Starting phenix.real_space_refine on Thu Dec 7 18:24:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8x_18264/12_2023/8q8x_18264.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8x_18264/12_2023/8q8x_18264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8x_18264/12_2023/8q8x_18264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8x_18264/12_2023/8q8x_18264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8x_18264/12_2023/8q8x_18264.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8x_18264/12_2023/8q8x_18264.pdb" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2154 2.51 5 N 630 2.21 5 O 645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B ASP 348": "OD1" <-> "OD2" Residue "B ASP 358": "OD1" <-> "OD2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D ASP 358": "OD1" <-> "OD2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F ASP 358": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3435 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 571 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 571 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 571 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 2.34, per 1000 atoms: 0.68 Number of scatterers: 3435 At special positions: 0 Unit cell: (133.768, 135.222, 56.706, 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 645 8.00 N 630 7.00 C 2154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 617.0 milliseconds 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 57.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.547A pdb=" N VAL A 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL C 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.878A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 325 removed outlier: 6.561A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLY C 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N CYS A 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU C 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER A 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.665A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 346 removed outlier: 6.773A pdb=" N LEU C 344 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASP A 345 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N PHE C 346 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 9.814A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 9.397A pdb=" N LEU E 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LYS A 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N PHE E 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 350 through 362 removed outlier: 8.982A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 10.259A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 9.061A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N SER C 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLY A 355 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ASP C 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU A 357 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE C 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N HIS C 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLN E 351 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N SER A 352 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS E 353 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE A 354 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLY E 355 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER A 356 " --> pdb=" O GLY E 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 368 through 378 removed outlier: 6.486A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU E 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS A 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE E 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR A 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.543A pdb=" N GLN B 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N TYR F 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.832A pdb=" N VAL B 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.295A pdb=" N LYS B 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N SER F 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR B 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N CYS F 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LYS B 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N SER F 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY B 323 " --> pdb=" O SER F 324 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.516A pdb=" N ILE B 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 336 through 340 removed outlier: 6.545A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 343 through 347 removed outlier: 6.418A pdb=" N LEU B 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LYS D 347 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE B 346 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.347A pdb=" N GLN B 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE F 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS B 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 357 through 362 Processing sheet with id=AB7, first strand: chain 'D' and resid 368 through 377 88 hydrogen bonds defined for protein. 264 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: 0.84 Time building geometry restraints manager: 1.31 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: 1021 1.33 - 1.46: 381 1.46 - 1.58: 2081 1.58 - 1.70: 0 1.70 - 1.82: 6 Bond restraints: 3489 Sorted by residual: bond pdb=" CZ ARG E 349 " pdb=" NH2 ARG E 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.69e+00 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.37e+00 bond pdb=" CZ ARG C 349 " pdb=" NH2 ARG C 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.66e+00 bond pdb=" CZ ARG A 379 " pdb=" NH2 ARG A 379 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.54e+00 bond pdb=" CA LYS C 331 " pdb=" C LYS C 331 " ideal model delta sigma weight residual 1.532 1.548 -0.016 6.50e-03 2.37e+04 6.24e+00 ... (remaining 3484 not shown) Histogram of bond angle deviations from ideal: 101.27 - 106.85: 162 106.85 - 112.43: 1614 112.43 - 118.01: 972 118.01 - 123.59: 1534 123.59 - 129.17: 386 Bond angle restraints: 4668 Sorted by residual: angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 118.91 -6.31 1.00e+00 1.00e+00 3.98e+01 angle pdb=" CA ASP F 358 " pdb=" CB ASP F 358 " pdb=" CG ASP F 358 " ideal model delta sigma weight residual 112.60 118.64 -6.04 1.00e+00 1.00e+00 3.65e+01 angle pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " ideal model delta sigma weight residual 112.60 118.56 -5.96 1.00e+00 1.00e+00 3.55e+01 angle pdb=" OE1 GLN A 336 " pdb=" CD GLN A 336 " pdb=" NE2 GLN A 336 " ideal