 0.7546 (tt0) cc_final: 0.7208 (tt0) REVERT: E 340 LYS cc_start: 0.7929 (tttt) cc_final: 0.7552 (tptp) REVERT: E 342 GLU cc_start: 0.7630 (mt-10) cc_final: 0.6089 (mp0) REVERT: E 347 LYS cc_start: 0.7584 (mttp) cc_final: 0.7039 (mmtm) REVERT: E 356 SER cc_start: 0.8275 (m) cc_final: 0.7897 (t) REVERT: E 369 LYS cc_start: 0.8566 (mttt) cc_final: 0.8191 (mttp) REVERT: E 379 ARG cc_start: 0.5523 (pmt170) cc_final: 0.5043 (pmt-80) REVERT: F 311 LYS cc_start: 0.8382 (mttt) cc_final: 0.6719 (pmtt) REVERT: F 338 GLU cc_start: 0.7900 (tt0) cc_final: 0.7525 (tt0) REVERT: F 345 ASP cc_start: 0.7946 (t0) cc_final: 0.7678 (t70) REVERT: F 347 LYS cc_start: 0.7700 (mttt) cc_final: 0.6974 (mtmm) REVERT: F 349 ARG cc_start: 0.7220 (mtt180) cc_final: 0.6768 (mtm180) REVERT: F 353 LYS cc_start: 0.8267 (tttt) cc_final: 0.7904 (tttt) REVERT: F 373 THR cc_start: 0.8392 (m) cc_final: 0.8031 (p) REVERT: G 311 LYS cc_start: 0.7699 (tttt) cc_final: 0.7435 (tttm) REVERT: G 317 LYS cc_start: 0.7454 (mttt) cc_final: 0.7148 (mtpm) REVERT: G 321 LYS cc_start: 0.7772 (mttt) cc_final: 0.7571 (mttm) REVERT: G 340 LYS cc_start: 0.7911 (mttt) cc_final: 0.7363 (mttm) REVERT: G 342 GLU cc_start: 0.7629 (mt-10) cc_final: 0.6661 (mp0) REVERT: G 343 LYS cc_start: 0.7738 (mttt) cc_final: 0.7436 (mttp) REVERT: G 345 ASP cc_start: 0.7423 (m-30) cc_final: 0.7138 (m-30) REVERT: G 349 ARG cc_start: 0.7226 (mtm180) cc_final: 0.6466 (mtm180) REVERT: G 353 LYS cc_start: 0.7503 (mttt) cc_final: 0.7249 (mtmt) REVERT: G 356 SER cc_start: 0.8072 (p) cc_final: 0.7698 (t) REVERT: G 369 LYS cc_start: 0.7369 (mttt) cc_final: 0.6943 (mttp) REVERT: G 371 ILE cc_start: 0.7896 (mt) cc_final: 0.7585 (mp) REVERT: H 317 LYS cc_start: 0.7534 (mtmt) cc_final: 0.7322 (mtpm) REVERT: H 321 LYS cc_start: 0.7826 (tttt) cc_final: 0.7049 (mptp) REVERT: H 331 LYS cc_start: 0.7946 (mttt) cc_final: 0.7679 (mttp) REVERT: H 336 GLN cc_start: 0.7540 (mt0) cc_final: 0.6966 (mt0) REVERT: H 341 SER cc_start: 0.7816 (m) cc_final: 0.7348 (t) REVERT: H 347 LYS cc_start: 0.7041 (mttp) cc_final: 0.6341 (mmtm) REVERT: H 356 SER cc_start: 0.8181 (m) cc_final: 0.7697 (t) REVERT: H 358 ASP cc_start: 0.6890 (m-30) cc_final: 0.6584 (m-30) REVERT: H 375 LYS cc_start: 0.7873 (tttt) cc_final: 0.7455 (tttm) REVERT: I 311 LYS cc_start: 0.7351 (mtpt) cc_final: 0.6549 (tttp) REVERT: I 317 LYS cc_start: 0.7652 (pttt) cc_final: 0.7338 (ptmt) REVERT: I 321 LYS cc_start: 0.7353 (ttmt) cc_final: 0.6843 (ttmm) REVERT: I 331 LYS cc_start: 0.6890 (mttt) cc_final: 0.6268 (mtpt) REVERT: I 341 SER cc_start: 0.7566 (p) cc_final: 0.7269 (t) REVERT: I 345 ASP cc_start: 0.7600 (t0) cc_final: 0.7351 (t0) REVERT: I 347 LYS cc_start: 0.7112 (mttt) cc_final: 0.5972 (mmtm) REVERT: I 349 ARG cc_start: 0.6822 (mtt180) cc_final: 0.6427 (mtm180) REVERT: I 353 LYS cc_start: 0.7864 (tttt) cc_final: 0.7616 (tttm) REVERT: I 369 LYS cc_start: 0.7434 (mttt) cc_final: 0.7182 (ttmm) outliers start: 4 outliers final: 0 residues processed: 194 average time/residue: 2.9641 time to fit residues: 593.8410 Evaluate side-chains 184 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 16 optimal weight: 0.0970 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN C 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5175 Z= 0.205 Angle : 0.549 4.697 6924 Z= 0.281 Chirality : 0.049 0.130 780 Planarity : 0.003 0.032 879 Dihedral : 5.952 17.226 681 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.85 % Allowed : 13.33 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.65 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 362 PHE 0.004 0.001 PHE D 378 TYR 0.008 0.002 TYR F 310 ARG 0.002 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 190 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.7651 (mt-10) cc_final: 0.6372 (mp0) REVERT: A 345 ASP cc_start: 0.6845 (t0) cc_final: 0.6537 (m-30) REVERT: B 311 LYS cc_start: 0.8054 (mttt) cc_final: 0.6986 (mmtm) REVERT: B 321 LYS cc_start: 0.7818 (tttt) cc_final: 0.7244 (tmmm) REVERT: B 336 GLN cc_start: 0.7667 (mt0) cc_final: 0.7466 (mt0) REVERT: B 338 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6554 (tt0) REVERT: B 340 LYS cc_start: 0.7491 (tttt) cc_final: 0.7191 (mtpp) REVERT: B 345 ASP cc_start: 0.7642 (t0) cc_final: 0.7359 (t0) REVERT: B 347 LYS cc_start: 0.6933 (mttp) cc_final: 0.6468 (mttp) REVERT: B 356 SER cc_start: 0.8444 (m) cc_final: 0.7995 (t) REVERT: B 358 ASP cc_start: 0.7242 (m-30) cc_final: 0.6803 (m-30) REVERT: B 379 ARG cc_start: 0.6328 (ttp-110) cc_final: 0.5870 (mtt90) REVERT: C 311 LYS cc_start: 0.7953 (mttt) cc_final: 0.7100 (mmtm) REVERT: C 321 LYS cc_start: 0.7323 (ttmt) cc_final: 0.6425 (tmtm) REVERT: C 331 LYS cc_start: 0.7320 (mttt) cc_final: 0.6834 (mtpt) REVERT: C 338 GLU cc_start: 0.7121 (tt0) cc_final: 0.6748 (tm-30) REVERT: C 345 ASP cc_start: 0.7563 (t0) cc_final: 0.6821 (t70) REVERT: C 347 LYS cc_start: 0.6904 (mttt) cc_final: 0.6581 (mtpp) REVERT: C 369 LYS cc_start: 0.7685 (mttt) cc_final: 0.7266 (ttmm) REVERT: D 311 LYS cc_start: 0.8263 (tttt) cc_final: 0.7824 (ttmt) REVERT: D 317 LYS cc_start: 0.7944 (mttt) cc_final: 0.7314 (mtpt) REVERT: D 321 LYS cc_start: 0.8190 (mttt) cc_final: 0.7503 (mmmt) REVERT: D 340 LYS cc_start: 0.8284 (mttt) cc_final: 0.7905 (mttm) REVERT: D 341 SER cc_start: 0.8666 (m) cc_final: 0.8423 (m) REVERT: D 342 GLU cc_start: 0.7754 (mt-10) cc_final: 0.6900 (mp0) REVERT: D 343 LYS cc_start: 