Starting phenix.real_space_refine on Mon Mar 11 04:21:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q27_18070/03_2024/8q27_18070.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q27_18070/03_2024/8q27_18070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q27_18070/03_2024/8q27_18070.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q27_18070/03_2024/8q27_18070.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q27_18070/03_2024/8q27_18070.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q27_18070/03_2024/8q27_18070.pdb" } resolution = 2.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2154 2.51 5 N 630 2.21 5 O 645 1.98 5 H 3567 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D ASP 358": "OD1" <-> "OD2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7002 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1162 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1162 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1162 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 3.61, per 1000 atoms: 0.52 Number of scatterers: 7002 At special positions: 0 Unit cell: (135.222, 135.949, 59.614, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 645 8.00 N 630 7.00 C 2154 6.00 H 3567 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.20 Conformation dependent library (CDL) restraints added in 785.8 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: 0.68 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.546A 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: 6.877A 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: 7.937A 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: 6.235A pdb=" N CYS A 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.709A 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: 6.666A 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: 6.774A 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: 6.948A 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: 10.260A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 9.062A 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: 6.781A 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: 7.887A pdb=" N HIS C 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.495A 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: 6.487A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.950A 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: 8.006A 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: 6.468A 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: 6.399A 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: 6.544A 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: 8.057A 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: 6.544A 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: 6.435A 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: 6.419A 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: 6.428A 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: 7.828A 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: 2.27 Time building geometry restraints manager: 5.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3561 1.12 - 1.29: 574 1.29 - 1.47: 1172 1.47 - 1.64: 1743 1.64 - 1.82: 6 Bond restraints: 7056 Sorted by residual: bond pdb=" N GLY C 367 " pdb=" H GLY C 367 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" NE2 GLN A 351 " pdb="HE21 GLN A 351 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N VAL E 318 " pdb=" H VAL E 318 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" NE2 GLN F 336 " pdb="HE21 GLN F 336 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N GLY A 367 " pdb=" H GLY A 367 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 7051 not shown) Histogram of bond angle deviations from ideal: 95.93 - 102.58: 18 102.58 - 109.23: 4577 109.23 - 115.88: 4600 115.88 - 122.53: 2888 122.53 - 129.18: 775 Bond angle restraints: 12858 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 112.60 118.92 -6.32 1.00e+00 1.00e+00 4.00e+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 112.60 118.53 -5.93 1.00e+00 1.00e+00 3.52e+01 angle pdb=" OE1 GLN A 336 " pdb=" CD GLN A 336 " pdb=" NE2 GLN A 336 " ideal model delta sigma weight residual 122.60 116.92 5.68 1.00e+00 1.00e+00 3.22e+01 angle pdb=" OE1 GLN C 336 " pdb=" CD GLN C 336 " pdb=" NE2 GLN C 336 " ideal model delta sigma weight residual 122.60 117.21 5.39 1.00e+00 1.00e+00 2.91e+01 ... (remaining 12853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 2931 17.68 - 