Starting phenix.real_space_refine (version: dev) on Sat Feb 18 03:08:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkj_14044/02_2023/7qkj_14044.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkj_14044/02_2023/7qkj_14044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkj_14044/02_2023/7qkj_14044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkj_14044/02_2023/7qkj_14044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkj_14044/02_2023/7qkj_14044.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qkj_14044/02_2023/7qkj_14044.pdb" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 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 Process input model Symmetric amino acids flipped Residue "A GLU 342": "OE1" <-> "OE2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A ARG 379": "NH1" <-> "NH2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "B ARG 379": "NH1" <-> "NH2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "E GLU 342": "OE1" <-> "OE2" Residue "E ARG 349": "NH1" <-> "NH2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 379": "NH1" <-> "NH2" Residue "F GLU 342": "OE1" <-> "OE2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F ARG 379": "NH1" <-> "NH2" Residue "G GLU 342": "OE1" <-> "OE2" Residue "G ARG 349": "NH1" <-> "NH2" Residue "H GLU 342": "OE1" <-> "OE2" Residue "H PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 349": "NH1" <-> "NH2" Residue "H ARG 379": "NH1" <-> "NH2" Residue "I GLU 342": "OE1" <-> "OE2" Residue "I PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 349": "NH1" <-> "NH2" Residue "I ARG 379": "NH1" <-> "NH2" Residue "J GLU 342": "OE1" <-> "OE2" Residue "J ARG 349": "NH1" <-> "NH2" Residue "J PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 342": "OE1" <-> "OE2" Residue "K ARG 349": "NH1" <-> "NH2" Residue "K ARG 379": "NH1" <-> "NH2" Residue "L GLU 342": "OE1" <-> "OE2" Residue "L ARG 349": "NH1" <-> "NH2" Residue "L ARG 379": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 6888 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "G" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "H" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "I" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "J" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "K" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "L" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 4.05, per 1000 atoms: 0.59 Number of scatterers: 6888 At special positions: 0 Unit cell: (159.032, 189.52, 46.144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 1284 8.00 N 1272 7.00 C 4320 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: 2.17 Conformation dependent library (CDL) restraints added in 1.1 seconds 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 37 sheets defined 0.0% alpha, 37.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.409A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL C 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE B 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.765A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.768A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 329 removed outlier: 6.372A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 337 through 341 removed outlier: 6.574A pdb=" N GLU A 338 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N SER C 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LYS A 340 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL B 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LYS C 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL B 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 346 removed outlier: 6.650A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 350 through 354 removed outlier: 6.422A pdb=" N VAL B 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N LYS C 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 361 removed outlier: 6.391A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 368 through 371 Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 377 removed outlier: 6.509A pdb=" N HIS B 374 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N THR C 377 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU B 376 " --> pdb=" O THR C 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 307 through 310 removed outlier: 6.352A pdb=" N ILE D 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.799A pdb=" N VAL D 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 319 through 322 removed outlier: 6.724A pdb=" N THR D 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N CYS F 322 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS D 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 328 through 329 removed outlier: 6.423A pdb=" N ILE D 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 337 through 341 removed outlier: 6.521A pdb=" N VAL D 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LYS E 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL D 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 345 through 346 removed outlier: 6.770A pdb=" N ASP D 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 350 through 358 removed outlier: 6.924A pdb=" N LEU E 357 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASP D 358 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER F 356 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU D 357 " --> pdb=" O SER F 356 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASP F 358 " --> pdb=" O LEU D 357 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 368 through 371 removed outlier: 6.483A