Starting phenix.real_space_refine on Thu Jul 18 19:38:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2l_18112/07_2024/8q2l_18112.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2l_18112/07_2024/8q2l_18112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2l_18112/07_2024/8q2l_18112.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2l_18112/07_2024/8q2l_18112.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2l_18112/07_2024/8q2l_18112.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2l_18112/07_2024/8q2l_18112.cif" } resolution = 2.2 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2076 2.51 5 N 600 2.21 5 O 618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 338": "OE1" <-> "OE2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F GLU 372": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3300 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "D" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "C" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "B" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "E" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "F" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Time building chain proxies: 2.85, per 1000 atoms: 0.86 Number of scatterers: 3300 At special positions: 0 Unit cell: (82.878, 119.955, 45.074, 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 6 16.00 O 618 8.00 N 600 7.00 C 2076 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: 0.91 Conformation dependent library (CDL) restraints added in 695.8 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 54.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 310 removed outlier: 6.639A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.908A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 324 removed outlier: 6.512A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N SER C 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY A 323 " --> pdb=" O SER C 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330 Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 346 removed outlier: 5.987A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N GLU C 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N SER A 341 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LEU C 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS A 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N PHE C 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL C 337 " --> pdb=" O GLN D 336 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLU D 338 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 354 removed outlier: 6.620A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 362 removed outlier: 6.605A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU D 357 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE C 360 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASN D 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N HIS C 362 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR D 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 368 through 377 removed outlier: 6.509A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 308 through 310 removed outlier: 6.604A pdb=" N VAL B 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.945A pdb=" N VAL B 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 317 through 324 removed outlier: 6.479A pdb=" N LYS B 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N SER F 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR B 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N CYS F 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS B 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N SER F 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY B 323 " --> pdb=" O SER F 324 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 328 through 330 Processing sheet with id=AB4, first strand: chain 'B' and resid 336 through 346 removed outlier: 5.885A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LYS F 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL B 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLU F 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER B 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU F 344 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LYS B 343 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N PHE F 346 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASP B 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL F 337 " --> pdb=" O GLN E 336 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU E 338 " --> pdb=" O VAL F 337 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 351 through 354 removed outlier: 6.600A pdb=" N GLN B 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ILE F 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS B 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 357 through 362 removed outlier: 6.427A pdb=" N LEU E 357 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE F 360 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASN E 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N HIS F 362 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR E 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 368 through 377 removed outlier: 6.539A pdb=" N LYS B 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLU F 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N HIS F 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR B 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LEU F 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS B 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) 73 hydrogen bonds defined for protein. 219 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: 0.69 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 969 1.33 - 1.45: 383 1.45 - 1.57: 1996 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3354 Sorted by residual: bond pdb=" CB VAL B 309 " pdb=" CG2 VAL B 309 " ideal model delta sigma weight residual 1.521 1.260 0.261 3.30e-02 9.18e+02 6.24e+01 bond pdb=" CB VAL B 318 " pdb=" CG1 VAL B 318 " ideal model delta sigma weight residual 1.521 1.407 0.114 3.30e-02 9.18e+02 1.19e+01 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.11e+00 bond pdb=" CZ ARG B 349 " pdb=" NH2 ARG B 349 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.06e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.63e+00 ... (remaining 3349 not shown) Histogram of bond angle deviations from ideal: 102.59 - 108.40: 335 108.40 - 114.20: 1663 114.20 - 120.01: 1036 120.01 - 125.82: 1364 125.82 - 131.63: 90 Bond angle restraints: 4488 Sorted by residual: angle pdb=" CA VAL F 309 " pdb=" CB VAL F 309 " pdb=" CG1 VAL F 309 " ideal model delta sigma weight residual 110.40 131.63 -21.23 1.70e+00 3.46e-01 1.56e+02 angle pdb=" CA VAL D 318 " pdb=" CB VAL D 318 " pdb=" CG1 VAL D 318 " ideal model delta sigma weight residual 110.40 130.38 -19.98 