Starting phenix.real_space_refine on Mon Mar 11 04:45:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9d_18277/03_2024/8q9d_18277.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9d_18277/03_2024/8q9d_18277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9d_18277/03_2024/8q9d_18277.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9d_18277/03_2024/8q9d_18277.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9d_18277/03_2024/8q9d_18277.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9d_18277/03_2024/8q9d_18277.pdb" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 H 3588 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7032 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "A" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 3.60, per 1000 atoms: 0.51 Number of scatterers: 7032 At special positions: 0 Unit cell: (113.712, 124.424, 41.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 642 8.00 N 636 7.00 C 2160 6.00 H 3588 1.00 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: 5.27 Conformation dependent library (CDL) restraints added in 724.0 milliseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 20 sheets defined 0.0% alpha, 49.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 306 through 310 removed outlier: 6.512A pdb=" N VAL E 306 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N VAL F 309 " --> pdb=" O VAL E 306 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE E 308 " --> pdb=" O VAL F 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.749A pdb=" N VAL A 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 317 through 320 removed outlier: 6.295A pdb=" N LYS A 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N SER F 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR A 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 323 through 325 removed outlier: 6.680A pdb=" N SER E 324 " --> pdb=" O LEU F 325 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 328 through 330 removed outlier: 6.605A pdb=" N HIS E 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 337 through 342 removed outlier: 6.468A pdb=" N GLU A 338 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N SER F 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS A 340 " --> pdb=" O SER F 341 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 345 through 346 removed outlier: 6.604A pdb=" N ASP A 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 350 through 362 removed outlier: 6.943A pdb=" N GLN E 351 " --> pdb=" O VAL F 350 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER F 352 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS E 353 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE F 354 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY E 355 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N SER F 356 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLN F 351 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N SER A 352 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS F 353 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE A 354 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY F 355 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N SER A 356 " --> pdb=" O GLY F 355 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 368 through 374 removed outlier: 6.693A pdb=" N ASN E 368 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE F 371 " --> pdb=" O ASN E 368 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS E 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N THR F 373 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU E 372 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS A 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N GLU F 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE A 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N HIS F 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR A 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 377 through 378 removed outlier: 6.776A pdb=" N THR A 377 " --> pdb=" O PHE F 378 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.598A pdb=" N VAL B 306 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL D 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE B 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLN C 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR D 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL C 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.759A pdb=" N VAL C 