pdb=" N ASN D 368 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ILE E 371 " --> pdb=" O ASN D 368 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LYS D 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 374 through 377 removed outlier: 6.687A pdb=" N HIS D 374 " --> pdb=" O LYS E 375 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N THR E 377 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU D 376 " --> pdb=" O THR E 377 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 306 through 310 removed outlier: 6.432A pdb=" N VAL G 306 " --> pdb=" O GLN H 307 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL H 309 " --> pdb=" O VAL G 306 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE G 308 " --> pdb=" O VAL H 309 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLN G 307 " --> pdb=" O ILE I 308 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N TYR I 310 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL G 309 " --> pdb=" O TYR I 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'H' and resid 313 through 314 removed outlier: 6.881A pdb=" N VAL G 313 " --> pdb=" O ASP I 314 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 319 through 322 removed outlier: 6.819A pdb=" N THR G 319 " --> pdb=" O SER I 320 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N CYS I 322 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS G 321 " --> pdb=" O CYS I 322 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 328 through 329 removed outlier: 6.438A pdb=" N ILE G 328 " --> pdb=" O HIS I 329 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 337 through 341 removed outlier: 6.646A pdb=" N VAL G 337 " --> pdb=" O GLU H 338 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N LYS H 340 " --> pdb=" O VAL G 337 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL G 339 " --> pdb=" O LYS H 340 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 345 through 346 removed outlier: 6.629A pdb=" N ASP G 345 " --> pdb=" O PHE I 346 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 350 through 358 removed outlier: 6.278A pdb=" N VAL G 350 " --> pdb=" O GLN H 351 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N LYS H 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER G 352 " --> pdb=" O LYS H 353 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N GLY H 355 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE G 354 " --> pdb=" O GLY H 355 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU H 357 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N SER G 356 " --> pdb=" O LEU H 357 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER I 356 " --> pdb=" O GLY G 355 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU G 357 " --> pdb=" O SER I 356 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASP I 358 " --> pdb=" O LEU G 357 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 368 through 377 removed outlier: 6.608A pdb=" N LYS G 369 " --> pdb=" O LYS I 370 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLU I 372 " --> pdb=" O LYS G 369 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE G 371 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N HIS I 374 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N THR G 373 " --> pdb=" O HIS I 374 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU I 376 " --> pdb=" O THR G 373 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LYS G 375 " --> pdb=" O LEU I 376 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 306 through 310 Processing sheet with id=AD2, first strand: chain 'K' and resid 313 through 314 removed outlier: 6.783A pdb=" N VAL J 313 " --> pdb=" O ASP L 314 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 319 through 322 removed outlier: 6.683A pdb=" N THR J 319 " --> pdb=" O SER L 320 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N CYS L 322 " --> pdb=" O THR J 319 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LYS J 321 " --> pdb=" O CYS L 322 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 328 through 329 removed outlier: 6.504A pdb=" N ILE J 328 " --> pdb=" O HIS L 329 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 337 through 341 Processing sheet with id=AD6, first strand: chain 'K' and resid 345 through 346 removed outlier: 6.664A pdb=" N ASP J 345 " --> pdb=" O PHE L 346 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 350 through 354 removed outlier: 6.416A pdb=" N VAL J 350 " --> pdb=" O GLN K 351 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N LYS K 353 " --> pdb=" O VAL J 350 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER J 352 " --> pdb=" O LYS K 353 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 357 through 361 removed outlier: 6.312A pdb=" N ASP J 358 " --> pdb=" O ASN L 359 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N THR L 361 " --> pdb=" O ASP J 358 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE J 360 " --> pdb=" O THR L 361 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 368 through 371 removed outlier: 6.550A pdb=" N LYS J 369 " --> pdb=" O LYS L 370 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 374 through 377 removed outlier: 6.476A pdb=" N HIS J 374 " --> pdb=" O LYS K 375 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N THR K 377 " --> pdb=" O HIS J 374 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU J 376 " --> pdb=" O THR K 377 " (cutoff:3.500A) 113 hydrogen bonds defined for protein. 