1.70e+00 3.46e-01 1.38e+02 angle pdb=" CA VAL C 318 " pdb=" CB VAL C 318 " pdb=" CG1 VAL C 318 " ideal model delta sigma weight residual 110.40 130.18 -19.78 1.70e+00 3.46e-01 1.35e+02 angle pdb=" CA VAL E 318 " pdb=" CB VAL E 318 " pdb=" CG1 VAL E 318 " ideal model delta sigma weight residual 110.40 129.81 -19.41 1.70e+00 3.46e-01 1.30e+02 angle pdb=" CA VAL B 313 " pdb=" CB VAL B 313 " pdb=" CG1 VAL B 313 " ideal model delta sigma weight residual 110.40 129.60 -19.20 1.70e+00 3.46e-01 1.28e+02 ... (remaining 4483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 1890 16.73 - 33.46: 112 33.46 - 50.19: 8 50.19 - 66.92: 21 66.92 - 83.65: 9 Dihedral angle restraints: 2040 sinusoidal: 852 harmonic: 1188 Sorted by residual: dihedral pdb=" CA PHE E 346 " pdb=" C PHE E 346 " pdb=" N LYS E 347 " pdb=" CA LYS E 347 " ideal model delta harmonic sigma weight residual -180.00 -156.90 -23.10 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA PHE D 346 " pdb=" C PHE D 346 " pdb=" N LYS D 347 " pdb=" CA LYS D 347 " ideal model delta harmonic sigma weight residual 180.00 -157.40 -22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA PHE C 346 " pdb=" C PHE C 346 " pdb=" N LYS C 347 " pdb=" CA LYS C 347 " ideal model delta harmonic sigma weight residual -180.00 -158.15 -21.85 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 2037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.225: 468 0.225 - 0.449: 14 0.449 - 0.674: 0 0.674 - 0.898: 13 0.898 - 1.123: 9 Chirality restraints: 504 Sorted by residual: chirality pdb=" CB VAL B 313 " pdb=" CA VAL B 313 " pdb=" CG1 VAL B 313 " pdb=" CG2 VAL B 313 " both_signs ideal model delta sigma weight residual False -2.63 -1.51 -1.12 2.00e-01 2.50e+01 3.15e+01 chirality pdb=" CB VAL B 309 " pdb=" CA VAL B 309 " pdb=" CG1 VAL B 309 " pdb=" CG2 VAL B 309 " both_signs ideal model delta sigma weight residual False -2.63 -1.53 -1.10 2.00e-01 2.50e+01 3.01e+01 chirality pdb=" CB VAL A 309 " pdb=" CA VAL A 309 " pdb=" CG1 VAL A 309 " pdb=" CG2 VAL A 309 " both_signs ideal model delta sigma weight residual False -2.63 -1.54 -1.09 2.00e-01 2.50e+01 2.96e+01 ... (remaining 501 not shown) Planarity restraints: 570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.062 2.00e-02 2.50e+03 3.65e-02 2.66e+01 pdb=" CG TYR A 310 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.052 2.00e-02 2.50e+03 3.07e-02 1.88e+01 pdb=" CG TYR F 310 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 374 " -0.027 2.00e-02 2.50e+03 2.11e-02 6.69e+00 pdb=" CG HIS E 374 " 0.029 2.00e-02 2.50e+03 pdb=" ND1 HIS E 374 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 HIS E 374 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 HIS E 374 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS E 374 " -0.024 2.00e-02 2.50e+03 ... (remaining 567 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.98: 1448 2.98 - 3.46: 2681 3.46 - 3.94: 5228 3.94 - 4.42: 5391 4.42 - 4.90: 10091 Nonbonded interactions: 24839 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.506 2.440 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.512 2.440 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.516 2.440 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.516 2.440 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.531 2.440 ... (remaining 24834 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: 2.480 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.440 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 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 : 0.013 0.261 3354 Z= 0.834 Angle : 2.223 21.228 4488 Z= 1.402 Chirality : 0.218 1.123 504 Planarity : 0.008 0.036 570 Dihedral : 14.082 83.649 1284 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Cbeta Deviations : 0.53 % 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: -2.11 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.004 HIS E 330 PHE 0.015 0.005 PHE F 346 TYR 0.062 0.014 TYR A 310 ARG 0.006 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 351 GLN cc_start: 0.8346 (mt0) cc_final: 0.8102 (mt0) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 1.2271 time to fit residues: 239.7600 Evaluate side-chains 141 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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: 5.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 0.0070 chunk 20 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN D 359 ASN C 359 ASN B 359 ASN E 359 ASN F 359 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3354 Z= 0.169 Angle : 0.603 4.997 4488 Z= 0.300 Chirality : 0.051 0.135 504 Planarity : 0.003 0.017 570 Dihedral : 5.357 15.765 438 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 4.23 % Allowed : 21.69 % Favored : 74.07 % 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: -1.85 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 374 PHE 0.005 0.001 PHE F 346 TYR 0.004 0.001 TYR E 310 ARG 0.004 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 0.395 Fit side-chains REVERT: D 351 GLN cc_start: 0.8407 (mt0) cc_final: 0.8182 (mt0) REVERT: E 308 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8380 (mm) outliers start: 16 outliers final: 5 residues processed: 151 average time/residue: 1.3448 time to fit residues: 207.4500 Evaluate side-chains 133 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 324 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.8624 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3354 Z= 0.265 Angle : 0.610 6.808 4488 Z= 0.301 Chirality : 0.050 0.135 504 Planarity : 0.002 0.014 570 Dihedral : 5.123 16.988 438 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 3.17 % Allowed : 22.49 % Favored : 74.34 % 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: -1.76 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 374 PHE 0.012 0.002 PHE E 378 TYR 0.007 0.001 TYR A 310 ARG 0.002 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 0.415 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 142 average time/residue: 1.3711 time to fit residues: 198.8316 Evaluate side-chains 135 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 130 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain F 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: 0.7980 chunk 18 optimal weight: 0.2980 chunk 25 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- 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: 0.8632 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3354 Z= 0.267 Angle : 0.585 8.004 4488 Z= 0.286 Chirality : 0.050 0.132 504 Planarity : 0.002 0.014 570 Dihedral : 4.978 17.690 438 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 2.91 % Allowed : 22.22 % Favored : 74.87 % 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: -1.80 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 374 PHE 0.013 0.002 PHE E 378 TYR 0.006 0.001 TYR A 310 ARG 0.001 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 