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 317 through 320 removed outlier: 6.387A pdb=" N LYS C 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N SER D 320 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR C 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 323 through 325 removed outlier: 6.633A pdb=" N SER B 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.549A pdb=" N HIS B 329 " --> pdb=" O HIS D 330 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE C 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 337 through 342 Processing sheet with id=AB8, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.707A pdb=" N ASP C 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 350 through 362 removed outlier: 6.228A pdb=" N VAL B 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LYS D 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER B 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLY D 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE B 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU D 357 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N SER B 356 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N ASN D 359 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N ASP B 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N THR D 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N ILE B 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU C 357 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASP D 358 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASN C 359 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE D 360 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR C 361 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N HIS D 362 " --> pdb=" O THR C 361 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 368 through 374 removed outlier: 6.442A pdb=" N LYS C 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N GLU D 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE C 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N HIS D 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N THR C 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 377 through 378 removed outlier: 6.837A pdb=" N THR C 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) 61 hydrogen bonds defined for protein. 183 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: 2.20 Time building geometry restraints manager: 5.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3582 1.12 - 1.29: 570 1.29 - 1.47: 1156 1.47 - 1.64: 1772 1.64 - 1.81: 6 Bond restraints: 7086 Sorted by residual: bond pdb=" N SER B 316 " pdb=" H SER B 316 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N LYS D 311 " pdb=" H LYS D 311 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" CE1 PHE C 346 " pdb=" HE1 PHE C 346 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N PHE E 378 " pdb=" H PHE E 378 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N VAL A 309 " pdb=" H VAL A 309 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 ... (remaining 7081 not shown) Histogram of bond angle deviations from ideal: 96.09 - 102.72: 24 102.72 - 109.36: 4878 109.36 - 115.99: 4365 115.99 - 122.62: 2963 122.62 - 129.25: 682 Bond angle restraints: 12912 Sorted by residual: angle pdb=" CB HIS D 330 " pdb=" CG HIS D 330 " pdb=" CD2 HIS D 330 " ideal model delta sigma weight residual 131.20 124.69 6.51 1.30e+00 5.92e-01 2.51e+01 angle pdb=" C ASP A 348 " pdb=" N ARG A 349 " pdb=" CA ARG A 349 " ideal model delta sigma weight residual 121.05 127.97 -6.92 1.43e+00 4.89e-01 2.35e+01 angle pdb=" CA ASP B 348 " pdb=" CB ASP B 348 " pdb=" CG ASP B 348 " ideal model delta sigma weight residual 112.60 117.28 -4.68 1.00e+00 1.00e+00 2.19e+01 angle pdb=" CB HIS A 330 " pdb=" CG HIS A 330 " pdb=" CD2 HIS A 330 " ideal model delta sigma weight residual 131.20 125.26 5.94 1.30e+00 5.92e-01 2.09e+01 angle pdb=" CB HIS C 330 " pdb=" CG HIS C 330 " pdb=" CD2 HIS C 330 " ideal model delta sigma weight residual 131.20 125.36 5.84 1.30e+00 5.92e-01 2.02e+01 ... (remaining 12907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.25: 2901 14.25 - 28.49: 173 28.49 - 42.73: 69 42.73 - 56.98: 58 56.98 - 71.22: 63 Dihedral angle restraints: 3264 sinusoidal: 1866 harmonic: 1398 Sorted by residual: dihedral pdb=" CA ASP F 358 " pdb=" C ASP F 358 " pdb=" N ASN F 359 " pdb=" CA ASN F 359 " ideal model delta harmonic sigma weight residual 180.00 160.44 19.56 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA ASP E 358 " pdb=" C ASP E 358 " pdb=" N ASN E 359 " pdb=" CA ASN E 359 " ideal model delta harmonic sigma weight residual 180.00 161.42 18.58 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA GLY A 333 " pdb=" C GLY A 333 " pdb=" N GLY A 334 " pdb=" CA GLY A 334 " ideal model delta harmonic sigma weight residual 180.00 161.60 18.40 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 3261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 273 0.061 - 0.121: 182 0.121 - 0.181: 57 0.181 - 0.241: 13 0.241 - 0.302: 3 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS C 347 " pdb=" N LYS C 347 " pdb=" C LYS C 347 " pdb=" CB LYS C 347 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA LYS A 347 " pdb=" N LYS A 347 " pdb=" C LYS A 347 " pdb=" CB LYS A 347 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA ASP B 348 " pdb=" N ASP B 348 " pdb=" C ASP B 348 " pdb=" CB ASP B 348 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 525 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.097 2.00e-02 2.50e+03 4.22e-02 5.33e+01 pdb=" CG TYR A 310 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " 0.073 2.00e-02 2.50e+03 pdb=" HD1 TYR A 310 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR A 310 " -0.051 2.00e-02 2.50e+03 pdb=" HE1 TYR A 310 " -0.028 2.00e-02 2.50e+03 pdb=" HE2 TYR A 310 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 330 " -0.083 2.00e-02 2.50e+03 4.61e-02 4.79e+01 pdb=" CG HIS F 330 " 0.048 2.00e-02 2.50e+03 pdb=" ND1 HIS F 330 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 HIS F 330 " 0.053 2.00e-02 2.50e+03 pdb=" CE1 HIS F 330 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS F 330 " 0.023 2.00e-02 2.50e+03 pdb=" HD2 HIS F 330 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 HIS F 330 " -0.022 2.00e-02 2.50e+03 pdb=" HE2 HIS F 330 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 362 " -0.064 2.00e-02 2.50e+03 3.80e-02 3.24e+01 pdb=" CG HIS E 362 " 0.053 2.00e-02 2.50e+03 pdb=" ND1 HIS E 362 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS E 362 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 HIS E 362 " 0.013 2.00e-02 2.50e+03 pdb=" NE2 HIS E 362 " 0.024 2.00e-02 2.50e+03 pdb=" HD2 HIS E 362 " -0.010 2.00e-02 2.50e+03 pdb=" HE1 HIS E 362 " -0.024 2.00e-02 2.50e+03 pdb=" HE2 HIS E 362 " -0.049 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 461 2.16 - 2.77: 11796 2.77 - 3.38: 18028 3.38 - 3.99: 24413 3.99 - 4.60: 33930 Nonbonded interactions: 88628 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.547 1.850 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.559 1.850 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.563 1.850 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.572 1.850 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.605 1.850 ... (remaining 88623 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' } 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: 2.920 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: 0.100 Extract box with map and model: 12.550 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.220 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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 : 0.011 0.035 3498 Z= 0.726 Angle : 1.800 6.925 4680 Z= 1.189 Chirality : 0.083 0.302 528 Planarity : 0.010 0.083 594 Dihedral : 9.918 46.311 1344 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -1.95 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS D 329 PHE 0.049 0.013 PHE E 346 TYR 0.084 0.016 TYR A 310 ARG 0.007 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.606 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 revert: symmetry clash REVERT: E 311 LYS cc_start: 0.7839 (mttt) cc_final: 0.7228 (pttp) REVERT: E 347 LYS cc_start: 0.8576 (mttt) cc_final: 0.7816 (mtmt) REVERT: E 369 LYS cc_start: 0.8128 (tttt) cc_final: 0.7668 (ttmm) REVERT: E 371 ILE cc_start: 0.8679 (mt) cc_final: 0.8055 (mt) REVERT: A 307 GLN cc_start: 0.6964 (tt0) cc_final: 0.6477 (mt0) REVERT: A 338 GLU cc_start: 0.6756 (tt0) cc_final: 0.6217 (tm-30) REVERT: A 369 LYS cc_start: 0.7458 (tttt) cc_final: 0.7171 (ttpp) REVERT: A 375 LYS cc_start: 0.7396 (tttt) cc_final: 0.7091 (tttt) REVERT: F 307 GLN cc_start: 0.7165 (tt0) cc_final: 0.6604 (mt0) REVERT: F 317 LYS cc_start: 0.6801 (mttt) cc_final: 0.6299 (mtpt) REVERT: F 338 GLU cc_start: 0.6879 (tt0) cc_final: 0.6548 (tm-30) REVERT: F 340 LYS cc_start: 0.7139 (tttt) cc_final: 0.6616 (mttm) REVERT: F 369 LYS cc_start: 0.7165 (tttt) cc_final: 0.6629 (ttmm) REVERT: F 371 ILE cc_start: 0.7782 (mt) cc_final: 0.7524 (mp) REVERT: B 307 GLN cc_start: 0.8218 (tt0) cc_final: 0.7395 (mt0) REVERT: B 317 LYS cc_start: 0.8017 (mttt) cc_final: 0.7306 (mtpt) REVERT: B 340 LYS cc_start: 0.8242 (tttt) cc_final: 0.7388 (ttmt) REVERT: B 353 LYS cc_start: 0.7157 (mttt) cc_final: 0.6773 (tttm) REVERT: B 369 LYS cc_start: 0.8225 (tttt) cc_final: 0.7650 (tttp) REVERT: C 311 LYS cc_start: 0.7575 (mttt) cc_final: 0.7343 (mttm) REVERT: C 317 LYS cc_start: 0.6972 (mttt) cc_final: 0.6681 (mtpp) REVERT: C 338 GLU cc_start: 0.7053 (tt0) cc_final: 0.6821 (tt0) REVERT: C 369 LYS cc_start: 0.7752 (tttt) cc_final: 0.7348 (tttp) REVERT: D 307 GLN cc_start: 0.7497 (tt0) cc_final: 0.7266 (tt0) REVERT: D 311 LYS cc_start: 0.7490 (mttt) cc_final: 0.7202 (mtmt) REVERT: D 317 LYS cc_start: 0.6932 (mttt) cc_final: 0.6344 (mtpp) REVERT: D 340 LYS cc_start: 0.7267 (tttt) cc_final: 0.6595 (ttmt) REVERT: D 369 LYS cc_start: 0.7547 (tttt) cc_final: 0.7034 (tttp) REVERT: D 372 GLU cc_start: 0.7486 (tt0) cc_final: 0.7270 (tt0) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.6971 time to fit residues: 98.7304 Evaluate side-chains 85 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN B 330 HIS D 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3498 Z= 0.280 Angle : 0.586 4.712 4680 Z= 0.305 Chirality : 0.052 0.134 528 Planarity : 0.003 0.027 594 Dihedral : 5.870 14.623 462 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.01 % Allowed : 5.05 % Favored : 93.94 % 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: -1.16 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.87 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.010 0.002 PHE D 346 TYR 0.010 0.002 TYR B 310 ARG 0.004 0.001 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.568 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 revert: symmetry clash REVERT: E 311 LYS cc_start: 0.7940 (mttt) cc_final: 0.7263 (pttp) REVERT: E 369 LYS cc_start: 0.8184 (tttt) cc_final: 0.7689 (ttmm) REVERT: A 307 GLN cc_start: 0.6975 (tt0) cc_final: 0.6486 (mt0) REVERT: A 317 LYS cc_start: 0.6940 (mttt) cc_final: 0.6560 (mtpt) REVERT: A 338 GLU cc_start: 0.6902 (tt0) cc_final: 0.6332 (tm-30) REVERT: A 369 LYS cc_start: 0.7442 (tttt) cc_final: 0.7184 (ttpp) REVERT: F 307 GLN cc_start: 0.7217 (tt0) cc_final: 0.6593 (mt0) REVERT: F 338 GLU cc_start: 0.6983 (tt0) cc_final: 0.6642 (tm-30) REVERT: F 342 GLU cc_start: 0.6739 (mp0) cc_final: 0.6496 (mp0) REVERT: F 371 ILE cc_start: 0.7726 (mt) cc_final: 0.7494 (mp) REVERT: B 317 LYS cc_start: 0.7942 (mttt) cc_final: 0.7302 (mtpt) REVERT: B 340 LYS cc_start: 0.8059 (tttt) cc_final: 0.7691 (ttmt) REVERT: B 353 LYS cc_start: 0.7158 (mttt) cc_final: 0.6794 (tttm) REVERT: B 369 LYS cc_start: 0.8307 (tttt) cc_final: 0.7732 (tttp) REVERT: C 307 GLN cc_start: 0.7586 (tt0) cc_final: 0.7282 (tt0) REVERT: C 311 LYS cc_start: 0.7689 (mttt) cc_final: 0.7361 (mttm) REVERT: C 317 LYS cc_start: 0.7089 (mttt) cc_final: 0.6740 (mtpp) REVERT: C 340 LYS cc_start: 0.7272 (tttt) cc_final: 0.6577 (mttm) REVERT: C 369 LYS cc_start: 0.7687 (tttt) cc_final: 0.7260 (tttp) REVERT: D 311 LYS cc_start: 0.7633 (mttt) cc_final: 0.7294 (mtmt) REVERT: D 317 LYS cc_start: 0.6943 (mttt) cc_final: 0.6393 (mtpp) REVERT: D 340 LYS cc_start: 0.7270 (tttt) cc_final: 0.6603 (mttm) REVERT: D 369 LYS cc_start: 0.7545 (tttt) cc_final: 0.6986 (tttp) outliers start: 4 outliers final: 4 residues processed: 85 average time/residue: 0.6694 time to fit residues: 63.1068 Evaluate side-chains 79 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain F residue 305 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3498 Z= 0.237 Angle : 0.529 4.577 4680 Z= 0.271 Chirality : 0.051 0.129 528 Planarity : 0.003 0.021 594 Dihedral : 5.287 13.923 462 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.77 % Allowed : 4.80 % Favored : 93.43 % 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: -0.92 (0.39), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.69 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 329 PHE 0.007 0.001 PHE D 346 TYR 0.011 0.002 TYR A 310 ARG 0.002 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 369 LYS cc_start: 0.8162 (tttt) cc_final: 0.7624 (ttmm) REVERT: A 307 GLN cc_start: 0.7048 (tt0) cc_final: 0.6515 (mt0) REVERT: A 317 LYS cc_start: 0.6993 (mttt) cc_final: 0.6585 (mtpt) REVERT: A 338 GLU cc_start: 0.7008 (tt0) cc_final: 0.6495 (tm-30) REVERT: A 347 LYS cc_start: 0.8567 (mttt) cc_final: 0.8078 (mtpp) REVERT: A 369 LYS