Starting phenix.real_space_refine on Sat Aug 3 04:10:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8e_18252/08_2024/8q8e_18252.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8e_18252/08_2024/8q8e_18252.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8e_18252/08_2024/8q8e_18252.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8e_18252/08_2024/8q8e_18252.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8e_18252/08_2024/8q8e_18252.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8e_18252/08_2024/8q8e_18252.cif" } resolution = 3.81 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 4278 2.51 5 N 1248 2.21 5 O 1272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 372": "OE1" <-> "OE2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F GLU 372": "OE1" <-> "OE2" Residue "G GLU 372": "OE1" <-> "OE2" Residue "H ARG 349": "NH1" <-> "NH2" Residue "H GLU 372": "OE1" <-> "OE2" Residue "I GLU 372": "OE1" <-> "OE2" Residue "J GLU 338": "OE1" <-> "OE2" Residue "J GLU 372": "OE1" <-> "OE2" Residue "K GLU 338": "OE1" <-> "OE2" Residue "K GLU 372": "OE1" <-> "OE2" Residue "L GLU 338": "OE1" <-> "OE2" Residue "L GLU 372": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6810 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "G" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "H" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "I" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "J" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "K" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 5.33, per 1000 atoms: 0.78 Number of scatterers: 6810 At special positions: 0 Unit cell: (166.448, 164.8, 50.264, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 1272 8.00 N 1248 7.00 C 4278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.2 seconds 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1560 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 34 sheets defined 0.0% alpha, 38.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.422A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 320 Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 330 removed outlier: 6.578A pdb=" N HIS A 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 336 through 340 removed outlier: 6.429A pdb=" N GLN A 336 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N VAL C 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLU A 338 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 343 through 346 removed outlier: 6.587A pdb=" N LEU A 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LYS E 347 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N PHE A 346 " --> pdb=" O LYS E 347 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 351 through 352 removed outlier: 6.226A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.153A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 370 through 373 Processing sheet with id=AA9, first strand: chain 'D' and resid 307 through 310 removed outlier: 6.959A pdb=" N ILE B 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.753A pdb=" N VAL B 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 317 through 325 Processing sheet with id=AB3, first strand: chain 'D' and resid 337 through 340 removed outlier: 6.689A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 343 through 346 removed outlier: 6.400A pdb=" N LYS B 343 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N PHE F 346 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP B 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 351 through 354 removed outlier: 6.213A pdb=" N GLN B 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE F 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS B 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.571A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 368 through 373 removed outlier: 6.298A pdb=" N ASN B 368 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ILE D 371 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS B 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N THR D 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLU B 372 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS B 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N GLU F 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE B 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 376 through 377 removed outlier: 6.742A pdb=" N LEU B 376 " --> pdb=" O THR D 377 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 306 through 310 removed outlier: 6.422A pdb=" N GLN G 307 " --> pdb=" O ILE H 308 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N TYR H 310 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL G 309 " --> pdb=" O TYR H 310 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 313 through 320 Processing sheet with id=AC2, first strand: chain 'H' and resid 329 through 330 removed outlier: 6.578A pdb=" N HIS G 329 " --> pdb=" O HIS H 330 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 336 through 340 removed outlier: 6.429A pdb=" N GLN G 336 " --> pdb=" O VAL H 337 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N VAL H 339 " --> pdb=" O GLN G 336 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLU G 338 " --> pdb=" O VAL H 339 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 343 through 346 removed outlier: 6.588A pdb=" N LEU G 344 " --> pdb=" O ASP I 345 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LYS I 347 " --> pdb=" O LEU G 344 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N PHE G 346 " --> pdb=" O LYS I 347 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 351 through 352 removed outlier: 6.226A pdb=" N GLN G 351 " --> pdb=" O SER H 352 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 357 through 362 removed outlier: 6.153A pdb=" N ASP G 358 " --> pdb=" O ASN H 359 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N THR H 361 " --> pdb=" O ASP G 358 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE G 360 " --> pdb=" O THR H 361 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 370 through 373 Processing sheet with id=AC8, first strand: chain 'K' and resid 307 through 310 removed outlier: 6.959A pdb=" N ILE J 308 " --> pdb=" O VAL K 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 