Starting phenix.real_space_refine on Mon Mar 11 03:31:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8e_18252/03_2024/8q8e_18252.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8e_18252/03_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_18252/03_2024/8q8e_18252.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8e_18252/03_2024/8q8e_18252.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8e_18252/03_2024/8q8e_18252.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8e_18252/03_2024/8q8e_18252.pdb" } 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 3.74, per 1000 atoms: 0.55 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: 2.32 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: 0.95 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: 1.76 Time building geometry restraints manager: 2.51 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 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: 3.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 13.350 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 20.670 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.130 ------------------------------------------------------------------------------- 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 : 0.796 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: 0.2437 time to fit residues: 56.6749 Evaluate side-chains 135 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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: 30.0000 chunk 63 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 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 E 362 HIS B 327 ASN B 330 HIS B 362 HIS ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 ASN D 362 HIS F 327 ASN ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 HIS ** G 329 HIS ** 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 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 362 HIS J 327 ASN ** K 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 327 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6022 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6918 Z= 0.275 Angle : 0.760 7.205 9258 Z= 0.404 Chirality : 0.051 0.156 1044 Planarity : 0.004 0.033 1176 Dihedral : 6.644 26.758 912 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.08 % Allowed : 10.90 % Favored : 86.03 % 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: -2.49 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.18), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS I 329 PHE 0.014 0.002 PHE G 346 TYR 0.020 0.003 TYR L 310 ARG 0.005 0.001 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 202 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 178 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8032 (mttt) cc_final: 0.7540 (ttmt) REVERT: A 336 GLN cc_start: 0.8460 (tm130) cc_final: 0.8035 (tm-30) REVERT: A 347 LYS cc_start: 0.8524 (mptt) cc_final: 0.8211 (mmtm) REVERT: A 353 LYS cc_start: 0.8407 (tttt) cc_final: 0.8057 (tttt) REVERT: C 321 LYS cc_start: 0.8285 (mttt) cc_final: 0.7781 (ttmt) REVERT: C 336 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8207 (tm-30) REVERT: C 349 ARG cc_start: 0.8174 (mtm180) cc_final: 0.7080 (ptt90) REVERT: E 311 LYS cc_start: 0.7996 (mttt) cc_final: 0.6991 (mmtm) REVERT: E 320 SER cc_start: 0.8829 (p) cc_final: 0.8595 (m) REVERT: E 321 LYS cc_start: 0.7963 (mttt) cc_final: 0.7675 (ttmt) REVERT: E 331 LYS cc_start: 0.8815 (mttt) cc_final: 0.8108 (mmmt) REVERT: E 349 ARG cc_start: 0.7917 (mtm180) cc_final: 0.7702 (mtp85) REVERT: E 376 LEU cc_start: 0.7565 (tt) cc_final: 0.7336 (mp) REVERT: B 314 ASP cc_start: 0.6839 (t0) cc_final: 0.6461 (t0) REVERT: B 369 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7691 (mptt) REVERT: D 348 ASP cc_start: 0.7952 (t0) cc_final: 0.7601 (t0) REVERT: D 369 LYS cc_start: 0.8355 (mtpt) cc_final: 0.7973 (mptt) REVERT: G 321 LYS cc_start: 0.8100 (mttt) cc_final: 0.7702 (ttpp) REVERT: G 362 HIS cc_start: 0.7977 (t70) cc_final: 0.7706 (t-90) REVERT: H 321 LYS cc_start: 0.7924 (mttt) cc_final: 0.7433 (ttmt) REVERT: H 345 ASP cc_start: 0.7690 (m-30) cc_final: 0.7189 (t0) REVERT: H 349 ARG cc_start: 0.6647 (mtm180) cc_final: 0.5487 (ptt-90) REVERT: I 322 CYS cc_start: 0.7997 (t) cc_final: 0.7641 (m) REVERT: I 349 ARG cc_start: 0.7292 (mtm180) cc_final: 0.6959 (mmp-170) REVERT: K 317 LYS cc_start: 0.7180 (pttt) cc_final: 0.6978 (pttt) REVERT: K 348 ASP cc_start: 0.7607 (t0) cc_final: 0.6938 (t0) REVERT: K 374 HIS cc_start: 0.6084 (m-70) cc_final: 0.5175 (p-80) outliers start: 24 outliers final: 17 residues processed: 191 average time/residue: 0.2981 time to