cc_start: 0.7517 (tttt) cc_final: 0.7004 (ttmm) REVERT: F 307 GLN cc_start: 0.7286 (tt0) cc_final: 0.6624 (mt0) REVERT: F 311 LYS cc_start: 0.7493 (mttt) cc_final: 0.6741 (pttp) REVERT: F 342 GLU cc_start: 0.6824 (mp0) cc_final: 0.6511 (mp0) REVERT: F 369 LYS cc_start: 0.7288 (tttt) cc_final: 0.6730 (ttmm) REVERT: F 371 ILE cc_start: 0.7819 (mt) cc_final: 0.7576 (mp) REVERT: B 317 LYS cc_start: 0.7935 (mttt) cc_final: 0.7341 (mtpt) REVERT: B 340 LYS cc_start: 0.8101 (tttt) cc_final: 0.7294 (mttm) REVERT: B 353 LYS cc_start: 0.7172 (mttt) cc_final: 0.6772 (tttm) REVERT: B 369 LYS cc_start: 0.8288 (tttt) cc_final: 0.7810 (tttp) REVERT: C 307 GLN cc_start: 0.7624 (tt0) cc_final: 0.7302 (tt0) REVERT: C 311 LYS cc_start: 0.7878 (mttt) cc_final: 0.7126 (tttt) REVERT: C 317 LYS cc_start: 0.7209 (mttt) cc_final: 0.6813 (mtpp) REVERT: C 369 LYS cc_start: 0.7608 (tttt) cc_final: 0.7205 (tttp) REVERT: D 311 LYS cc_start: 0.7589 (mttt) cc_final: 0.7272 (mtmt) REVERT: D 317 LYS cc_start: 0.6960 (mttt) cc_final: 0.6398 (mtpp) REVERT: D 369 LYS cc_start: 0.7496 (tttt) cc_final: 0.6912 (tttp) outliers start: 7 outliers final: 5 residues processed: 78 average time/residue: 0.6565 time to fit residues: 57.0627 Evaluate side-chains 71 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3498 Z= 0.295 Angle : 0.529 4.377 4680 Z= 0.272 Chirality : 0.050 0.132 528 Planarity : 0.003 0.022 594 Dihedral : 5.214 13.879 462 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.53 % Allowed : 5.81 % Favored : 91.67 % 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: -0.86 (0.40), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.64 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 329 PHE 0.007 0.001 PHE B 346 TYR 0.011 0.003 TYR E 310 ARG 0.002 0.001 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 351 GLN cc_start: 0.8132 (tt0) cc_final: 0.7776 (mt0) REVERT: A 307 GLN cc_start: 0.7112 (tt0) cc_final: 0.6549 (mt0) REVERT: A 317 LYS cc_start: 0.7082 (mttt) cc_final: 0.6614 (mtpt) REVERT: A 338 GLU cc_start: 0.7031 (tt0) cc_final: 0.6522 (tm-30) REVERT: A 347 LYS cc_start: 0.8516 (mttt) cc_final: 0.8124 (mtpp) REVERT: A 369 LYS cc_start: 0.7517 (tttt) cc_final: 0.6997 (ttmm) REVERT: A 372 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6833 (tm-30) REVERT: F 307 GLN cc_start: 0.7370 (tt0) cc_final: 0.6633 (mt0) REVERT: F 311 LYS cc_start: 0.7455 (mttt) cc_final: 0.6666 (pttm) REVERT: F 341 SER cc_start: 0.8519 (m) cc_final: 0.7963 (m) REVERT: F 342 GLU cc_start: 0.6779 (mp0) cc_final: 0.6539 (mp0) REVERT: F 369 LYS cc_start: 0.7373 (tttt) cc_final: 0.6813 (ttmm) REVERT: F 371 ILE cc_start: 0.7833 (mt) cc_final: 0.7586 (mp) REVERT: B 317 LYS cc_start: 0.7952 (mttt) cc_final: 0.7243 (mtpp) REVERT: B 340 LYS cc_start: 0.8044 (tttt) cc_final: 0.7371 (mttm) REVERT: B 353 LYS cc_start: 0.7215 (mttt) cc_final: 0.6863 (tttm) REVERT: B 369 LYS cc_start: 0.8500 (tttt) cc_final: 0.8008 (tttp) REVERT: C 307 GLN cc_start: 0.7632 (tt0) cc_final: 0.7362 (tt0) REVERT: C 311 LYS cc_start: 0.7887 (mttt) cc_final: 0.7112 (tttt) REVERT: C 317 LYS cc_start: 0.7260 (mttt) cc_final: 0.6850 (mtpp) REVERT: D 311 LYS cc_start: 0.7576 (mttt) cc_final: 0.7256 (mtmt) REVERT: D 317 LYS cc_start: 0.7035 (mttt) cc_final: 0.6434 (mtpp) REVERT: D 369 LYS cc_start: 0.7503 (tttt) cc_final: 0.6880 (tttp) outliers start: 10 outliers final: 8 residues processed: 77 average time/residue: 0.6046 time to fit residues: 52.1241 Evaluate side-chains 76 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3498 Z= 0.179 Angle : 0.466 4.282 4680 Z= 0.237 Chirality : 0.050 0.130 528 Planarity : 0.002 0.019 594 Dihedral : 4.821 13.941 462 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.52 % Allowed : 6.57 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.40), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.63 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 PHE 0.004 0.001 PHE B 346 TYR 0.006 0.002 TYR B 310 ARG 0.002 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 349 ARG cc_start: 0.6432 (mtm180) cc_final: 0.6023 (pmt-80) REVERT: E 351 GLN cc_start: 0.8090 (tt0) cc_final: 0.7751 (mt0) REVERT: A 307 GLN cc_start: 0.7061 (tt0) cc_final: 0.6505 (mt0) REVERT: A 317 LYS cc_start: 0.7028 (mttt) cc_final: 0.6584 (mtpt) REVERT: A 338 GLU cc_start: 0.7036 (tt0) cc_final: 0.6521 (tm-30) REVERT: A 347 LYS cc_start: 0.8528 (mttt) cc_final: 0.8144 (mtpp) REVERT: A 369 LYS cc_start: 0.7448 (tttt) cc_final: 0.6961 (ttmm) REVERT: F 307 GLN cc_start: 0.7272 (tt0) cc_final: 