Starting phenix.real_space_refine on Fri Apr 5 21:11:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seh_40411/04_2024/8seh_40411_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seh_40411/04_2024/8seh_40411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seh_40411/04_2024/8seh_40411.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seh_40411/04_2024/8seh_40411.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seh_40411/04_2024/8seh_40411_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seh_40411/04_2024/8seh_40411_neut.pdb" } resolution = 2.9 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= 0.003 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 10 5.16 5 C 3510 2.51 5 N 1010 2.21 5 O 1040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5570 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" 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: "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: "C" 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: "E" 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: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "H" 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: "I" 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: "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} Time building chain proxies: 3.36, per 1000 atoms: 0.60 Number of scatterers: 5570 At special positions: 0 Unit cell: (79.05, 144.398, 44.268, 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 10 16.00 O 1040 8.00 N 1010 7.00 C 3510 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: 2.05 Conformation dependent library (CDL) restraints added in 1.1 seconds 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1280 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 54.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 307 through 310 removed outlier: 6.485A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLN C 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N TYR E 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL C 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLN E 307 " --> pdb=" O ILE G 308 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N TYR G 310 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL E 309 " --> pdb=" O TYR G 310 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLN G 307 " --> pdb=" O ILE I 308 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N TYR I 310 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL G 309 " --> pdb=" O TYR I 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 314 through 324 removed outlier: 6.734A pdb=" N SER C 324 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER E 324 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER G 324 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER I 324 " --> pdb=" O GLY G 323 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 330 removed outlier: 6.416A pdb=" N HIS A 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N HIS C 329 " --> pdb=" O HIS E 330 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N HIS E 329 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N HIS G 329 " --> pdb=" O HIS I 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 340 Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 347 removed outlier: 6.187A pdb=" N LYS A 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE C 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LYS C 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE E 346 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP C 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LYS E 343 " --> pdb=" O LEU G 344 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE G 346 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP E 345 " --> pdb=" O PHE G 346 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LYS G 343 " --> pdb=" O LEU I 344 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE I 346 " --> pdb=" O LYS G 343 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP G 345 " --> pdb=" O PHE I 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 356 removed outlier: 6.623A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER C 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLY A 355 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN C 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE E 354 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS C 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER E 356 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLY C 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN E 351 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE G 354 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS E 353 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER G 356 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLY E 355 " --> pdb=" O SER G 356 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN G 351 " --> pdb=" O SER I 352 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE I 354 " --> pdb=" O GLN G 351 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS G 353 " --> pdb=" O ILE I 354 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER I 356 " --> pdb=" O LYS G 353 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N GLY G 355 " --> pdb=" O SER I 356 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 359 through 362 Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 377 Processing sheet with id=AA9, first strand: chain 'B' and resid 307 through 310 removed outlier: 6.485A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLN D 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N TYR F 