model delta sigma weight residual 122.60 116.93 5.67 1.00e+00 1.00e+00 3.22e+01 angle pdb=" CA GLY C 355 " pdb=" C GLY C 355 " pdb=" N SER C 356 " ideal model delta sigma weight residual 114.58 119.19 -4.61 8.60e-01 1.35e+00 2.88e+01 ... (remaining 4663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 2014 17.67 - 35.35: 76 35.35 - 53.02: 18 53.02 - 70.69: 7 70.69 - 88.37: 3 Dihedral angle restraints: 2118 sinusoidal: 879 harmonic: 1239 Sorted by residual: dihedral pdb=" CA LYS F 343 " pdb=" C LYS F 343 " pdb=" N LEU F 344 " pdb=" CA LEU F 344 " ideal model delta harmonic sigma weight residual 180.00 155.22 24.78 0 5.00e+00 4.00e-02 2.46e+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 180.00 155.72 24.28 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA SER B 341 " pdb=" C SER B 341 " pdb=" N GLU B 342 " pdb=" CA GLU B 342 " ideal model delta harmonic sigma weight residual 180.00 156.72 23.28 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 2115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 276 0.058 - 0.117: 185 0.117 - 0.175: 48 0.175 - 0.233: 14 0.233 - 0.291: 2 Chirality restraints: 525 Sorted by residual: chirality pdb=" CA THR A 319 " pdb=" N THR A 319 " pdb=" C THR A 319 " pdb=" CB THR A 319 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA THR E 319 " pdb=" N THR E 319 " pdb=" C THR E 319 " pdb=" CB THR E 319 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA GLU E 342 " pdb=" N GLU E 342 " pdb=" C GLU E 342 " pdb=" CB GLU E 342 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 522 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.110 2.00e-02 2.50e+03 6.34e-02 8.03e+01 pdb=" CG TYR C 310 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.052 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.044 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " -0.014 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.064 2.00e-02 2.50e+03 3.56e-02 2.53e+01 pdb=" CG TYR A 310 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.049 2.00e-02 2.50e+03 2.60e-02 1.35e+01 pdb=" CG TYR E 310 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.036 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 1594 2.99 - 3.47: 2668 3.47 - 3.95: 5618 3.95 - 4.42: 5438 4.42 - 4.90: 10758 Nonbonded interactions: 26076 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.517 2.440 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.521 2.440 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.529 2.440 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.532 2.440 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.535 2.440 ... (remaining 26071 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' and resid 305 through 378) selection = (chain 'B' and resid 305 through 378) selection = (chain 'C' and resid 305 through 378) selection = (chain 'D' and resid 305 through 378) selection = (chain 'E' and resid 305 through 378) selection = (chain 'F' and resid 305 through 378) } 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: 2.310 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: 11.380 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 14.170 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 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 0.036 3489 Z= 0.747 Angle : 1.745 6.308 4668 Z= 1.165 Chirality : 0.079 0.291 525 Planarity : 0.009 0.063 594 Dihedral : 11.916 88.368 1332 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.27 % Allowed : 4.33 % Favored : 94.40 % 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: -1.63 (0.34), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS C 362 PHE 0.034 0.011 PHE E 346 TYR 0.110 0.022 TYR C 310 ARG 0.005 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 193 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 193 average time/residue: 1.2191 time to fit residues: 241.0404 Evaluate side-chains 109 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.447 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5947 ------------------------------------------------------------------------------- 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: 0.9990 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN C 351 GLN D 351 GLN E 327 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3489 Z= 0.176 Angle : 0.624 8.672 4668 Z= 0.298 Chirality : 0.049 0.129 525 Planarity : 0.003 0.019 594 Dihedral : 5.430 15.878 462 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.54 % Allowed : 16.79 % Favored : 80.66 % 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: -1.40 (0.34), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 PHE 0.009 0.002 PHE C 346 TYR 0.018 0.003 TYR B 310 ARG 0.002 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 0.444 Fit side-chains outliers start: 10 outliers final: 1 residues processed: 121 average time/residue: 1.2343 time to fit residues: 153.2403 Evaluate side-chains 111 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 0.445 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0279 time to fit residues: 0.5380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 10 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN C 336 GLN C 351 GLN E 336 GLN E 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3489 Z= 0.268 Angle : 0.617 9.753 4668 Z= 0.297 Chirality : 0.050 0.120 525 Planarity : 0.003 0.025 594 Dihedral : 5.145 13.201 462 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.54 % Allowed : 20.61 % Favored : 76.84 % 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: -1.58 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 PHE 0.011 0.002 PHE C 346 TYR 0.018 0.002 TYR B 310 ARG 0.002 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 119 time to evaluate : 0.484 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 121 average time/residue: 1.4068 time to fit residues: 174.1509 Evaluate side-chains 115 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 0.479 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.0359 time to fit residues: 0.7432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 327 ASN C 351 GLN E 336 GLN E 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 3489 Z= 0.373 Angle : 0.634 6.627 4668 Z= 0.309 Chirality : 0.049 0.120 525 Planarity : 0.003 0.044 594 Dihedral : 5.215 13.301 462 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.80 % Allowed : 19.34 % Favored : 77.86 % 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: -1.78 (0.32), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.011 0.002 PHE C 346 TYR 0.021 0.002 TYR B 310 ARG 0.005 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 0.358 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 107 average time/residue: 1.3881 time to fit residues: 152.0023 Evaluate side-chains 105 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 0.459 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 0.0359 time to fit residues: 0.7752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 9.9990 chunk 16 optimal weight: 0.1980 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 0 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 overall best weight: 3.