Starting phenix.real_space_refine on Fri Dec 8 03:35:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8e_18252/12_2023/8q8e_18252.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8e_18252/12_2023/8q8e_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_18252/12_2023/8q8e_18252.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8e_18252/12_2023/8q8e_18252.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8e_18252/12_2023/8q8e_18252.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8e_18252/12_2023/8q8e_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 3.97, per 1000 atoms: 0.58 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: 2.27 Conformation dependent library (CDL) restraints added in 1.4 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: 0.83 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: 1.56 Time building geometry restraints manager: 2.48 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: 5.820 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: 11.740 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 21.060 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.010 ------------------------------------------------------------------------------- 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 : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2513 time to fit residues: 58.8857 Evaluate side-chains 127 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0744 ------------------------------------------------------------------------------- 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: 0.9980 chunk 63 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 0.0870 chunk 49 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 overall best weight: 2.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN B 330 HIS B 362 HIS ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 ASN D 359 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 ** both conformations clash, **PLEASE CHECK MANUALLY** J 327 ASN L 327 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5976 moved from start: 0.5152 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= 0.278 Angle : 0.794 7.195 9258 Z= 0.421 Chirality : 0.052 0.152 1044 Planarity : 0.004 0.044 1176 Dihedral : 6.485 25.868 912 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.33 % Allowed : 11.54 % Favored : 85.13 % 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: -2.56 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.17), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS I 329 PHE 0.018 0.002 PHE H 346 TYR 0.022 0.003 TYR L 310 ARG 0.008 0.002 ARG E 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 205 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 179 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 17 residues processed: 191 average time/residue: 0.2672 time to fit residues: 62.7659 Evaluate side-chains 145 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 0.781 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0622 time to fit residues: 3.0151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 63 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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** C 368 ASN D 368 ASN F 330 HIS ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 362 HIS J 330 HIS J 359 ASN ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 329 HIS ** L 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 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= 0.443 Angle : 1.011 11.871 9258 Z= 0.538 Chirality : 0.059 0.254 1044 Planarity : 0.006 0.056 1176 Dihedral : 7.839 39.714 912 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.10 % Allowed : 15.64 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.22), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.17), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS I 329 PHE 0.019 0.003 PHE F 378 TYR 0.040 0.005 TYR I 310 ARG 0.008 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 204 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 172 time to evaluate : 0.837 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 16 residues processed: 198 average time/residue: 0.2374 time to fit residues: 58.4234 Evaluate side-chains 154 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 138 time to evaluate : 0.738 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0578 time to fit residues: 2.7354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 36 optimal weight: 0.5980 chunk 51 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- 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** C 336 GLN C 368 ASN H 336 GLN I 351 GLN J 362 HIS ** J 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6873 moved from start: 0.9309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6918 Z= 0.293 Angle : 0.796 8.582 9258 Z= 0.417 Chirality : 0.052 0.186 1044 Planarity : 0.005 0.052 1176 Dihedral : 6.806 27.995 912 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 3.72 % Allowed : 18.33 % Favored : 77.95 % 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: -3.07 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.17), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 374 PHE 0.018 0.002 PHE E 378 TYR 0.032 0.004 TYR A 310 ARG 0.011 0.001 ARG J 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 176 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 147 time to evaluate : 0.863 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 167 average time/residue: 0.2443 time to fit residues: 50.8545 Evaluate side-chains 147 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 0.793 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0599 time to fit residues: 3.2733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 chunk 1 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 69 optimal weight: 20.0000 chunk 56 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 20 optimal weight: 0.0060 overall best weight: 3.