310 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL D 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN F 307 " --> pdb=" O ILE H 308 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N TYR H 310 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL F 309 " --> pdb=" O TYR H 310 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLN H 307 " --> pdb=" O ILE J 308 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N TYR J 310 " --> pdb=" O GLN H 307 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL H 309 " --> pdb=" O TYR J 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 314 through 324 removed outlier: 6.734A pdb=" N SER D 324 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER F 324 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER H 324 " --> pdb=" O GLY F 323 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER J 324 " --> pdb=" O GLY H 323 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.416A pdb=" N HIS B 329 " --> pdb=" O HIS D 330 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N HIS D 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N HIS F 329 " --> pdb=" O HIS H 330 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N HIS H 329 " --> pdb=" O HIS J 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 336 through 340 Processing sheet with id=AB4, first strand: chain 'B' and resid 343 through 347 removed outlier: 6.187A pdb=" N LYS B 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE D 346 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LYS D 343 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N PHE F 346 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP D 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LYS F 343 " --> pdb=" O LEU H 344 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N PHE H 346 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP F 345 " --> pdb=" O PHE H 346 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LYS H 343 " --> pdb=" O LEU J 344 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N PHE J 346 " --> pdb=" O LYS H 343 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP H 345 " --> pdb=" O PHE J 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 350 through 356 removed outlier: 6.624A pdb=" N GLN B 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE D 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS B 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER D 356 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLY B 355 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN D 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE F 354 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS D 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER F 356 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLY D 355 " --> pdb=" O SER F 356 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN F 351 " --> pdb=" O SER H 352 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE H 354 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS F 353 " --> pdb=" O ILE H 354 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER H 356 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLY F 355 " --> pdb=" O SER H 356 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN H 351 " --> pdb=" O SER J 352 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE J 354 " --> pdb=" O GLN H 351 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS H 353 " --> pdb=" O ILE J 354 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER J 356 " --> pdb=" O LYS H 353 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N GLY H 355 " --> pdb=" O SER J 356 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 359 through 362 Processing sheet with id=AB7, first strand: chain 'B' and resid 369 through 377 192 hydrogen bonds defined for protein. 576 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: 1.59 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.31: 1358 1.31 - 1.43: 1055 1.43 - 1.55: 3207 1.55 - 1.67: 30 1.67 - 1.79: 10 Bond restraints: 5660 Sorted by residual: bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.419 0.078 1.40e-02 5.10e+03 3.11e+01 bond pdb=" CB HIS H 374 " pdb=" CG HIS H 374 " ideal model delta sigma weight residual 1.497 1.419 0.078 1.40e-02 5.10e+03 3.08e+01 bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.420 0.077 1.40e-02 5.10e+03 3.06e+01 bond pdb=" CB HIS D 374 " pdb=" CG HIS D 374 " ideal model delta sigma weight residual 1.497 1.420 0.077 1.40e-02 5.10e+03 3.03e+01 bond pdb=" CB HIS F 374 " pdb=" CG HIS F 374 " ideal model delta sigma weight residual 1.497 1.420 0.077 1.40e-02 5.10e+03 3.03e+01 ... (remaining 5655 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.53: 299 106.53 - 113.02: 2828 113.02 - 119.51: 1966 119.51 - 126.00: 2397 126.00 - 132.49: 90 Bond angle restraints: 7580 Sorted by residual: angle pdb=" CA PHE H 346 " pdb=" CB PHE H 346 " pdb=" CG PHE H 346 " ideal model delta sigma weight residual 113.80 122.53 -8.73 1.00e+00 1.00e+00 7.63e+01 angle pdb=" CA PHE C 346 " pdb=" CB PHE C 346 " pdb=" CG PHE C 346 " ideal model delta sigma weight residual 113.80 122.53 -8.73 1.00e+00 1.00e+00 7.62e+01 angle pdb=" CA PHE D 346 " pdb=" CB PHE D 346 " pdb=" CG PHE D 346 " ideal model delta sigma weight residual 113.80 122.53 -8.73 1.00e+00 1.00e+00 7.62e+01 angle pdb=" CA PHE B 346 " pdb=" CB PHE B 346 " pdb=" CG PHE B 346 " ideal model delta sigma weight residual 113.80 122.52 -8.72 1.00e+00 1.00e+00 7.60e+01 angle pdb=" CA PHE E 346 " pdb=" CB PHE E 346 " pdb=" CG PHE E 346 " ideal model delta sigma weight residual 113.80 122.49 -8.69 1.00e+00 1.00e+00 7.54e+01 ... (remaining 