0.8231 (mttt) cc_final: 0.7918 (mttm) REVERT: D 347 LYS cc_start: 0.8005 (mtpt) cc_final: 0.7777 (mtpt) REVERT: D 369 LYS cc_start: 0.8065 (mttt) cc_final: 0.7703 (mttp) REVERT: E 317 LYS cc_start: 0.7752 (mtmt) cc_final: 0.7497 (mtpm) REVERT: E 320 SER cc_start: 0.7897 (t) cc_final: 0.7509 (p) REVERT: E 321 LYS cc_start: 0.8043 (tttt) cc_final: 0.7603 (tmmt) REVERT: E 336 GLN cc_start: 0.8108 (mt0) cc_final: 0.7657 (mt0) REVERT: E 338 GLU cc_start: 0.7617 (tt0) cc_final: 0.7280 (tt0) REVERT: E 340 LYS cc_start: 0.7991 (tttt) cc_final: 0.7601 (tptp) REVERT: E 342 GLU cc_start: 0.7470 (mt-10) cc_final: 0.6102 (mp0) REVERT: E 347 LYS cc_start: 0.7601 (mttp) cc_final: 0.7051 (mmtm) REVERT: E 356 SER cc_start: 0.8553 (m) cc_final: 0.8093 (t) REVERT: E 369 LYS cc_start: 0.8568 (mttt) cc_final: 0.8198 (mttp) REVERT: F 311 LYS cc_start: 0.8305 (mttt) cc_final: 0.6729 (pmtt) REVERT: F 338 GLU cc_start: 0.7926 (tt0) cc_final: 0.7575 (tt0) REVERT: F 349 ARG cc_start: 0.7266 (mtt180) cc_final: 0.6721 (mtm180) REVERT: F 353 LYS cc_start: 0.8234 (tttt) cc_final: 0.7875 (tttt) REVERT: F 370 LYS cc_start: 0.7543 (tttp) cc_final: 0.7309 (ttpt) REVERT: G 311 LYS cc_start: 0.7734 (tttt) cc_final: 0.7501 (tttm) REVERT: G 317 LYS cc_start: 0.7372 (mttt) cc_final: 0.7055 (mtpm) REVERT: G 321 LYS cc_start: 0.7746 (mttt) cc_final: 0.6951 (mtpp) REVERT: G 340 LYS cc_start: 0.7881 (mttt) cc_final: 0.7359 (mttm) REVERT: G 342 GLU cc_start: 0.7586 (mt-10) cc_final: 0.6612 (mp0) REVERT: G 343 LYS cc_start: 0.7736 (mttt) cc_final: 0.7463 (mttp) REVERT: G 345 ASP cc_start: 0.7465 (m-30) cc_final: 0.7193 (m-30) REVERT: G 349 ARG cc_start: 0.7236 (mtm180) cc_final: 0.6421 (mtm180) REVERT: G 353 LYS cc_start: 0.7496 (mttt) cc_final: 0.7224 (mtmt) REVERT: G 356 SER cc_start: 0.8104 (p) cc_final: 0.7706 (t) REVERT: G 369 LYS cc_start: 0.7387 (mttt) cc_final: 0.6964 (mttp) REVERT: G 371 ILE cc_start: 0.7846 (mt) cc_final: 0.7534 (mp) REVERT: H 317 LYS cc_start: 0.7558 (mtmt) cc_final: 0.7324 (mtpm) REVERT: H 321 LYS cc_start: 0.7777 (tttt) cc_final: 0.6932 (mptp) REVERT: H 331 LYS cc_start: 0.7970 (mttt) cc_final: 0.7702 (mttp) REVERT: H 336 GLN cc_start: 0.7519 (mt0) cc_final: 0.6982 (mt0) REVERT: H 341 SER cc_start: 0.7797 (OUTLIER) cc_final: 0.7354 (t) REVERT: H 345 ASP cc_start: 0.7675 (t0) cc_final: 0.7102 (t70) REVERT: H 347 LYS cc_start: 0.6990 (mttp) cc_final: 0.6305 (mmtm) REVERT: H 356 SER cc_start: 0.8233 (m) cc_final: 0.7791 (t) REVERT: H 358 ASP cc_start: 0.6927 (m-30) cc_final: 0.6680 (m-30) REVERT: H 375 LYS cc_start: 0.7897 (tttt) cc_final: 0.7411 (tttm) REVERT: I 311 LYS cc_start: 0.7302 (mtpt) cc_final: 0.6507 (tttp) REVERT: I 317 LYS cc_start: 0.7639 (pttt) cc_final: 0.7269 (ptmt) REVERT: I 321 LYS cc_start: 0.7349 (ttmt) cc_final: 0.6838 (ttmm) REVERT: I 331 LYS cc_start: 0.6697 (mttt) cc_final: 0.6082 (mtpt) REVERT: I 338 GLU cc_start: 0.7505 (tt0) cc_final: 0.7287 (tt0) REVERT: I 341 SER cc_start: 0.7554 (p) cc_final: 0.7274 (t) REVERT: I 347 LYS cc_start: 0.6927 (mttt) cc_final: 0.5812 (mptp) REVERT: I 349 ARG cc_start: 0.6810 (mtt180) cc_final: 0.6422 (mtm180) REVERT: I 353 LYS cc_start: 0.7858 (tttt) cc_final: 0.7621 (tttm) REVERT: I 369 LYS cc_start: 0.7466 (mttt) cc_final: 0.7186 (ttmm) outliers start: 5 outliers final: 1 residues processed: 191 average time/residue: 2.9826 time to fit residues: 588.0588 Evaluate side-chains 188 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 186 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain H residue 341 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN C 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5175 Z= 0.206 Angle : 0.537 4.977 6924 Z= 0.274 Chirality : 0.049 0.130 780 Planarity : 0.003 0.033 879 Dihedral : 5.864 17.233 681 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.34 % Allowed : 15.04 % Favored : 84.62 % 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: -2.65 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 362 PHE 0.011 0.001 PHE E 378 TYR 0.008 0.002 TYR F 310 ARG 0.002 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7813 (mttt) cc_final: 0.7167 (mttp) REVERT: A 342 GLU cc_start: 0.7554 (mt-10) cc_final: 0.6249 (mp0) REVERT: A 345 ASP cc_start: 0.6909 (t0) cc_final: 0.6567 (m-30) REVERT: B 311 LYS cc_start: 0.8087 (mttt) cc_final: 0.7022 (mmtm) REVERT: B 321 LYS cc_start: 0.7835 (tttt) cc_final: 0.7217 (tmmt) REVERT: B 336 GLN cc_start: 0.7674 (mt0) cc_final: 0.7439 (mt0) REVERT: B 338 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6561 (tt0) REVERT: B 340 LYS cc_start: 0.7529 (tttt) cc_final: 0.7220 (mtpp) REVERT: B 345 ASP cc_start: 0.7637 (t0) cc_final: 0.7358 (t0) REVERT: B 347 LYS cc_start: 0.6934 (mttp) cc_final: 0.6469 (mttp) REVERT: B 356 SER cc_start: 0.8448 (m) cc_final: 0.7994 (t) REVERT: B 358 ASP cc_start: 0.7123 (m-30) cc_final: 0.6675 (m-30) REVERT: B 375 LYS cc_start: 0.7683 (tttt) cc_final: 0.7296 (ttpp) REVERT: B 379 ARG cc_start: 0.6318 (ttp-110) cc_final: 0.5856 (mtt90) REVERT: C 311 LYS cc_start: 0.7959 (mttt) cc_final: 0.7113 (mmtm) REVERT: C 321 LYS cc_start: 0.7308 (ttmt) cc_final: 0.6405 (tmtm) REVERT: C 331 LYS cc_start: 0.7324 (mttt) cc_final: 0.6850 (mtpt) REVERT: C 338 GLU cc_start: 0.7113 (tt0) cc_final: 0.6736 (tm-30) REVERT: C 345 ASP cc_start: 0.7522 (t0) cc_final: 0.6810 (t70) REVERT: C 347 LYS cc_start: 0.6843 (mttt) cc_final: 0.6495 (mtpp) REVERT: C 369 LYS cc_start: 0.7706 (mttt) cc_final: 0.7261 (ttmm) REVERT: D 311 LYS cc_start: 0.8257 (tttt) cc_final: 0.7818 (ttmt) REVERT: D 317 LYS cc_start: 0.7871 (mttt) cc_final: 0.7322 (mtpt) REVERT: D 321 LYS cc_start: 0.8225 (mttt) cc_final: 0.7502 (mmmt) REVERT: D 340 LYS cc_start: 0.8305 (mttt) cc_final: 0.7922 (mttm) REVERT: D 341 SER cc_start: 0.8654 (m) cc_final: 0.8398 (m) REVERT: D 342 GLU cc_start: 0.7752 (mt-10) cc_final: 0.6897 (mp0) REVERT: D 343 LYS cc_start: 0.8266 (mttt) cc_final: 0.7842 (mttm) REVERT: D 347 LYS cc_start: 0.7924 (mtpt) cc_final: 0.7721 (mtpt) REVERT: D 369 LYS cc_start: 0.8076 (mttt) cc_final: 0.7629 (mmtp) REVERT: E 317 LYS cc_start: 0.7762 (mtmt) cc_final: 0.7509 (mtpm) REVERT: E 320 SER cc_start: 0.7817 (t) cc_final: 0.7404 (p) REVERT: E 321 LYS cc_start: 0.8037 (tttt) cc_final: 0.7598 (tmmt) REVERT: E 336 GLN cc_start: 0.8073 (mt0) cc_final: 0.7604 (mt0) REVERT: E 338 GLU cc_start: 0.7636 (tt0) cc_final: 0.7266 (tt0) REVERT: E 340 LYS cc_start: 0.7944 (tttt) cc_final: 0.7466 (tptp) REVERT: E 342 GLU cc_start: 0.7493 (mt-10) cc_final: 0.6022 (mp0) REVERT: E 347 LYS cc_start: 0.7558 (mttp) cc_final: 0.6970 (mmtm) REVERT: E 369 LYS cc_start: 0.8564 (mttt) cc_final: 0.8221 (mttp) REVERT: F 311 LYS cc_start: 0.8307 (mttt) cc_final: 0.6753 (pmtt) REVERT: F 338 GLU cc_start: 0.7929 (tt0) cc_final: 0.7548 (tt0) REVERT: F 349 ARG cc_start: 0.7303 (mtt180) cc_final: 0.6760 (mtm180) REVERT: F 353 LYS cc_start: 0.8228 (tttt) cc_final: 0.7868 (tttt) REVERT: F 370 LYS cc_start: 0.7529 (tttp) cc_final: 0.7309 (ttpt) REVERT: G 311 LYS cc_start: 0.7749 (tttt) cc_final: 0.7525 (tttm) REVERT: G 317 LYS cc_start: 0.7386 (mttt) cc_final: 0.7067 (mtpm) REVERT: G 321 LYS cc_start: 0.7718 (mttt) cc_final: 0.6920 (mtpp) REVERT: G 340 LYS cc_start: 0.7934 (mttt) cc_final: 0.7400 (mttm) REVERT: G 342 GLU cc_start: 0.7502 (mt-10) cc_final: 0.6401 (mp0) REVERT: G 343 LYS cc_start: 0.7724 (mttt) cc_final: 0.7481 (mttp) REVERT: G 345 ASP cc_start: 0.7451 (m-30) cc_final: 0.7220 (m-30) REVERT: G 348 ASP cc_start: 0.7220 (t0) cc_final: 0.7003 (t0) REVERT: G 349 ARG cc_start: 0.7315 (mtm180) cc_final: 0.6665 (mtm180) REVERT: G 353 LYS cc_start: 0.7478 (mttt) cc_final: 0.7218 (mtmt) REVERT: G 356 SER cc_start: 0.8069 (p) cc_final: 0.7728 (t) REVERT: G 369 LYS cc_start: 0.7392 (mttt) cc_final: 0.6989 (mttp) REVERT: G 371 ILE cc_start: 0.7846 (mt) cc_final: 0.7525 (mp) REVERT: H 317 LYS cc_start: 0.7573 (mtmt) cc_final: 0.7356 (mtpm) REVERT: H 321 LYS cc_start: 0.7848 (tttt) cc_final: 0.6948 (mptp) REVERT: H 331 LYS cc_start: 0.7977 (mttt) cc_final: 0.7702 (mttp) REVERT: H 336 GLN cc_start: 0.7545 (mt0) cc_final: 0.7001 (mt0) REVERT: H 341 SER cc_start: 0.7804 (m) cc_final: 0.7348 (t) REVERT: H 345 ASP cc_start: 0.7679 (t0) cc_final: 0.7087 (t70) REVERT: H 347 LYS cc_start: 0.6952 (mttp) cc_final: 0.6275 (mmtm) REVERT: H 356 SER cc_start: 0.8385 (m) cc_final: 0.7890 (t) REVERT: H 358 ASP cc_start: 0.6934 (m-30) cc_final: 0.6694 (m-30) REVERT: H 375 LYS cc_start: 0.7906 (tttt) cc_final: 0.7474 (tttm) REVERT: I 311 LYS cc_start: 0.7388 (mtpt) cc_final: 0.6545 (tttp) REVERT: I 317 LYS cc_start: 0.7639 (pttt) cc_final: 0.7285 (ptmt) REVERT: I 321 LYS cc_start: 0.7397 (ttmt) cc_final: 0.6891 (ttmm) REVERT: I 331 LYS cc_start: 0.6749 (mttt) cc_final: 0.6114 (mtpt) REVERT: I 341 SER cc_start: 0.7568 (p) cc_final: 0.7269 (t) REVERT: I 347 LYS cc_start: 0.6950 (mttt) cc_final: 0.5836 (mptp) REVERT: I 349 ARG cc_start: 0.6841 (mtt180) cc_final: 0.6381 (mtm180) REVERT: I 353 LYS cc_start: 0.7849 (tttt) cc_final: 0.7613 (tttm) REVERT: I 369 LYS cc_start: 0.7469 (mttt) cc_final: 0.7177 (ttmm) outliers start: 2 outliers final: 1 residues processed: 192 average time/residue: 3.0336 time to fit residues: 600.5538 Evaluate side-chains 189 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 345 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 0.0060 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5175 Z= 0.226 Angle : 0.542 5.335 6924 Z= 0.277 Chirality : 0.049 0.132 780 Planarity : 0.004 0.033 879 Dihedral : 5.857 17.290 681 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.68 % Allowed : 15.90 % Favored : 83.42 % 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: -2.72 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 362 PHE 0.013 0.001 PHE E 378 TYR 0.009 0.002 TYR F 310 ARG 0.005 0.001 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 189 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7785 (mttt) cc_final: 0.7157 (mttp) REVERT: A 342 GLU cc_start: 0.7542 (mt-10) cc_final: 0.6235 (mp0) REVERT: A 345 ASP cc_start: 0.6906 (t0) cc_final: 0.6577 (m-30) REVERT: B 311 LYS cc_start: 0.8185 (mttt) cc_final: 0.7037 (mmtm) REVERT: B 321 LYS cc_start: 0.7780 (tttt) cc_final: 0.7209 (tmmm) REVERT: B 336 GLN cc_start: 0.7674 (mt0) cc_final: 0.7462 (mt0) REVERT: B 338 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6590 (tt0) REVERT: B 340 LYS cc_start: 0.7510 (tttt) cc_final: 0.7192 (mtpp) REVERT: B 345 ASP cc_start: 0.7633 (t0) cc_final: 0.7355 (t0) REVERT: B 347 LYS cc_start: 0.6923 (mttp) cc_final: 0.6485 (mttp) REVERT: B 356 SER cc_start: 0.8456 (m) cc_final: 0.8019 (t) REVERT: B 375 LYS cc_start: 0.7813 (tttt) cc_final: 0.7404 (ttpp) REVERT: B 379 ARG cc_start: 0.6350 (ttp-110) cc_final: 0.5880 (mtt90) REVERT: C 311 LYS cc_start: 0.7972 (mttt) cc_final: 