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS C 336 GLN ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 HIS I 374 HIS K 327 ASN 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.9932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6918 Z= 0.266 Angle : 0.755 8.016 9258 Z= 0.393 Chirality : 0.051 0.150 1044 Planarity : 0.005 0.055 1176 Dihedral : 6.561 29.956 912 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.31 % Allowed : 20.26 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.17), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS J 374 PHE 0.019 0.002 PHE F 378 TYR 0.028 0.004 TYR C 310 ARG 0.005 0.001 ARG A 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 162 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 144 time to evaluate : 0.824 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 154 average time/residue: 0.2470 time to fit residues: 48.5271 Evaluate side-chains 134 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 0.727 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0723 time to fit residues: 2.8259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN D 359 ASN ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 368 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 1.0365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6918 Z= 0.286 Angle : 0.750 7.637 9258 Z= 0.394 Chirality : 0.052 0.157 1044 Planarity : 0.005 0.059 1176 Dihedral : 6.532 29.240 912 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 2.31 % Allowed : 19.87 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.18), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS I 330 PHE 0.017 0.002 PHE F 378 TYR 0.026 0.004 TYR C 310 ARG 0.008 0.001 ARG G 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 156 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 149 average time/residue: 0.3080 time to fit residues: 56.7722 Evaluate side-chains 131 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 1.023 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0670 time to fit residues: 2.8815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN C 336 GLN ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 351 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 1.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6918 Z= 0.338 Angle : 0.806 7.642 9258 Z= 0.423 Chirality : 0.053 0.174 1044 Planarity : 0.006 0.064 1176 Dihedral : 6.844 28.483 912 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 2.69 % Allowed : 20.51 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.18), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS I 330 PHE 0.015 0.002 PHE F 378 TYR 0.028 0.004 TYR I 310 ARG 0.004 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 148 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 18 residues processed: 159 average time/residue: 0.2606 time to fit residues: 51.1093 Evaluate side-chains 147 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 0.678 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0673 time to fit residues: 3.0799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN C 336 GLN ** J 368 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 1.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6918 Z= 0.216 Angle : 0.709 7.213 9258 Z= 0.364 Chirality : 0.051 0.154 1044 Planarity : 0.005 0.065 1176 Dihedral : 6.262 22.741 912 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.90 % Allowed : 22.18 % Favored : 76.92 % 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: -3.34 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.18), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS I 330 PHE 0.021 0.001 PHE D 378 TYR 0.020 0.003 TYR A 310 ARG 0.004 0.000 ARG J 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 142 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 135 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 137 average time/residue: 0.2448 time to fit residues: 41.9101 Evaluate side-chains 132 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 0.803 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0667 time to fit residues: 1.8567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 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: 0.7018 moved from start: 1.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6918 Z= 0.250 Angle : 0.733 7.165 9258 Z= 0.378 Chirality : 0.051 0.155 1044 Planarity : 0.005 0.064 1176 Dihedral : 6.203 22.892 912 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 1.28 % Allowed : 22.82 % Favored : 75.90 % 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: -3.37 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.18), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS I 330 PHE 0.021 0.002 PHE F 378 TYR 0.018 0.003 TYR A 310 ARG 0.005 0.001 ARG K 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1740 Ramachandran restraints generated. 870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 129 average time/residue: 0.2432 time to fit residues: 40.0633 Evaluate side-chains 127 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 0.820 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0639 time to fit residues: 2.0342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 51 optimal weight: 0.0980 chunk 40 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN C 336 GLN D 359 ASN ** J 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 1.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6918 Z= 0.311 Angle : 0.785 7.168 9258 Z= 0.408 Chirality : 0.053 0.177 1044 Planarity : 0.006 0.066 1176 Dihedral : 6.604 23.692 912 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 0.64 % Allowed : 23.97 % Favored : 75.38 % 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: -3.54 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.18), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS I 330 PHE 0.024 0.002 PHE G 378 TYR 0.020 0.004 TYR E 310 ARG 0.004 0.001 ARG K 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 131 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 126 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 129 average time/residue: 0.2304 time to fit residues: 38.1952 Evaluate side-chains 125 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 0.781 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0761 time to fit residues: 1.6449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 27 optimal weight: 0.0470 chunk 68 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 3 optimal weight: 40.0000 chunk 48 optimal weight: 0.9990 overall best weight: 4.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5053 r_free = 0.5053 target = 0.283561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.223862 restraints weight = 9509.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.4983 r_free = 0.4983 target = 0.221431 restraints weight = 15968.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.220924 restraints weight = 14360.206| |-----------------------------------------------------------------------------| r_work (final): 0.4596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 1.1657 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= 0.289 Angle : 0.765 7.139 9258 Z= 0.396 Chirality : 0.053 0.157 1044 Planarity : 0.005 0.065 1176 Dihedral : 6.414 23.837 912 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 0.77 % Allowed : 24.23 % 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: -3.54 (0.23), residues: 870 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.18), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS I 330 PHE 0.021 0.002 PHE F 378 TYR 0.017 0.003 TYR E 310 ARG 0.005 0.001 ARG K 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1865.12 seconds wall clock time: 34 minutes 57.66 seconds (2097.66 seconds total)