7575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.66: 3280 15.66 - 31.31: 110 31.31 - 46.96: 20 46.96 - 62.62: 20 62.62 - 78.27: 10 Dihedral angle restraints: 3440 sinusoidal: 1430 harmonic: 2010 Sorted by residual: dihedral pdb=" C PHE A 346 " pdb=" N PHE A 346 " pdb=" CA PHE A 346 " pdb=" CB PHE A 346 " ideal model delta harmonic sigma weight residual -122.60 -133.33 10.73 0 2.50e+00 1.60e-01 1.84e+01 dihedral pdb=" C PHE F 346 " pdb=" N PHE F 346 " pdb=" CA PHE F 346 " pdb=" CB PHE F 346 " ideal model delta harmonic sigma weight residual -122.60 -133.33 10.73 0 2.50e+00 1.60e-01 1.84e+01 dihedral pdb=" C PHE E 346 " pdb=" N PHE E 346 " pdb=" CA PHE E 346 " pdb=" CB PHE E 346 " ideal model delta harmonic sigma weight residual -122.60 -133.30 10.70 0 2.50e+00 1.60e-01 1.83e+01 ... (remaining 3437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 590 0.103 - 0.206: 238 0.206 - 0.309: 22 0.309 - 0.412: 0 0.412 - 0.515: 10 Chirality restraints: 860 Sorted by residual: chirality pdb=" CA PHE F 346 " pdb=" N PHE F 346 " pdb=" C PHE F 346 " pdb=" CB PHE F 346 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" CA PHE E 346 " pdb=" N PHE E 346 " pdb=" C PHE E 346 " pdb=" CB PHE E 346 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.62e+00 chirality pdb=" CA PHE D 346 " pdb=" N PHE D 346 " pdb=" C PHE D 346 " pdb=" CB PHE D 346 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.61e+00 ... (remaining 857 not shown) Planarity restraints: 960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 346 " 0.048 2.00e-02 2.50e+03 2.97e-02 1.54e+01 pdb=" CG PHE G 346 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE G 346 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE G 346 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE G 346 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE G 346 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE G 346 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 346 " 0.048 2.00e-02 2.50e+03 2.97e-02 1.54e+01 pdb=" CG PHE I 346 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE I 346 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE I 346 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE I 346 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE I 346 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE I 346 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 346 " -0.048 2.00e-02 2.50e+03 2.96e-02 1.53e+01 pdb=" CG PHE F 346 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE F 346 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE F 346 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE F 346 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE F 346 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE F 346 " -0.021 2.00e-02 2.50e+03 ... (remaining 957 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 3119 2.99 - 3.46: 4765 3.46 - 3.94: 8642 3.94 - 4.42: 10487 4.42 - 4.90: 20246 Nonbonded interactions: 47259 Sorted by model distance: nonbonded pdb=" CB GLU E 372 " pdb=" OE1 GLU E 372 " model vdw 2.507 2.752 nonbonded pdb=" CB GLU J 372 " pdb=" OE1 GLU J 372 " model vdw 2.507 2.752 nonbonded pdb=" CB GLU G 372 " pdb=" OE1 GLU G 372 " model vdw 2.507 2.752 nonbonded pdb=" CB GLU B 372 " pdb=" OE1 GLU B 372 " model vdw 2.507 2.752 nonbonded pdb=" CB GLU H 372 " pdb=" OE1 GLU H 372 " model vdw 2.507 2.752 ... (remaining 47254 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.670 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.570 Find NCS groups from input model: 0.390 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: 0.010 Load rotamer database and sin/cos tables:13.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 : 0.026 0.138 5660 Z= 1.751 Angle : 2.088 9.108 7580 Z= 1.335 Chirality : 0.117 0.515 860 Planarity : 0.010 0.035 960 Dihedral : 10.929 78.268 2160 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 1.56 % 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: -2.29 (0.26), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.004 HIS E 362 PHE 0.051 0.015 PHE G 346 TYR 0.013 0.008 TYR A 310 ARG 0.002 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: C 342 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7075 (mt-10) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 1.5988 time to fit residues: 234.4323 Evaluate side-chains 88 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN B 362 HIS B 368 ASN C 327 ASN C 368 ASN D 368 ASN F 336 GLN H 368 ASN J 368 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5660 Z= 0.244 Angle : 0.655 5.727 7580 Z= 0.341 Chirality : 0.051 0.134 860 Planarity : 0.004 0.031 960 Dihedral : 5.875 17.470 740 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.19 % Allowed : 11.72 % Favored : 86.09 % 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: -2.26 (0.28), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 374 PHE 0.021 0.003 PHE F 346 TYR 0.010 0.002 TYR H 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7429 (tt0) cc_final: 0.7205 (tm-30) REVERT: A 340 LYS cc_start: 0.8394 (ttmm) cc_final: 0.7998 (ttmt) REVERT: B 340 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8109 (ttmt) REVERT: B 375 LYS cc_start: 0.8024 (ttmt) cc_final: 0.7709 (ttmp) outliers start: 14 outliers final: 2 residues processed: 122 average time/residue: 1.3654 time to fit residues: 173.0739 Evaluate side-chains 104 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain G residue 357 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 336 GLN D 362 HIS F 336 GLN F 368 ASN ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 336 GLN I 362 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 