339 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1982 1.34 - 1.46: 867 1.46 - 1.58: 4132 1.58 - 1.70: 3 1.70 - 1.82: 12 Bond restraints: 6996 Sorted by residual: bond pdb=" CA GLU J 372 " pdb=" CB GLU J 372 " ideal model delta sigma weight residual 1.527 1.566 -0.039 7.60e-03 1.73e+04 2.63e+01 bond pdb=" N GLY L 355 " pdb=" CA GLY L 355 " ideal model delta sigma weight residual 1.442 1.468 -0.026 7.70e-03 1.69e+04 1.15e+01 bond pdb=" CA ILE K 371 " pdb=" CB ILE K 371 " ideal model delta sigma weight residual 1.538 1.582 -0.044 1.30e-02 5.92e+03 1.12e+01 bond pdb=" CZ ARG K 379 " pdb=" NH2 ARG K 379 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.12e+00 bond pdb=" CZ ARG J 379 " pdb=" NH2 ARG J 379 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.03e+00 ... (remaining 6991 not shown) Histogram of bond angle deviations from ideal: 100.22 - 106.68: 322 106.68 - 113.15: 3467 113.15 - 119.62: 2260 119.62 - 126.08: 3129 126.08 - 132.55: 182 Bond angle restraints: 9360 Sorted by residual: angle pdb=" N GLU B 372 " pdb=" CA GLU B 372 " pdb=" C GLU B 372 " ideal model delta sigma weight residual 110.44 125.38 -14.94 1.20e+00 6.94e-01 1.55e+02 angle pdb=" N GLU C 372 " pdb=" CA GLU C 372 " pdb=" C GLU C 372 " ideal model delta sigma weight residual 110.44 124.79 -14.35 1.20e+00 6.94e-01 1.43e+02 angle pdb=" N ASN F 327 " pdb=" CA ASN F 327 " pdb=" C ASN F 327 " ideal model delta sigma weight residual 110.35 126.12 -15.77 1.36e+00 5.41e-01 1.35e+02 angle pdb=" CA ILE J 371 " pdb=" CB ILE J 371 " pdb=" CG1 ILE J 371 " ideal model delta sigma weight residual 110.40 130.01 -19.61 1.70e+00 3.46e-01 1.33e+02 angle pdb=" N GLU A 372 " pdb=" CA GLU A 372 " pdb=" C GLU A 372 " ideal model delta sigma weight residual 110.88 124.29 -13.41 1.28e+00 6.10e-01 1.10e+02 ... (remaining 9355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.61: 3493 10.61 - 21.23: 552 21.23 - 31.84: 169 31.84 - 42.46: 43 42.46 - 53.07: 15 Dihedral angle restraints: 4272 sinusoidal: 1788 harmonic: 2484 Sorted by residual: dihedral pdb=" C GLU L 372 " pdb=" N GLU L 372 " pdb=" CA GLU L 372 " pdb=" CB GLU L 372 " ideal model delta harmonic sigma weight residual -122.60 -151.85 29.25 0 2.50e+00 1.60e-01 1.37e+02 dihedral pdb=" C GLU B 372 " pdb=" N GLU B 372 " pdb=" CA GLU B 372 " pdb=" CB GLU B 372 " ideal model delta harmonic sigma weight residual -122.60 -151.00 28.40 0 2.50e+00 1.60e-01 1.29e+02 dihedral pdb=" C GLU C 372 " pdb=" N GLU C 372 " pdb=" CA GLU C 372 " pdb=" CB GLU C 372 " ideal model delta harmonic sigma weight residual -122.60 -150.98 28.38 0 2.50e+00 1.60e-01 1.29e+02 ... (remaining 4269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.259: 1029 0.259 - 0.519: 14 0.519 - 0.778: 2 0.778 - 1.037: 2 1.037 - 1.297: 9 Chirality restraints: 1056 Sorted by residual: chirality pdb=" CA GLU L 372 " pdb=" N GLU L 372 " pdb=" C GLU L 372 " pdb=" CB GLU L 372 " both_signs ideal model delta sigma weight residual False 2.51 1.21 1.30 2.00e-01 2.50e+01 4.20e+01 chirality pdb=" CA ASN F 327 " pdb=" N ASN F 327 " pdb=" C ASN F 327 " pdb=" CB ASN F 327 " both_signs ideal model delta sigma weight residual False 2.51 1.26 1.25 2.00e-01 2.50e+01 3.92e+01 chirality pdb=" CA GLU B 372 " pdb=" N GLU B 372 " pdb=" C GLU B 372 " pdb=" CB GLU B 372 " both_signs ideal model delta sigma weight residual False 2.51 1.28 1.23 2.00e-01 2.50e+01 3.79e+01 ... (remaining 1053 not shown) Planarity restraints: 1188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 359 " 0.024 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C ASN D 359 " -0.079 2.00e-02 2.50e+03 pdb=" O ASN D 359 " 0.029 2.00e-02 2.50e+03 pdb=" N ILE D 360 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 359 " 0.022 2.00e-02 2.50e+03 4.33e-02 1.87e+01 pdb=" C ASN F 359 " -0.075 2.00e-02 2.50e+03 pdb=" O ASN F 359 " 0.028 2.00e-02 2.50e+03 pdb=" N ILE F 360 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 359 " 0.022 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C ASN E 359 " -0.074 2.00e-02 2.50e+03 pdb=" O ASN E 359 " 0.027 2.00e-02 2.50e+03 pdb=" N ILE E 360 " 0.025 2.00e-02 2.50e+03 ... (remaining 1185 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 3200 2.99 - 3.47: 5386 3.47 - 3.94: 11041 3.94 - 4.42: 10462 4.42 - 4.90: 20856 Nonbonded interactions: 50945 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.510 2.440 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.527 2.440 nonbonded pdb=" OD1 ASP K 314 " pdb=" OG SER K 316 " model vdw 2.538 2.440 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.552 2.440 nonbonded pdb=" OD1 ASP J 314 " pdb=" OG SER J 316 " model vdw 2.570 2.440 ... (remaining 50940 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' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 4320 2.51 5 N 1272 2.21 5 O 1284 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 3.690 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: 12.040 Check model and map are aligned: 0.110 Process input model: 19.710 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.060 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.058 6996 Z= 0.802 Angle : 2.043 19.606 9360 Z= 1.314 Chirality : 0.155 1.297 1056 Planarity : 0.010 0.068 1188 Dihedral : 11.594 53.069 2688 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 0.