Starting phenix.real_space_refine on Tue Feb 13 11:49:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nrv_12551/02_2024/7nrv_12551.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nrv_12551/02_2024/7nrv_12551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nrv_12551/02_2024/7nrv_12551.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nrv_12551/02_2024/7nrv_12551.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nrv_12551/02_2024/7nrv_12551.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nrv_12551/02_2024/7nrv_12551.pdb" } resolution = 3.0 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= 0.001 sd= 0.007 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 3670 2.51 5 N 1080 2.21 5 O 1110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5870 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "F" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "C" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "D" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "E" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "G" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "H" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "I" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "J" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Time building chain proxies: 3.51, per 1000 atoms: 0.60 Number of scatterers: 5870 At special positions: 0 Unit cell: (155.25, 71.3, 44.85, 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 1110 8.00 N 1080 7.00 C 3670 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: 1.80 Conformation dependent library (CDL) restraints added in 1.2 seconds 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1340 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 39.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.211A pdb=" N VAL B 306 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL D 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE B 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL A 306 " --> pdb=" O GLN I 307 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL I 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE A 308 " --> pdb=" O VAL I 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.913A pdb=" N VAL A 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL G 313 " --> pdb=" O ASP I 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 321 removed outlier: 6.183A pdb=" N VAL B 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N LYS D 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.433A pdb=" N LEU A 325 " --> pdb=" O GLY I 326 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 329 through 330 removed outlier: 6.448A pdb=" N HIS A 329 " --> pdb=" O HIS D 330 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS G 329 " --> pdb=" O HIS I 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 337 through 340 removed outlier: 6.302A pdb=" N GLU A 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLU G 338 " --> pdb=" O VAL I 339 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 343 through 356 removed outlier: 6.468A pdb=" N LEU B 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LYS D 347 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N PHE B 346 " --> pdb=" O LYS D 347 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ARG D 349 " --> pdb=" O PHE B 346 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ASP B 348 " --> pdb=" O ARG D 349 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N GLN D 351 " --> pdb=" O ASP B 348 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL B 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LYS D 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER B 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N GLY D 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ILE B 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP D 348 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG A 349 " --> pdb=" O ASP D 348 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY A 355 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER D 356 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU A 344 " --> pdb=" O ASP I 345 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LYS I 347 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N PHE A 346 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ARG I 349 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ASP A 348 " --> pdb=" O ARG I 349 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N GLN I 351 " --> pdb=" O ASP A 348 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL A 350 " --> pdb=" O GLN I 351 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LYS I 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER A 352 " --> pdb=" O LYS I 353 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N GLY I 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ILE A 354 " --> pdb=" O GLY I 355 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASP I 348 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG G 349 " --> pdb=" O ASP I 348 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLY G 355 " --> pdb=" O ILE I 354 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N SER I 356 " --> pdb=" O GLY G 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 359 through 362 removed outlier: 6.438A pdb=" N ILE A 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN A 359 " --> pdb=" O ILE I 360 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N HIS I 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR A 361 " --> pdb=" O HIS I 362 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE G 360 " --> pdb=" O THR I 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 374 through 378 removed outlier: 6.491A pdb=" N LYS A 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N PHE D 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR A 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS G 375 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N PHE I 378 " --> pdb=" O LYS G 375 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N THR G 377 " --> pdb=" O PHE I 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.684A pdb=" N GLN F 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N TYR E 310 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL F 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N VAL F 306 " --> pdb=" O GLN J 307 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL J 309 " --> pdb=" O VAL F 306 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE F 308 " --> pdb=" O VAL J 309 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLN H 307 " --> pdb=" O ILE J 308 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N TYR J 310 " --> pdb=" O GLN H 307 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL H 309 " --> pdb=" O TYR J 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.723A pdb=" N VAL F 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL H 313 " --> pdb=" O ASP J 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 317 through 319 removed outlier: 6.228A pdb=" N VAL C 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL F 318 " --> pdb=" O THR J 319 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.690A pdb=" N ILE C 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE F 328 " --> pdb=" O HIS J 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 337 through 340 removed outlier: 6.430A pdb=" N VAL C 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N LYS E 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL C 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU F 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL F 337 " --> pdb=" O GLU J 338 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LYS J 340 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL F 339 " --> pdb=" O LYS J 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 343 through 351 removed outlier: 6.275A pdb=" N LEU C 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LYS E 347 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N PHE C 346 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG E 349 " --> pdb=" O PHE C 346 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ASP C 348 " --> pdb=" O ARG E 349 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N GLN E 351 " --> pdb=" O ASP C 348 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL C 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP E 348 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG F 349 " --> pdb=" O ASP E 348 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU F 344 " --> pdb=" O ASP J 345 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS J 347 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N PHE F 346 " --> pdb=" O LYS J 347 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG J 349 " --> pdb=" O PHE F 346 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ASP F 348 " --> pdb=" O ARG J 349 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N GLN J 351 " --> pdb=" O ASP F 348 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL F 350 " --> pdb=" O GLN J 351 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASP J 348 " --> pdb=" O LYS H 347 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG H 349 " --> pdb=" O ASP J 348 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 355 through 356 removed outlier: 6.695A pdb=" N GLY C 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLY F 355 " --> pdb=" O SER J 356 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.559A pdb=" N ASN C 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N HIS E 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR C 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 374 through 378 removed outlier: 6.488A pdb=" N LYS F 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N PHE E 378 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N THR F 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS H 375 " --> pdb=" O LEU J 376 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE J 378 " --> pdb=" O LYS H 375 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N THR H 377 " --> pdb=" O PHE J 378 " (cutoff:3.500A) 107 hydrogen bonds defined for protein. 