0.406 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 146 average time/residue: 1.3991 time to fit residues: 208.4519 Evaluate side-chains 145 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 138 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain F 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: 10.0000 chunk 16 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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: 0.8655 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 3354 Z= 0.440 Angle : 0.634 7.415 4488 Z= 0.322 Chirality : 0.051 0.136 504 Planarity : 0.003 0.014 570 Dihedral : 5.312 20.911 438 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.44 % Allowed : 22.22 % Favored : 74.34 % 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: -1.90 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 362 PHE 0.019 0.002 PHE E 378 TYR 0.007 0.001 TYR A 310 ARG 0.002 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 136 time to evaluate : 0.369 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 142 average time/residue: 1.4670 time to fit residues: 212.4104 Evaluate side-chains 143 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain F 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: 0.9990 chunk 40 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3354 Z= 0.153 Angle : 0.512 6.402 4488 Z= 0.251 Chirality : 0.049 0.129 504 Planarity : 0.002 0.013 570 Dihedral : 4.638 16.449 438 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 2.38 % Allowed : 22.75 % Favored : 74.87 % 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: -1.84 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 374 PHE 0.016 0.002 PHE E 378 TYR 0.007 0.001 TYR A 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 138 time to evaluate : 0.438 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 145 average time/residue: 1.3728 time to fit residues: 203.1667 Evaluate side-chains 145 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 139 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain F 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: 0.0470 chunk 34 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 overall best weight: 3.7484 ------------------------------------------------------------------------------- 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: 0.8643 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 3354 Z= 0.309 Angle : 0.579 7.583 4488 Z= 0.286 Chirality : 0.049 0.128 504 Planarity : 0.002 0.014 570 Dihedral : 4.933 18.613 438 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.12 % Allowed : 23.54 % Favored : 74.34 % 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: -1.84 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 374 PHE 0.018 0.002 PHE E 378 TYR 0.007 0.001 TYR A 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 138 time to evaluate : 0.390 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 144 average time/residue: 1.4813 time to fit residues: 217.5253 Evaluate side-chains 143 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain F 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: 7.9990 chunk 36 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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: 0.8639 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3354 Z= 0.280 Angle : 0.552 6.961 4488 Z= 0.277 Chirality : 0.049 0.131 504 Planarity : 0.002 0.014 570 Dihedral : 4.876 18.177 438 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 2.12 % Allowed : 23.81 % Favored : 74.07 % 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: -1.82 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 374 PHE 0.020 0.002 PHE E 378 TYR 0.007 0.001 TYR A 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 138 time to evaluate : 0.419 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 144 average time/residue: 1.4533 time to fit residues: 213.5377 Evaluate side-chains 145 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 138 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 overall best weight: 2.3584 ------------------------------------------------------------------------------- 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: 0.8629 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3354 Z= 0.211 Angle : 0.525 6.759 4488 Z= 0.260 Chirality : 0.049 0.132 504 Planarity : 0.002 0.013 570 Dihedral : 4.690 17.299 438 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.85 % Allowed : 23.81 % Favored : 74.34 % 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: -1.83 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 374 PHE 0.019 0.002 PHE E 378 TYR 0.009 0.001 TYR A 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 139 time to evaluate : 0.430 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 145 average time/residue: 1.4524 time to fit residues: 214.9619 Evaluate side-chains 143 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain F 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: 10.0000 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 0.0060 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- 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: 0.8640 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3354 Z= 0.285 Angle : 0.576 8.616 4488 Z= 0.283 Chirality : 0.049 0.139 504 Planarity : 0.002 0.013 570 Dihedral : 4.871 18.238 438 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.85 % Allowed : 24.34 % Favored : 73.81 % 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: -1.82 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 374 PHE 0.022 0.002 PHE E 378 TYR 0.006 0.001 TYR A 310 ARG 0.001 0.000 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 137 time to evaluate : 0.441 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 143 average time/residue: 1.5440 time to fit residues: 225.1787 Evaluate side-chains 143 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 28 optimal weight: 0.0050 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 41 optimal weight: 9.9990 overall best weight: 3.9200 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.109564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.100833 restraints weight = 4061.042| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.32 r_work: 0.3396 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3354 Z= 0.325 Angle : 0.579 7.209 4488 Z= 0.292 Chirality : 0.049 0.129 504 Planarity : 0.002 0.012 570 Dihedral : 4.988 19.203 438 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.12 % Allowed : 24.07 % Favored : 73.81 % 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: -1.82 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 374 PHE 0.023 0.002 PHE E 378 TYR 0.006 0.001 TYR A 310 ARG 0.001 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3304.90 seconds wall clock time: 58 minutes 50.24 seconds (3530.24 seconds total)