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer Outliers : 0.00 % Cbeta Deviations : 1.52 % 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: -2.24 (0.25), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.19), residues: 876 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.2976 time to fit residues: 82.7982 Evaluate side-chains 158 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.880 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 76 optimal weight: 0.0770 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 HIS C 368 ASN D 327 ASN E 327 ASN F 327 ASN H 307 GLN I 336 GLN K 327 ASN L 327 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 6996 Z= 0.172 Angle : 0.636 7.387 9360 Z= 0.326 Chirality : 0.049 0.183 1056 Planarity : 0.004 0.036 1188 Dihedral : 5.680 17.557 924 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.26), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.20), residues: 876 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 182 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 188 average time/residue: 0.2490 time to fit residues: 58.0708 Evaluate side-chains 164 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 160 time to evaluate : 0.853 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0648 time to fit residues: 1.6225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 40.0000 chunk 23 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 51 optimal weight: 0.0770 chunk 21 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 overall best weight: 2.9144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS A 330 HIS E 359 ASN F 327 ASN G 307 GLN H 307 GLN J 327 ASN L 307 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 6996 Z= 0.234 Angle : 0.631 6.574 9360 Z= 0.324 Chirality : 0.049 0.174 1056 Planarity : 0.004 0.041 1188 Dihedral : 5.113 16.572 924 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer Outliers : 1.26 % 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: -2.10 (0.26), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.20), residues: 876 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 163 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 164 average time/residue: 0.2409 time to fit residues: 48.7881 Evaluate side-chains 160 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 155 time to evaluate : 0.756 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0571 time to fit residues: 1.6152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 9.9990 chunk 57 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 40.0000 chunk 36 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 307 GLN H 307 GLN L 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 6996 Z= 0.173 Angle : 0.580 6.252 9360 Z= 0.295 Chirality : 0.047 0.178 1056 Planarity : 0.004 0.041 1188 Dihedral : 4.685 16.236 924 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer Outliers : 0.88 % 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: -2.10 (0.26), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.20), residues: 876 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 162 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 164 average time/residue: 0.2581 time to fit residues: 52.7053 Evaluate side-chains 160 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 156 time to evaluate : 0.889 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0639 time to fit residues: 1.7006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 1 optimal weight: 30.0000 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 69 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 0.0170 chunk 20 optimal weight: 20.0000 overall best weight: 3.2824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN H 307 GLN J 307 GLN K 329 HIS L 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 6996 Z= 0.250 Angle : 0.615 5.514 9360 Z= 0.316 Chirality : 0.049 0.166 1056 Planarity : 0.004 0.041 1188 Dihedral : 4.954 15.918 924 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer Outliers : 1.77 % 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: -2.14 (0.26), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.20), residues: 876 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 164 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 170 average time/residue: 0.2570 time to fit residues: 54.1894 Evaluate side-chains 160 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 155 time to evaluate : 0.848 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0582 time to fit residues: 1.7144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 16 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 20 optimal weight: 40.0000 chunk 81 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 0.0570 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 30.0000 overall best weight: 1.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 HIS H 330 HIS L 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 6996 Z= 0.177 Angle : 0.568 7.042 9360 Z= 0.289 Chirality : 0.047 0.182 1056 Planarity : 0.004 0.035 1188 Dihedral : 4.535 14.433 924 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer Outliers : 1.01 % 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: -2.16 (0.26), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.20), residues: 876 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 162 time to evaluate : 0.859 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 163 average time/residue: 0.2473 time to fit residues: 50.7751 Evaluate side-chains 158 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 154 time to evaluate : 0.916 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0626 time to fit residues: 1.6945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 59 optimal weight: 30.0000 chunk 45 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 50 optimal weight: 0.0070 chunk 49 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 overall best weight: 6.