321 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: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 990 1.31 - 1.43: 1380 1.43 - 1.56: 3580 1.56 - 1.68: 0 1.68 - 1.80: 10 Bond restraints: 5960 Sorted by residual: bond pdb=" CG GLN E 336 " pdb=" CD GLN E 336 " ideal model delta sigma weight residual 1.516 1.436 0.080 2.50e-02 1.60e+03 1.03e+01 bond pdb=" CG GLN H 336 " pdb=" CD GLN H 336 " ideal model delta sigma weight residual 1.516 1.436 0.080 2.50e-02 1.60e+03 1.03e+01 bond pdb=" CG GLN J 336 " pdb=" CD GLN J 336 " ideal model delta sigma weight residual 1.516 1.436 0.080 2.50e-02 1.60e+03 1.02e+01 bond pdb=" CG GLN C 336 " pdb=" CD GLN C 336 " ideal model delta sigma weight residual 1.516 1.436 0.080 2.50e-02 1.60e+03 1.02e+01 bond pdb=" CG GLN F 336 " pdb=" CD GLN F 336 " ideal model delta sigma weight residual 1.516 1.436 0.080 2.50e-02 1.60e+03 1.01e+01 ... (remaining 5955 not shown) Histogram of bond angle deviations from ideal: 98.02 - 104.68: 90 104.68 - 111.34: 2591 111.34 - 118.00: 2094 118.00 - 124.65: 3104 124.65 - 131.31: 91 Bond angle restraints: 7970 Sorted by residual: angle pdb=" CB GLN J 336 " pdb=" CG GLN J 336 " pdb=" CD GLN J 336 " ideal model delta sigma weight residual 112.60 122.72 -10.12 1.70e+00 3.46e-01 3.54e+01 angle pdb=" CB GLN C 336 " pdb=" CG GLN C 336 " pdb=" CD GLN C 336 " ideal model delta sigma weight residual 112.60 122.71 -10.11 1.70e+00 3.46e-01 3.54e+01 angle pdb=" CB GLN H 336 " pdb=" CG GLN H 336 " pdb=" CD GLN H 336 " ideal model delta sigma weight residual 112.60 122.69 -10.09 1.70e+00 3.46e-01 3.52e+01 angle pdb=" CB GLN F 336 " pdb=" CG GLN F 336 " pdb=" CD GLN F 336 " ideal model delta sigma weight residual 112.60 122.68 -10.08 1.70e+00 3.46e-01 3.52e+01 angle pdb=" CB GLN E 336 " pdb=" CG GLN E 336 " pdb=" CD GLN E 336 " ideal model delta sigma weight residual 112.60 122.67 -10.07 1.70e+00 3.46e-01 3.51e+01 ... (remaining 7965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.82: 3146 13.82 - 27.63: 384 27.63 - 41.45: 65 41.45 - 55.27: 30 55.27 - 69.09: 5 Dihedral angle restraints: 3630 sinusoidal: 1520 harmonic: 2110 Sorted by residual: dihedral pdb=" CD ARG A 379 " pdb=" NE ARG A 379 " pdb=" CZ ARG A 379 " pdb=" NH1 ARG A 379 " ideal model delta sinusoidal sigma weight residual 0.00 -45.09 45.09 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CD ARG B 379 " pdb=" NE ARG B 379 " pdb=" CZ ARG B 379 " pdb=" NH1 ARG B 379 " ideal model delta sinusoidal sigma weight residual 0.00 -45.06 45.06 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CD ARG I 379 " pdb=" NE ARG I 379 " pdb=" CZ ARG I 379 " pdb=" NH1 ARG I 379 " ideal model delta sinusoidal sigma weight residual 0.00 -45.06 45.06 1 1.00e+01 1.00e-02 2.82e+01 ... (remaining 3627 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.111: 816 0.111 - 0.221: 64 0.221 - 0.332: 5 0.332 - 0.442: 0 0.442 - 0.552: 5 Chirality restraints: 890 Sorted by residual: chirality pdb=" CG LEU B 344 " pdb=" CB LEU B 344 " pdb=" CD1 LEU B 344 " pdb=" CD2 LEU B 344 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.62e+00 chirality pdb=" CG LEU A 344 " pdb=" CB LEU A 344 " pdb=" CD1 LEU A 344 " pdb=" CD2 LEU A 344 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.53e+00 chirality pdb=" CG LEU I 344 " pdb=" CB LEU I 344 " pdb=" CD1 LEU I 344 " pdb=" CD2 LEU I 344 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.53e+00 ... (remaining 887 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 379 " 0.776 9.50e-02 1.11e+02 3.48e-01 7.35e+01 pdb=" NE ARG A 379 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARG A 379 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 379 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 379 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 379 " 0.776 9.50e-02 1.11e+02 3.48e-01 7.35e+01 pdb=" NE ARG B 379 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARG B 379 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 379 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 379 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 379 " 0.776 9.50e-02 1.11e+02 3.48e-01 7.35e+01 pdb=" NE ARG I 379 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARG I 379 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG I 379 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG I 379 " 0.023 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 2024 2.89 - 3.39: 4719 3.39 - 3.89: 10111 3.89 - 4.40: 