0.7092 (mmtm) REVERT: C 321 LYS cc_start: 0.7206 (ttmt) cc_final: 0.6238 (tmtm) REVERT: C 331 LYS cc_start: 0.7320 (mttt) cc_final: 0.6849 (mtpt) REVERT: C 338 GLU cc_start: 0.7090 (tt0) cc_final: 0.6656 (tm-30) REVERT: C 345 ASP cc_start: 0.7520 (t0) cc_final: 0.6828 (t70) REVERT: C 347 LYS cc_start: 0.6852 (mttt) cc_final: 0.6492 (mtpp) REVERT: C 349 ARG cc_start: 0.7009 (mtt180) cc_final: 0.6615 (mtm180) REVERT: D 311 LYS cc_start: 0.8251 (tttt) cc_final: 0.7812 (ttmt) REVERT: D 317 LYS cc_start: 0.7836 (mttt) cc_final: 0.7315 (mtpt) REVERT: D 321 LYS cc_start: 0.8255 (mttt) cc_final: 0.7508 (mmmt) REVERT: D 340 LYS cc_start: 0.8302 (mttt) cc_final: 0.7934 (mttm) REVERT: D 341 SER cc_start: 0.8663 (m) cc_final: 0.8398 (m) REVERT: D 342 GLU cc_start: 0.7732 (mt-10) cc_final: 0.6895 (mp0) REVERT: D 343 LYS cc_start: 0.8276 (mttt) cc_final: 0.8030 (mttm) REVERT: E 317 LYS cc_start: 0.7776 (mtmt) cc_final: 0.7504 (mtpm) REVERT: E 320 SER cc_start: 0.7758 (t) cc_final: 0.7320 (p) REVERT: E 321 LYS cc_start: 0.8052 (tttt) cc_final: 0.7623 (tmmt) REVERT: E 336 GLN cc_start: 0.8089 (mt0) cc_final: 0.7606 (mt0) REVERT: E 338 GLU cc_start: 0.7618 (tt0) cc_final: 0.7239 (tt0) REVERT: E 340 LYS cc_start: 0.7953 (tttt) cc_final: 0.7520 (tptp) REVERT: E 342 GLU cc_start: 0.7502 (mt-10) cc_final: 0.6028 (mp0) REVERT: E 347 LYS cc_start: 0.7456 (mttp) cc_final: 0.6916 (mmtm) REVERT: E 369 LYS cc_start: 0.8621 (mttt) cc_final: 0.8290 (mttp) REVERT: E 379 ARG cc_start: 0.5883 (OUTLIER) cc_final: 0.3355 (ptt90) REVERT: F 311 LYS cc_start: 0.8306 (mttt) cc_final: 0.6770 (pmtt) REVERT: F 338 GLU cc_start: 0.7810 (tt0) cc_final: 0.7472 (tt0) REVERT: F 347 LYS cc_start: 0.7688 (mttt) cc_final: 0.7393 (mtmm) REVERT: F 349 ARG cc_start: 0.7243 (mtt180) cc_final: 0.6836 (mtm180) REVERT: F 353 LYS cc_start: 0.8223 (tttt) cc_final: 0.7864 (tttt) REVERT: F 370 LYS cc_start: 0.7434 (tttp) cc_final: 0.7200 (ttpt) REVERT: G 317 LYS cc_start: 0.7351 (mttt) cc_final: 0.7018 (mtpm) REVERT: G 321 LYS cc_start: 0.7722 (mttt) cc_final: 0.6897 (mtpp) REVERT: G 340 LYS cc_start: 0.7918 (mttt) cc_final: 0.7093 (mttp) REVERT: G 342 GLU cc_start: 0.7509 (mt-10) cc_final: 0.6355 (mp0) REVERT: G 343 LYS cc_start: 0.7794 (mttt) cc_final: 0.7512 (mttp) REVERT: G 345 ASP cc_start: 0.7443 (m-30) cc_final: 0.7219 (m-30) REVERT: G 349 ARG cc_start: 0.7177 (mtm180) cc_final: 0.6492 (mtm180) REVERT: G 353 LYS cc_start: 0.7450 (mttt) cc_final: 0.7173 (mtmt) REVERT: G 356 SER cc_start: 0.8080 (p) cc_final: 0.7708 (t) REVERT: G 369 LYS cc_start: 0.7474 (mttt) cc_final: 0.7090 (mttp) REVERT: G 371 ILE cc_start: 0.7835 (mt) cc_final: 0.7516 (mp) REVERT: H 317 LYS cc_start: 0.7595 (mtmt) cc_final: 0.7360 (mtpm) REVERT: H 321 LYS cc_start: 0.7852 (tttt) cc_final: 0.6961 (mttp) REVERT: H 331 LYS cc_start: 0.7985 (mttt) cc_final: 0.7693 (mttp) REVERT: H 336 GLN cc_start: 0.7531 (mt0) cc_final: 0.6991 (mt0) REVERT: H 341 SER cc_start: 0.7801 (m) cc_final: 0.7331 (t) REVERT: H 345 ASP cc_start: 0.7681 (t0) cc_final: 0.7082 (t70) REVERT: H 347 LYS cc_start: 0.6948 (mttp) cc_final: 0.6268 (mmtm) REVERT: H 356 SER cc_start: 0.8346 (m) cc_final: 0.7894 (t) REVERT: H 358 ASP cc_start: 0.7023 (m-30) cc_final: 0.6750 (m-30) REVERT: H 375 LYS cc_start: 0.7900 (tttt) cc_final: 0.7441 (tttm) REVERT: I 311 LYS cc_start: 0.7433 (mtpt) cc_final: 0.6573 (tttp) REVERT: I 317 LYS cc_start: 0.7636 (pttt) cc_final: 0.7298 (ptmt) REVERT: I 321 LYS cc_start: 0.7399 (ttmt) cc_final: 0.6889 (ttmm) REVERT: I 331 LYS cc_start: 0.6743 (mttt) cc_final: 0.6542 (mttm) REVERT: I 338 GLU cc_start: 0.7600 (tt0) cc_final: 0.7272 (tt0) REVERT: I 341 SER cc_start: 0.7570 (p) cc_final: 0.7273 (t) REVERT: I 345 ASP cc_start: 0.7565 (t0) cc_final: 0.7081 (t0) REVERT: I 347 LYS cc_start: 0.6951 (mttt) cc_final: 0.5811 (mptp) REVERT: I 349 ARG cc_start: 0.6842 (mtt180) cc_final: 0.6318 (mtm180) REVERT: I 353 LYS cc_start: 0.7838 (tttt) cc_final: 0.7602 (tttm) REVERT: I 369 LYS cc_start: 0.7500 (mttt) cc_final: 0.7193 (ttmm) outliers start: 4 outliers final: 2 residues processed: 190 average time/residue: 3.0710 time to fit residues: 601.5855 Evaluate side-chains 190 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 187 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5175 Z= 0.276 Angle : 0.563 5.237 6924 Z= 0.287 Chirality : 0.049 0.133 780 Planarity : 0.004 0.035 879 Dihedral : 5.959 17.433 681 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.68 % Allowed : 15.90 % Favored : 83.42 % 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: -2.80 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS G 330 PHE 0.007 0.001 PHE A 378 TYR 0.010 0.002 TYR F 310 ARG 0.003 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 188 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7769 (mttt) cc_final: 0.7182 (mttp) REVERT: A 342 GLU cc_start: 0.7537 (mt-10) cc_final: 0.6244 (mp0) REVERT: A 345 ASP cc_start: 0.7005 (t0) cc_final: 0.6419 (m-30) REVERT: B 311 LYS cc_start: 0.8265 (mttt) cc_final: 0.7112 (mmtm) REVERT: B 321 LYS cc_start: 0.7738 (tttt) cc_final: 0.7160 (tmmm) REVERT: B 338 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6573 (tt0) REVERT: B 340 LYS cc_start: 0.7506 (tttt) cc_final: 0.7175 (mtpp) REVERT: B 345 ASP cc_start: 0.7746 (t0) cc_final: 0.7372 (t0) REVERT: B 347 LYS cc_start: 0.6891 (mttp) cc_final: 0.6440 (mttp) REVERT: B 356 SER cc_start: 