313 through 314 removed outlier: 6.754A pdb=" N VAL J 313 " --> pdb=" O ASP L 314 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 317 through 325 Processing sheet with id=AD2, first strand: chain 'K' and resid 337 through 340 removed outlier: 6.689A pdb=" N VAL J 337 " --> pdb=" O GLU K 338 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N LYS K 340 " --> pdb=" O VAL J 337 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL J 339 " --> pdb=" O LYS K 340 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 343 through 346 removed outlier: 6.400A pdb=" N LYS J 343 " --> pdb=" O LEU L 344 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N PHE L 346 " --> pdb=" O LYS J 343 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASP J 345 " --> pdb=" O PHE L 346 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 351 through 354 removed outlier: 6.213A pdb=" N GLN J 351 " --> pdb=" O SER L 352 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE L 354 " --> pdb=" O GLN J 351 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS J 353 " --> pdb=" O ILE L 354 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 361 through 362 removed outlier: 6.571A pdb=" N THR J 361 " --> pdb=" O HIS K 362 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 368 through 373 removed outlier: 6.299A pdb=" N ASN J 368 " --> pdb=" O LYS K 369 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ILE K 371 " --> pdb=" O ASN J 368 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS J 370 " --> pdb=" O ILE K 371 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N THR K 373 " --> pdb=" O LYS J 370 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLU J 372 " --> pdb=" O THR K 373 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS J 369 " --> pdb=" O LYS L 370 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N GLU L 372 " --> pdb=" O LYS J 369 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE J 371 " --> pdb=" O GLU L 372 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'K' and resid 376 through 377 removed outlier: 6.742A pdb=" N LEU J 376 " --> pdb=" O THR K 377 " (cutoff:3.500A) 136 hydrogen bonds defined for protein. 408 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1827 1.33 - 1.45: 955 1.45 - 1.57: 4124 1.57 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 6918 Sorted by residual: bond pdb=" N LYS H 370 " pdb=" CA LYS H 370 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.21e-02 6.83e+03 1.07e+01 bond pdb=" N LYS C 370 " pdb=" CA LYS C 370 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.21e-02 6.83e+03 1.04e+01 bond pdb=" CZ ARG K 349 " pdb=" NH2 ARG K 349 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.01e+01 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.92e+00 bond pdb=" CZ ARG B 349 " pdb=" NH2 ARG B 349 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 8.88e+00 ... (remaining 6913 not shown) Histogram of bond angle deviations from ideal: 101.92 - 107.38: 475 107.38 - 112.83: 3148 112.83 - 118.29: 1775 118.29 - 123.74: 3220 123.74 - 129.19: 640 Bond angle restraints: 9258 Sorted by residual: angle pdb=" O SER E 352 " pdb=" C SER E 352 " pdb=" N LYS E 353 " ideal model delta sigma weight residual 123.24 111.67 11.57 1.32e+00 5.74e-01 7.69e+01 angle pdb=" O SER I 352 " pdb=" C SER I 352 " pdb=" N LYS I 353 " ideal model delta sigma weight residual 123.24 111.68 11.56 1.32e+00 5.74e-01 7.67e+01 angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 119.08 -6.48 1.00e+00 1.00e+00 4.20e+01 angle pdb=" CA ASP J 358 " pdb=" CB ASP J 358 " pdb=" CG ASP J 358 " ideal model delta sigma weight residual 112.60 119.08 -6.48 1.00e+00 1.00e+00 4.20e+01 angle pdb=" CA PHE J 346 " pdb=" CB PHE J 346 " pdb=" CG PHE J 346 " ideal model delta sigma weight residual 113.80 119.89 -6.09 1.00e+00 1.00e+00 3.71e+01 ... (remaining 9253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.69: 3845 14.69 - 29.38: 291 29.38 - 44.07: 46 44.07 - 58.76: 20 58.76 - 73.45: 4 Dihedral angle restraints: 4206 sinusoidal: 1752 harmonic: 2454 Sorted by residual: dihedral pdb=" CA LYS C 343 " pdb=" C LYS C 343 " pdb=" N LEU C 344 " pdb=" CA LEU C 344 " ideal model delta harmonic sigma weight residual 180.00 150.92 29.08 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA LYS H 343 " pdb=" C LYS H 343 " pdb=" N LEU H 344 " pdb=" CA LEU H 344 " ideal model delta harmonic sigma weight residual 180.00 150.93 29.07 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA SER F 341 " pdb=" C SER F 341 " pdb=" N GLU F 342 " pdb=" CA GLU F 342 " ideal model delta harmonic sigma weight residual 180.00 151.23 28.77 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 4203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 716 0.100 - 0.199: 263 0.199 - 0.299: 47 0.299 - 0.398: 8 0.398 - 0.498: 10 Chirality restraints: 1044 Sorted by residual: chirality pdb=" CA LYS B 347 " pdb=" N LYS B 347 " pdb=" C LYS B 347 " pdb=" CB LYS B 347 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" CA LYS J 347 " pdb=" N LYS J 347 " pdb=" C LYS J 347 " pdb=" CB LYS J 347 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.09e+00 chirality pdb=" CA LYS D 311 " pdb=" N LYS D 311 " pdb=" C LYS D 311 " pdb=" CB LYS D 311 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.10e+00 ... (remaining 1041 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.153 2.00e-02 2.50e+03 8.17e-02 1.34e+02 pdb=" CG TYR A 310 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " -0.071 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 310 " 0.153 2.00e-02 2.50e+03 8.17e-02 1.34e+02 pdb=" CG TYR G 310 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR G 310 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 TYR G 310 " -0.071 2.00e-02 2.50e+03 pdb=" CE1 TYR G 310 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TYR G 310 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR G 310 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR G 310 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 352 " -0.055 2.00e-02 2.50e+03 1.04e-01 1.08e+02 pdb=" C SER E 352 " 0.180 2.00e-02 2.50e+03 pdb=" O SER E 352 " -0.066 2.00e-02 2.50e+03 pdb=" N LYS E 353 " -0.058 2.00e-02 2.50e+03 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 