10378 4.40 - 4.90: 22082 Nonbonded interactions: 49314 Sorted by model distance: nonbonded pdb=" NZ LYS I 370 " pdb=" OE2 GLU I 372 " model vdw 2.385 2.520 nonbonded pdb=" NZ LYS A 370 " pdb=" OE2 GLU A 372 " model vdw 2.385 2.520 nonbonded pdb=" NZ LYS B 370 " pdb=" OE2 GLU B 372 " model vdw 2.385 2.520 nonbonded pdb=" NZ LYS D 370 " pdb=" OE2 GLU D 372 " model vdw 2.385 2.520 nonbonded pdb=" NZ LYS G 370 " pdb=" OE2 GLU G 372 " model vdw 2.386 2.520 ... (remaining 49309 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: 0.940 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: 3.690 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.570 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 : 0.007 0.080 5960 Z= 0.484 Angle : 1.149 12.675 7970 Z= 0.557 Chirality : 0.074 0.552 890 Planarity : 0.025 0.348 1020 Dihedral : 12.811 69.085 2290 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -3.05 (0.26), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 329 PHE 0.014 0.005 PHE E 346 TYR 0.008 0.003 TYR A 310 ARG 0.001 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.687 Fit side-chains REVERT: F 315 LEU cc_start: 0.8087 (mp) cc_final: 0.7787 (tt) REVERT: B 321 LYS cc_start: 0.7958 (mttt) cc_final: 0.7742 (tttm) REVERT: B 356 SER cc_start: 0.9066 (p) cc_final: 0.8684 (p) REVERT: C 315 LEU cc_start: 0.8344 (mp) cc_final: 0.8071 (tt) REVERT: D 315 LEU cc_start: 0.7912 (mp) cc_final: 0.7684 (tt) REVERT: G 315 LEU cc_start: 0.8060 (mp) cc_final: 0.7769 (tt) REVERT: I 315 LEU cc_start: 0.8116 (mp) cc_final: 0.7895 (tt) REVERT: J 353 LYS cc_start: 0.8839 (tttt) cc_final: 0.8584 (tttp) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 1.1103 time to fit residues: 108.7668 Evaluate side-chains 77 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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: 6.9990 chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN C 368 ASN J 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5960 Z= 0.277 Angle : 0.674 12.037 7970 Z= 0.320 Chirality : 0.050 0.149 890 Planarity : 0.004 0.031 1020 Dihedral : 5.597 16.362 790 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.04 % Allowed : 8.36 % Favored : 90.60 % 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: -2.85 (0.27), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 330 PHE 0.007 0.002 PHE J 346 TYR 0.014 0.003 TYR D 310 ARG 0.002 0.000 ARG G 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.718 Fit side-chains REVERT: A 321 LYS cc_start: 0.8062 (mttt) cc_final: 0.7674 (tttm) REVERT: F 331 LYS cc_start: 0.8725 (ttmm) cc_final: 0.8405 (mtpt) REVERT: B 369 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8154 (mttm) REVERT: C 315 LEU cc_start: 0.8349 (mp) cc_final: 0.8040 (tt) REVERT: C 331 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8595 (mtpt) REVERT: D 315 LEU cc_start: 0.8119 (mp) cc_final: 0.7843 (tt) REVERT: E 315 LEU cc_start: 0.7903 (mp) cc_final: 0.7563 (tt) REVERT: E 331 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8505 (mtpt) REVERT: G 315 LEU cc_start: 0.8249 (mp) cc_final: 0.7852 (tt) REVERT: H 331 LYS cc_start: 0.8805 (ttmm) cc_final: 0.8566 (mtmt) REVERT: I 315 LEU cc_start: 0.8252 (mp) cc_final: 0.7983 (tt) REVERT: J 331 LYS cc_start: 0.8666 (ttmt) cc_final: 0.8401 (ttmm) REVERT: J 353 LYS cc_start: 0.8802 (tttt) cc_final: 0.8601 (tttm) outliers start: 7 outliers final: 2 residues processed: 73 average time/residue: 1.1922 time to fit residues: 91.5688 Evaluate side-chains 72 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain E residue 331 LYS 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: 8.9990 chunk 19 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 17 optimal weight: 0.0060 chunk 63 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 overall best weight: 6.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 336 GLN J 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 5960 Z= 0.535 Angle : 0.763 11.334 7970 Z= 0.379 Chirality : 0.052 0.125 890 Planarity : 0.004 0.030 1020 Dihedral : 5.914 17.328 790 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 1.04 % Allowed : 12.54 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.25), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 330 PHE 0.009 0.002 PHE J 378 TYR 0.021 0.005 TYR B 310 ARG 0.002 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.702 Fit side-chains REVERT: A 315 LEU cc_start: 0.7970 (tt) cc_final: 0.7534 (mp) REVERT: A 321 LYS cc_start: 0.8052 (mttt) cc_final: 0.7737 (ttpp) REVERT: F 331 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8429 (mtpt) REVERT: B 316 SER cc_start: 0.8717 (p) cc_final: 0.8510 (p) REVERT: B 321 LYS cc_start: 0.8140 (mttt) cc_final: 0.7619 (tttm) REVERT: B 369 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8292 (mttm) REVERT: C 315 LEU cc_start: 0.8501 (mp) cc_final: 0.8119 (tt) REVERT: C 331 LYS