0.8469 (m) cc_final: 0.8043 (t) REVERT: B 375 LYS cc_start: 0.7826 (tttt) cc_final: 0.7362 (ttpp) REVERT: C 311 LYS cc_start: 0.8016 (mttt) cc_final: 0.7145 (mmtm) REVERT: C 331 LYS cc_start: 0.7270 (mttt) cc_final: 0.6789 (mtpt) REVERT: C 338 GLU cc_start: 0.7118 (tt0) cc_final: 0.6658 (tm-30) REVERT: C 345 ASP cc_start: 0.7519 (t0) cc_final: 0.6833 (t0) REVERT: C 347 LYS cc_start: 0.6868 (mttt) cc_final: 0.6491 (mtpp) REVERT: C 349 ARG cc_start: 0.7017 (mtt180) cc_final: 0.6609 (mtm180) REVERT: D 311 LYS cc_start: 0.8228 (tttt) cc_final: 0.7800 (ttmt) REVERT: D 317 LYS cc_start: 0.7850 (mttt) cc_final: 0.7364 (mtpt) REVERT: D 321 LYS cc_start: 0.8350 (mttt) cc_final: 0.7476 (tptm) REVERT: D 340 LYS cc_start: 0.8332 (mttt) cc_final: 0.7935 (mttm) REVERT: D 341 SER cc_start: 0.8669 (m) cc_final: 0.8389 (m) REVERT: D 342 GLU cc_start: 0.7718 (mt-10) cc_final: 0.6859 (mp0) REVERT: D 343 LYS cc_start: 0.8286 (mttt) cc_final: 0.8039 (mttm) REVERT: D 378 PHE cc_start: 0.5663 (t80) cc_final: 0.5258 (m-80) REVERT: E 317 LYS cc_start: 0.7802 (mtmt) cc_final: 0.7504 (mtpm) REVERT: E 320 SER cc_start: 0.7823 (t) cc_final: 0.7363 (p) REVERT: E 321 LYS cc_start: 0.8049 (tttt) cc_final: 0.7620 (tmmt) REVERT: E 336 GLN cc_start: 0.8076 (mt0) cc_final: 0.7606 (mt0) REVERT: E 338 GLU cc_start: 0.7649 (tt0) cc_final: 0.7251 (tt0) REVERT: E 340 LYS cc_start: 0.7927 (tttt) cc_final: 0.7487 (tptp) REVERT: E 342 GLU cc_start: 0.7514 (mt-10) cc_final: 0.6115 (mp0) REVERT: E 347 LYS cc_start: 0.7457 (mttp) cc_final: 0.6915 (mmtm) REVERT: E 369 LYS cc_start: 0.8652 (mttt) cc_final: 0.8314 (mttp) REVERT: E 379 ARG cc_start: 0.5960 (OUTLIER) cc_final: 0.3384 (ptt90) REVERT: F 311 LYS cc_start: 0.8301 (mttt) cc_final: 0.6878 (pmtt) REVERT: F 338 GLU cc_start: 0.7811 (tt0) cc_final: 0.7520 (tt0) REVERT: F 347 LYS cc_start: 0.7742 (mttt) cc_final: 0.7396 (mtmm) REVERT: F 349 ARG cc_start: 0.7225 (mtt180) cc_final: 0.6823 (mtm180) REVERT: F 353 LYS cc_start: 0.8274 (tttt) cc_final: 0.7930 (tttt) REVERT: F 370 LYS cc_start: 0.7458 (tttp) cc_final: 0.7210 (ttpt) REVERT: G 317 LYS cc_start: 0.7377 (mttt) cc_final: 0.7082 (mtpm) REVERT: G 321 LYS cc_start: 0.7727 (mttt) cc_final: 0.7199 (mttm) REVERT: G 342 GLU cc_start: 0.7541 (mt-10) cc_final: 0.6416 (mp0) REVERT: G 343 LYS cc_start: 0.7816 (mttt) cc_final: 0.7586 (mttp) REVERT: G 349 ARG cc_start: 0.7197 (mtm180) cc_final: 0.6523 (mtm180) REVERT: G 353 LYS cc_start: 0.7446 (mttt) cc_final: 0.7171 (mtmt) REVERT: G 356 SER cc_start: 0.8109 (p) cc_final: 0.7694 (t) REVERT: G 369 LYS cc_start: 0.7478 (mttt) cc_final: 0.7098 (mttp) REVERT: G 371 ILE cc_start: 0.7830 (mt) cc_final: 0.7516 (mp) REVERT: G 378 PHE cc_start: 0.5742 (t80) cc_final: 0.5388 (m-80) REVERT: H 317 LYS cc_start: 0.7612 (mtmt) cc_final: 0.7353 (mtpm) REVERT: H 321 LYS cc_start: 0.7874 (tttt) cc_final: 0.6940 (mttp) REVERT: H 331 LYS cc_start: 0.7997 (mttt) cc_final: 0.7681 (mttp) REVERT: H 336 GLN cc_start: 0.7676 (mt0) cc_final: 0.7132 (mt0) REVERT: H 341 SER cc_start: 0.7984 (m) cc_final: 0.7481 (t) REVERT: H 345 ASP cc_start: 0.7766 (t0) cc_final: 0.7072 (t70) REVERT: H 347 LYS cc_start: 0.6953 (mttp) cc_final: 0.6267 (mmtm) REVERT: H 353 LYS cc_start: 0.7701 (ttpt) cc_final: 0.7455 (ttpt) REVERT: H 375 LYS cc_start: 0.7926 (tttt) cc_final: 0.7451 (tttm) REVERT: I 311 LYS cc_start: 0.7442 (mtpt) cc_final: 0.6577 (tttp) REVERT: I 317 LYS cc_start: 0.7636 (pttt) cc_final: 0.7294 (ptmt) REVERT: I 321 LYS cc_start: 0.7403 (ttmt) cc_final: 0.6909 (ttmm) REVERT: I 331 LYS cc_start: 0.6700 (mttt) cc_final: 0.6478 (mttm) REVERT: I 338 GLU cc_start: 0.7647 (tt0) cc_final: 0.7197 (tt0) REVERT: I 341 SER cc_start: 0.7628 (OUTLIER) cc_final: 0.7334 (t) REVERT: I 345 ASP cc_start: 0.7459 (t0) cc_final: 0.6996 (t0) REVERT: I 347 LYS cc_start: 0.6967 (mttt) cc_final: 0.5814 (mptp) REVERT: I 349 ARG cc_start: 0.6812 (mtt180) cc_final: 0.6339 (mtm180) REVERT: I 353 LYS cc_start: 0.7827 (tttt) cc_final: 0.7530 (tttm) REVERT: I 369 LYS cc_start: 0.7545 (mttt) cc_final: 0.7133 (ttmm) outliers start: 4 outliers final: 2 residues processed: 188 average time/residue: 3.1708 time to fit residues: 614.3726 Evaluate side-chains 190 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 186 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain I residue 341 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN B 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5175 Z= 0.171 Angle : 0.520 5.800 6924 Z= 0.266 Chirality : 0.049 0.130 780 Planarity : 0.004 0.055 879 Dihedral : 5.720 17.015 681 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.34 % Allowed : 16.92 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.79 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 329 PHE 0.004 0.001 PHE E 378 TYR 0.006 0.001 TYR E 310 ARG 0.004 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 189 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7759 (mttt) cc_final: 0.7159 (mttp) REVERT: A 342 GLU cc_start: 0.7532 (mt-10) cc_final: 0.6238 (mp0) REVERT: A 345 ASP cc_start: 0.6925 (t0) cc_final: 0.6568 (m-30) REVERT: B 311 LYS cc_start: 0.8266 (mttt) cc_final: 0.7110 (mmtm) REVERT: B 321 LYS cc_start: 0.7636 (tttt) cc_final: 0.7049 (tmmm) REVERT: B 338 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6576 (tt0) REVERT: B 340 LYS cc_start: 0.7496 (tttt) cc_final: 0.7189 (mtpp) REVERT: B 345 ASP cc_start: 