7 2.20 - 2.87: 2010 2.87 - 3.55: 8455 3.55 - 4.22: 14788 4.22 - 4.90: 25944 Nonbonded interactions: 51204 Sorted by model distance: nonbonded pdb=" CG GLN F 336 " pdb=" CB GLN L 336 " model vdw 1.524 3.840 nonbonded pdb=" NZ LYS F 340 " pdb=" NZ LYS L 331 " model vdw 1.609 3.200 nonbonded pdb=" CE LYS F 340 " pdb=" NZ LYS L 331 " model vdw 1.729 3.520 nonbonded pdb=" CG GLN F 336 " pdb=" CG GLN L 336 " model vdw 1.852 3.840 nonbonded pdb=" CG GLN B 336 " pdb=" CB GLN J 336 " model vdw 1.943 3.840 ... (remaining 51199 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 306 through 378) selection = chain 'B' selection = (chain 'C' and resid 306 through 378) selection = chain 'D' selection = (chain 'E' and resid 306 through 378) selection = chain 'F' selection = (chain 'G' and resid 306 through 378) selection = (chain 'H' and resid 306 through 378) selection = (chain 'I' and resid 306 through 378) selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.460 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5163 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 : 0.012 0.041 6918 Z= 0.790 Angle : 2.007 11.574 9258 Z= 1.324 Chirality : 0.109 0.498 1044 Planarity : 0.012 0.104 1176 Dihedral : 11.636 73.452 2646 Min Nonbonded Distance : 1.524 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.77 % 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: -2.95 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.17), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.004 HIS I 362 PHE 0.040 0.010 PHE B 346 TYR 0.153 0.042 TYR G 310 ARG 0.009 0.001 ARG K 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7960 (mttt) cc_final: 0.7431 (ttmt) REVERT: A 346 PHE cc_start: 0.9093 (m-10) cc_final: 0.8765 (m-10) REVERT: A 349 ARG cc_start: 0.8143 (mtm180) cc_final: 0.7866 (mtm-85) REVERT: A 359 ASN cc_start: 0.8475 (m-40) cc_final: 0.8226 (m110) REVERT: C 321 LYS cc_start: 0.8286 (mttt) cc_final: 0.7602 (ttmt) REVERT: C 349 ARG cc_start: 0.7971 (mtm180) cc_final: 0.6817 (ppt170) REVERT: E 311 LYS cc_start: 0.7997 (mttt) cc_final: 0.7192 (mmtm) REVERT: E 321 LYS cc_start: 0.7964 (mttt) cc_final: 0.7494 (ttmt) REVERT: E 331 LYS cc_start: 0.8711 (mttt) cc_final: 0.8089 (mmtt) REVERT: E 347 LYS cc_start: 0.8392 (mttp) cc_final: 0.8104 (ttmm) REVERT: E 349 ARG cc_start: 0.7824 (mtm180) cc_final: 0.6745 (mmp-170) REVERT: B 320 SER cc_start: 0.8655 (m) cc_final: 0.8365 (m) REVERT: B 349 ARG cc_start: 0.7358 (mtm180) cc_final: 0.7129 (mtm-85) REVERT: B 369 LYS cc_start: 0.8037 (mtpt) cc_final: 0.7622 (mptt) REVERT: D 349 ARG cc_start: 0.7475 (mtm180) cc_final: 0.7009 (mtm-85) REVERT: D 369 LYS cc_start: 0.8023 (mtpt) cc_final: 0.7596 (mptt) REVERT: H 346 PHE cc_start: 0.8255 (m-10) cc_final: 0.7885 (m-80) REVERT: I 349 ARG cc_start: 0.7113 (mtm180) cc_final: 0.6572 (mmp80) REVERT: K 374 HIS cc_start: 0.5785 (m-70) cc_final: 0.5240 (p-80) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2494 time to fit residues: 58.3641 Evaluate side-chains 135 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 40.0000 chunk 63 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 327 ASN B 330 HIS B 362 HIS D 327 ASN D 359 ASN D 362 HIS F 327 ASN ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 HIS ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 HIS ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 362 HIS ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 362 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6918 Z= 0.287 Angle : 0.805 7.387 9258 Z= 0.428 Chirality : 0.053 0.163 1044 Planarity : 0.004 0.027 1176 Dihedral : 6.637 27.698 912 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.82 % Allowed : 10.90 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.17), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS I 329 PHE 0.013 0.002 PHE B 378 TYR 0.020 0.003 TYR L 310 ARG 0.008 0.002 ARG J 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 177 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7995 (mttt) cc_final: 0.7514 (ttmt) REVERT: A 336 GLN cc_start: 0.8464 (tm130) cc_final: 0.8093 (tm-30) REVERT: A 347 LYS cc_start: 0.8525 (mptt) cc_final: 0.8166 (mmtm) REVERT: C 321 LYS cc_start: 0.8271 (mttt) cc_final: 0.7793 (ttmt) REVERT: C 336 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8083 (tm-30) REVERT: C 349 ARG cc_start: 0.8106 (mtm180) cc_final: 0.7860 (mtt90) REVERT: C 351 GLN cc_start: 0.7752 (mp10) cc_final: 0.7039 (mp10) REVERT: C 368 ASN cc_start: 0.8347 (m-40) cc_final: 0.8058 (m-40) REVERT: E 311 LYS cc_start: 0.7986 (mttt) cc_final: 0.7044 (mmtm) REVERT: E 320 SER cc_start: 0.8867 (p) cc_final: 0.8662 (m) REVERT: E 321 LYS cc_start: 0.7968 (mttt) cc_final: 0.7695 (ttmt) REVERT: E 331 LYS cc_start: 0.8778 (mttt) cc_final: 0.8034 (mmmt) REVERT: E 336 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8087 (tm-30) REVERT: E 349 ARG cc_start: 0.7877 (mtm180) cc_final: 0.6808 (mmp-170) REVERT: B 322 CYS cc_start: 0.7869 (p) cc_final: 0.7435 (p) REVERT: B 369 LYS cc_start: 0.8131 (mtpt) cc_final: 0.7749 (mptt) REVERT: D 369 LYS cc_start: 0.8390 (mtpt) cc_final: 0.8056 (mptt) REVERT: G 321 LYS cc_start: 0.8068 (mttt) cc_final: 0.7751 (ttpp) REVERT: G 362 HIS cc_start: 0.8117 (t70) cc_final: 0.7758 (t-90) REVERT: G 369 LYS cc_start: 0.7856 (ptpp) cc_final: 0.7648 (ptpp) REVERT: H 321 LYS cc_start: 0.8104 (mttt) cc_final: 0.7605 (ttmt) REVERT: H 344 LEU cc_start: 0.8908 (mp) cc_final: 0.8167 (tt) REVERT: H 345 ASP cc_start: 0.7533 (m-30) cc_final: 0.7124 (t0) REVERT: H 349 ARG cc_start: 0.6949 (mtm180) cc_final: 0.5772 (ptt-90) REVERT: I 322 CYS cc_start: 0.8188 (t) cc_final: 0.7754 (m) REVERT: I 349 ARG cc_start: 0.7338 (mtm180) cc_final: 0.6998 (mmp-170) REVERT: K 340 LYS cc_start: 0.7696 (mtpt) cc_final: 0.7477 (mtmm) REVERT: K 348 ASP cc_start: 0.7520 (t0) cc_final: 0.6923 (t0) REVERT: K 376 LEU cc_start: 0.5951 (pt) cc_final: 0.5630 (tt) outliers start: 22 outliers final: 13 residues processed: 189 average time/residue: 0.2323 time to fit residues: 53.6608 Evaluate side-chains 150 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 137 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain G residue 306 VAL Chi-restraints excluded: chain H residue 322 