fit residues: 69.3494 Evaluate side-chains 152 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 C residue 359 ASN Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 368 ASN 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 G residue 359 ASN 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 K residue 345 ASP 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: 20.0000 chunk 23 optimal weight: 9.9990 chunk 63 optimal weight: 30.0000 chunk 51 optimal weight: 10.0000 chunk 21 optimal weight: 30.0000 chunk 76 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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** D 368 ASN ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 336 GLN ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 359 ASN ** K 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 329 HIS K 362 HIS ** L 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.8553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 6918 Z= 0.498 Angle : 1.060 13.051 9258 Z= 0.567 Chirality : 0.062 0.296 1044 Planarity : 0.006 0.064 1176 Dihedral : 8.179 39.624 912 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 5.90 % Allowed : 13.59 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.59 % 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: -3.17 (0.22), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.17), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS B 330 PHE 0.017 0.003 PHE L 346 TYR 0.042 0.006 TYR I 310 ARG 0.010 0.001 ARG G 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 222 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 176 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8242 (mttt) cc_final: 0.7618 (ttmt) REVERT: A 336 GLN cc_start: 0.8588 (tm130) cc_final: 0.8192 (tm-30) REVERT: A 347 LYS cc_start: 0.8693 (mptt) cc_final: 0.8269 (mmtm) REVERT: A 353 LYS cc_start: 0.8648 (tttt) cc_final: 0.8294 (tttt) REVERT: A 379 ARG cc_start: 0.7443 (mtt180) cc_final: 0.7229 (ttm110) REVERT: C 321 LYS cc_start: 0.8408 (mttt) cc_final: 0.7894 (ttmt) REVERT: C 336 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7999 (tm-30) REVERT: C 345 ASP cc_start: 0.7584 (m-30) cc_final: 0.7320 (t0) REVERT: C 351 GLN cc_start: 0.8017 (mp10) cc_final: 0.7649 (mp10) REVERT: E 311 LYS cc_start: 0.8087 (mttt) cc_final: 0.7022 (mmtt) REVERT: E 321 LYS cc_start: 0.8186 (mttt) cc_final: 0.7698 (ttmt) REVERT: E 349 ARG cc_start: 0.8071 (mtm180) cc_final: 0.6943 (mmp-170) REVERT: E 376 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7611 (mp) REVERT: E 379 ARG cc_start: 0.7466 (mtt180) cc_final: 0.7197 (ttm110) REVERT: B 347 LYS cc_start: 0.8710 (ptmt) cc_final: 0.8148 (ttmm) REVERT: B 360 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.7556 (mt) REVERT: B 369 LYS cc_start: 0.8044 (mtpt) cc_final: 0.7815 (mptt) REVERT: D 347 LYS cc_start: 0.8886 (ptmt) cc_final: 0.7912 (ttpp) REVERT: D 348 ASP cc_start: 0.8168 (t0) cc_final: 0.7917 (t0) REVERT: D 369 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7660 (mptt) REVERT: F 347 LYS cc_start: 0.8914 (mtpp) cc_final: 0.8567 (ttmm) REVERT: G 321 LYS cc_start: 0.8118 (mttt) cc_final: 0.7637 (tttm) REVERT: G 363 VAL cc_start: 0.9177 (t) cc_final: 0.8910 (t) REVERT: H 311 LYS cc_start: 0.7707 (pttp) cc_final: 0.7247 (mtpt) REVERT: H 321 LYS cc_start: 0.8253 (mttt) cc_final: 0.7624 (ttmt) REVERT: H 349 ARG cc_start: 0.8116 (mtm180) cc_final: 0.6411 (ptt-90) REVERT: I 349 ARG cc_start: 0.7814 (mtm180) cc_final: 0.7431 (mmp-170) REVERT: I 375 LYS cc_start: 0.8338 (ttmt) cc_final: 0.8090 (ttmm) REVERT: J 347 LYS cc_start: 0.8799 (ptmt) cc_final: 0.8422 (mtmt) REVERT: J 353 LYS cc_start: 0.8290 (mttt) cc_final: 0.8067 (mttp) REVERT: K 346 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.7979 (m-10) REVERT: K 349 ARG cc_start: 0.7569 (mtm180) cc_final: 0.6995 (mtm-85) REVERT: K 371 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8132 (mp) REVERT: L 347 LYS cc_start: 0.8854 (ptmt) cc_final: 0.8307 (ttmm) REVERT: L 348 ASP cc_start: 0.8279 (t0) cc_final: 0.7341 (p0) outliers start: 46 outliers final: 26 residues processed: 205 average time/residue: 0.2477 time to fit residues: 63.1378 Evaluate side-chains 186 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 C residue 359 ASN Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 320 SER 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 G residue 359 ASN Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 351 GLN Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 327 ASN Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain K residue 346 PHE Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain K residue 371 ILE Chi-restraints excluded: chain L residue 316 SER Chi-restraints excluded: chain L residue 346 PHE 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: 6.9990 chunk 57 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 76 optimal weight: 20.0000 chunk 81 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 72 optimal weight: 0.0010 chunk 21 optimal weight: 20.0000 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS C 368 ASN F 330 HIS ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 327 ASN L 362 HIS ** L 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.8813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6918 Z= 0.215 Angle : 0.704 7.684 9258 Z= 0.366 Chirality : 0.050 0.145 1044 Planarity : 0.005 0.051 1176 Dihedral : 6.586 27.155 912 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 5.51 % Allowed : 16.15 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.17), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS J 330 PHE 0.019 0.002 PHE F 378 TYR 0.021 0.003 TYR I 310 ARG 0.006 0.001 ARG D 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 197 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 154 time to evaluate : 0.868 Fit side-chains REVERT: A 321 LYS cc_start: 0.8298 (mttt) cc_final: 0.7674 (ttmt) REVERT: A 336 GLN cc_start: 0.8609 (tm130) cc_final: 0.8123 (tm-30) REVERT: A 347 LYS cc_start: 0.8619 (mptt) cc_final: 0.8228 (mmtm) REVERT: A 349 ARG cc_start: 0.8110 (mtt90) cc_final: 0.7479 (mmm-85) REVERT: C 336 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8085 (tm-30) REVERT: C 349 ARG cc_start: 0.8144 (mtm180) cc_final: 0.6353 (ppt170) REVERT: C 351 GLN cc_start: 0.8043 (mp10) cc_final: 0.7715 (mp10) REVERT: C 379 ARG cc_start: 0.6887 (mtt180) cc_final: 0.6507 (ttm110) REVERT: E 311 LYS cc_start: 0.8022 (mttt) cc_final: 0.6928 (mmtt) REVERT: E 321 LYS cc_start: 0.8175 (mttt) cc_final: 0.7709 (ttmt) REVERT: E 336 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8087 (tm-30) REVERT: E 349 ARG cc_start: 0.7966 (mtm180) cc_final: 0.7734 (mmm-85) REVERT: E 376 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7471 (mp) REVERT: B 314 ASP cc_start: 0.7413 (t0) cc_final: 0.7206 (t0) REVERT: B 347 LYS cc_start: 0.8372 (ptmt) cc_final: 0.7846 (ttmm) REVERT: D 347 LYS cc_start: 0.8455 (ptmt) cc_final: 0.8048 (ptmm) REVERT: D 348 ASP cc_start: 0.8006 (t0) cc_final: 0.7675 (t0) REVERT: D 369 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7738 (mptt) REVERT: F 347 LYS cc_start: 0.8897 (mtpp) cc_final: 0.8532 (ttmm) REVERT: G 321 LYS cc_start: 0.8006 (mttt) cc_final: 0.7565 (tttm) REVERT: H 349 ARG cc_start: 0.8113 (mtm180) cc_final: 0.6435 (ptt-90) REVERT: I 310 TYR cc_start: 0.5842 (OUTLIER) cc_final: 0.4237 (t80) REVERT: I 349 ARG cc_start: 0.7981 (mtm180) cc_final: 0.7556 (mmp-170) REVERT: I 375 LYS cc_start: 0.8291 (ttmt) cc_final: 0.7297 (ttmm) REVERT: J 347 LYS cc_start: 0.8546 (ptmt) cc_final: 0.7522 (ptpp) REVERT: K 314 ASP cc_start: 0.5338 (p0) cc_final: 0.5133 (p0) REVERT: K 349 ARG cc_start: 0.7477 (mtm180) cc_final: 0.7181 (mtm-85) REVERT: K 371 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8142 (mp) REVERT: L 347 LYS cc_start: 0.8546 (ptmt) cc_final: 0.7862 (ttmm) REVERT: L 348 ASP cc_start: 0.8196 (t0) cc_final: 0.7115 (p0) outliers start: 43 outliers final: 27 residues processed: 180 average time/residue: 0.2368 time to fit residues: 53.3380 Evaluate side-chains 166 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 327 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain D residue 319 THR 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 327 ASN Chi-restraints excluded: chain G residue 306 VAL Chi-restraints excluded: chain G residue 337 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 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 L residue 313 VAL 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: 7.9990 chunk 46 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 69 optimal weight: 40.0000 chunk 56 optimal weight: 0.0980 chunk 0 optimal weight: 20.0000 chunk 41 optimal weight: 7.9990 chunk 72 optimal weight: 0.0980 chunk 20 optimal weight: 20.0000 overall best weight: 4.4386 ------------------------------------------------------------------------------- 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** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 362 HIS L 362 HIS ** L 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.9546 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= 0.287 Angle : 0.752 8.787 9258 Z= 0.397 Chirality : 0.052 0.178 1044 Planarity : 0.005 0.055 1176 Dihedral : 6.705 31.135 912 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 6.54 % Allowed : 16.54 % Favored : 76.92 % 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: -3.14 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.17), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS J 330 PHE 0.017 0.002 PHE F 378 TYR 0.028 0.004 TYR I 310 ARG 0.005 0.001 ARG F 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 198 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 147 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8273 (mttt) cc_final: 0.7703 (ttmt) REVERT: A 336 GLN cc_start: 0.8616 (tm130) cc_final: 0.8078 (tm-30) REVERT: A 347 LYS cc_start: 0.8707 (mptt) cc_final: 0.8288 (mmtm) REVERT: A 353 LYS cc_start: 0.8802 (tttt) cc_final: 0.8465 (tttt) REVERT: C 321 LYS cc_start: 0.8452 (mttt) cc_final: 0.7896 (ttmt) REVERT: C 336 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8074 (tm-30) REVERT: C 351 GLN cc_start: 0.8116 (mp10) cc_final: 0.7775 (mp10) REVERT: C 379 ARG cc_start: 0.6696 (mtt180) cc_final: 0.6452 (ttm110) REVERT: E 311 LYS cc_start: 0.8031 (mttt) cc_final: 0.6899 (mmtt) REVERT: E 321 LYS cc_start: 0.8198 (mttt) cc_final: 0.7690 (ttmt) REVERT: E 336 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8108 (tm-30) REVERT: E 349 ARG cc_start: 0.8005 (mtm180) cc_final: 0.6979 (mmp-170) REVERT: B 347 LYS cc_start: 0.8608 (ptmt) cc_final: 0.8090 (ttmm) REVERT: D 347 LYS cc_start: 0.8730 (ptmt) cc_final: 0.8359 (ptmm) REVERT: D 348 ASP cc_start: 0.7953 (t0) cc_final: 0.7751 (t0) REVERT: D 369 LYS cc_start: 0.8123 (mtpt) cc_final: 0.7728 (mptt) REVERT: F 347 LYS cc_start: 0.9021 (mtpp) cc_final: 0.8637 (ttmm) REVERT: G 321 LYS cc_start: 0.8014 (mttt) cc_final: 0.7396 (ttpp) REVERT: G 340 LYS cc_start: 0.7528 (tptp) cc_final: 0.6146 (mttm) REVERT: H 349 ARG cc_start: 0.8155 (mtm180) cc_final: 0.6445 (ptt-90) REVERT: I 310 TYR cc_start: 0.6283 (OUTLIER) cc_final: 0.4516 (t80) REVERT: I 349 ARG cc_start: 0.8004 (mtm180) cc_final: 0.7491 (mmp-170) REVERT: I 375 LYS cc_start: 0.8561 (ttmt) cc_final: 0.7343 (ttmm) REVERT: J 347 LYS cc_start: 0.8721 (ptmt) cc_final: 0.8147 (ptmm) REVERT: L 347 LYS cc_start: 0.8825 (ptmt) cc_final: 0.8090 (ttmm) REVERT: L 348 ASP cc_start: 0.8347 (t0) cc_final: 0.7208 (p0) outliers start: 51 outliers final: 45 residues processed: 182 average time/residue: 0.2284 time to fit residues: 52.3281 Evaluate side-chains 185 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 139 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 327 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 322 CYS 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 G residue 306 VAL Chi-restraints excluded: chain G residue 337 VAL Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 351 GLN Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 310 TYR Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain I residue 327 ASN Chi-restraints excluded: chain I residue 330 HIS Chi-restraints excluded: chain J residue 313 VAL 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 L residue 313 VAL Chi-restraints excluded: chain L residue 319 THR 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: 10.0000 chunk 73 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 20 optimal weight: 0.0670 chunk 81 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 overall best weight: 5.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 368 ASN ** 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: 0.7067 moved from start: 1.0031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6918 Z= 0.310 Angle : 0.751 7.968 9258 Z= 0.396 Chirality : 0.053 0.179 1044 Planarity : 0.005 0.061 1176 Dihedral : 6.712 30.366 912 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 6.03 % Allowed : 18.21 % Favored : 75.77 % 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: -3.32 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.17), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS J 330 PHE 0.021 0.002 PHE F 378 TYR 0.029 0.004 TYR I 310 ARG 0.003 0.001 ARG K 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 199 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 152 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8286 (mttt) cc_final: 0.7743 (ttmt) REVERT: A 336 GLN cc_start: 0.8662 (tm130) cc_final: 0.8110 (tm-30) REVERT: A 347 LYS cc_start: 0.8756 (mptt) cc_final: 0.8328 (mmtm) REVERT: C 321 LYS cc_start: 0.8443 (mttt) cc_final: 0.7902 (ttmt) REVERT: C 336 GLN cc_start: 0.8463 (tm-30) cc_final: 0.8015 (tm-30) REVERT: C 351 GLN cc_start: 0.8098 (mp10) cc_final: 0.7750 (mp10) REVERT: E 311 LYS cc_start: 