cc_start: 0.8957 (ttmt) cc_final: 0.8645 (mtpt) REVERT: E 315 LEU cc_start: 0.8023 (mp) cc_final: 0.7663 (tt) REVERT: E 321 LYS cc_start: 0.8127 (mttt) cc_final: 0.7876 (mttm) REVERT: E 331 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8439 (mtpt) REVERT: H 315 LEU cc_start: 0.8383 (tt) cc_final: 0.7868 (mp) REVERT: H 331 LYS cc_start: 0.8858 (ttmm) cc_final: 0.8618 (mtmt) REVERT: J 331 LYS cc_start: 0.8756 (ttmt) cc_final: 0.8539 (ttmm) REVERT: J 349 ARG cc_start: 0.7071 (mtm180) cc_final: 0.6831 (mmm160) outliers start: 7 outliers final: 3 residues processed: 88 average time/residue: 1.1898 time to fit residues: 110.0413 Evaluate side-chains 89 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain I residue 320 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 ASN ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 336 GLN J 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5960 Z= 0.270 Angle : 0.628 8.562 7970 Z= 0.306 Chirality : 0.049 0.127 890 Planarity : 0.003 0.021 1020 Dihedral : 5.383 15.165 790 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.04 % Allowed : 15.22 % Favored : 83.73 % 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: -2.89 (0.25), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.005 0.001 PHE J 378 TYR 0.012 0.002 TYR B 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.683 Fit side-chains REVERT: A 315 LEU cc_start: 0.7794 (tt) cc_final: 0.7447 (mp) REVERT: A 321 LYS cc_start: 0.8071 (mttt) cc_final: 0.7767 (ttpp) REVERT: F 331 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8458 (mtpt) REVERT: B 315 LEU cc_start: 0.8224 (tt) cc_final: 0.7869 (mp) REVERT: B 369 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8169 (mttm) REVERT: C 315 LEU cc_start: 0.8448 (mp) cc_final: 0.8068 (tt) REVERT: C 331 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8578 (mtpt) REVERT: E 315 LEU cc_start: 0.7897 (mp) cc_final: 0.7559 (tt) REVERT: E 321 LYS cc_start: 0.8110 (mttt) cc_final: 0.7876 (mttp) REVERT: E 331 LYS cc_start: 0.8705 (ttmt) cc_final: 0.8393 (mtpt) REVERT: H 315 LEU cc_start: 0.8484 (tt) cc_final: 0.7992 (mp) REVERT: J 331 LYS cc_start: 0.8669 (ttmt) cc_final: 0.8453 (ttmm) REVERT: J 349 ARG cc_start: 0.7138 (mtm180) cc_final: 0.6879 (mmm160) outliers start: 7 outliers final: 4 residues processed: 83 average time/residue: 1.1073 time to fit residues: 96.8697 Evaluate side-chains 81 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain E residue 349 ARG Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain I residue 320 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 ASN ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 5960 Z= 0.467 Angle : 0.702 8.880 7970 Z= 0.352 Chirality : 0.051 0.132 890 Planarity : 0.003 0.024 1020 Dihedral : 5.625 15.982 790 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.13 % Allowed : 15.37 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.25), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 330 PHE 0.008 0.002 PHE J 378 TYR 0.017 0.004 TYR D 310 ARG 0.002 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 77 time to evaluate : 0.717 Fit side-chains REVERT: A 315 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7484 (mp) REVERT: A 321 LYS cc_start: 0.8135 (mttt) cc_final: 0.7792 (tttp) REVERT: F 331 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8420 (mtpt) REVERT: F 353 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8687 (ttpp) REVERT: B 315 LEU cc_start: 0.8348 (tt) cc_final: 0.8023 (mp) REVERT: B 321 LYS cc_start: 0.8175 (mttt) cc_final: 0.7623 (tttp) REVERT: B 342 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: B 369 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8229 (mttm) REVERT: C 331 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8583 (mtpt) REVERT: E 315 LEU cc_start: 0.8038 (mp) cc_final: 0.7692 (tt) REVERT: E 321 LYS cc_start: 0.8227 (mttt) cc_final: 0.8001 (mttm) REVERT: E 331 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8335 (mtpt) REVERT: H 315 LEU cc_start: 0.8451 (tt) cc_final: 0.7956 (mp) REVERT: H 357 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9047 (tt) REVERT: J 331 LYS cc_start: 0.8723 (ttmt) cc_final: 0.8519 (ttmm) REVERT: J 349 ARG cc_start: 0.7159 (mtm180) cc_final: 0.6727 (mmm160) outliers start: 21 outliers final: 9 residues processed: 90 average time/residue: 1.1316 time to fit residues: 107.1630 Evaluate side-chains 95 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain F residue 353 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain E residue 349 ARG Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 336 GLN Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 357 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN F 368 ASN ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 5960 Z= 0.453 Angle : 0.703 8.942 7970 Z= 0.353 Chirality : 0.051 0.143 890 Planarity : 0.003 