0.6586 (mt0) REVERT: F 311 LYS cc_start: 0.7468 (mttt) cc_final: 0.6751 (pttt) REVERT: F 341 SER cc_start: 0.8495 (m) cc_final: 0.7956 (m) REVERT: F 342 GLU cc_start: 0.6804 (mp0) cc_final: 0.6567 (mp0) REVERT: F 369 LYS cc_start: 0.7348 (tttt) cc_final: 0.6802 (ttmm) REVERT: F 371 ILE cc_start: 0.7813 (mt) cc_final: 0.7573 (mp) REVERT: B 317 LYS cc_start: 0.7956 (mttt) cc_final: 0.7300 (mtpp) REVERT: B 340 LYS cc_start: 0.8081 (tttt) cc_final: 0.7582 (ttmt) REVERT: B 353 LYS cc_start: 0.7134 (mttt) cc_final: 0.6821 (tttm) REVERT: B 369 LYS cc_start: 0.8482 (tttt) cc_final: 0.8056 (tttp) REVERT: C 307 GLN cc_start: 0.7663 (tt0) cc_final: 0.7384 (tt0) REVERT: C 317 LYS cc_start: 0.7232 (mttt) cc_final: 0.6821 (mtpp) REVERT: D 311 LYS cc_start: 0.7603 (mttt) cc_final: 0.7233 (mtmt) REVERT: D 317 LYS cc_start: 0.7008 (mttt) cc_final: 0.6403 (mtpp) REVERT: D 369 LYS cc_start: 0.7490 (tttt) cc_final: 0.6898 (tttp) outliers start: 6 outliers final: 6 residues processed: 72 average time/residue: 0.6351 time to fit residues: 51.2736 Evaluate side-chains 68 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3498 Z= 0.212 Angle : 0.467 4.174 4680 Z= 0.238 Chirality : 0.050 0.130 528 Planarity : 0.003 0.019 594 Dihedral : 4.733 12.237 462 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.02 % Allowed : 6.82 % Favored : 91.16 % 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: -0.78 (0.40), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.59 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 PHE 0.006 0.001 PHE B 346 TYR 0.009 0.002 TYR E 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 349 ARG cc_start: 0.6505 (mtm180) cc_final: 0.6058 (pmt-80) REVERT: E 351 GLN cc_start: 0.8079 (tt0) cc_final: 0.7755 (mt0) REVERT: A 307 GLN cc_start: 0.7081 (tt0) cc_final: 0.6504 (mt0) REVERT: A 317 LYS cc_start: 0.7023 (mttt) cc_final: 0.6573 (mtpt) REVERT: A 338 GLU cc_start: 0.7029 (tt0) cc_final: 0.6528 (tm-30) REVERT: A 347 LYS cc_start: 0.8512 (mttt) cc_final: 0.8125 (mtpp) REVERT: A 369 LYS cc_start: 0.7448 (tttt) cc_final: 0.6961 (ttmm) REVERT: F 307 GLN cc_start: 0.7282 (tt0) cc_final: 0.6673 (mt0) REVERT: F 311 LYS cc_start: 0.7435 (mttt) cc_final: 0.6670 (pttt) REVERT: F 341 SER cc_start: 0.8502 (m) cc_final: 0.7953 (m) REVERT: F 342 GLU cc_start: 0.6783 (mp0) cc_final: 0.6546 (mp0) REVERT: F 369 LYS cc_start: 0.7365 (tttt) cc_final: 0.6814 (ttmm) REVERT: F 371 ILE cc_start: 0.7775 (mt) cc_final: 0.7539 (mp) REVERT: B 317 LYS cc_start: 0.8040 (mttt) cc_final: 0.7393 (mtpp) REVERT: B 340 LYS cc_start: 0.8087 (tttt) cc_final: 0.7313 (mttm) REVERT: B 353 LYS cc_start: 0.7179 (mttt) cc_final: 0.6837 (tttm) REVERT: B 369 LYS cc_start: 0.8516 (tttt) cc_final: 0.8075 (tttp) REVERT: C 307 GLN cc_start: 0.7640 (tt0) cc_final: 0.7366 (tt0) REVERT: C 311 LYS cc_start: 0.7824 (mttt) cc_final: 0.7085 (tttt) REVERT: C 317 LYS cc_start: 0.7189 (mttt) cc_final: 0.6800 (mtpp) REVERT: D 311 LYS cc_start: 0.7579 (mttt) cc_final: 0.7222 (mtmm) REVERT: D 317 LYS cc_start: 0.6975 (mttt) cc_final: 0.6428 (mtpp) REVERT: D 369 LYS cc_start: 0.7487 (tttt) cc_final: 0.6858 (tttp) outliers start: 8 outliers final: 8 residues processed: 72 average time/residue: 0.6582 time to fit residues: 53.0184 Evaluate side-chains 72 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3498 Z= 0.355 Angle : 0.524 4.327 4680 Z= 0.271 Chirality : 0.050 0.131 528 Planarity : 0.003 0.020 594 Dihedral : 5.028 13.809 462 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.78 % Allowed : 6.82 % Favored : 90.40 % 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: -0.97 (0.40), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.73 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 329 PHE 0.007 0.002 PHE B 346 TYR 0.013 0.003 TYR A 310 ARG 0.002 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 347 LYS cc_start: 0.8735 (mttt) cc_final: 0.8298 (mtpp) REVERT: E 349 ARG cc_start: 0.6547 (mtm180) cc_final: 0.6055 (pmt-80) REVERT: E 369 LYS cc_start: 0.8166 (tttt) cc_final: 0.7636 (ttmm) REVERT: A 307 GLN cc_start: 0.7085 (tt0) cc_final: 0.6515 (mt0) REVERT: A 338 GLU cc_start: 0.7086 (tt0) cc_final: 0.6554 (tm-30) REVERT: A 347 LYS cc_start: 0.8487 (mttt) cc_final: 0.8121 (mtpp) REVERT: A 369 LYS cc_start: 0.7491 (tttt) cc_final: 0.6968 (ttmm) REVERT: F 307 GLN cc_start: 0.7337 (tt0) cc_final: 0.6700 (mt0) REVERT: F 311 LYS cc_start: 0.7470 (mttt) cc_final: 0.6633 (pttt) REVERT: F 341 SER cc_start: 0.8507 (m) cc_final: 0.7909 (m) REVERT: F 342 GLU