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS I 336 GLN ** I 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 329 HIS L 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.5864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 6996 Z= 0.417 Angle : 0.723 8.507 9360 Z= 0.371 Chirality : 0.051 0.164 1056 Planarity : 0.005 0.044 1188 Dihedral : 5.494 16.930 924 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.25), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.19), residues: 876 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 0.775 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 153 average time/residue: 0.2440 time to fit residues: 46.8591 Evaluate side-chains 149 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 141 time to evaluate : 0.866 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0961 time to fit residues: 2.4105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 30.0000 chunk 24 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 51 optimal weight: 0.0770 chunk 55 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 7 optimal weight: 40.0000 chunk 63 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 overall best weight: 3.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 336 GLN ** I 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.6120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 6996 Z= 0.253 Angle : 0.629 6.355 9360 Z= 0.322 Chirality : 0.048 0.144 1056 Planarity : 0.004 0.039 1188 Dihedral : 4.876 15.553 924 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer Outliers : 0.25 % 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: -2.43 (0.25), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.19), residues: 876 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 0.881 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 152 average time/residue: 0.2364 time to fit residues: 45.5867 Evaluate side-chains 149 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 0.863 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0615 time to fit residues: 1.3301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 45 optimal weight: 40.0000 chunk 32 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 49 optimal weight: 0.0980 chunk 79 optimal weight: 7.9990 chunk 48 optimal weight: 30.0000 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS H 307 GLN ** 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: 0.7361 moved from start: 0.6423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 6996 Z= 0.350 Angle : 0.701 8.729 9360 Z= 0.359 Chirality : 0.050 0.157 1056 Planarity : 0.004 0.042 1188 Dihedral : 5.205 17.418 924 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer Outliers : 0.51 % 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: -2.57 (0.25), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.19), residues: 876 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 154 time to evaluate : 0.883 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 154 average time/residue: 0.2355 time to fit residues: 45.5998 Evaluate side-chains 157 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 155 time to evaluate : 0.785 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0613 time to fit residues: 1.3485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 83 optimal weight: 0.3980 chunk 77 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 6 optimal weight: 40.0000 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.6528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 6996 Z= 0.164 Angle : 0.604 8.106 9360 Z= 0.306 Chirality : 0.047 0.142 1056 Planarity : 0.003 0.035 1188 Dihedral : 4.470 13.505 924 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 0.51 % 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: -2.50 (0.25), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.19), residues: 876 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 170 time to evaluate : 0.867 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 171 average time/residue: 0.2524 time to fit residues: 53.7885 Evaluate side-chains 159 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 157 time to evaluate : 0.841 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0639 time to fit residues: 1.4070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 30.0000 chunk 9 optimal weight: 8.9990 chunk 18 optimal weight: 30.0000 chunk 66 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 58 optimal weight: 0.0070 chunk 3 optimal weight: 0.0020 chunk 48 optimal weight: 40.0000 overall best weight: 4.4012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 307 GLN ** I 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.221033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.148530 restraints weight = 7088.619| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 1.69 r_work: 0.4114 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.4019 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.6670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 6996 Z= 0.323 Angle : 0.688 9.557 9360 Z= 0.350 Chirality : 0.049 0.149 1056 Planarity : 0.004 0.065 1188 Dihedral : 4.912 14.931 924 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer Outliers : 0.25 % 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: -2.54 (0.25), residues: 876 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.19), residues: 876 =============================================================================== Job complete usr+sys time: 2179.04 seconds wall clock time: 40 minutes 12.01 seconds (2412.01 seconds total)