0.8059 (mttt) cc_final: 0.6875 (mmtt) REVERT: E 321 LYS cc_start: 0.8219 (mttt) cc_final: 0.7632 (ttmt) REVERT: E 336 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8121 (tm-30) REVERT: E 349 ARG cc_start: 0.8007 (mtm180) cc_final: 0.6995 (mmp-170) REVERT: B 347 LYS cc_start: 0.8538 (ptmt) cc_final: 0.8056 (ttmm) REVERT: D 347 LYS cc_start: 0.8763 (ptmt) cc_final: 0.8393 (ptmm) REVERT: D 369 LYS cc_start: 0.8089 (mtpt) cc_final: 0.7706 (mptt) REVERT: F 347 LYS cc_start: 0.8969 (mtpp) cc_final: 0.8473 (ttmm) REVERT: G 321 LYS cc_start: 0.7986 (mttt) cc_final: 0.7360 (ttpp) REVERT: G 340 LYS cc_start: 0.7394 (tptp) cc_final: 0.6159 (mttm) REVERT: H 311 LYS cc_start: 0.7485 (pttp) cc_final: 0.7034 (mtpt) REVERT: H 321 LYS cc_start: 0.8486 (mttt) cc_final: 0.7824 (ttmt) REVERT: H 349 ARG cc_start: 0.8188 (mtm180) cc_final: 0.6487 (ptt-90) REVERT: I 310 TYR cc_start: 0.6314 (OUTLIER) cc_final: 0.4551 (t80) REVERT: I 349 ARG cc_start: 0.8018 (mtm180) cc_final: 0.7434 (mmp-170) REVERT: I 369 LYS cc_start: 0.8147 (tttt) cc_final: 0.7833 (ttmm) REVERT: I 375 LYS cc_start: 0.8584 (ttmt) cc_final: 0.7514 (ttmt) REVERT: J 347 LYS cc_start: 0.8735 (ptmt) cc_final: 0.8037 (ptmm) REVERT: K 348 ASP cc_start: 0.8183 (t0) cc_final: 0.7772 (t0) REVERT: K 351 GLN cc_start: 0.7815 (mp10) cc_final: 0.7318 (mp10) REVERT: L 327 ASN cc_start: 0.8408 (m110) cc_final: 0.8064 (m110) REVERT: L 347 LYS cc_start: 0.8860 (ptmt) cc_final: 0.8081 (ttmm) REVERT: L 348 ASP cc_start: 0.8408 (t0) cc_final: 0.7250 (p0) outliers start: 47 outliers final: 43 residues processed: 184 average time/residue: 0.2546 time to fit residues: 58.5304 Evaluate side-chains 179 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 135 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 327 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 319 THR 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 337 VAL Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain G residue 359 ASN 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 320 SER Chi-restraints excluded: chain I residue 327 ASN Chi-restraints excluded: chain J residue 313 VAL 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 313 VAL Chi-restraints excluded: chain L residue 319 THR 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: 8.9990 chunk 9 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 351 GLN ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 374 HIS ** L 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 1.0422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6918 Z= 0.265 Angle : 0.715 7.548 9258 Z= 0.373 Chirality : 0.052 0.165 1044 Planarity : 0.005 0.062 1176 Dihedral : 6.415 26.645 912 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 7.05 % Allowed : 17.95 % Favored : 75.00 % 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: -3.39 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.17), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS J 330 PHE 0.019 0.002 PHE F 378 TYR 0.023 0.003 TYR I 310 ARG 0.006 0.001 ARG B 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 210 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 155 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: A 336 GLN cc_start: 0.8686 (tm130) cc_final: 0.8165 (tm-30) REVERT: C 321 LYS cc_start: 0.8478 (mttt) cc_final: 0.7868 (ttmt) REVERT: C 336 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8024 (tm-30) REVERT: C 351 GLN cc_start: 0.8141 (mp10) cc_final: 0.7817 (mp10) REVERT: E 311 LYS cc_start: 0.7974 (mttt) cc_final: 0.6811 (mmtt) REVERT: E 321 LYS cc_start: 0.8220 (mttt) cc_final: 0.7653 (ttmt) REVERT: E 336 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8159 (tm-30) REVERT: E 349 ARG cc_start: 0.8032 (mtm180) cc_final: 0.7083 (mmp-170) REVERT: B 347 LYS cc_start: 0.8532 (ptmt) cc_final: 0.8017 (ttmm) REVERT: B 348 ASP cc_start: 0.8259 (t0) cc_final: 0.7933 (t0) REVERT: D 347 LYS cc_start: 0.8618 (ptmt) cc_final: 0.8272 (ptmm) REVERT: D 360 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7097 (mt) REVERT: D 369 LYS cc_start: 0.8034 (mtpt) cc_final: 0.7672 (mptt) REVERT: F 347 LYS cc_start: 0.8914 (mtpp) cc_final: 0.8206 (ttmm) REVERT: G 321 LYS cc_start: 0.8006 (mttt) cc_final: 0.7413 (ttpp) REVERT: G 340 LYS cc_start: 0.7503 (tptp) cc_final: 0.6394 (mttm) REVERT: H 311 LYS cc_start: 0.7305 (pttp) cc_final: 0.6874 (mtpp) REVERT: H 321 LYS cc_start: 0.8451 (mttt) cc_final: 0.7825 (ttmt) REVERT: H 349 ARG cc_start: 0.8168 (mtm180) cc_final: 0.6454 (ptt-90) REVERT: I 310 TYR cc_start: 0.6265 (OUTLIER) cc_final: 0.4416 (t80) REVERT: I 353 LYS cc_start: 0.6762 (ptpt) cc_final: 