0.024 1020 Dihedral : 5.580 15.749 790 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.58 % Allowed : 16.12 % Favored : 80.30 % 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: -2.85 (0.25), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.008 0.002 PHE J 378 TYR 0.018 0.004 TYR B 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 83 time to evaluate : 0.723 Fit side-chains REVERT: A 315 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7512 (mp) REVERT: A 321 LYS cc_start: 0.8131 (mttt) cc_final: 0.7733 (tttp) REVERT: F 331 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8452 (mtpt) REVERT: B 342 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: B 369 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8227 (mttm) REVERT: C 331 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8573 (mtpt) REVERT: C 349 ARG cc_start: 0.7558 (mtm180) cc_final: 0.6878 (mmm160) REVERT: D 321 LYS cc_start: 0.7845 (mttt) cc_final: 0.7622 (mttm) REVERT: E 321 LYS cc_start: 0.8299 (mttt) cc_final: 0.8012 (mttm) REVERT: E 331 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8328 (mtpt) REVERT: H 315 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7944 (mp) REVERT: J 349 ARG cc_start: 0.7229 (mtm180) cc_final: 0.6766 (mmm160) outliers start: 24 outliers final: 11 residues processed: 95 average time/residue: 1.0560 time to fit residues: 105.6538 Evaluate side-chains 100 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain E residue 349 ARG Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain H residue 336 GLN Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain I residue 340 LYS Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 325 LEU Chi-restraints excluded: chain J residue 357 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 ASN ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 336 GLN J 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5960 Z= 0.276 Angle : 0.628 8.368 7970 Z= 0.307 Chirality : 0.050 0.134 890 Planarity : 0.003 0.022 1020 Dihedral : 5.287 14.445 790 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.13 % Allowed : 16.27 % Favored : 80.60 % 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: -2.73 (0.26), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 329 PHE 0.005 0.001 PHE J 378 TYR 0.011 0.002 TYR B 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 76 time to evaluate : 0.738 Fit side-chains REVERT: A 315 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7550 (mp) REVERT: A 321 LYS cc_start: 0.8108 (mttt) cc_final: 0.7783 (tttp) REVERT: F 331 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8464 (mtpt) REVERT: F 353 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8612 (ttpp) REVERT: B 342 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: B 369 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8178 (mttm) REVERT: C 331 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8535 (mtpt) REVERT: D 321 LYS cc_start: 0.7834 (mttt) cc_final: 0.7609 (mttp) REVERT: E 321 LYS cc_start: 0.8277 (mttt) cc_final: 0.7990 (mttp) REVERT: E 331 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8351 (mtpt) REVERT: H 315 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7952 (mp) REVERT: J 349 ARG cc_start: 0.7126 (mtm180) cc_final: 0.6717 (mmm160) outliers start: 21 outliers final: 10 residues processed: 88 average time/residue: 1.1471 time to fit residues: 106.2390 Evaluate side-chains 93 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain F residue 353 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain E residue 349 ARG Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 325 LEU Chi-restraints excluded: chain J residue 357 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 5960 Z= 0.482 Angle : 0.721 8.855 7970 Z= 0.362 Chirality : 0.051 0.139 890 Planarity : 0.003 0.022 1020 Dihedral : 5.534 16.063 790 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.13 % Allowed : 17.01 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.25), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 330 PHE 0.008 0.002 PHE J 378 TYR 0.019 0.004 TYR D 310 ARG 0.002 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 0.712 Fit side-chains REVERT: A 315 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7675 (mp) REVERT: A 321 LYS cc_start: 0.8138 (mttt) cc_final: 0.7796 (tttp) REVERT: F 331 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8442 (mtpt) REVERT: F 353 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8713 (tttp) REVERT: B 342 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: B 369 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8232 (mttm) REVERT: C 331 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8583 (mtpt) REVERT: C 349 ARG cc_start: 0.7619 (mtm180) cc_final: 0.6911 (mmm160) REVERT: D 321 LYS cc_start: 0.7856 (mttt) cc_final: 0.7630 (mttm) REVERT: E 321 LYS cc_start: 