CYS Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain L residue 350 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 63 optimal weight: 20.0000 chunk 51 optimal weight: 0.2980 chunk 21 optimal weight: 40.0000 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 68 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 HIS ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 330 HIS H 336 GLN H 368 ASN ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 359 ASN L 327 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.6416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6918 Z= 0.226 Angle : 0.715 7.217 9258 Z= 0.368 Chirality : 0.051 0.159 1044 Planarity : 0.004 0.039 1176 Dihedral : 6.003 22.050 912 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.46 % Allowed : 12.69 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.24), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.18), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 330 PHE 0.013 0.002 PHE F 378 TYR 0.026 0.003 TYR I 310 ARG 0.006 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 158 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8054 (mttt) cc_final: 0.7576 (ttmt) REVERT: A 325 LEU cc_start: 0.8812 (mt) cc_final: 0.8590 (mp) REVERT: A 336 GLN cc_start: 0.8429 (tm130) cc_final: 0.8017 (tm-30) REVERT: A 347 LYS cc_start: 0.8509 (mptt) cc_final: 0.8159 (mmtm) REVERT: C 321 LYS cc_start: 0.8252 (mttt) cc_final: 0.7628 (ttmt) REVERT: C 336 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8029 (tm-30) REVERT: C 349 ARG cc_start: 0.8092 (mtm180) cc_final: 0.7635 (mtm-85) REVERT: C 350 VAL cc_start: 0.8262 (OUTLIER) cc_final: 0.7887 (p) REVERT: C 351 GLN cc_start: 0.7646 (mp10) cc_final: 0.7272 (mp10) REVERT: E 311 LYS cc_start: 0.7834 (mttt) cc_final: 0.6847 (mmtt) REVERT: E 321 LYS cc_start: 0.8016 (mttt) cc_final: 0.7737 (ttmt) REVERT: E 336 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8121 (tm-30) REVERT: E 349 ARG cc_start: 0.7694 (mtm180) cc_final: 0.6834 (mmp-170) REVERT: E 379 ARG cc_start: 0.7389 (mtt180) cc_final: 0.7076 (ttm110) REVERT: B 360 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7482 (mp) REVERT: B 369 LYS cc_start: 0.8037 (mtpt) cc_final: 0.7688 (mptt) REVERT: D 348 ASP cc_start: 0.8017 (t0) cc_final: 0.7525 (t0) REVERT: D 369 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7971 (mptt) REVERT: F 347 LYS cc_start: 0.8699 (mtpp) cc_final: 0.8244 (ttmm) REVERT: F 348 ASP cc_start: 0.8360 (t0) cc_final: 0.7523 (p0) REVERT: G 321 LYS cc_start: 0.8032 (mttt) cc_final: 0.7608 (tttm) REVERT: G 369 LYS cc_start: 0.8162 (ptpp) cc_final: 0.7942 (ptpp) REVERT: H 321 LYS cc_start: 0.8151 (mttt) cc_final: 0.7506 (ttmt) REVERT: H 349 ARG cc_start: 0.7427 (mtm180) cc_final: 0.6023 (ptt-90) REVERT: I 349 ARG cc_start: 0.7301 (mtm180) cc_final: 0.7016 (mmp-170) REVERT: I 372 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: I 375 LYS cc_start: 0.7320 (mmtm) cc_final: 0.7041 (mptt) REVERT: J 348 ASP cc_start: 0.8050 (t0) cc_final: 0.7686 (t0) REVERT: J 349 ARG cc_start: 0.7408 (mtm-85) cc_final: 0.7021 (mtm-85) REVERT: J 374 HIS cc_start: 0.5781 (m90) cc_final: 0.5411 (m-70) REVERT: K 317 LYS cc_start: 0.7573 (pttt) cc_final: 0.7364 (mmtt) REVERT: K 349 ARG cc_start: 0.7459 (mtm180) cc_final: 0.7103 (mtm-85) REVERT: K 376 LEU cc_start: 0.6118 (pt) cc_final: 0.5836 (tt) outliers start: 27 outliers final: 14 residues processed: 169 average time/residue: 0.2798 time to fit residues: 56.9316 Evaluate side-chains 153 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 136 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain G residue 306 VAL Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 372 GLU Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain L residue 337 VAL Chi-restraints excluded: chain L residue 350 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 330 HIS ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 368 ASN L 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.8316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6918 Z= 0.291 Angle : 0.805 8.856 9258 Z= 0.423 Chirality : 0.053 0.194 1044 Planarity : 0.006 0.092 1176 Dihedral : 6.613 32.508 912 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.46 % Allowed : 15.13 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.62 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.18), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 374 PHE 0.024 0.002 PHE B 378 TYR 0.031 0.004 TYR I 310 ARG 0.010 0.001 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 169 time to evaluate : 0.799 Fit side-chains REVERT: A 321 LYS cc_start: 0.8205 (mttt) cc_final: 0.7642 (ttmt) REVERT: A 336 GLN cc_start: 0.8561 (tm130) cc_final: 0.8023 (tm-30) REVERT: A 347 LYS cc_start: 0.8615 (mptt) cc_final: 0.8215 (mmtm) REVERT: C 321 LYS cc_start: 0.8364 (mttt) cc_final: 0.7782 (ttmt) REVERT: C 336 GLN cc_start: 0.8429 (tm-30) cc_final: 0.7977 (tm-30) REVERT: C 351 GLN cc_start: 0.7725 (mp10) cc_final: 0.7308 (mp10) REVERT: E 311 LYS cc_start: 0.7983 (mttt) cc_final: 0.6881 (mmtt) REVERT: E 321 LYS cc_start: 0.8036 (mttt) cc_final: 0.7729 (ttmt) REVERT: E 336 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8086 (tm-30) REVERT: E 349 ARG cc_start: 0.7886 (mtm180) cc_final: 0.6934 (mmp-170) REVERT: E 379 ARG cc_start: 0.7423 (mtt180) cc_final: 0.7171 (ttm110) REVERT: B 347 LYS cc_start: 0.8423 (ptmt) cc_final: 0.8009 (ttmm) REVERT: B 369 LYS cc_start: 0.8043 (mtpt) cc_final: 0.7690 (mptt) REVERT: D 369 LYS cc_start: 0.8143 (mtpt) cc_final: 0.7791 (mptt) REVERT: F 347 LYS cc_start: 0.8894 (mtpp) cc_final: 0.8454 (ttmm) REVERT: F 348 ASP cc_start: 0.8247 (t0) cc_final: 0.7090 (p0) REVERT: F 378 PHE cc_start: 0.6405 (t80) cc_final: 0.5918 (t80) REVERT: G 321 LYS cc_start: 0.8041 (mttt) cc_final: 0.7553 (ttpp) REVERT: H 311 LYS cc_start: 0.7688 (pttm) cc_final: 0.7287 (mtpt) REVERT: H 321 LYS cc_start: 0.8270 (mttt) cc_final: 0.7584 (ttmt) REVERT: H 349 ARG cc_start: 0.7910 (mtm180) cc_final: 0.6269 (ptt-90) REVERT: I 349 ARG cc_start: 0.7616 (mtm180) cc_final: 0.7239 (mmp-170) REVERT: J 347 LYS cc_start: 0.8500 (ptmt) cc_final: 0.8274 (mtmt) REVERT: J 374 HIS cc_start: 0.5678 (m90) cc_final: 0.5420 (m-70) REVERT: K 317 LYS cc_start: 0.7861 (pttt) cc_final: 0.7470 (mmmt) REVERT: K 348 ASP cc_start: 0.8297 (t0) cc_final: 0.7978 (t0) REVERT: K 371 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7989 (mp) REVERT: K 376 LEU cc_start: 0.6003 (pt) cc_final: 0.5732 (tt) REVERT: L 347 LYS cc_start: 0.8620 (ptmt) cc_final: 0.8136 (ttmm) REVERT: L 348 ASP cc_start: 0.8131 (t0) cc_final: 0.7302 (p0) REVERT: L 374 HIS cc_start: 0.6377 (m90) cc_final: 0.5737 (m90) outliers start: 27 outliers final: 20 residues processed: 184 average time/residue: 0.2650 time to fit residues: 59.4510 Evaluate side-chains 170 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 149 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain G residue 306 VAL Chi-restraints excluded: chain G residue 331 LYS Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain J residue 322 CYS Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain L residue 337 VAL Chi-restraints excluded: chain L residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 60 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN F 368 ASN ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 HIS ** J 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 362 HIS J 368 ASN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 368 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.9545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6918 Z= 0.361 Angle : 0.820 8.839 9258 Z= 0.435 Chirality : 0.055 0.192 1044 Planarity : 0.005 0.054 1176 Dihedral : 7.053 30.348 912 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 5.13 % Allowed : 17.56 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.17), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 362 PHE 0.015 0.003 PHE H 378 TYR 0.035 0.005 TYR I 310 ARG 0.007 0.001 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 157 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8316 (mttt) cc_final: 0.7710 (ttmt) REVERT: A 336 GLN cc_start: 0.8623 (tm130) cc_final: 0.8083 (tm-30) REVERT: A 347 LYS cc_start: 0.8702 (mptt) cc_final: 0.8259 (mmtm) REVERT: A 353 LYS cc_start: 0.8691 (tttt) cc_final: 0.8484 (tttt) REVERT: C 321 LYS cc_start: 0.8439 (mttt) cc_final: 0.7825 (ttmt) REVERT: C 336 GLN cc_start: 0.8463 (tm130) cc_final: 0.8048 (tm-30) REVERT: C 349 ARG cc_start: 0.8107 (mtm180) cc_final: 0.7665 (mtt90) REVERT: C 351 GLN cc_start: 0.7683 (mp10) cc_final: 0.6903 (mp10) REVERT: E 311 LYS cc_start: 0.8054 (mttt) cc_final: 0.6887 (mmtt) REVERT: E 321 LYS cc_start: 0.8015 (mttt) cc_final: 0.7707 (ttmt) REVERT: E 336 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8101 (tm-30) REVERT: E 349 ARG cc_start: 0.7963 (mtm180) cc_final: 0.6927 (mmp-170) REVERT: B 347 LYS cc_start: 0.8599 (ptmt) cc_final: 0.8135 (ttmm) REVERT: D 347 LYS cc_start: 0.8780 (ptmt) cc_final: 0.8089 (ttmm) REVERT: D 369 LYS cc_start: 0.8226 (mtpt) cc_final: 0.7805 (mptt) REVERT: D 375 LYS cc_start: 0.7055 (tptt) cc_final: 0.6807 (tptp) REVERT: F 347 LYS cc_start: 0.9005 (mtpp) cc_final: 0.8600 (ttmm) REVERT: F 378 PHE cc_start: 0.6586 (t80) cc_final: 0.5948 (t80) REVERT: G 321 LYS cc_start: 0.8078 (mttt) cc_final: 0.7448 (ttpp) REVERT: G 350 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8682 (p) REVERT: G 376 LEU cc_start: 0.7857 (mt) cc_final: 0.5986 (mt) REVERT: H 311 LYS cc_start: 0.7608 (pttm) cc_final: 0.7135 (mtpt) REVERT: H 321 LYS cc_start: 0.8466 (mttt) cc_final: 0.7725 (ttmt) REVERT: H 349 ARG cc_start: 0.8076 (mtm180) cc_final: 0.6329 (ptt-90) REVERT: I 310 TYR cc_start: 0.6007 (OUTLIER) cc_final: 0.4360 (t80) REVERT: I 349 ARG cc_start: 0.7969 (mtm180) cc_final: 0.7334 (mmp-170) REVERT: J 347 LYS cc_start: 0.8631 (ptmt) cc_final: 0.8078 (ttmm) REVERT: K 371 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8136 (mp) REVERT: L 340 LYS cc_start: 0.8602 (mmtp) cc_final: 0.8228 (mmtp) REVERT: L 347 LYS cc_start: 0.8806 (ptmt) cc_final: 0.8557 (ptmm) REVERT: L 348 ASP cc_start: 0.8298 (t0) cc_final: 0.7188 (p0) outliers start: 40 outliers final: 31 residues processed: 182 average time/residue: 0.2721 time to fit residues: 60.4469 Evaluate side-chains 177 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 143 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 322 CYS Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain G residue 306 VAL Chi-restraints excluded: chain G residue 331 LYS Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 310 TYR Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain J residue 322 CYS Chi-restraints excluded: chain J residue 341 SER Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain K residue 322 CYS Chi-restraints excluded: chain K residue 341 SER Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain K residue 375 LYS Chi-restraints excluded: chain L residue 330 HIS Chi-restraints excluded: chain L residue 337 VAL Chi-restraints excluded: chain L residue 341 SER Chi-restraints excluded: chain L residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 81 optimal weight: 0.5980 chunk 67 optimal weight: 0.0970 chunk 37 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 overall best weight: 3.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 327 ASN K 327 ASN ** L 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.9808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6918 Z= 0.233 Angle : 0.706 7.590 9258 Z= 0.366 Chirality : 0.051 0.159 1044 Planarity : 0.005 0.052 1176 Dihedral : 6.358 27.600 912 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.74 % Allowed : 18.85 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.17), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 330 PHE 0.013 0.001 PHE G 378 TYR 0.021 0.003 TYR A 310 ARG 0.008 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 150 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8267 (mttt) cc_final: 0.7648 (ttmt) REVERT: A 336 GLN cc_start: 0.8655 (tm130) cc_final: 0.8106 (tm-30) REVERT: C 321 LYS cc_start: 0.8398 (mttt) cc_final: 0.7757 (ttmt) REVERT: C 336 GLN cc_start: 0.8474 (tm130) cc_final: 0.8073 (tm-30) REVERT: C 349 ARG cc_start: 0.8056 (mtm180) cc_final: 0.7707 (mtt90) REVERT: C 351 GLN cc_start: 0.7706 (mp10) cc_final: 0.7281 (mp10) REVERT: E 311 LYS cc_start: 0.7994 (mttt) cc_final: 0.6820 (mmtt) REVERT: E 321 LYS cc_start: 0.7983 (mttt) cc_final: 0.7662 (ttmt) REVERT: E 336 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8132 (tm-30) REVERT: E 349 ARG cc_start: 0.7822 (mtm180) cc_final: 0.6941 (mmp-170) REVERT: B 347 LYS cc_start: 0.8437 (ptmt) cc_final: 0.7943 (ttmm) REVERT: B 360 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.7534 (mt) REVERT: D 347 LYS cc_start: 0.8493 (ptmt) cc_final: 0.8129 (ptmm) REVERT: D 369 LYS cc_start: 0.8199 (mtpt) cc_final: 0.7785 (mptt) REVERT: F 347 LYS cc_start: 0.8909 (mtpp) cc_final: 0.8430 (ttmm) REVERT: F 378 PHE cc_start: 0.6424 (t80) cc_final: 0.5745 (t80) REVERT: G 321 LYS cc_start: 0.8031 (mttt) cc_final: 0.7457 (ttmt) REVERT: G 340 LYS cc_start: 0.7453 (tptp) cc_final: 0.6070 (mttm) REVERT: G 350 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8582 (p) REVERT: H 311 LYS cc_start: 0.7549 (pttm) cc_final: 0.7071 (mtpt) REVERT: H 321 LYS cc_start: 0.8362 (mttt) cc_final: 0.7826 (tttm) REVERT: H 349 ARG cc_start: 0.8040 (mtm180) cc_final: 0.6353 (ptt-90) REVERT: I 349 ARG cc_start: 0.8058 (mtm180) cc_final: 0.7518 (mmp-170) REVERT: J 347 LYS cc_start: 0.8461 (ptmt) cc_final: 0.7808 (ptmm) REVERT: K 351 GLN cc_start: 0.7848 (mp10) cc_final: 0.7343 (mp10) REVERT: K 371 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8088 (mp) REVERT: L 340 LYS cc_start: 0.8527 (mmtp) cc_final: 0.8317 (mmtp) REVERT: L 347 LYS cc_start: 0.8759 (ptmt) cc_final: 0.8016 (ttmm) REVERT: L 348 ASP cc_start: 0.8211 (t0) cc_final: 0.7066 (p0) outliers start: 37 outliers final: 33 residues processed: 172 average time/residue: 0.2333 time to fit residues: 49.9028 Evaluate side-chains 179 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 143 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain F residue 322 CYS Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain G residue 306 VAL Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 331 LYS Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 361 THR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain J residue 322 CYS Chi-restraints excluded: chain J residue 341 SER Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain K residue 341 SER Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain K residue 375 LYS Chi-restraints excluded: chain L residue 322 CYS Chi-restraints excluded: chain L residue 330 HIS Chi-restraints excluded: chain L residue 337 VAL Chi-restraints excluded: chain L residue 341 SER Chi-restraints excluded: chain L residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 chunk 46 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 49 optimal weight: 40.0000 chunk 37 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 1.0245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6918 Z= 0.281 Angle : 0.747 7.777 9258 Z= 0.390 Chirality : 0.052 0.176 1044 Planarity : 0.005 0.057 1176 Dihedral : 6.455 27.093 912 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 5.13 % Allowed : 18.85 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.18), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS G 362 PHE 0.019 0.002 PHE H 378 TYR 0.025 0.004 TYR I 310 ARG 0.007 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 152 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8245 (mttt) cc_final: 0.7637 (ttmt) REVERT: A 336 GLN cc_start: 0.8650 (tm130) cc_final: 0.8086 (tm-30) REVERT: C 321 LYS cc_start: 0.8415 (mttt) cc_final: 0.7799 (ttmt) REVERT: C 336 GLN cc_start: 0.8472 (tm130) cc_final: 0.8071 (tm-30) REVERT: C 351 GLN cc_start: 0.7716 (mp10) cc_final: 0.7301 (mp10) REVERT: E 311 LYS cc_start: 0.7995 (mttt) cc_final: 0.6807 (mmtt) REVERT: E 321 LYS cc_start: 0.8017 (mttt) cc_final: 0.7678 (ttmt) REVERT: E 336 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8143 (tm-30) REVERT: E 349 ARG cc_start: 0.7874 (mtm180) cc_final: 0.6889 (mmp-170) REVERT: B 347 LYS cc_start: 0.8534 (ptmt) cc_final: 0.8108 (ttmm) REVERT: B 360 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.7600 (mt) REVERT: D 347 LYS cc_start: 0.8656 (ptmt) cc_final: 0.7933 (ttmm) REVERT: D 360 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.6848 (mt) REVERT: D 369 LYS cc_start: 0.8102 (mtpt) cc_final: 0.7783 (mptt) REVERT: F 347 LYS cc_start: 0.8949 (mtpp) cc_final: 0.8269 (ttmm) REVERT: F 378 PHE cc_start: 0.6500 (t80) cc_final: 0.5720 (t80) REVERT: G 321 LYS cc_start: 0.8018 (mttt) cc_final: 0.7487 (ttmt) REVERT: G 340 LYS cc_start: 0.7193 (tptp) cc_final: 0.6134 (mttm) REVERT: G 345 ASP cc_start: 0.7833 (t0) cc_final: 0.7410 (m-30) REVERT: G 350 VAL cc_start: 0.8757 (OUTLIER) cc_final: 0.8522 (p) REVERT: G 376 LEU cc_start: 0.7899 (mt) cc_final: 0.6472 (mt) REVERT: H 311 LYS cc_start: 0.7642 (pttm) cc_final: 0.7127 (mtpt) REVERT: H 321 LYS cc_start: 0.8386 (mttt) cc_final: 0.7672 (ttmt) REVERT: H 349 ARG cc_start: 0.8147 (mtm180) cc_final: 0.6476 (ptt-90) REVERT: I 310 TYR cc_start: 0.6193 (OUTLIER) cc_final: 0.4781 (t80) REVERT: I 369 LYS cc_start: 0.7916 (tttt) cc_final: 0.7550 (mttm) REVERT: J 347 LYS cc_start: 0.8597 (ptmt) cc_final: 0.7876 (ttmm) REVERT: K 351 GLN cc_start: 0.7886 (mp10) cc_final: 0.7283 (mp10) REVERT: L 347 LYS cc_start: 0.8886 (ptmt) cc_final: 0.8221 (ttmm) REVERT: L 348 ASP cc_start: 0.8327 (t0) cc_final: 0.7122 (p0) outliers start: 40 outliers final: 34 residues processed: 176 average time/residue: 0.2430 time to fit residues: 52.9766 Evaluate side-chains 184 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 146 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 322 CYS Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain G residue 306 VAL Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 331 LYS Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 310 TYR Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain J residue 322 CYS Chi-restraints excluded: chain J residue 341 SER Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain K residue 322 CYS Chi-restraints excluded: chain K residue 341 SER Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain L residue 322 CYS Chi-restraints excluded: chain L residue 330 HIS Chi-restraints excluded: chain L residue 337 VAL Chi-restraints excluded: chain L residue 341 SER Chi-restraints excluded: chain L residue 350 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 0.2980 chunk 7 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 