0.6506 (ptmt) REVERT: I 369 LYS cc_start: 0.8367 (tttt) cc_final: 0.8087 (ttmm) REVERT: I 375 LYS cc_start: 0.8599 (ttmt) cc_final: 0.7489 (ttmm) REVERT: J 311 LYS cc_start: 0.6369 (ptpp) cc_final: 0.6152 (mmmt) REVERT: J 347 LYS cc_start: 0.8626 (ptmt) cc_final: 0.7971 (ptmm) REVERT: K 347 LYS cc_start: 0.8953 (mtpp) cc_final: 0.8616 (ttmm) REVERT: L 327 ASN cc_start: 0.8453 (m110) cc_final: 0.8102 (m110) REVERT: L 347 LYS cc_start: 0.8893 (ptmt) cc_final: 0.8096 (ttmm) REVERT: L 348 ASP cc_start: 0.8368 (t0) cc_final: 0.7254 (p0) REVERT: L 370 LYS cc_start: 0.6377 (tptt) cc_final: 0.6157 (tppt) outliers start: 55 outliers final: 51 residues processed: 191 average time/residue: 0.2220 time to fit residues: 53.3832 Evaluate side-chains 198 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 145 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASN 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 327 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 322 CYS 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 337 VAL Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain G residue 359 ASN Chi-restraints excluded: chain G residue 361 THR Chi-restraints excluded: chain G residue 368 ASN Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 351 GLN 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 I residue 359 ASN Chi-restraints excluded: chain J residue 313 VAL 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 313 VAL Chi-restraints excluded: chain L residue 319 THR 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 Chi-restraints excluded: chain L residue 351 GLN 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: 8.9990 chunk 15 optimal weight: 10.0000 chunk 51 optimal weight: 0.0870 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 63 optimal weight: 30.0000 chunk 73 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 overall best weight: 5.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 351 GLN ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 1.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6918 Z= 0.312 Angle : 0.754 7.246 9258 Z= 0.396 Chirality : 0.053 0.179 1044 Planarity : 0.006 0.063 1176 Dihedral : 6.561 26.313 912 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 6.92 % Allowed : 19.62 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.18), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS J 330 PHE 0.021 0.002 PHE I 378 TYR 0.030 0.004 TYR I 310 ARG 0.004 0.001 ARG I 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 201 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 147 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8223 (mttt) cc_final: 0.7708 (ttmt) REVERT: A 336 GLN cc_start: 0.8706 (tm130) cc_final: 0.8161 (tm-30) REVERT: A 347 LYS cc_start: 0.8808 (mptt) cc_final: 0.8381 (mmtm) REVERT: C 321 LYS cc_start: 0.8494 (mttt) cc_final: 0.7925 (tttm) REVERT: C 336 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8045 (tm-30) REVERT: C 351 GLN cc_start: 0.8158 (mp10) cc_final: 0.7833 (mp10) REVERT: E 336 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8162 (tm-30) REVERT: E 349 ARG cc_start: 0.8039 (mtm180) cc_final: 0.7184 (mmp-170) REVERT: B 347 LYS cc_start: 0.8572 (ptmt) cc_final: 0.8048 (ttmm) REVERT: B 360 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7589 (mt) REVERT: D 347 LYS cc_start: 0.8759 (ptmt) cc_final: 0.8398 (ptmm) REVERT: D 360 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.6912 (mt) REVERT: D 369 LYS cc_start: 0.8057 (mtpt) cc_final: 0.7713 (mptt) REVERT: F 347 LYS cc_start: 0.8898 (mtpp) cc_final: 0.8221 (ttmm) REVERT: G 321 LYS cc_start: 0.7999 (mttt) cc_final: 0.7360 (ttpp) REVERT: H 311 LYS cc_start: 0.7272 (pttp) cc_final: 0.6841 (mtpp) REVERT: H 321 LYS cc_start: 0.8476 (mttt) cc_final: 0.7852 (ttmt) REVERT: H 349 ARG cc_start: 0.8184 (mtm180) cc_final: 0.6611 (ptt-90) REVERT: I 310 TYR cc_start: 0.6532 (OUTLIER) cc_final: 0.4537 (t80) REVERT: I 353 LYS cc_start: 0.6872 (ptpt) cc_final: 0.6544 (ptmt) REVERT: I 369 LYS cc_start: 0.8408 (tttt) cc_final: 0.8120 (ttmm) REVERT: I 375 LYS cc_start: 0.8689 (ttmt) cc_final: 0.7583 (ttmm) REVERT: J 311 LYS cc_start: 0.6420 (ptpp) cc_final: 0.5814 (mmmt) REVERT: K 347 LYS cc_start: 0.9000 (mtpp) cc_final: 0.8640 (ttmm) REVERT: L 347 LYS cc_start: 0.8855 (ptmt) cc_final: 0.8632 (ptmm) REVERT: L 348 ASP cc_start: 0.8407 (t0) cc_final: 0.7092 (p0) outliers start: 54 outliers final: 49 residues processed: 183 average time/residue: 0.2299 time to fit residues: 52.6510 Evaluate side-chains 194 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 142 