0.7619 (t0) cc_final: 0.7330 (t0) REVERT: B 347 LYS cc_start: 0.6910 (mttp) cc_final: 0.6472 (mttp) REVERT: B 356 SER cc_start: 0.8471 (m) cc_final: 0.8033 (t) REVERT: C 311 LYS cc_start: 0.8015 (mttt) cc_final: 0.7134 (mmtm) REVERT: C 331 LYS cc_start: 0.7308 (mttt) cc_final: 0.6836 (mtpt) REVERT: C 338 GLU cc_start: 0.7110 (tt0) cc_final: 0.6668 (tm-30) REVERT: C 345 ASP cc_start: 0.7557 (t0) cc_final: 0.6891 (t0) REVERT: C 347 LYS cc_start: 0.6847 (mttt) cc_final: 0.6473 (mtpp) REVERT: C 349 ARG cc_start: 0.7022 (mtt180) cc_final: 0.6622 (mtm180) REVERT: D 311 LYS cc_start: 0.8234 (tttt) cc_final: 0.7811 (ttmt) REVERT: D 317 LYS cc_start: 0.7847 (mttt) cc_final: 0.7378 (mtpt) REVERT: D 321 LYS cc_start: 0.8335 (mttt) cc_final: 0.7388 (tptm) REVERT: D 340 LYS cc_start: 0.8339 (mttt) cc_final: 0.7922 (mttm) REVERT: D 341 SER cc_start: 0.8640 (m) cc_final: 0.8364 (m) REVERT: D 342 GLU cc_start: 0.7719 (mt-10) cc_final: 0.6892 (mp0) REVERT: D 343 LYS cc_start: 0.8280 (mttt) cc_final: 0.8038 (mttm) REVERT: D 378 PHE cc_start: 0.5729 (t80) cc_final: 0.5302 (m-80) REVERT: E 317 LYS cc_start: 0.7773 (mtmt) cc_final: 0.7426 (mtpm) REVERT: E 320 SER cc_start: 0.7758 (t) cc_final: 0.7318 (p) REVERT: E 321 LYS cc_start: 0.8030 (tttt) cc_final: 0.7609 (tmmt) REVERT: E 336 GLN cc_start: 0.8002 (mt0) cc_final: 0.7515 (mt0) REVERT: E 338 GLU cc_start: 0.7644 (tt0) cc_final: 0.7257 (tt0) REVERT: E 340 LYS cc_start: 0.7933 (tttt) cc_final: 0.7464 (tptp) REVERT: E 342 GLU cc_start: 0.7458 (mt-10) cc_final: 0.6004 (mp0) REVERT: E 347 LYS cc_start: 0.7435 (mttp) cc_final: 0.6960 (mttm) REVERT: E 369 LYS cc_start: 0.8627 (mttt) cc_final: 0.8282 (mttp) REVERT: F 311 LYS cc_start: 0.8314 (mttt) cc_final: 0.6819 (pmtt) REVERT: F 338 GLU cc_start: 0.7809 (tt0) cc_final: 0.7557 (tt0) REVERT: F 347 LYS cc_start: 0.7691 (mttt) cc_final: 0.7074 (mtmm) REVERT: F 349 ARG cc_start: 0.7201 (mtt180) cc_final: 0.6824 (mtm180) REVERT: F 353 LYS cc_start: 0.8255 (tttt) cc_final: 0.7923 (tttt) REVERT: F 370 LYS cc_start: 0.7437 (tttp) cc_final: 0.7211 (ttpt) REVERT: F 379 ARG cc_start: 0.7047 (mmm-85) cc_final: 0.5811 (mtm110) REVERT: G 317 LYS cc_start: 0.7377 (mttt) cc_final: 0.7069 (mtpm) REVERT: G 321 LYS cc_start: 0.7727 (mttt) cc_final: 0.7233 (mttm) REVERT: G 342 GLU cc_start: 0.7507 (mt-10) cc_final: 0.6383 (mp0) REVERT: G 343 LYS cc_start: 0.7775 (mttt) cc_final: 0.7546 (mttp) REVERT: G 349 ARG cc_start: 0.7183 (mtm180) cc_final: 0.6501 (mtm180) REVERT: G 353 LYS cc_start: 0.7400 (mttt) cc_final: 0.7159 (mtmt) REVERT: G 356 SER cc_start: 0.8073 (p) cc_final: 0.7674 (t) REVERT: G 369 LYS cc_start: 0.7405 (mttt) cc_final: 0.7068 (mttp) REVERT: G 371 ILE cc_start: 0.7821 (mt) cc_final: 0.7505 (mp) REVERT: G 378 PHE cc_start: 0.5821 (t80) cc_final: 0.5437 (m-80) REVERT: H 317 LYS cc_start: 0.7631 (mtmt) cc_final: 0.7275 (mtmm) REVERT: H 321 LYS cc_start: 0.7863 (tttt) cc_final: 0.6938 (mttp) REVERT: H 331 LYS cc_start: 0.7984 (mttt) cc_final: 0.7666 (mttp) REVERT: H 336 GLN cc_start: 0.7550 (mt0) cc_final: 0.7022 (mt0) REVERT: H 341 SER cc_start: 0.7673 (OUTLIER) cc_final: 0.7215 (t) REVERT: H 345 ASP cc_start: 0.7648 (t0) cc_final: 0.7106 (t70) REVERT: H 347 LYS cc_start: 0.6936 (mttp) cc_final: 0.6251 (mmtm) REVERT: H 353 LYS cc_start: 0.7699 (ttpt) cc_final: 0.7463 (ttpt) REVERT: H 356 SER cc_start: 0.8261 (m) cc_final: 0.7770 (t) REVERT: H 375 LYS cc_start: 0.7912 (tttt) cc_final: 0.7384 (tttm) REVERT: I 311 LYS cc_start: 0.7395 (mtpt) cc_final: 0.6536 (tttp) REVERT: I 317 LYS cc_start: 0.7639 (pttt) cc_final: 0.7301 (ptmt) REVERT: I 321 LYS cc_start: 0.7405 (ttmt) cc_final: 0.6908 (ttmm) REVERT: I 331 LYS cc_start: 0.6822 (mttt) cc_final: 0.6566 (mttm) REVERT: I 338 GLU cc_start: 0.7567 (tt0) cc_final: 0.7213 (tt0) REVERT: I 341 SER cc_start: 0.7562 (p) cc_final: 0.7281 (t) REVERT: I 345 ASP cc_start: 0.7466 (t0) cc_final: 0.6984 (t0) REVERT: I 347 LYS cc_start: 0.6939 (mttt) cc_final: 0.5780 (mptp) REVERT: I 349 ARG cc_start: 0.6820 (mtt180) cc_final: 0.6358 (mtm180) REVERT: I 369 LYS cc_start: 0.7512 (mttt) cc_final: 0.7199 (ttmm) outliers start: 2 outliers final: 1 residues processed: 189 average time/residue: 3.1160 time to fit residues: 606.9488 Evaluate side-chains 190 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 188 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain H residue 341 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.0770 chunk 41 optimal weight: 1.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN B 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5175 Z= 0.223 Angle : 0.533 5.824 6924 Z= 0.271 Chirality : 0.048 0.131 780 Planarity : 0.004 0.034 879 Dihedral : 5.731 16.980 681 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.51 % Allowed : 17.09 % Favored : 82.39 % 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: -2.83 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS G 330 PHE 0.004 0.001 PHE F 346 TYR 0.009 0.002 TYR F 310 ARG 0.006 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 191 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7759 (mttt) cc_final: 0.7158 (mttp) REVERT: A 342 GLU cc_start: 0.7580 (mt-10) cc_final: 0.6354 (mp0) REVERT: A 345 ASP cc_start: 0.6949 (t0) cc_final: 0.6546 (m-30) REVERT: B 311 LYS cc_start: 0.8223 (mttt) cc_final: 0.7093 (mmtm) REVERT: B 321 LYS cc_start: 0.7616 (tttt) cc_final: 0.7100 (tmmm) REVERT: B 338 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6585 (tt0) REVERT: B 340 LYS cc_start: 0.7508 (tttt) cc_final: 0.7198 (mtpp) REVERT: B 345 ASP cc_start: 0.7622 (t0) cc_final: 0.7319 (t0) REVERT: B 347 LYS cc_start: 0.6890 (mttp) cc_final: 0.6455 (mttp) REVERT: B 356 SER cc_start: 0.8470 (m) cc_final: 0.8028 (t) REVERT: C 311 LYS cc_start: 0.8022 (mttt) cc_final: 0.7140 (mmtm) REVERT: C 331 LYS cc_start: 0.7312 (mttt) cc_final: 0.6840 (mtpt) REVERT: C 338 GLU cc_start: 0.7116 (tt0) cc_final: 0.6652 (tm-30) REVERT: C 340 LYS cc_start: 0.7654 (tttt) cc_final: 0.6641 (tptt) REVERT: C 345 ASP cc_start: 0.7559 (t0) cc_final: 0.6907 (t0) REVERT: C 347 LYS cc_start: 0.6861 (mttt) cc_final: 0.6477 (mtpp) REVERT: C 349 ARG cc_start: 0.7024 (mtt180) cc_final: 0.6620 (mtm180) REVERT: D 311 LYS cc_start: 0.8237 (tttt) cc_final: 0.7719 (ttmp) REVERT: D 317 LYS cc_start: 0.7869 (mttt) cc_final: 0.7404 (mtpt) REVERT: D 321 LYS cc_start: 0.8391 (mttt) cc_final: 0.7448 (tptm) REVERT: D 340 LYS cc_start: 0.8333 (mttt) cc_final: 0.7960 (mttm) REVERT: D 341 SER cc_start: 0.8647 (m) cc_final: 0.8404 (m) REVERT: D 342 GLU cc_start: 0.7710 (mt-10) cc_final: 0.6877 (mp0) REVERT: D 343 LYS cc_start: 0.8264 (mttt) cc_final: 0.8021 (mttm) REVERT: D 378 PHE cc_start: 0.5680 (t80) cc_final: 0.5300 (m-80) REVERT: E 317 LYS cc_start: 0.7782 (mtmt) cc_final: 0.7428 (mtpm) REVERT: E 320 SER cc_start: 0.7771 (t) cc_final: 0.7330 (p) REVERT: E 321 LYS cc_start: 0.8035 (tttt) cc_final: 0.7603 (tmmt) REVERT: E 336 GLN cc_start: 0.8010 (mt0) cc_final: 0.7522 (mt0) REVERT: E 338 GLU cc_start: 0.7652 (tt0) cc_final: 0.7218 (tt0) REVERT: E 340 LYS cc_start: 0.7879 (tttt) cc_final: 0.7492 (tptp) REVERT: E 342 GLU cc_start: 0.7483 (mt-10) cc_final: 0.5996 (mp0) REVERT: E 347 LYS cc_start: 0.7465 (mttp) cc_final: 0.6992 (mttm) REVERT: E 369 LYS cc_start: 0.8634 (mttt) cc_final: 0.8285 (mttp) REVERT: F 311 LYS cc_start: 0.8315 (mttt) cc_final: 0.6833 (pmtt) REVERT: F 338 GLU cc_start: 0.7814 (tt0) cc_final: 0.7535 (tt0) REVERT: F 347 LYS cc_start: 0.7607 (mttt) cc_final: 0.7267 (mtmm) REVERT: F 349 ARG cc_start: 0.7205 (mtt180) cc_final: 0.6836 (mtm180) REVERT: F 353 LYS cc_start: 0.8257 (tttt) cc_final: 0.7917 (tttt) REVERT: F 370 LYS cc_start: 0.7389 (tttp) cc_final: 0.7127 (ttpt) REVERT: F 379 ARG cc_start: 0.7004 (mmm-85) cc_final: 0.5975 (mtm110) REVERT: G 317 LYS cc_start: 0.7392 (mttt) cc_final: 0.7103 (mtpm) REVERT: G 321 LYS cc_start: 0.7751 (mttt) cc_final: 0.7223 (mttm) REVERT: G 342 GLU cc_start: 0.7545 (mt-10) cc_final: 0.6385 (mp0) REVERT: G 343 LYS cc_start: 0.7819 (mttt) cc_final: 0.7593 (mttp) REVERT: G 349 ARG cc_start: 0.7148 (mtm180) cc_final: 0.6496 (mtm180) REVERT: G 353 LYS cc_start: 0.7421 (mttt) cc_final: 0.7172 (mtmt) REVERT: G 356 SER cc_start: 0.8083 (p) cc_final: 0.7699 (t) REVERT: G 369 LYS cc_start: 0.7487 (mttt) cc_final: 0.7151 (mttp) REVERT: G 371 ILE cc_start: 0.7815 (mt) cc_final: 0.7597 (mp) REVERT: G 378 PHE cc_start: 0.5840 (t80) cc_final: 0.5460 (m-80) REVERT: H 317 LYS cc_start: 0.7625 (mtmt) cc_final: 0.7255 (mtmm) REVERT: H 321 LYS cc_start: 0.7877 (tttt) cc_final: 0.6944 (mptp) REVERT: H 331 LYS cc_start: 0.8026 (mttt) cc_final: 0.7707 (mttp) REVERT: H 336 GLN cc_start: 0.7604 (mt0) cc_final: 0.7057 (mt0) REVERT: H 341 SER cc_start: 0.7861 (m) cc_final: 0.7377 (t) REVERT: H 345 ASP cc_start: 0.7651 (t0) cc_final: 0.7072 (t70) REVERT: H 347 LYS cc_start: 0.6941 (mttp) cc_final: 0.6252 (mmtm) REVERT: H 356 SER cc_start: 0.8266 (m) cc_final: 0.7775 (t) REVERT: H 375 LYS cc_start: 0.7899 (tttt) cc_final: 0.7367 (tttm) REVERT: I 311 LYS cc_start: 0.7428 (mtpt) cc_final: 0.6569 (tttp) REVERT: I 317 LYS cc_start: 0.7635 (pttt) cc_final: 0.7302 (ptmt) REVERT: I 321 LYS cc_start: 0.7397 (ttmt) cc_final: 0.6903 (ttmm) REVERT: I 331 LYS cc_start: 0.6761 (mttt) cc_final: 0.6492 (mttm) REVERT: I 338 GLU cc_start: 0.7567 (tt0) cc_final: 0.7152 (tt0) REVERT: I 341 SER cc_start: 0.7609 (p) cc_final: 0.7325 (t) REVERT: I 345 ASP cc_start: 0.7492 (t0) cc_final: 0.7022 (t0) REVERT: I 347 LYS cc_start: 0.6931 (mttt) cc_final: 0.5755 (mptp) REVERT: I 349 ARG cc_start: 0.6833 (mtt180) cc_final: 0.6356 (mtm180) REVERT: I 353 LYS cc_start: 0.7809 (tttt) cc_final: 0.7523 (tttm) REVERT: I 369 LYS cc_start: 0.7533 (mttt) cc_final: 0.7135 (ttmm) outliers start: 3 outliers final: 2 residues processed: 191 average time/residue: 3.1633 time to fit residues: 623.5321 Evaluate side-chains 190 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 188 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain E residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5175 Z= 0.170 Angle : 0.510 6.022 6924 Z= 0.261 Chirality : 0.049 0.129 780 Planarity : 0.004 0.035 879 Dihedral : 5.601 16.801 681 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.51 % Allowed : 17.44 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.79 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 329 PHE 0.003 0.001 PHE E 378 TYR 0.006 0.001 TYR E 310 ARG 0.005 0.000 ARG B 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 190 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7731 (mttt) cc_final: 0.7139 (mttp) REVERT: A 342 GLU cc_start: 0.7577 (mt-10) cc_final: 0.6444 (mp0) REVERT: A 345 ASP cc_start: 0.6892 (t0) cc_final: 0.6448 (m-30) REVERT: B 311 LYS cc_start: 0.8223 (mttt) cc_final: 0.7094 (mmtm) REVERT: B 321 LYS cc_start: 0.7555 (tttt) cc_final: 0.7009 (tmmm) REVERT: B 338 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6578 (tt0) REVERT: B 340 LYS cc_start: 0.7507 (tttt) cc_final: 0.7213 (mtpp) REVERT: B 347 LYS cc_start: 0.6905 (mttp) cc_final: 0.6512 (mttp) REVERT: B 356 SER cc_start: 0.8482 (m) cc_final: 0.8039 (t) REVERT: C 311 LYS cc_start: 0.8014 (mttt) cc_final: 0.7150 (mmtm) REVERT: C 331 LYS cc_start: 0.7307 (mttt) cc_final: 0.6837 (mtpt) REVERT: C 338 GLU cc_start: 0.7107 (tt0) cc_final: 0.6671 (tm-30) REVERT: C 340 LYS cc_start: 0.7692 (tttt) cc_final: 0.6640 (tptt) REVERT: C 345 ASP cc_start: 0.7486 (t0) cc_final: 0.6757 (t0) REVERT: C 347 LYS cc_start: 0.6852 (mttt) cc_final: 0.6483 (mtpp) REVERT: C 349 ARG cc_start: 0.7025 (mtt180) cc_final: 0.6627 (mtm180) REVERT: D 311 LYS cc_start: 0.8246 (tttt) cc_final: 0.7720 (ttmp) REVERT: D 317 LYS cc_start: 0.7852 (mttt) cc_final: 0.7388 (mtpt) REVERT: D 321 LYS cc_start: 0.8314 (mttt) cc_final: 0.7332 (tptm) REVERT: D 340 LYS cc_start: 0.8339 (mttt) cc_final: 0.7940 (mttm) REVERT: D 341 SER cc_start: 0.8630 (m) cc_final: 0.8340 (m) REVERT: D 342 GLU cc_start: 0.7690 (mt-10) cc_final: 0.6857 (mp0) REVERT: D 345 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7211 (m-30) REVERT: D 378 PHE cc_start: 0.5653 (t80) cc_final: 0.5272 (m-80) REVERT: E 317 LYS cc_start: 0.7764 (mtmt) cc_final: 0.7415 (mtpm) REVERT: E 320 SER cc_start: 0.7756 (t) cc_final: 0.7320 (p) REVERT: E 321 LYS cc_start: 0.8018 (tttt) cc_final: 0.7598 (tmmt) REVERT: E 336 GLN cc_start: 0.8003 (mt0) cc_final: 0.7514 (mt0) REVERT: E 338 GLU cc_start: 0.7666 (tt0) cc_final: 0.7263 (tt0) REVERT: E 340 LYS cc_start: 0.7887 (tttt) cc_final: 0.7501 (tptp) REVERT: E 342 GLU cc_start: 0.7420 (mt-10) cc_final: 0.5957 (mp0) REVERT: E 347 LYS cc_start: 0.7456 (mttp) cc_final: 0.6938 (mttm) REVERT: E 369 LYS cc_start: 0.8612 (mttt) cc_final: 0.8255 (mttp) REVERT: F 311 LYS cc_start: 0.8314 (mttt) cc_final: 0.6816 (pmtt) REVERT: F 338 GLU cc_start: 0.7816 (tt0) cc_final: 0.7545 (tt0) REVERT: F 347 LYS cc_start: 0.7466 (mttt) cc_final: 0.7129 (mtmm) REVERT: F 349 ARG cc_start: 0.7188 (mtt180) cc_final: 0.6838 (mtm180) REVERT: F 353 LYS cc_start: 0.8227 (tttt) cc_final: 0.7896 (tttt) REVERT: F 370 LYS cc_start: 0.7431 (tttp) cc_final: 0.7198 (ttpt) REVERT: F 379 ARG cc_start: 0.6999 (mmm-85) cc_final: 0.5994 (mtm110) REVERT: G 317 LYS cc_start: 0.7395 (mttt) cc_final: 0.7113 (mtpm) REVERT: G 321 LYS cc_start: 0.7701 (mttt) cc_final: 0.7159 (mttm) REVERT: G 340 LYS cc_start: 0.7887 (mttt) cc_final: 0.7021 (mttp) REVERT: G 342 GLU cc_start: 0.7500 (mt-10) cc_final: 0.6462 (mp0) REVERT: G 343 LYS cc_start: 0.7778 (mttt) cc_final: 0.7545 (mttp) REVERT: G 349 ARG cc_start: 0.7123 (mtm180) cc_final: 0.6466 (mtm180) REVERT: G 353 LYS cc_start: 0.7385 (mttt) cc_final: 0.7169 (mtmt) REVERT: G 356 SER cc_start: 0.8058 (p) cc_final: 0.7702 (t) REVERT: G 369 LYS cc_start: 0.7405 (mttt) cc_final: 0.7073 (mttp) REVERT: G 371 ILE cc_start: 0.7733 (mt) cc_final: 0.7517 (mp) REVERT: G 378 PHE cc_start: 0.5848 (t80) cc_final: 0.5463 (m-80) REVERT: H 317 LYS cc_start: 0.7624 (mtmt) cc_final: 0.7258 (mtmm) REVERT: H 321 LYS cc_start: 0.7868 (tttt) cc_final: 0.6925 (mptp) REVERT: H 331 LYS cc_start: 0.8032 (mttt) cc_final: 0.7710 (mttp) REVERT: H 336 GLN cc_start: 0.7548 (mt0) cc_final: 0.7020 (mt0) REVERT: H 341 SER cc_start: 0.7840 (OUTLIER) cc_final: 0.7373 (t) REVERT: H 345 ASP cc_start: 0.7635 (t0) cc_final: 0.6999 (t70) REVERT: H 356 SER cc_start: 0.8145 (m) cc_final: 0.7823 (t) REVERT: H 375 LYS cc_start: 0.7906 (tttt) cc_final: 0.7370 (tttm) REVERT: I 311 LYS cc_start: 0.7410 (mtpt) cc_final: 0.6534 (tttp) REVERT: I 317 LYS cc_start: 0.7636 (pttt) cc_final: 0.7311 (ptmt) REVERT: I 321 LYS cc_start: 0.7393 (ttmt) cc_final: 0.6901 (ttmm) REVERT: I 331 LYS cc_start: 0.6826 (mttt) cc_final: 0.6546 (mttm) REVERT: I 338 GLU cc_start: 0.7569 (tt0) cc_final: 0.7204 (tt0) REVERT: I 341 SER cc_start: 0.7553 (p) cc_final: 0.7274 (t) REVERT: I 345 ASP cc_start: 0.7517 (t0) cc_final: 0.6955 (t0) REVERT: I 347 LYS cc_start: 0.6923 (mttt) cc_final: 0.5745 (mmtm) REVERT: I 349 ARG cc_start: 0.6796 (mtt180) cc_final: 0.6331 (mtm180) REVERT: I 369 LYS cc_start: 0.7531 (mttt) cc_final: 0.7140 (ttmm) outliers start: 3 outliers final: 1 residues processed: 190 average time/residue: 3.1462 time to fit residues: 615.9060 Evaluate side-chains 188 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 185 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain H residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.137267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.121693 restraints weight = 19227.624| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.42 r_work: 0.3742 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5175 Z= 0.281 Angle : 0.559 6.008 6924 Z= 0.285 Chirality : 0.049 0.133 780 Planarity : 0.004 0.034 879 Dihedral : 5.824 17.293 681 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.85 % Allowed : 17.44 % Favored : 81.71 % 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: -2.87 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS G 330 PHE 0.005 0.001 PHE F 346 TYR 0.009 0.002 TYR E 310 ARG 0.005 0.001 ARG B 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9130.21 seconds wall clock time: 156 minutes 54.73 seconds (9414.73 seconds total)