5660 Z= 0.466 Angle : 0.766 5.376 7580 Z= 0.405 Chirality : 0.053 0.175 860 Planarity : 0.005 0.046 960 Dihedral : 6.493 17.841 740 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 4.53 % Allowed : 15.16 % Favored : 80.31 % 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: -2.67 (0.26), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 329 PHE 0.034 0.006 PHE G 346 TYR 0.014 0.003 TYR D 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8492 (ttmm) cc_final: 0.8077 (ttmt) REVERT: A 375 LYS cc_start: 0.7951 (ttmt) cc_final: 0.7732 (ttmp) REVERT: B 338 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: C 346 PHE cc_start: 0.7121 (OUTLIER) cc_final: 0.6550 (p90) REVERT: H 321 LYS cc_start: 0.8743 (mttp) cc_final: 0.8526 (mttp) REVERT: H 352 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.8437 (t) outliers start: 29 outliers final: 16 residues processed: 139 average time/residue: 1.4898 time to fit residues: 214.3154 Evaluate side-chains 120 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 346 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 346 PHE Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain J residue 352 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.0060 chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5660 Z= 0.298 Angle : 0.636 5.756 7580 Z= 0.335 Chirality : 0.050 0.129 860 Planarity : 0.005 0.043 960 Dihedral : 6.026 16.217 740 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 5.00 % Allowed : 20.78 % Favored : 74.22 % 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: -2.88 (0.26), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 329 PHE 0.022 0.004 PHE H 346 TYR 0.012 0.002 TYR H 310 ARG 0.001 0.000 ARG J 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 96 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8360 (ttmm) cc_final: 0.8090 (ttmt) REVERT: B 357 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8623 (tp) REVERT: C 338 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6569 (tm-30) REVERT: G 338 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: H 352 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8503 (t) REVERT: I 317 LYS cc_start: 0.7539 (pttp) cc_final: 0.7338 (pttt) outliers start: 32 outliers final: 13 residues processed: 116 average time/residue: 1.4437 time to fit residues: 173.7572 Evaluate side-chains 104 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain I residue 352 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 60 optimal weight: 0.4980 chunk 17 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 5660 Z= 0.440 Angle : 0.715 5.442 7580 Z= 0.378 Chirality : 0.052 0.168 860 Planarity : 0.005 0.052 960 Dihedral : 6.349 18.483 740 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 5.94 % Allowed : 19.84 % Favored : 74.22 % 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: -3.15 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 329 PHE 0.029 0.005 PHE C 346 TYR 0.014 0.003 TYR D 310 ARG 0.002 0.000 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 103 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 338 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6542 (tm-30) REVERT: C 346 PHE cc_start: 0.7081 (OUTLIER) cc_final: 0.6399 (p90) REVERT: D 346 PHE cc_start: 0.7082 (OUTLIER) cc_final: 0.6540 (p90) REVERT: F 346 PHE cc_start: 0.7201 (OUTLIER) cc_final: 0.6952 (p90) REVERT: G 338 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7234 (tt0) REVERT: H 321 LYS cc_start: 0.8712 (mttp) cc_final: 0.8483 (mttp) REVERT: H 352 SER cc_start: 0.8784 (OUTLIER) cc_final: 0.8452 (t) outliers start: 38 outliers final: 19 residues processed: 126 average time/residue: 1.4941 time to fit residues: 194.8597 Evaluate side-chains 124 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 346 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 346 PHE Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 346 PHE Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain J residue 356 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 56 optimal weight: 0.0060 chunk 31 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5660 Z= 0.191 Angle : 0.560 3.971 7580 Z= 0.292 Chirality : 0.048 0.124 860 Planarity : 0.004 0.040 960 Dihedral : 5.570 14.458 740 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.91 % Allowed : 22.50 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 374 PHE 0.014 0.002 PHE C 346 TYR 0.010 0.002 TYR H 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.6281 (OUTLIER) cc_final: 0.5994 (mmpt) REVERT: A 338 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7150 (tm-30) REVERT: D 369 LYS cc_start: 0.8275 (ttmm) cc_final: 0.7990 (mtpt) REVERT: F 357 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8603 (tt) REVERT: H 352 SER cc_start: 0.8810 (OUTLIER) cc_final: 0.8495 (t) outliers start: 25 outliers final: 5 residues processed: 116 average time/residue: 1.3238 time to fit residues: 159.7628 Evaluate side-chains 101 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain H residue 352 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 0.0010 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.5648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5660 Z= 0.298 Angle : 0.629 4.636 7580 Z= 0.329 Chirality : 0.049 0.124 860 Planarity : 0.005 0.048 960 Dihedral : 5.815 17.234 740 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 4.53 % Allowed : 22.97 % Favored : 72.50 % 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: -3.12 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 329 PHE 0.021 0.004 PHE C 346 TYR 0.010 0.002 TYR H 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.6316 (OUTLIER) cc_final: 0.6001 (mmpt) REVERT: B 331 LYS cc_start: 0.8243 (mtpm) cc_final: 0.8000 (mtpm) REVERT: C 338 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7421 (tm-30) REVERT: H 352 SER cc_start: 0.8843 (OUTLIER) cc_final: 0.8509 (t) outliers start: 29 outliers final: 14 residues processed: 109 average time/residue: 1.3444 time to fit residues: 152.4077 Evaluate side-chains 104 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 346 PHE Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain I residue 352 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 5660 Z= 0.464 Angle : 0.747 6.910 7580 Z= 0.394 Chirality : 0.053 0.173 860 Planarity : 0.005 0.048 960 Dihedral : 6.397 25.134 740 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 5.00 % Allowed : 22.81 % Favored : 72.19 % 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: -3.36 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.18), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 329 PHE 0.031 0.006 PHE C 346 TYR 0.014 0.003 TYR D 310 ARG 0.002 0.000 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 101 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.6316 (OUTLIER) cc_final: 0.5982 (mmpt) REVERT: B 347 LYS cc_start: 0.7632 (pttt) cc_final: 0.7428 (ptpt) REVERT: C 346 PHE cc_start: 0.7032 (OUTLIER) cc_final: 0.6490 (p90) REVERT: G 321 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7866 (mtmm) REVERT: G 338 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7066 (tp30) REVERT: G 343 LYS cc_start: 0.8043 (tttp) cc_final: 0.7735 (mmmm) REVERT: H 321 LYS cc_start: 0.8691 (mttp) cc_final: 0.8462 (mttp) REVERT: H 352 SER cc_start: 0.8787 (OUTLIER) cc_final: 0.8461 (t) outliers start: 32 outliers final: 15 residues processed: 121 average time/residue: 1.5025 time to fit residues: 188.1958 Evaluate side-chains 114 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 346 PHE Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 346 PHE Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain J residue 356 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 0.0980 chunk 41 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5660 Z= 0.337 Angle : 0.675 7.685 7580 Z= 0.355 Chirality : 0.050 0.131 860 Planarity : 0.005 0.046 960 Dihedral : 6.080 22.056 740 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 4.53 % Allowed : 23.28 % Favored : 72.19 % 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 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 PHE 0.023 0.004 PHE C 346 TYR 0.012 0.002 TYR H 310 ARG 0.002 0.000 ARG H 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 85 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.6328 (OUTLIER) cc_final: 0.6001 (mmpt) REVERT: A 338 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6820 (tm-30) REVERT: B 347 LYS cc_start: 0.7519 (pttt) cc_final: 0.7286 (ptpt) REVERT: C 346 PHE cc_start: 0.6815 (OUTLIER) cc_final: 0.6339 (p90) REVERT: G 338 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7323 (tm-30) REVERT: H 352 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.8449 (t) outliers start: 29 outliers final: 15 residues processed: 101 average time/residue: 1.3786 time to fit residues: 144.8068 Evaluate side-chains 102 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 346 PHE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 346 PHE Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain J residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5660 Z= 0.266 Angle : 0.638 7.489 7580 Z= 0.334 Chirality : 0.049 0.125 860 Planarity : 0.005 0.047 960 Dihedral : 5.824 19.611 740 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.28 % Allowed : 24.84 % Favored : 71.88 % 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: -3.29 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 329 PHE 0.018 0.003 PHE C 346 TYR 0.010 0.002 TYR H 310 ARG 0.001 0.000 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.6364 (mmtm) cc_final: 0.5762 (mmpt) REVERT: A 338 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6856 (tm-30) REVERT: B 347 LYS cc_start: 0.7495 (pttt) cc_final: 0.7261 (ptpt) REVERT: C 346 PHE cc_start: 0.6634 (OUTLIER) cc_final: 0.6247 (p90) REVERT: F 357 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8629 (tt) REVERT: G 338 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7259 (tm-30) REVERT: H 352 SER cc_start: 0.8810 (OUTLIER) cc_final: 0.8490 (t) outliers start: 21 outliers final: 14 residues processed: 101 average time/residue: 1.3080 time to fit residues: 137.6906 Evaluate side-chains 101 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 346 PHE Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 346 PHE Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain J residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.128873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.106933 restraints weight = 6245.097| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.86 r_work: 0.3601 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 5660 Z= 0.435 Angle : 0.726 7.447 7580 Z= 0.383 Chirality : 0.052 0.163 860 Planarity : 0.005 0.050 960 Dihedral : 6.304 23.313 740 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 4.06 % Allowed : 24.69 % Favored : 71.25 % 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: -3.40 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.18), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 329 PHE 0.029 0.005 PHE C 346 TYR 0.013 0.003 TYR D 310 ARG 0.002 0.001 ARG H 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3079.41 seconds wall clock time: 55 minutes 57.48 seconds (3357.48 seconds total)