329 HIS ** L 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 1.0509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6918 Z= 0.262 Angle : 0.728 7.188 9258 Z= 0.379 Chirality : 0.052 0.165 1044 Planarity : 0.005 0.057 1176 Dihedral : 6.322 23.271 912 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 5.38 % Allowed : 18.97 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.18), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS G 362 PHE 0.020 0.002 PHE I 378 TYR 0.024 0.003 TYR I 310 ARG 0.006 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 148 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8242 (mttt) cc_final: 0.7677 (ttmt) REVERT: A 336 GLN cc_start: 0.8674 (tm130) cc_final: 0.8137 (tm-30) REVERT: C 321 LYS cc_start: 0.8388 (mttt) cc_final: 0.7766 (ttmt) REVERT: C 336 GLN cc_start: 0.8470 (tm130) cc_final: 0.8089 (tm-30) REVERT: C 351 GLN cc_start: 0.7740 (mp10) cc_final: 0.7334 (mp10) REVERT: E 311 LYS cc_start: 0.7987 (mttt) cc_final: 0.6799 (mmtt) REVERT: E 321 LYS cc_start: 0.8047 (mttt) cc_final: 0.7642 (ttmt) REVERT: E 336 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8157 (tm-30) REVERT: E 349 ARG cc_start: 0.7879 (mtm180) cc_final: 0.6960 (mmp-170) REVERT: B 347 LYS cc_start: 0.8412 (ptmt) cc_final: 0.8025 (ttmm) REVERT: B 360 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7626 (mt) REVERT: D 347 LYS cc_start: 0.8576 (ptmt) cc_final: 0.7866 (ttmm) REVERT: D 348 ASP cc_start: 0.7954 (t0) cc_final: 0.7336 (t0) REVERT: D 360 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.6881 (mt) REVERT: D 369 LYS cc_start: 0.8136 (mtpt) cc_final: 0.7817 (mptt) REVERT: F 347 LYS cc_start: 0.8808 (mtpp) cc_final: 0.8111 (ttmm) REVERT: F 378 PHE cc_start: 0.6580 (t80) cc_final: 0.5753 (t80) REVERT: G 321 LYS cc_start: 0.8028 (mttt) cc_final: 0.7506 (ttmt) REVERT: G 345 ASP cc_start: 0.7734 (t0) cc_final: 0.7403 (m-30) REVERT: G 350 VAL cc_start: 0.8711 (OUTLIER) cc_final: 0.8473 (p) REVERT: H 311 LYS cc_start: 0.7503 (pttm) cc_final: 0.7054 (mtpt) REVERT: H 321 LYS cc_start: 0.8396 (mttt) cc_final: 0.7647 (ttmt) REVERT: H 349 ARG cc_start: 0.8125 (mtm180) cc_final: 0.6371 (ptt-90) REVERT: I 369 LYS cc_start: 0.8156 (tttt) cc_final: 0.7844 (ttmm) REVERT: J 311 LYS cc_start: 0.5773 (mtmm) cc_final: 0.5334 (mmmm) REVERT: J 347 LYS cc_start: 0.8498 (ptmt) cc_final: 0.7765 (ttmm) REVERT: J 360 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.7455 (mp) REVERT: K 314 ASP cc_start: 0.5588 (p0) cc_final: 0.4822 (t70) REVERT: K 347 LYS cc_start: 0.8832 (mtpp) cc_final: 0.8355 (ttmm) REVERT: K 351 GLN cc_start: 0.7934 (mp10) cc_final: 0.7312 (mp10) REVERT: L 347 LYS cc_start: 0.8865 (ptmt) cc_final: 0.8215 (ttmm) REVERT: L 348 ASP cc_start: 0.8285 (t0) cc_final: 0.7100 (p0) outliers start: 42 outliers final: 37 residues processed: 170 average time/residue: 0.2211 time to fit residues: 47.5410 Evaluate side-chains 185 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 144 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 322 CYS Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain G residue 306 VAL Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 331 LYS Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain J residue 322 CYS Chi-restraints excluded: chain J residue 341 SER Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain K residue 322 CYS Chi-restraints excluded: chain K residue 328 ILE Chi-restraints excluded: chain K residue 341 SER Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain K residue 375 LYS Chi-restraints excluded: chain K residue 376 LEU Chi-restraints excluded: chain L residue 322 CYS Chi-restraints excluded: chain L residue 330 HIS Chi-restraints excluded: chain L residue 337 VAL Chi-restraints excluded: chain L residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 1.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6918 Z= 0.360 Angle : 0.816 11.711 9258 Z= 0.427 Chirality : 0.055 0.203 1044 Planarity : 0.006 0.063 1176 Dihedral : 6.807 25.103 912 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 6.41 % Allowed : 18.85 % Favored : 74.74 % 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: -3.38 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.18), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS G 362 PHE 0.022 0.002 PHE H 378 TYR 0.034 0.004 TYR I 310 ARG 0.005 0.001 ARG J 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 150 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8250 (mttt) cc_final: 0.7656 (ttmt) REVERT: A 336 GLN cc_start: 0.8690 (tm130) cc_final: 0.8155 (tm-30) REVERT: A 353 LYS cc_start: 0.8732 (tttt) cc_final: 0.8492 (tttt) REVERT: C 321 LYS cc_start: 0.8429 (mttt) cc_final: 0.7816 (ttmt) REVERT: C 336 GLN cc_start: 0.8472 (tm130) cc_final: 0.8040 (tm-30) REVERT: C 351 GLN cc_start: 0.7779 (mp10) cc_final: 0.7004 (mp10) REVERT: E 311 LYS cc_start: 0.8018 (mttt) cc_final: 0.6788 (mmtt) REVERT: E 321 LYS cc_start: 0.8175 (mttt) cc_final: 0.7665 (ttmt) REVERT: E 336 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8144 (tm-30) REVERT: E 349 ARG cc_start: 0.7920 (mtm180) cc_final: 0.6966 (mmp-170) REVERT: E 351 GLN cc_start: 0.7027 (mp10) cc_final: 0.6740 (mp10) REVERT: B 347 LYS cc_start: 0.8574 (ptmt) cc_final: 0.8149 (ttmm) REVERT: B 360 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.7517 (mt) REVERT: D 347 LYS cc_start: 0.8825 (ptmt) cc_final: 0.8127 (ttmm) REVERT: D 369 LYS cc_start: 0.8069 (mtpt) cc_final: 0.7727 (mptt) REVERT: F 347 LYS cc_start: 0.8870 (mtpp) cc_final: 0.8372 (ttmm) REVERT: F 378 PHE cc_start: 0.6741 (t80) cc_final: 0.6180 (t80) REVERT: G 311 LYS cc_start: 0.7106 (ttmm) cc_final: 0.6857 (ttmt) REVERT: G 321 LYS cc_start: 0.8021 (mttt) cc_final: 0.7448 (ttmt) REVERT: G 345 ASP cc_start: 0.7794 (t0) cc_final: 0.7402 (t0) REVERT: G 350 VAL cc_start: 0.8678 (OUTLIER) cc_final: 0.8424 (p) REVERT: H 311 LYS cc_start: 0.7724 (pttm) cc_final: 0.7198 (mtpt) REVERT: H 321 LYS cc_start: 0.8406 (mttt) cc_final: 0.7723 (ttmt) REVERT: H 349 ARG cc_start: 0.8165 (mtm180) cc_final: 0.6562 (ptt-90) REVERT: I 310 TYR cc_start: 0.6379 (OUTLIER) cc_final: 0.4626 (t80) REVERT: I 369 LYS cc_start: 0.8320 (tttt) cc_final: 0.8036 (ttmm) REVERT: I 375 LYS cc_start: 0.8490 (tppt) cc_final: 0.7734 (tppt) REVERT: J 311 LYS cc_start: 0.6150 (mtmm) cc_final: 0.5582 (mmmm) REVERT: J 347 LYS cc_start: 0.8743 (ptmt) cc_final: 0.8187 (ttmm) REVERT: K 347 LYS cc_start: 0.8943 (mtpp) cc_final: 0.8507 (ttmm) REVERT: K 351 GLN cc_start: 0.7905 (mp10) cc_final: 0.7265 (mp10) REVERT: L 348 ASP cc_start: 0.8369 (t0) cc_final: 0.7192 (p0) outliers start: 50 outliers final: 44 residues processed: 178 average time/residue: 0.2373 time to fit residues: 52.6209 Evaluate side-chains 192 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 145 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 322 CYS Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain G residue 306 VAL Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 331 LYS Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 363 VAL Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 310 TYR Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain I residue 327 ASN Chi-restraints excluded: chain J residue 313 VAL Chi-restraints excluded: chain J residue 341 SER Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain K residue 322 CYS Chi-restraints excluded: chain K residue 328 ILE Chi-restraints excluded: chain K residue 341 SER Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain K residue 375 LYS Chi-restraints excluded: chain L residue 322 CYS Chi-restraints excluded: chain L residue 330 HIS Chi-restraints excluded: chain L residue 337 VAL Chi-restraints excluded: chain L residue 341 SER Chi-restraints excluded: chain L residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 83 optimal weight: 0.0070 chunk 77 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 362 HIS ** L 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 1.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6918 Z= 0.190 Angle : 0.704 10.631 9258 Z= 0.359 Chirality : 0.051 0.245 1044 Planarity : 0.005 0.066 1176 Dihedral : 6.098 24.701 912 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.87 % Allowed : 20.51 % Favored : 74.62 % 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: -3.26 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.18), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS G 362 PHE 0.023 0.002 PHE E 378 TYR 0.016 0.002 TYR A 310 ARG 0.005 0.001 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 147 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8199 (mttt) cc_final: 0.7636 (ttmt) REVERT: A 336 GLN cc_start: 0.8705 (tm130) cc_final: 0.8167 (tm-30) REVERT: C 321 LYS cc_start: 0.8324 (mttt) cc_final: 0.7687 (ttmt) REVERT: C 336 GLN cc_start: 0.8487 (tm130) cc_final: 0.8119 (tm-30) REVERT: C 351 GLN cc_start: 0.7730 (mp10) cc_final: 0.7008 (mp10) REVERT: E 311 LYS cc_start: 0.7873 (mttt) cc_final: 0.6683 (mmtt) REVERT: E 321 LYS cc_start: 0.8055 (mttt) cc_final: 0.7626 (ttmt) REVERT: E 336 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8207 (tm-30) REVERT: E 349 ARG cc_start: 0.7861 (mtm180) cc_final: 0.7106 (mmp-170) REVERT: B 347 LYS cc_start: 0.8304 (ptmt) cc_final: 0.7774 (ttmm) REVERT: B 360 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.7506 (mt) REVERT: D 369 LYS cc_start: 0.8108 (mtpt) cc_final: 0.7805 (mptt) REVERT: F 347 LYS cc_start: 0.8785 (mtpp) cc_final: 0.8169 (ttmm) REVERT: F 349 ARG cc_start: 0.7523 (mpp80) cc_final: 0.6960 (ptt90) REVERT: F 378 PHE cc_start: 0.6581 (t80) cc_final: 0.5932 (t80) REVERT: G 350 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8414 (p) REVERT: H 311 LYS cc_start: 0.7466 (pttm) cc_final: 0.7069 (mtpt) REVERT: H 321 LYS cc_start: 0.8367 (mttt) cc_final: 0.7800 (tttm) REVERT: H 349 ARG cc_start: 0.8175 (mtm180) cc_final: 0.6471 (ptt-90) REVERT: I 369 LYS cc_start: 0.8204 (tttt) cc_final: 0.7923 (ttmm) REVERT: J 311 LYS cc_start: 0.6069 (mtmm) cc_final: 0.5738 (mmmm) REVERT: K 351 GLN cc_start: 0.7979 (mp10) cc_final: 0.7333 (mp10) REVERT: L 347 LYS cc_start: 0.8637 (ptmm) cc_final: 0.7930 (ttmm) REVERT: L 348 ASP cc_start: 0.8191 (t0) cc_final: 0.7027 (p0) outliers start: 38 outliers final: 35 residues processed: 161 average time/residue: 0.2167 time to fit residues: 44.2971 Evaluate side-chains 181 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 144 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 322 CYS Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain G residue 306 VAL Chi-restraints excluded: chain G residue 331 LYS Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 362 HIS Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain J residue 313 VAL Chi-restraints excluded: chain J residue 341 SER Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain K residue 322 CYS Chi-restraints excluded: chain K residue 328 ILE Chi-restraints excluded: chain K residue 341 SER Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain K residue 375 LYS Chi-restraints excluded: chain K residue 376 LEU Chi-restraints excluded: chain L residue 322 CYS Chi-restraints excluded: chain L residue 330 HIS Chi-restraints excluded: chain L residue 341 SER Chi-restraints excluded: chain L residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 3 optimal weight: 40.0000 chunk 48 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 368 ASN ** L 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.172413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.139258 restraints weight = 9317.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.141771 restraints weight = 4910.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.143359 restraints weight = 3377.758| |-----------------------------------------------------------------------------| r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 1.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6918 Z= 0.366 Angle : 0.824 12.762 9258 Z= 0.432 Chirality : 0.055 0.223 1044 Planarity : 0.006 0.066 1176 Dihedral : 6.628 23.959 912 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 4.74 % Allowed : 20.90 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.18), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.002 HIS G 362 PHE 0.018 0.002 PHE E 378 TYR 0.039 0.004 TYR I 310 ARG 0.006 0.001 ARG K 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1781.46 seconds wall clock time: 35 minutes 59.20 seconds (2159.20 seconds total)