35.36: 138 35.36 - 53.04: 78 53.04 - 70.73: 101 70.73 - 88.41: 4 Dihedral angle restraints: 3252 sinusoidal: 1857 harmonic: 1395 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 180.00 155.20 24.80 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 180.00 155.71 24.29 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 180.00 156.71 23.29 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 3249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 276 0.059 - 0.117: 185 0.117 - 0.176: 49 0.176 - 0.234: 13 0.234 - 0.293: 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 2.15e+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 1.67e+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 1.36e+00 ... (remaining 522 not shown) Planarity restraints: 1023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.121 2.00e-02 2.50e+03 5.40e-02 8.75e+01 pdb=" CG TYR C 310 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " -0.022 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.114 2.00e-02 2.50e+03 pdb=" HD1 TYR C 310 " -0.006 2.00e-02 2.50e+03 pdb=" HD2 TYR C 310 " -0.036 2.00e-02 2.50e+03 pdb=" HE1 TYR C 310 " -0.026 2.00e-02 2.50e+03 pdb=" HE2 TYR C 310 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 327 " 0.034 2.00e-02 2.50e+03 7.06e-02 7.48e+01 pdb=" CG ASN C 327 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN C 327 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN C 327 " -0.140 2.00e-02 2.50e+03 pdb="HD21 ASN C 327 " 0.046 2.00e-02 2.50e+03 pdb="HD22 ASN C 327 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 368 " 0.073 2.00e-02 2.50e+03 6.82e-02 6.98e+01 pdb=" CG ASN A 368 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 368 " -0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN A 368 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN A 368 " -0.094 2.00e-02 2.50e+03 pdb="HD22 ASN A 368 " 0.097 2.00e-02 2.50e+03 ... (remaining 1020 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 567 2.17 - 2.77: 11740 2.77 - 3.38: 18325 3.38 - 3.99: 24870 3.99 - 4.60: 34541 Nonbonded interactions: 90043 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.558 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.566 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.570 1.850 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.577 1.850 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.578 1.850 ... (remaining 90038 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: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 11.720 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 26.380 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 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 : 1.744 6.322 4668 Z= 1.165 Chirality : 0.079 0.293 525 Planarity : 0.009 0.063 594 Dihedral : 11.916 88.408 1332 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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 0.111 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 171 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 166 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7207 (ttmt) cc_final: 0.6941 (mttt) REVERT: A 314 ASP cc_start: 0.7168 (t0) cc_final: 0.6705 (t0) REVERT: A 324 SER cc_start: 0.8126 (m) cc_final: 0.7733 (t) REVERT: A 331 LYS cc_start: 0.7114 (mtpt) cc_final: 0.6740 (mttt) REVERT: A 336 GLN cc_start: 0.7075 (tt0) cc_final: 0.6662 (tt0) REVERT: A 338 GLU cc_start: 0.6818 (mt-10) cc_final: 0.6298 (mt-10) REVERT: A 340 LYS cc_start: 0.6516 (mttt) cc_final: 0.6098 (mtpm) REVERT: A 353 LYS cc_start: 0.5855 (mttt) cc_final: 0.5619 (tttm) REVERT: A 358 ASP cc_start: 0.6256 (m-30) cc_final: 0.6042 (m-30) REVERT: A 369 LYS cc_start: 0.6831 (ttmt) cc_final: 0.6531 (ttpt) REVERT: A 372 GLU cc_start: 0.7144 (tt0) cc_final: 0.6468 (mm-30) REVERT: A 375 LYS cc_start: 0.7108 (ttmt) cc_final: 0.6881 (ttmp) REVERT: B 315 LEU cc_start: 0.7881 (mt) cc_final: 0.7615 (mt) REVERT: B 340 LYS cc_start: 0.6897 (tttt) cc_final: 0.6639 (tttp) REVERT: B 342 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6367 (mm-30) REVERT: B 369 LYS cc_start: 0.6998 (tttt) cc_final: 0.6777 (tppt) REVERT: C 311 LYS cc_start: 0.7409 (ttmt) cc_final: 0.7127 (mttt) REVERT: C 317 LYS cc_start: 0.6710 (mttt) cc_final: 0.6487 (mtpt) REVERT: C 321 LYS cc_start: 0.6685 (mttt) cc_final: 0.6437 (mtpt) REVERT: C 331 LYS cc_start: 0.7068 (mtpt) cc_final: 0.6837 (mttt) REVERT: C 338 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6650 (mt-10) REVERT: C 345 ASP cc_start: 0.6667 (t0) cc_final: 0.6334 (t70) REVERT: C 353 LYS cc_start: 0.5917 (mttt) cc_final: 0.5652 (tttp) REVERT: C 356 SER cc_start: 0.7566 (m) cc_final: 0.7344 (t) REVERT: C 369 LYS cc_start: 0.7122 (ttmt) cc_final: 0.6598 (ttpt) REVERT: C 372 GLU cc_start: 0.7560 (tt0) cc_final: 0.6954 (mm-30) REVERT: C 375 LYS cc_start: 0.7212 (ttmt) cc_final: 0.7005 (ttmp) REVERT: D 315 LEU cc_start: 0.7874 (mp) cc_final: 0.7671 (mt) REVERT: D 340 LYS cc_start: 0.6688 (tttt) cc_final: 0.5987 (tptt) REVERT: D 343 LYS cc_start: 0.7005 (ttmt) cc_final: 0.6749 (ttmt) REVERT: D 369 LYS cc_start: 0.7132 (tttt) cc_final: 0.6907 (tttt) REVERT: D 375 LYS cc_start: 0.6900 (tttt) cc_final: 0.6570 (ttpt) REVERT: E 311 LYS cc_start: 0.7503 (ttmt) cc_final: 0.7181 (mttt) REVERT: E 314 ASP cc_start: 0.7355 (t0) cc_final: 0.6757 (t0) REVERT: E 320 SER cc_start: 0.8122 (m) cc_final: 0.7546 (p) REVERT: E 331 LYS cc_start: 0.7193 (mtpt) cc_final: 0.6902 (mttm) REVERT: E 338 GLU cc_start: 0.7336 (mt-10) cc_final: 0.6665 (tt0) REVERT: E 340 LYS cc_start: 0.7293 (mttt) cc_final: 0.6804 (mttp) REVERT: E 353 LYS cc_start: 0.6701 (mttt) cc_final: 0.6352 (tttm) REVERT: E 358 ASP cc_start: 0.6858 (m-30) cc_final: 0.6645 (m-30) REVERT: E 369 LYS cc_start: 0.7510 (ttmt) cc_final: 0.7237 (ttpt) REVERT: E 372 GLU cc_start: 0.7036 (tt0) cc_final: 0.6740 (mm-30) REVERT: F 338 GLU cc_start: 0.7215 (tt0) cc_final: 0.6989 (tt0) outliers start: 5 outliers final: 0 residues processed: 171 average time/residue: 2.7688 time to fit residues: 484.6192 Evaluate side-chains 126 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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: 7.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 307 GLN C 351 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2921 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= 0.276 Angle : 0.634 4.359 4668 Z= 0.328 Chirality : 0.051 0.132 525 Planarity : 0.004 0.030 594 Dihedral : 5.977 19.467 462 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.51 % Allowed : 8.40 % Favored : 91.09 % 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: -1.30 (0.35), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.98 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.010 0.002 PHE E 378 TYR 0.009 0.002 TYR A 310 ARG 0.002 0.000 ARG C 379 *********************** 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: 2 poor density : 123 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7200 (ttmt) cc_final: 0.6993 (mttt) REVERT: A 314 ASP cc_start: 0.7377 (t0) cc_final: 0.6892 (t0) REVERT: A 324 SER cc_start: 0.8101 (m) cc_final: 0.7589 (t) REVERT: A 331 LYS cc_start: 0.6944 (mtpt) cc_final: 0.6566 (mttt) REVERT: A 336 GLN cc_start: 0.7002 (tt0) cc_final: 0.6635 (tt0) REVERT: A 338 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6446 (mt-10) REVERT: A 353 LYS cc_start: 0.5795 (mttt) cc_final: 0.5567 (tttm) REVERT: A 369 LYS cc_start: 0.6791 (ttmt) cc_final: 0.6532 (ttpt) REVERT: A 372 GLU cc_start: 0.7022 (tt0) cc_final: 0.6424 (mm-30) REVERT: A 375 LYS cc_start: 0.7185 (ttmt) cc_final: 0.6970 (ttmt) REVERT: B 315 LEU cc_start: 0.7824 (mp) cc_final: 0.7588 (mt) REVERT: B 340 LYS cc_start: 0.6908 (tttt) cc_final: 0.6673 (tttp) REVERT: B 369 LYS cc_start: 0.7010 (tttt) cc_final: 0.6763 (tppt) REVERT: C 311 LYS cc_start: 0.7423 (ttmt) cc_final: 0.7206 (mttt) REVERT: C 317 LYS cc_start: 0.6806 (mttt) cc_final: 0.6595 (mtpt) REVERT: C 321 LYS cc_start: 0.6630 (mttt) cc_final: 0.6369 (mtpt) REVERT: C 331 LYS cc_start: 0.7000 (mtpt) cc_final: 0.6789 (mttt) REVERT: C 336 GLN cc_start: 0.7031 (tt0) cc_final: 0.6806 (tt0) REVERT: C 345 ASP cc_start: 0.6737 (t0) cc_final: 0.6303 (t70) REVERT: C 369 LYS cc_start: 0.7132 (ttmt) cc_final: 0.6591 (ttpt) REVERT: C 372 GLU cc_start: 0.7573 (tt0) cc_final: 0.7001 (mm-30) REVERT: D 340 LYS cc_start: 0.6724 (tttt) cc_final: 0.6195 (tptm) REVERT: D 343 LYS cc_start: 0.7079 (ttmt) cc_final: 0.6612 (ttpt) REVERT: D 351 GLN cc_start: 0.7611 (tt0) cc_final: 0.7365 (tt0) REVERT: D 369 LYS cc_start: 0.7112 (tttt) cc_final: 0.6895 (tttt) REVERT: D 375 LYS cc_start: 0.6850 (tttt) cc_final: 0.6354 (ttpt) REVERT: E 311 LYS cc_start: 0.7509 (ttmt) cc_final: 0.7125 (mttt) REVERT: E 314 ASP cc_start: 0.7522 (t0) cc_final: 0.6953 (t0) REVERT: E 320 SER cc_start: 0.8147 (m) cc_final: 0.7593 (p) REVERT: E 338 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6813 (tt0) REVERT: E 340 LYS cc_start: 0.7284 (mttt) cc_final: 0.7016 (mttp) REVERT: E 349 ARG cc_start: 0.5909 (mtm180) cc_final: 