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 351 GLN E 336 GLN E 351 GLN F 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3489 Z= 0.277 Angle : 0.577 6.924 4668 Z= 0.280 Chirality : 0.048 0.118 525 Planarity : 0.003 0.021 594 Dihedral : 4.984 13.081 462 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.29 % Allowed : 18.58 % Favored : 79.13 % 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: -1.88 (0.32), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 329 PHE 0.009 0.002 PHE C 346 TYR 0.023 0.002 TYR B 310 ARG 0.002 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 0.478 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 109 average time/residue: 1.4431 time to fit residues: 160.8731 Evaluate side-chains 111 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 0.439 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 0.0347 time to fit residues: 0.7707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 351 GLN E 351 GLN F 307 GLN F 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3489 Z= 0.272 Angle : 0.575 7.245 4668 Z= 0.278 Chirality : 0.048 0.123 525 Planarity : 0.003 0.020 594 Dihedral : 4.922 13.139 462 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.54 % Allowed : 19.34 % Favored : 78.12 % 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: -1.92 (0.32), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.009 0.002 PHE C 346 TYR 0.024 0.002 TYR B 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.412 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 110 average time/residue: 1.3700 time to fit residues: 154.1311 Evaluate side-chains 109 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 0.408 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 0.0381 time to fit residues: 0.8054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 overall best weight: 6.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 351 GLN E 351 GLN F 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 3489 Z= 0.546 Angle : 0.689 7.629 4668 Z= 0.342 Chirality : 0.050 0.125 525 Planarity : 0.004 0.042 594 Dihedral : 5.313 18.240 462 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.29 % Allowed : 18.58 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.31), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 329 PHE 0.013 0.002 PHE C 346 TYR 0.026 0.003 TYR B 310 ARG 0.003 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.471 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 101 average time/residue: 1.4585 time to fit residues: 150.8208 Evaluate side-chains 103 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 0.441 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 0.0346 time to fit residues: 0.8747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 351 GLN D 307 GLN D 351 GLN E 336 GLN E 351 GLN F 307 GLN F 351 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3489 Z= 0.275 Angle : 0.586 7.745 4668 Z= 0.282 Chirality : 0.048 0.118 525 Planarity : 0.003 0.022 594 Dihedral : 5.027 18.731 462 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.27 % Allowed : 20.36 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.31), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 329 PHE 0.008 0.002 PHE C 346 TYR 0.024 0.002 TYR B 310 ARG 0.002 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 0.454 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 108 average time/residue: 1.3777 time to fit residues: 152.3585 Evaluate side-chains 107 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.503 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.1008 time to fit residues: 0.8448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 38 optimal weight: 0.0770 chunk 33 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 351 GLN D 307 GLN E 351 GLN F 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3489 Z= 0.335 Angle : 0.601 8.378 4668 Z= 0.294 Chirality : 0.048 0.116 525 Planarity : 0.003 0.027 594 Dihedral : 5.061 19.129 462 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.53 % Allowed : 20.87 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.31), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.009 0.002 PHE C 346 TYR 0.027 0.003 TYR B 310 ARG 0.002 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 0.457 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 104 average time/residue: 1.4384 time to fit residues: 153.0569 Evaluate side-chains 104 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.450 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.7298 time to fit residues: 2.1003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 351 GLN D 307 GLN D 351 GLN E 351 GLN F 307 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3489 Z= 0.145 Angle : 0.529 8.725 4668 Z= 0.251 Chirality : 0.049 0.120 525 Planarity : 0.002 0.020 594 Dihedral : 4.581 16.733 462 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.51 % Allowed : 21.37 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.32), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 329 PHE 0.004 0.001 PHE C 346 TYR 0.024 0.002 TYR B 310 ARG 0.001 0.000 ARG C 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 0.472 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 115 average time/residue: 1.3983 time to fit residues: 164.5353 Evaluate side-chains 106 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.446 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 0.0010 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 307 GLN C 351 GLN D 351 GLN E 351 GLN F 307 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.114817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.101292 restraints weight = 4125.094| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.40 r_work: 0.3338 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3489 Z= 0.214 Angle : 0.561 8.665 4668 Z= 0.268 Chirality : 0.048 0.121 525 Planarity : 0.003 0.020 594 Dihedral : 4.665 16.671 462 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.53 % Allowed : 22.14 % Favored : 76.34 % 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: -1.96 (0.32), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 362 PHE 0.007 0.001 PHE C 346 TYR 0.007 0.002 TYR F 310 ARG 0.001 0.000 ARG D 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2849.76 seconds wall clock time: 50 minutes 56.94 seconds (3056.94 seconds total)