0.8338 (mttt) cc_final: 0.8059 (mttm) REVERT: E 331 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8314 (mtpt) REVERT: G 328 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8495 (mt) REVERT: H 315 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7947 (mp) REVERT: J 349 ARG cc_start: 0.7277 (mtm180) cc_final: 0.6774 (mmm160) outliers start: 21 outliers final: 9 residues processed: 92 average time/residue: 1.0361 time to fit residues: 100.7064 Evaluate side-chains 98 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain F residue 353 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain E residue 349 ARG Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 357 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5960 Z= 0.227 Angle : 0.621 8.287 7970 Z= 0.302 Chirality : 0.050 0.136 890 Planarity : 0.003 0.038 1020 Dihedral : 5.172 14.212 790 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.09 % Allowed : 17.91 % Favored : 80.00 % 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: -2.68 (0.26), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 330 PHE 0.004 0.001 PHE F 346 TYR 0.009 0.002 TYR D 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.693 Fit side-chains REVERT: A 315 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7551 (mp) REVERT: A 321 LYS cc_start: 0.8107 (mttt) cc_final: 0.7795 (tttp) REVERT: F 331 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8464 (mtpt) REVERT: B 342 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: B 369 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8157 (mttm) REVERT: C 331 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8521 (mtpt) REVERT: C 349 ARG cc_start: 0.7519 (mtm180) cc_final: 0.6888 (mmm160) REVERT: E 321 LYS cc_start: 0.8277 (mttt) cc_final: 0.7993 (mttm) REVERT: E 331 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8418 (mtpt) REVERT: H 315 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7953 (mp) REVERT: J 349 ARG cc_start: 0.7170 (mtm180) cc_final: 0.6734 (mmm160) outliers start: 14 outliers final: 2 residues processed: 81 average time/residue: 1.1385 time to fit residues: 97.0887 Evaluate side-chains 83 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain J residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.6980 chunk 64 optimal weight: 0.0470 chunk 55 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 0.0370 chunk 59 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN E 336 GLN J 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5960 Z= 0.141 Angle : 0.570 9.322 7970 Z= 0.272 Chirality : 0.049 0.126 890 Planarity : 0.003 0.041 1020 Dihedral : 4.753 14.075 790 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.34 % Allowed : 18.66 % Favored : 80.00 % 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: -2.58 (0.27), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS J 362 PHE 0.005 0.001 PHE F 346 TYR 0.006 0.001 TYR I 310 ARG 0.001 0.000 ARG E 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.700 Fit side-chains REVERT: A 321 LYS cc_start: 0.8084 (mttt) cc_final: 0.7778 (tttp) REVERT: F 331 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8454 (mtpt) REVERT: B 342 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: B 369 LYS cc_start: 0.8433 (mtmt) cc_final: 0.8099 (mttm) REVERT: C 331 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8466 (mtpt) REVERT: E 321 LYS cc_start: 0.8315 (mttt) cc_final: 0.8042 (mttm) REVERT: E 331 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8284 (mtpt) REVERT: H 315 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8046 (mp) REVERT: J 315 LEU cc_start: 0.8322 (mp) cc_final: 0.8045 (tt) REVERT: J 349 ARG cc_start: 0.7147 (mtm180) cc_final: 0.6899 (mmm160) outliers start: 9 outliers final: 0 residues processed: 82 average time/residue: 1.3029 time to fit residues: 112.5331 Evaluate side-chains 78 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain H residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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** F 368 ASN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.146595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.111743 restraints weight = 6639.256| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.58 r_work: 0.3844 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 5960 Z= 0.474 Angle : 0.744 11.417 7970 Z= 0.366 Chirality : 0.052 0.151 890 Planarity : 0.004 0.047 1020 Dihedral : 5.394 15.513 790 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.19 % Allowed : 19.40 % Favored : 79.40 % 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: -2.70 (0.26), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.008 0.002 PHE J 378 TYR 0.018 0.004 TYR D 310 ARG 0.002 0.000 ARG D 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2211.59 seconds wall clock time: 40 minutes 31.12 seconds (2431.12 seconds total)