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASN 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 327 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain B 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 319 THR Chi-restraints excluded: chain D residue 322 CYS 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 337 VAL Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain G residue 359 ASN 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 H residue 351 GLN 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 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 376 LEU Chi-restraints excluded: chain L residue 313 VAL Chi-restraints excluded: chain L residue 319 THR 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 Chi-restraints excluded: chain L residue 351 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 1.9990 chunk 77 optimal weight: 40.0000 chunk 45 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 327 ASN ** L 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 1.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 6918 Z= 0.236 Angle : 0.695 7.028 9258 Z= 0.361 Chirality : 0.051 0.153 1044 Planarity : 0.005 0.065 1176 Dihedral : 6.195 21.698 912 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 6.41 % Allowed : 21.03 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.17), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS J 330 PHE 0.021 0.002 PHE F 378 TYR 0.022 0.003 TYR I 310 ARG 0.003 0.000 ARG H 379 *********************** 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 196 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 146 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8189 (mttt) cc_final: 0.7663 (ttmt) REVERT: A 336 GLN cc_start: 0.8751 (tm130) cc_final: 0.8213 (tm-30) REVERT: A 347 LYS cc_start: 0.8799 (mptt) cc_final: 0.8400 (mmtm) REVERT: C 321 LYS cc_start: 0.8484 (mttt) cc_final: 0.7863 (ttmt) REVERT: C 336 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8105 (tm-30) REVERT: C 351 GLN cc_start: 0.8096 (mp10) cc_final: 0.7795 (mp10) REVERT: E 311 LYS cc_start: 0.7870 (mttt) cc_final: 0.6716 (mmtt) REVERT: E 321 LYS cc_start: 0.8293 (mttt) cc_final: 0.7627 (ttmt) REVERT: E 336 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8193 (tm-30) REVERT: E 349 ARG cc_start: 0.8046 (mtm180) cc_final: 0.7164 (mmp-170) REVERT: B 347 LYS cc_start: 0.8383 (ptmt) cc_final: 0.7910 (ttmm) REVERT: D 347 LYS cc_start: 0.8555 (ptmt) cc_final: 0.8224 (ptmm) REVERT: D 369 LYS cc_start: 0.8039 (mtpt) cc_final: 0.7721 (mptt) REVERT: F 347 LYS cc_start: 0.8869 (mtpp) cc_final: 0.8241 (ttmm) REVERT: H 311 LYS cc_start: 0.7184 (pttp) cc_final: 0.6810 (mtpp) REVERT: H 321 LYS cc_start: 0.8445 (mttt) cc_final: 0.7797 (ttmt) REVERT: H 349 ARG cc_start: 0.8168 (mtm180) cc_final: 0.6440 (ptt-90) REVERT: I 310 TYR cc_start: 0.6423 (OUTLIER) cc_final: 0.4387 (t80) REVERT: I 349 ARG cc_start: 0.8278 (mtp180) cc_final: 0.7231 (mmp-170) REVERT: I 369 LYS cc_start: 0.8410 (tttt) cc_final: 0.8181 (ttmm) REVERT: I 375 LYS cc_start: 0.8591 (ttmt) cc_final: 0.7680 (ttmm) REVERT: J 311 LYS cc_start: 0.6507 (ptpp) cc_final: 0.6177 (mmmt) REVERT: L 347 LYS cc_start: 0.8847 (ptmt) cc_final: 0.8067 (ttmm) REVERT: L 348 ASP cc_start: 0.8387 (t0) cc_final: 0.7125 (p0) outliers start: 50 outliers final: 48 residues processed: 178 average time/residue: 0.2340 time to fit residues: 52.2189 Evaluate side-chains 189 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 140 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 327 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 322 CYS 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 337 VAL Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain G residue 359 ASN 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 H residue 351 GLN 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 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 327 ASN 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 376 LEU Chi-restraints excluded: chain L residue 313 VAL Chi-restraints excluded: chain L residue 319 THR 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 Chi-restraints excluded: chain L residue 351 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 0.0870 chunk 52 optimal weight: 0.9990 chunk 70 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 368 ASN ** 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: 0.7058 moved from start: 1.