cc_start: 0.6809 (mp0) cc_final: 0.6592 (mp0) REVERT: F 369 LYS cc_start: 0.7414 (tttt) cc_final: 0.6855 (ttmm) REVERT: F 371 ILE cc_start: 0.7795 (mt) cc_final: 0.7547 (mp) REVERT: B 317 LYS cc_start: 0.8085 (mttt) cc_final: 0.7442 (mtpp) REVERT: B 340 LYS cc_start: 0.8139 (tttt) cc_final: 0.7659 (ttmt) REVERT: B 353 LYS cc_start: 0.7208 (mttt) cc_final: 0.6903 (tttm) REVERT: B 369 LYS cc_start: 0.8512 (tttt) cc_final: 0.8039 (tttp) REVERT: C 307 GLN cc_start: 0.7651 (tt0) cc_final: 0.7390 (tt0) REVERT: C 311 LYS cc_start: 0.7905 (mttt) cc_final: 0.7055 (tttt) REVERT: C 317 LYS cc_start: 0.7193 (mttt) cc_final: 0.6802 (mtpp) REVERT: D 311 LYS cc_start: 0.7590 (mttt) cc_final: 0.7242 (mtmt) REVERT: D 317 LYS cc_start: 0.7111 (mttt) cc_final: 0.6560 (mtpp) REVERT: D 369 LYS cc_start: 0.7536 (tttt) cc_final: 0.6902 (tttp) outliers start: 11 outliers final: 9 residues processed: 76 average time/residue: 0.6401 time to fit residues: 54.2849 Evaluate side-chains 76 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3498 Z= 0.172 Angle : 0.456 4.316 4680 Z= 0.232 Chirality : 0.050 0.128 528 Planarity : 0.002 0.018 594 Dihedral : 4.685 13.136 462 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.27 % Allowed : 7.58 % Favored : 90.15 % 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: -0.93 (0.40), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.70 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 329 PHE 0.004 0.001 PHE B 346 TYR 0.007 0.002 TYR A 310 ARG 0.001 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 342 GLU cc_start: 0.7329 (tt0) cc_final: 0.7086 (tt0) REVERT: E 347 LYS cc_start: 0.8731 (mttt) cc_final: 0.8274 (mtpp) REVERT: E 349 ARG cc_start: 0.6526 (mtm180) cc_final: 0.6088 (pmt-80) REVERT: E 369 LYS cc_start: 0.8210 (tttt) cc_final: 0.7648 (ttmm) REVERT: A 307 GLN cc_start: 0.7050 (tt0) cc_final: 0.6505 (mt0) REVERT: A 317 LYS cc_start: 0.7014 (mttt) cc_final: 0.6551 (mtpt) REVERT: A 338 GLU cc_start: 0.7037 (tt0) cc_final: 0.6529 (tm-30) REVERT: A 347 LYS cc_start: 0.8522 (mttt) cc_final: 0.8139 (mtpp) REVERT: A 369 LYS cc_start: 0.7471 (tttt) cc_final: 0.6965 (ttmm) REVERT: F 307 GLN cc_start: 0.7211 (tt0) cc_final: 0.6687 (mt0) REVERT: F 311 LYS cc_start: 0.7461 (mttt) cc_final: 0.6671 (pttt) REVERT: F 341 SER cc_start: 0.8492 (m) cc_final: 0.7951 (m) REVERT: F 342 GLU cc_start: 0.6780 (mp0) cc_final: 0.6562 (mp0) REVERT: F 369 LYS cc_start: 0.7400 (tttt) cc_final: 0.6818 (ttmm) REVERT: F 371 ILE cc_start: 0.7732 (mt) cc_final: 0.7496 (mp) REVERT: B 317 LYS cc_start: 0.7974 (mttt) cc_final: 0.7383 (mtpp) REVERT: B 340 LYS cc_start: 0.8065 (tttt) cc_final: 0.7618 (ttmt) REVERT: B 353 LYS cc_start: 0.7183 (mttt) cc_final: 0.6824 (tttm) REVERT: B 369 LYS cc_start: 0.8485 (tttt) cc_final: 0.8037 (tttp) REVERT: C 307 GLN cc_start: 0.7647 (tt0) cc_final: 0.7381 (tt0) REVERT: C 317 LYS cc_start: 0.7240 (mttt) cc_final: 0.6826 (mtpp) REVERT: D 311 LYS cc_start: 0.7559 (mttt) cc_final: 0.7155 (mtmm) REVERT: D 317 LYS cc_start: 0.7046 (mttt) cc_final: 0.6505 (mtpp) REVERT: D 369 LYS cc_start: 0.7563 (tttt) cc_final: 0.6939 (tttp) outliers start: 9 outliers final: 8 residues processed: 78 average time/residue: 0.6896 time to fit residues: 59.8757 Evaluate side-chains 76 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3498 Z= 0.269 Angle : 0.485 4.346 4680 Z= 0.249 Chirality : 0.050 0.131 528 Planarity : 0.003 0.019 594 Dihedral : 4.803 13.009 462 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.02 % Allowed : 7.58 % Favored : 90.40 % 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: -1.01 (0.40), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.76 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 PHE 0.006 0.001 PHE B 346 TYR 0.010 0.002 TYR E 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 342 GLU cc_start: 0.7403 (tt0) cc_final: 0.7187 (tt0) REVERT: E 347 LYS cc_start: 0.8739 (mttt) cc_final: 0.8291 (mtpp) REVERT: E 349 ARG cc_start: 0.6555 (mtm180) cc_final: 0.6102 (pmt-80) REVERT: E 369 LYS cc_start: 0.8183 (tttt) cc_final: 0.7642 (ttmm) REVERT: A 307 GLN cc_start: 0.7072 (tt0) cc_final: 0.6506 (mt0) REVERT: A 338 GLU cc_start: 0.7051 (tt0) cc_final: 0.6534 (tm-30) REVERT: A 347 LYS cc_start: 0.8516 (mttt) cc_final: 0.8128 (mtpp) REVERT: A 369 LYS cc_start: 0.7478 (tttt) cc_final: 0.6965 (ttmm) REVERT: A 379 ARG cc_start: 0.4780 (tmm160) cc_final: 0.4550 (tmm160) REVERT: F 307 GLN cc_start: 0.7251 (tt0) cc_final: 0.6685 (mt0) REVERT: F 311 LYS cc_start: 0.7438 (mttt) cc_final: 0.6605 (pttt) REVERT: F 341 SER cc_start: 0.8489 (m) cc_final: 0.7885 (m) REVERT: F 342 GLU cc_start: 0.6774 (mp0) cc_final: 0.6572 (mp0) REVERT: F 369 LYS cc_start: 0.7418 (tttt) cc_final: 0.6855 (ttmm) REVERT: F 371 ILE cc_start: 0.7676 (mt) cc_final: 0.7209 (mp) REVERT: F 372 GLU cc_start: 0.7419 (tt0) cc_final: 0.7109 (mp0) REVERT: B 317 LYS cc_start: 0.8012 (mttt) cc_final: 0.7416 (mtpp) REVERT: B 340 LYS cc_start: 0.8137 (tttt) cc_final: 0.7740 (ttmt) REVERT: B 353 LYS cc_start: 0.7218 (mttt) cc_final: 0.6870 (tttm) REVERT: B 369 LYS cc_start: 0.8526 (tttt) cc_final: 0.8059 (tttp) REVERT: C 307 GLN cc_start: 0.7692 (tt0) cc_final: 0.7423 (tt0) REVERT: C 311 LYS cc_start: 0.7869 (mttt) cc_final: 0.7084 (tttt) REVERT: C 317 LYS cc_start: 0.7230 (mttt) cc_final: 0.6804 (mtpp) REVERT: D 311 LYS cc_start: 0.7578 (mttt) cc_final: 0.7227 (mtmt) REVERT: D 317 LYS cc_start: 0.7119 (mttt) cc_final: 0.6578 (mtpp) REVERT: D 369 LYS cc_start: 0.7541 (tttt) cc_final: 0.6914 (tttp) outliers start: 8 outliers final: 8 residues processed: 75 average time/residue: 0.6771 time to fit residues: 56.7708 Evaluate side-chains 75 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 34 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3498 Z= 0.202 Angle : 0.453 4.283 4680 Z= 0.230 Chirality : 0.049 0.127 528 Planarity : 0.002 0.018 594 Dihedral : 4.608 11.888 462 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.02 % Allowed : 7.32 % Favored : 90.66 % 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: -1.00 (0.40), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.75 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 329 PHE 0.004 0.001 PHE B 346 TYR 0.007 0.002 TYR A 310 ARG 0.001 0.000 ARG A 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 347 LYS cc_start: 0.8736 (mttt) cc_final: 0.8291 (mtpp) REVERT: E 349 ARG cc_start: 0.6547 (mtm180) cc_final: 0.6102 (pmt-80) REVERT: E 369 LYS cc_start: 0.8216 (tttt) cc_final: 0.7654 (ttmm) REVERT: A 307 GLN cc_start: 0.7083 (tt0) cc_final: 0.6510 (mt0) REVERT: A 338 GLU cc_start: 0.7044 (tt0) cc_final: 0.6531 (tm-30) REVERT: A 347 LYS cc_start: 0.8511 (mttt) cc_final: 0.8129 (mtpp) REVERT: A 369 LYS cc_start: 0.7464 (tttt) cc_final: 0.6953 (ttmm) REVERT: A 379 ARG cc_start: 0.4811 (tmm160) cc_final: 0.4580 (tmm160) REVERT: F 307 GLN cc_start: 0.7204 (tt0) cc_final: 0.6672 (mt0) REVERT: F 311 LYS cc_start: 0.7454 (mttt) cc_final: 0.6669 (pttt) REVERT: F 341 SER cc_start: 0.8476 (m) cc_final: 0.7893 (m) REVERT: F 342 GLU cc_start: 0.6741 (mp0) cc_final: 0.6526 (mp0) REVERT: F 369 LYS cc_start: 0.7431 (tttt) cc_final: 0.6861 (ttmm) REVERT: F 371 ILE cc_start: 0.7650 (mt) cc_final: 0.7171 (mp) REVERT: F 372 GLU cc_start: 0.7367 (tt0) cc_final: 0.7087 (mp0) REVERT: B 317 LYS cc_start: 0.8016 (mttt) cc_final: 0.7437 (mtpp) REVERT: B 340 LYS cc_start: 0.8086 (tttt) cc_final: 0.7352 (mttm) REVERT: B 353 LYS cc_start: 0.7180 (mttt) cc_final: 0.6825 (tttm) REVERT: B 369 LYS cc_start: 0.8505 (tttt) cc_final: 0.8077 (tttp) REVERT: C 307 GLN cc_start: 0.7709 (tt0) cc_final: 0.7439 (tt0) REVERT: C 317 LYS cc_start: 0.7263 (mttt) cc_final: 0.6836 (mtpp) REVERT: D 311 LYS cc_start: 0.7571 (mttt) cc_final: 0.7171 (mtmm) REVERT: D 317 LYS cc_start: 0.7084 (mttt) cc_final: 0.6552 (mtpp) REVERT: D 369 LYS cc_start: 0.7572 (tttt) cc_final: 0.6942 (tttp) outliers start: 8 outliers final: 8 residues processed: 77 average time/residue: 0.6983 time to fit residues: 59.7535 Evaluate side-chains 75 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.4980 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 0.1980 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.126010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.111328 restraints weight = 13370.382| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.85 r_work: 0.3694 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3498 Z= 0.130 Angle : 0.433 4.046 4680 Z= 0.218 Chirality : 0.050 0.126 528 Planarity : 0.002 0.017 594 Dihedral : 4.321 13.715 462 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.77 % Allowed : 8.84 % Favored : 89.39 % 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: -0.87 (0.40), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.66 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 362 PHE 0.004 0.001 PHE F 378 TYR 0.006 0.001 TYR B 310 ARG 0.001 0.000 ARG F 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3149.50 seconds wall clock time: 56 minutes 2.46 seconds (3362.46 seconds total)