0.5565 (mtt90) REVERT: E 353 LYS cc_start: 0.6612 (mttt) cc_final: 0.6312 (tttm) REVERT: E 369 LYS cc_start: 0.7485 (ttmt) cc_final: 0.7179 (ttpt) REVERT: E 372 GLU cc_start: 0.7126 (tt0) cc_final: 0.6773 (mm-30) REVERT: F 338 GLU cc_start: 0.7396 (tt0) cc_final: 0.7047 (tt0) REVERT: F 343 LYS cc_start: 0.7407 (ttmt) cc_final: 0.7022 (ttmm) outliers start: 2 outliers final: 1 residues processed: 124 average time/residue: 3.2648 time to fit residues: 413.2561 Evaluate side-chains 115 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN C 351 GLN D 307 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3489 Z= 0.134 Angle : 0.504 4.985 4668 Z= 0.252 Chirality : 0.052 0.132 525 Planarity : 0.003 0.026 594 Dihedral : 5.360 17.039 462 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % 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: -1.26 (0.35), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.007 0.001 PHE E 378 TYR 0.008 0.002 TYR B 310 ARG 0.004 0.000 ARG C 379 *********************** 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 119 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7126 (ttmt) cc_final: 0.6862 (mttt) REVERT: A 314 ASP cc_start: 0.7428 (t0) cc_final: 0.6982 (t0) REVERT: A 324 SER cc_start: 0.8055 (m) cc_final: 0.7577 (t) REVERT: A 331 LYS cc_start: 0.6928 (mtpt) cc_final: 0.6547 (mttt) REVERT: A 336 GLN cc_start: 0.6879 (tt0) cc_final: 0.6497 (tt0) REVERT: A 338 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6473 (mt-10) REVERT: A 369 LYS cc_start: 0.6800 (ttmt) cc_final: 0.6569 (ttpt) REVERT: A 372 GLU cc_start: 0.6996 (tt0) cc_final: 0.6481 (mm-30) REVERT: A 375 LYS cc_start: 0.7214 (ttmt) cc_final: 0.6987 (ttmt) REVERT: B 315 LEU cc_start: 0.7791 (mp) cc_final: 0.7568 (mt) REVERT: B 340 LYS cc_start: 0.6936 (tttt) cc_final: 0.6695 (tttp) REVERT: B 369 LYS cc_start: 0.7005 (tttt) cc_final: 0.6775 (tppt) REVERT: C 321 LYS cc_start: 0.6659 (mttt) cc_final: 0.6379 (mtpt) REVERT: C 340 LYS cc_start: 0.6775 (ttmm) cc_final: 0.6389 (mttp) REVERT: C 345 ASP cc_start: 0.6723 (t0) cc_final: 0.6274 (t70) REVERT: C 369 LYS cc_start: 0.7144 (ttmt) cc_final: 0.6566 (tttt) REVERT: C 372 GLU cc_start: 0.7553 (tt0) cc_final: 0.7034 (mm-30) REVERT: D 340 LYS cc_start: 0.6717 (tttt) cc_final: 0.6181 (tptm) REVERT: D 343 LYS cc_start: 0.7194 (ttmt) cc_final: 0.6753 (ttpt) REVERT: D 369 LYS cc_start: 0.7107 (tttt) cc_final: 0.6897 (tttt) REVERT: D 375 LYS cc_start: 0.6881 (tttt) cc_final: 0.6296 (ttpp) REVERT: E 311 LYS cc_start: 0.7445 (ttmt) cc_final: 0.7097 (mttt) REVERT: E 314 ASP cc_start: 0.7555 (t0) cc_final: 0.6937 (t0) REVERT: E 320 SER cc_start: 0.8075 (m) cc_final: 0.7503 (p) REVERT: E 338 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6781 (tt0) REVERT: E 340 LYS cc_start: 0.7321 (mttt) cc_final: 0.7047 (mttp) REVERT: E 349 ARG cc_start: 0.5807 (mtm180) cc_final: 0.5594 (mtt90) REVERT: E 353 LYS cc_start: 0.6600 (mttt) cc_final: 0.6296 (tttm) REVERT: E 369 LYS cc_start: 0.7492 (ttmt) cc_final: 0.7214 (tttt) REVERT: E 372 GLU cc_start: 0.7068 (tt0) cc_final: 0.6730 (mm-30) REVERT: F 338 GLU cc_start: 0.7371 (tt0) cc_final: 0.7077 (tt0) REVERT: F 343 LYS cc_start: 0.7443 (ttmt) cc_final: 0.6992 (ttmm) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 3.2559 time to fit residues: 395.7019 Evaluate side-chains 106 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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: 8.9990 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 307 GLN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN D 307 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3489 Z= 0.157 Angle : 0.486 4.893 4668 Z= 0.246 Chirality : 0.051 0.130 525 Planarity : 0.003 0.025 594 Dihedral : 5.109 16.308 462 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.25 % Allowed : 7.89 % Favored : 91.86 % 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: -1.21 (0.35), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.91 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.008 0.001 PHE E 378 TYR 0.007 0.002 TYR C 310 ARG 0.001 0.000 ARG A 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 106 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7156 (ttmt) cc_final: 0.6939 (mttt) REVERT: A 314 ASP cc_start: 0.7505 (t0) cc_final: 0.7039 (t0) REVERT: A 324 SER cc_start: 0.8036 (m) cc_final: 0.7549 (t) REVERT: A 331 LYS cc_start: 0.6905 (mtpt) cc_final: 0.6527 (mttt) REVERT: A 336 GLN cc_start: 0.6945 (tt0) cc_final: 0.6696 (tt0) REVERT: A 338 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6499 (mt-10) REVERT: A 369 LYS cc_start: 0.6823 (ttmt) cc_final: 0.6561 (ttpt) REVERT: A 372 GLU cc_start: 0.7020 (tt0) cc_final: 0.6477 (mm-30) REVERT: A 375 LYS cc_start: 0.7206 (ttmt) cc_final: 0.6974 (ttmt) REVERT: B 315 LEU cc_start: 0.7712 (mp) cc_final: 0.7505 (mt) REVERT: B 340 LYS cc_start: 0.6945 (tttt) cc_final: 0.6631 (tttp) REVERT: B 369 LYS cc_start: 0.6986 (tttt) cc_final: 0.6761 (tppt) REVERT: C 314 ASP cc_start: 0.7928 (t0) cc_final: 0.7685 (t0) REVERT: C 319 THR cc_start: 0.7419 (p) cc_final: 0.7060 (t) REVERT: C 345 ASP cc_start: 0.6747 (t0) cc_final: 0.6278 (t70) REVERT: C 369 LYS cc_start: 0.7157 (ttmt) cc_final: 0.6588 (tttt) REVERT: C 372 GLU cc_start: 0.7563 (tt0) cc_final: 0.7028 (mm-30) REVERT: D 340 LYS cc_start: 0.6727 (tttt) cc_final: 0.6179 (tptm) REVERT: D 343 LYS cc_start: 0.7237 (ttmt) cc_final: 0.6988 (ttmt) REVERT: D 369 LYS cc_start: 0.7122 (tttt) cc_final: 0.6903 (tttt) REVERT: D 375 LYS cc_start: 0.6886 (tttt) cc_final: 0.6304 (ttpp) REVERT: E 311 LYS cc_start: 0.7414 (ttmt) cc_final: 0.7075 (mttt) REVERT: E 314 ASP cc_start: 0.7612 (t0) cc_final: 0.6866 (t0) REVERT: E 320 SER cc_start: 0.8092 (m) cc_final: 0.7509 (p) REVERT: E 338 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6820 (tt0) REVERT: E 340 LYS cc_start: 0.7332 (mttt) cc_final: 0.7069 (mttp) REVERT: E 349 ARG cc_start: 0.5803 (mtm180) cc_final: 0.5570 (mtt90) REVERT: E 353 LYS cc_start: 0.6646 (mttt) cc_final: 0.6344 (tttm) REVERT: E 369 LYS cc_start: 0.7517 (ttmt) cc_final: 0.7264 (tttt) REVERT: E 372 GLU cc_start: 0.7165 (tt0) cc_final: 0.6758 (mm-30) REVERT: F 338 GLU cc_start: 0.7449 (tt0) cc_final: 0.7189 (tt0) REVERT: F 340 LYS cc_start: 0.7330 (tttt) cc_final: 0.6764 (tptm) outliers start: 1 outliers final: 1 residues processed: 106 average time/residue: 3.1323 time to fit residues: 339.4312 Evaluate side-chains 106 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 375 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.0170 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 0.0470 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 307 GLN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN D 307 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3489 Z= 0.130 Angle : 0.465 4.846 4668 Z= 0.234 Chirality : 0.051 0.129 525 Planarity : 0.003 0.024 594 Dihedral : 4.892 15.258 462 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.36), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.88 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.006 0.001 PHE E 378 TYR 0.007 0.002 TYR C 310 ARG 0.001 0.000 ARG E 379 *********************** 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 108 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7133 (ttmt) cc_final: 0.6902 (mttt) REVERT: A 314 ASP cc_start: 0.7533 (t0) cc_final: 0.7010 (t0) REVERT: A 324 SER cc_start: 0.8045 (m) cc_final: 0.7540 (t) REVERT: A 331 LYS cc_start: 0.6902 (mtpt) cc_final: 0.6527 (mttt) REVERT: A 338 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6551 (mt-10) REVERT: A 369 LYS cc_start: 0.6827 (ttmt) cc_final: 0.6544 (ttpt) REVERT: A 372 GLU cc_start: 0.7020 (tt0) cc_final: 0.6489 (mm-30) REVERT: A 375 LYS cc_start: 0.7206 (ttmt) cc_final: 0.6993 (ttmp) REVERT: B 340 LYS cc_start: 0.6957 (tttt) cc_final: 0.6698 (tttm) REVERT: B 369 LYS cc_start: 0.6994 (tttt) cc_final: 0.6785 (tppt) REVERT: C 319 THR cc_start: 0.7388 (p) cc_final: 0.7062 (t) REVERT: C 345 ASP cc_start: 0.6748 (t0) cc_final: 0.6257 (t70) REVERT: C 369 LYS cc_start: 0.7184 (ttmt) cc_final: 0.6716 (tttt) REVERT: C 372 GLU cc_start: 0.7526 (tt0) cc_final: 0.7008 (mm-30) REVERT: D 340 LYS cc_start: 0.6720 (tttt) cc_final: 0.6023 (tptt) REVERT: D 343 LYS cc_start: 0.7253 (ttmt) cc_final: 0.6986 (ttmt) REVERT: D 369 LYS cc_start: 0.7138 (tttt) cc_final: 0.6924 (tttt) REVERT: D 375 LYS cc_start: 0.6870 (tttt) cc_final: 0.6346 (ttpp) REVERT: E 311 LYS cc_start: 0.7401 (ttmt) cc_final: 0.7078 (mttt) REVERT: E 314 ASP cc_start: 0.7608 (t0) cc_final: 0.6818 (t0) REVERT: E 320 SER cc_start: 0.8047 (m) cc_final: 0.7489 (p) REVERT: E 338 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6830 (tt0) REVERT: E 340 LYS cc_start: 0.7330 (mttt) cc_final: 0.7055 (mttp) REVERT: E 353 LYS cc_start: 0.6635 (mttt) cc_final: 0.6338 (tttm) REVERT: E 369 LYS cc_start: 0.7526 (ttmt) cc_final: 0.7279 (tttt) REVERT: E 372 GLU cc_start: 0.7123 (tt0) cc_final: 0.6703 (mm-30) REVERT: F 338 GLU cc_start: 0.7432 (tt0) cc_final: 0.7198 (tt0) REVERT: F 343 LYS cc_start: 0.7344 (ttmt) cc_final: 0.7007 (ttmm) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 3.0772 time to fit residues: 339.8562 Evaluate side-chains 102 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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: 8.9990 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 351 GLN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN D 307 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3489 Z= 0.149 Angle : 0.472 4.653 4668 Z= 0.238 Chirality : 0.051 0.128 525 Planarity : 0.003 0.021 594 Dihedral : 4.856 15.649 462 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.36), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.88 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.006 0.001 PHE C 346 TYR 0.009 0.002 TYR C 310 ARG 0.001 0.000 ARG E 379 *********************** 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 102 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7103 (ttmt) cc_final: 0.6893 (mttt) REVERT: A 314 ASP cc_start: 0.7568 (t0) cc_final: 0.7124 (t0) REVERT: A 324 SER cc_start: 0.8018 (m) cc_final: 0.7540 (t) REVERT: A 331 LYS cc_start: 0.6867 (mtpt) cc_final: 0.6501 (mttt) REVERT: A 369 LYS cc_start: 0.6835 (ttmt) cc_final: 0.6565 (ttpt) REVERT: A 372 GLU cc_start: 0.7091 (tt0) cc_final: 0.6484 (mm-30) REVERT: A 375 LYS cc_start: 0.7206 (ttmt) cc_final: 0.6573 (ttmt) REVERT: B 340 LYS cc_start: 0.6907 (tttt) cc_final: 0.6685 (tttp) REVERT: C 314 ASP cc_start: 0.8112 (t0) cc_final: 0.7704 (t0) REVERT: C 319 THR cc_start: 0.7382 (p) cc_final: 0.7083 (t) REVERT: C 345 ASP cc_start: 0.6735 (t0) cc_final: 0.6507 (t70) REVERT: C 369 LYS cc_start: 0.7173 (ttmt) cc_final: 0.6702 (tttt) REVERT: C 372 GLU cc_start: 0.7567 (tt0) cc_final: 0.7019 (mm-30) REVERT: D 340 LYS cc_start: 0.6732 (tttt) cc_final: 0.6029 (tptt) REVERT: D 343 LYS cc_start: 0.7229 (ttmt) cc_final: 0.6965 (ttmt) REVERT: D 369 LYS cc_start: 0.7159 (tttt) cc_final: 0.6936 (tttt) REVERT: D 375 LYS cc_start: 0.6905 (tttt) cc_final: 0.6357 (ttpp) REVERT: E 311 LYS cc_start: 0.7377 (ttmt) cc_final: 0.7049 (mttt) REVERT: E 320 SER cc_start: 0.8049 (m) cc_final: 0.7477 (p) REVERT: E 338 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6814 (tt0) REVERT: E 340 LYS cc_start: 0.7315 (mttt) cc_final: 0.6889 (mttp) REVERT: E 353 LYS cc_start: 0.6639 (mttt) cc_final: 0.6349 (tttm) REVERT: E 369 LYS cc_start: 0.7552 (ttmt) cc_final: 0.7309 (tttt) REVERT: E 372 GLU cc_start: 0.7165 (tt0) cc_final: 0.6762 (mm-30) REVERT: F 338 GLU cc_start: 0.7434 (tt0) cc_final: 0.7196 (tt0) REVERT: F 343 LYS cc_start: 0.7401 (ttmt) cc_final: 0.7007 (ttmm) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 3.0838 time to fit residues: 321.6297 Evaluate side-chains 99 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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: 0.9980 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 0.0370 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3489 Z= 0.145 Angle : 0.471 4.656 4668 Z= 0.237 Chirality : 0.051 0.124 525 Planarity : 0.003 0.022 594 Dihedral : 4.795 15.162 462 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % 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: -1.17 (0.36), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.88 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.005 0.001 PHE C 346 TYR 0.008 0.002 TYR C 310 ARG 0.001 0.000 ARG E 379 *********************** 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 99 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7096 (ttmt) cc_final: 0.6842 (mttt) REVERT: A 314 ASP cc_start: 0.7626 (t0) cc_final: 0.7189 (t0) REVERT: A 324 SER cc_start: 0.7934 (m) cc_final: 0.7531 (t) REVERT: A 331 LYS cc_start: 0.6866 (mtpt) cc_final: 0.6501 (mttt) REVERT: A 369 LYS cc_start: 0.6831 (ttmt) cc_final: 0.6563 (ttpt) REVERT: A 372 GLU cc_start: 0.7173 (tt0) cc_final: 0.6588 (mm-30) REVERT: B 340 LYS cc_start: 0.6933 (tttt) cc_final: 0.6678 (tttm) REVERT: C 314 ASP cc_start: 0.8122 (t0) cc_final: 0.7725 (t0) REVERT: C 345 ASP cc_start: 0.6731 (t0) cc_final: 0.6507 (t70) REVERT: C 369 LYS cc_start: 0.7177 (ttmt) cc_final: 0.6713 (tttt) REVERT: C 372 GLU cc_start: 0.7598 (tt0) cc_final: 0.7013 (mm-30) REVERT: D 340 LYS cc_start: 0.6727 (tttt) cc_final: 0.6016 (tptt) REVERT: D 343 LYS cc_start: 0.7211 (ttmt) cc_final: 0.6962 (ttmt) REVERT: D 369 LYS cc_start: 0.7105 (tttt) cc_final: 0.6898 (tttt) REVERT: D 375 LYS cc_start: 0.6891 (tttt) cc_final: 0.6340 (ttpp) REVERT: E 311 LYS cc_start: 0.7376 (ttmt) cc_final: 0.7027 (mttt) REVERT: E 314 ASP cc_start: 0.7557 (t0) cc_final: 0.6975 (t0) REVERT: E 320 SER cc_start: 0.8050 (m) cc_final: 0.7481 (p) REVERT: E 338 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6852 (tt0) REVERT: E 340 LYS cc_start: 0.7323 (mttt) cc_final: 0.6890 (mttp) REVERT: E 353 LYS cc_start: 0.6606 (mttt) cc_final: 0.6320 (tttm) REVERT: E 369 LYS cc_start: 0.7537 (ttmt) cc_final: 0.7303 (ttpt) REVERT: F 338 GLU cc_start: 0.7471 (tt0) cc_final: 0.7231 (tt0) REVERT: F 343 LYS cc_start: 0.7421 (ttmt) cc_final: 0.7021 (ttmm) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 3.1320 time to fit residues: 317.0058 Evaluate side-chains 99 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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: 8.9990 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.0770 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3489 Z= 0.117 Angle : 0.438 4.483 4668 Z= 0.218 Chirality : 0.052 0.129 525 Planarity : 0.002 0.016 594 Dihedral : 4.481 14.653 462 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % 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: -1.02 (0.37), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.77 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 362 PHE 0.004 0.001 PHE E 378 TYR 0.004 0.001 TYR B 310 ARG 0.001 0.000 ARG C 379 *********************** 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 103 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7078 (ttmt) cc_final: 0.6841 (mttt) REVERT: A 314 ASP cc_start: 0.7619 (t0) cc_final: 0.7195 (t0) REVERT: A 324 SER cc_start: 0.7955 (m) cc_final: 0.7483 (t) REVERT: A 331 LYS cc_start: 0.6861 (mtpt) cc_final: 0.6488 (mttt) REVERT: A 369 LYS cc_start: 0.6847 (ttmt) cc_final: 0.6583 (ttpt) REVERT: A 372 GLU cc_start: 0.7119 (tt0) cc_final: 0.6600 (mm-30) REVERT: B 340 LYS cc_start: 0.6919 (tttt) cc_final: 0.6671 (tttm) REVERT: C 314 ASP cc_start: 0.8112 (t0) cc_final: 0.7743 (t0) REVERT: C 345 ASP cc_start: 0.6730 (t0) cc_final: 0.6261 (t70) REVERT: C 369 LYS cc_start: 0.7200 (ttmt) cc_final: 0.6737 (tttt) REVERT: C 372 GLU cc_start: 0.7551 (tt0) cc_final: 0.6974 (mm-30) REVERT: D 340 LYS cc_start: 0.6739 (tttt) cc_final: 0.6032 (tptt) REVERT: D 343 LYS cc_start: 0.7281 (ttmt) cc_final: 0.7018 (ttmt) REVERT: D 369 LYS cc_start: 0.7168 (tttt) cc_final: 0.6965 (tttt) REVERT: D 375 LYS cc_start: 0.6891 (tttt) cc_final: 0.6347 (ttpp) REVERT: E 311 LYS cc_start: 0.7450 (ttmt) cc_final: 0.7129 (mttt) REVERT: E 314 ASP cc_start: 0.7546 (t0) cc_final: 0.6948 (t0) REVERT: E 320 SER cc_start: 0.7976 (m) cc_final: 0.7445 (p) REVERT: E 338 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6840 (tt0) REVERT: E 340 LYS cc_start: 0.7369 (mttt) cc_final: 0.6929 (mttp) REVERT: E 353 LYS cc_start: 0.6483 (mttt) cc_final: 0.6256 (tttm) REVERT: E 369 LYS cc_start: 0.7504 (ttmt) cc_final: 0.7168 (tttt) REVERT: F 338 GLU cc_start: 0.7472 (tt0) cc_final: 0.7248 (tt0) REVERT: F 343 LYS cc_start: 0.7423 (ttmt) cc_final: 0.7102 (ttpt) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 3.0538 time to fit residues: 321.8237 Evaluate side-chains 102 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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: 8.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3489 Z= 0.203 Angle : 0.497 4.586 4668 Z= 0.253 Chirality : 0.050 0.125 525 Planarity : 0.003 0.021 594 Dihedral : 4.867 15.004 462 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % 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: -1.15 (0.36), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.87 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 362 PHE 0.009 0.002 PHE A 378 TYR 0.010 0.003 TYR C 310 ARG 0.001 0.000 ARG C 379 *********************** 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 101 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7101 (ttmt) cc_final: 0.6860 (mttt) REVERT: A 314 ASP cc_start: 0.7686 (t0) cc_final: 0.7253 (t0) REVERT: A 324 SER cc_start: 0.7950 (m) cc_final: 0.7513 (t) REVERT: A 331 LYS cc_start: 0.6865 (mtpt) cc_final: 0.6498 (mttt) REVERT: A 369 LYS cc_start: 0.6839 (ttmt) cc_final: 0.6554 (ttpt) REVERT: A 372 GLU cc_start: 0.7177 (tt0) cc_final: 0.6520 (mm-30) REVERT: B 340 LYS cc_start: 0.6929 (tttt) cc_final: 0.6685 (tttm) REVERT: C 314 ASP cc_start: 0.8143 (t0) cc_final: 0.7754 (t0) REVERT: C 345 ASP cc_start: 0.6740 (t0) cc_final: 0.6260 (t70) REVERT: C 