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6918 Z= 0.178 Angle : 0.659 7.161 9258 Z= 0.337 Chirality : 0.050 0.140 1044 Planarity : 0.005 0.060 1176 Dihedral : 5.844 19.891 912 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 6.28 % Allowed : 21.15 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.22), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.17), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS J 330 PHE 0.021 0.002 PHE I 378 TYR 0.014 0.003 TYR I 310 ARG 0.004 0.000 ARG D 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 192 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 143 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8184 (mttt) cc_final: 0.7681 (ttmt) REVERT: A 325 LEU cc_start: 0.8749 (mt) cc_final: 0.8469 (mp) REVERT: A 336 GLN cc_start: 0.8750 (tm130) cc_final: 0.8198 (tm-30) REVERT: A 347 LYS cc_start: 0.8677 (mptt) cc_final: 0.8287 (mmtm) REVERT: C 321 LYS cc_start: 0.8452 (mttt) cc_final: 0.7808 (ttmt) REVERT: C 336 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8151 (tm-30) REVERT: C 351 GLN cc_start: 0.8089 (mp10) cc_final: 0.7785 (mp10) REVERT: E 311 LYS cc_start: 0.7778 (mttt) cc_final: 0.6600 (mmtt) REVERT: E 321 LYS cc_start: 0.8251 (mttt) cc_final: 0.7596 (ttmt) REVERT: E 336 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8232 (tm-30) REVERT: D 369 LYS cc_start: 0.8013 (mtpt) cc_final: 0.7719 (mptt) REVERT: G 348 ASP cc_start: 0.8358 (t0) cc_final: 0.8086 (t0) REVERT: G 378 PHE cc_start: 0.6420 (t80) cc_final: 0.6205 (t80) REVERT: H 311 LYS cc_start: 0.7168 (pttp) cc_final: 0.6824 (mtpp) REVERT: H 321 LYS cc_start: 0.8399 (mttt) cc_final: 0.7741 (ttmt) REVERT: H 349 ARG cc_start: 0.8131 (mtm180) cc_final: 0.6367 (ptt-90) REVERT: I 349 ARG cc_start: 0.8281 (mtp180) cc_final: 0.7396 (mmp-170) REVERT: I 369 LYS cc_start: 0.8360 (tttt) cc_final: 0.8147 (ttmm) REVERT: I 375 LYS cc_start: 0.8482 (ttmt) cc_final: 0.8244 (ttmt) REVERT: J 311 LYS cc_start: 0.6606 (ptpp) cc_final: 0.6250 (mmmt) REVERT: K 360 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7161 (mt) REVERT: L 348 ASP cc_start: 0.8239 (t0) cc_final: 0.6952 (p0) outliers start: 49 outliers final: 45 residues processed: 171 average time/residue: 0.2347 time to fit residues: 51.8075 Evaluate side-chains 186 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 140 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASN 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 327 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 322 CYS Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain F residue 309 VAL 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 337 VAL Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain G residue 359 ASN Chi-restraints excluded: chain G residue 361 THR Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 351 GLN Chi-restraints excluded: chain H residue 363 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 I residue 327 ASN Chi-restraints excluded: chain J residue 322 CYS Chi-restraints excluded: chain J residue 327 ASN Chi-restraints excluded: chain J residue 341 SER Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain K residue 327 ASN Chi-restraints excluded: chain K residue 341 SER Chi-restraints excluded: chain K residue 360 ILE Chi-restraints excluded: chain K residue 376 LEU 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 61 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 18 optimal weight: 20.0000 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 351 GLN ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 359 ASN ** L 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5110 r_free = 0.5110 target = 0.292105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.5022 r_free = 0.5022 target = 0.227644 restraints weight = 9305.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 107)---------------| | r_work = 0.5066 r_free = 0.5066 target = 0.224483 restraints weight = 12547.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5072 r_free = 0.5072 target = 0.223829 restraints weight = 11396.890| |-----------------------------------------------------------------------------| r_work (final): 0.4567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 1.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6918 Z= 0.176 Angle : 0.657 7.686 9258 Z= 0.335 Chirality : 0.050 0.141 1044 Planarity : 0.005 0.063 1176 Dihedral : 5.678 19.462 912 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 5.90 % Allowed : 21.92 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.17), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS J 330 PHE 0.021 0.001 PHE F 378 TYR 0.016 0.002 TYR F 310 ARG 0.007 0.001 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1977.25 seconds wall clock time: 37 minutes 29.72 seconds (2249.72 seconds total)