369 LYS cc_start: 0.7152 (ttmt) cc_final: 0.6708 (tttt) REVERT: C 372 GLU cc_start: 0.7623 (tt0) cc_final: 0.6997 (mm-30) REVERT: D 340 LYS cc_start: 0.6697 (tttt) cc_final: 0.6006 (tptt) REVERT: D 343 LYS cc_start: 0.7217 (ttmt) cc_final: 0.6974 (ttmt) REVERT: D 369 LYS cc_start: 0.7134 (tttt) cc_final: 0.6915 (tttt) REVERT: D 375 LYS cc_start: 0.6887 (tttt) cc_final: 0.6308 (ttpp) REVERT: E 311 LYS cc_start: 0.7418 (ttmt) cc_final: 0.7089 (mttt) REVERT: E 314 ASP cc_start: 0.7617 (t0) cc_final: 0.6981 (t0) REVERT: E 320 SER cc_start: 0.8057 (m) cc_final: 0.7475 (p) REVERT: E 338 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6793 (tt0) REVERT: E 340 LYS cc_start: 0.7329 (mttt) cc_final: 0.6900 (mttp) REVERT: E 353 LYS cc_start: 0.6608 (mttt) cc_final: 0.6331 (tttm) REVERT: E 369 LYS cc_start: 0.7521 (ttmt) cc_final: 0.7291 (ttpt) REVERT: F 338 GLU cc_start: 0.7473 (tt0) cc_final: 0.7207 (tt0) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 3.3530 time to fit residues: 346.4155 Evaluate side-chains 101 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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: 0.6980 chunk 26 optimal weight: 0.0970 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3489 Z= 0.137 Angle : 0.467 4.559 4668 Z= 0.234 Chirality : 0.051 0.124 525 Planarity : 0.003 0.020 594 Dihedral : 4.716 15.277 462 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % 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: -1.10 (0.36), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.83 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.008 0.001 PHE A 378 TYR 0.007 0.002 TYR C 310 ARG 0.001 0.000 ARG A 379 ********************** 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 103 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7077 (ttmt) cc_final: 0.6836 (mttt) REVERT: A 314 ASP cc_start: 0.7691 (t0) cc_final: 0.7255 (t0) REVERT: A 324 SER cc_start: 0.7934 (m) cc_final: 0.7479 (t) REVERT: A 331 LYS cc_start: 0.6861 (mtpt) cc_final: 0.6490 (mttt) REVERT: A 369 LYS cc_start: 0.6841 (ttmt) cc_final: 0.6579 (ttpt) REVERT: A 372 GLU cc_start: 0.7174 (tt0) cc_final: 0.6510 (mm-30) REVERT: B 340 LYS cc_start: 0.6933 (tttt) cc_final: 0.6691 (tttm) REVERT: C 314 ASP cc_start: 0.8119 (t0) cc_final: 0.7745 (t0) REVERT: C 338 GLU cc_start: 0.6761 (mt-10) cc_final: 0.6504 (mt-10) REVERT: C 345 ASP cc_start: 0.6716 (t0) cc_final: 0.6484 (t70) REVERT: C 369 LYS cc_start: 0.7163 (ttmt) cc_final: 0.6714 (tttt) REVERT: C 372 GLU cc_start: 0.7629 (tt0) cc_final: 0.6975 (mm-30) REVERT: D 340 LYS cc_start: 0.6705 (tttt) cc_final: 0.6010 (tptt) REVERT: D 343 LYS cc_start: 0.7239 (ttmt) cc_final: 0.7009 (ttmt) REVERT: D 369 LYS cc_start: 0.7133 (tttt) cc_final: 0.6928 (tttt) REVERT: D 375 LYS cc_start: 0.6902 (tttt) cc_final: 0.6321 (ttpp) REVERT: E 311 LYS cc_start: 0.7397 (ttmt) cc_final: 0.7050 (mttt) REVERT: E 314 ASP cc_start: 0.7615 (t0) cc_final: 0.6976 (t0) REVERT: E 320 SER cc_start: 0.8041 (m) cc_final: 0.7477 (p) REVERT: E 338 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6848 (tt0) REVERT: E 340 LYS cc_start: 0.7364 (mttt) cc_final: 0.6937 (mttp) REVERT: E 353 LYS cc_start: 0.6606 (mttt) cc_final: 0.6330 (tttm) REVERT: E 369 LYS cc_start: 0.7507 (ttmt) cc_final: 0.7183 (ttpt) REVERT: F 338 GLU cc_start: 0.7452 (tt0) cc_final: 0.7229 (tt0) REVERT: F 343 LYS cc_start: 0.7441 (ttmt) cc_final: 0.7097 (ttpt) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 3.1616 time to fit residues: 332.7278 Evaluate side-chains 101 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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: 8.9990 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.146470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.130132 restraints weight = 10468.939| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 1.05 r_work: 0.3846 rms_B_bonded: 1.10 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3489 Z= 0.180 Angle : 0.490 4.521 4668 Z= 0.247 Chirality : 0.050 0.125 525 Planarity : 0.003 0.024 594 Dihedral : 4.849 15.229 462 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % 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: -1.21 (0.36), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.91 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.008 0.002 PHE A 378 TYR 0.009 0.002 TYR C 310 ARG 0.001 0.000 ARG C 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6491.74 seconds wall clock time: 113 minutes 5.21 seconds (6785.21 seconds total)