Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 13:47:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q27_18070/10_2023/8q27_18070.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q27_18070/10_2023/8q27_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_18070/10_2023/8q27_18070.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q27_18070/10_2023/8q27_18070.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q27_18070/10_2023/8q27_18070.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q27_18070/10_2023/8q27_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-1.21rc1-5097/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: 3.45, per 1000 atoms: 0.49 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: 5.41 Conformation dependent library (CDL) restraints added in 610.7 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: 0.58 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: 2.26 Time building geometry restraints manager: 5.63 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: 2509 17.68 - 35.36: 90 35.36 - 53.04: 29 53.04 - 70.73: 80 70.73 - 88.41: 4 Dihedral angle restraints: 2712 sinusoidal: 1317 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 2709 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: 3.270 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: 0.110 Extract box with map and model: 11.890 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 25.910 Find NCS groups from input model: 0.360 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:12.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.950 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.611 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 outliers start: 5 outliers final: 0 residues processed: 171 average time/residue: 2.7816 time to fit residues: 486.7604 Evaluate side-chains 101 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.669 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7791 ------------------------------------------------------------------------------- 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: 6.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN A 336 GLN A 351 GLN B 307 GLN C 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3489 Z= 0.239 Angle : 0.624 4.328 4668 Z= 0.318 Chirality : 0.051 0.130 525 Planarity : 0.004 0.028 594 Dihedral : 5.969 19.546 462 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.02 % Allowed : 11.70 % Favored : 87.28 % 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: -1.27 (0.35), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.96 (0.27), residues: 441 *********************** 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 106 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 103 average time/residue: 3.0585 time to fit residues: 322.0249 Evaluate side-chains 90 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.557 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.6781 ------------------------------------------------------------------------------- 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: 7.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 F 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.4494 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= 0.261 Angle : 0.583 5.131 4668 Z= 0.300 Chirality : 0.051 0.134 525 Planarity : 0.004 0.026 594 Dihedral : 5.607 17.662 462 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.27 % Allowed : 11.70 % Favored : 87.02 % 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: -1.37 (0.35), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.03 (0.26), residues: 441 *********************** 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 92 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 87 average time/residue: 2.8099 time to fit residues: 250.5482 Evaluate side-chains 83 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.560 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7346 ------------------------------------------------------------------------------- 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: 7.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.4611 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= 0.211 Angle : 0.548 4.961 4668 Z= 0.275 Chirality : 0.051 0.131 525 Planarity : 0.003 0.025 594 Dihedral : 5.325 16.534 462 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.76 % Allowed : 11.96 % Favored : 87.28 % 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: -1.36 (0.35), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.02 (0.27), residues: 441 *********************** 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 90 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 87 average time/residue: 2.7532 time to fit residues: 245.7506 Evaluate side-chains 84 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.652 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8029 ------------------------------------------------------------------------------- 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: 6.9990 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3489 Z= 0.264 Angle : 0.560 4.767 4668 Z= 0.287 Chirality : 0.051 0.134 525 Planarity : 0.004 0.025 594 Dihedral : 5.374 16.480 462 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.27 % Allowed : 11.20 % Favored : 87.53 % 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: -1.42 (0.35), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.26), residues: 441 *********************** 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 89 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 85 average time/residue: 2.7468 time to fit residues: 239.5409 Evaluate side-chains 86 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.600 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.0967 time to fit residues: 3.0752 ------------------------------------------------------------------------------- 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: 10.0000 chunk 40 optimal weight: 3.9990 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: 7.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.4832 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= 0.222 Angle : 0.540 4.727 4668 Z= 0.274 Chirality : 0.051 0.129 525 Planarity : 0.003 0.024 594 Dihedral : 5.267 15.981 462 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.27 % Allowed : 12.47 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.35), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.26), residues: 441 *********************** 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 89 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 84 average time/residue: 2.8739 time to fit residues: 247.4847 Evaluate side-chains 84 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.611 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.9724 time to fit residues: 2.7828 ------------------------------------------------------------------------------- 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: 5.9990 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 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** C 351 GLN D 307 GLN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3489 Z= 0.180 Angle : 0.522 4.591 4668 Z= 0.261 Chirality : 0.051 0.129 525 Planarity : 0.003 0.022 594 Dihedral : 5.139 15.736 462 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.02 % Allowed : 12.72 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.35), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.27), residues: 441 *********************** 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 87 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 84 average time/residue: 2.7670 time to fit residues: 238.2446 Evaluate side-chains 84 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.622 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.9932 time to fit residues: 2.7685 ------------------------------------------------------------------------------- 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: 2.9990 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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** C 351 GLN D 307 GLN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3489 Z= 0.141 Angle : 0.492 5.204 4668 Z= 0.244 Chirality : 0.051 0.124 525 Planarity : 0.003 0.020 594 Dihedral : 4.911 15.508 462 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.76 % Allowed : 13.23 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.35), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.05 (0.27), residues: 441 *********************** 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 87 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 85 average time/residue: 2.8467 time to fit residues: 248.0535 Evaluate side-chains 84 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.623 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.7410 ------------------------------------------------------------------------------- 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: 7.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- 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 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3489 Z= 0.270 Angle : 0.546 4.791 4668 Z= 0.280 Chirality : 0.050 0.125 525 Planarity : 0.003 0.024 594 Dihedral : 5.165 15.343 462 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.76 % Allowed : 13.23 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.35), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.26), residues: 441 *********************** 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 87 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 85 average time/residue: 2.7909 time to fit residues: 243.1539 Evaluate side-chains 84 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.618 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.9025 time to fit residues: 2.7303 ------------------------------------------------------------------------------- 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: 3.9990 chunk 26 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 0.0040 chunk 6 optimal weight: 1.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- 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** C 351 GLN D 307 GLN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3489 Z= 0.209 Angle : 0.530 4.648 4668 Z= 0.268 Chirality : 0.051 0.127 525 Planarity : 0.003 0.023 594 Dihedral : 5.102 15.486 462 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.51 % Allowed : 13.23 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.35), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.27), residues: 441 ********************** 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 85 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 85 average time/residue: 2.7463 time to fit residues: 239.4947 Evaluate side-chains 84 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.641 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.7795 ------------------------------------------------------------------------------- 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: 0.4980 chunk 1 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 41 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** C 351 GLN D 307 GLN E 362 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.147379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.131161 restraints weight = 10485.443| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 1.05 r_work: 0.3865 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.3803 rms_B_bonded: 1.90 restraints_weight: 0.2500 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.5133 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= 0.131 Angle : 0.470 4.267 4668 Z= 0.233 Chirality : 0.052 0.122 525 Planarity : 0.002 0.018 594 Dihedral : 4.678 15.223 462 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.51 % Allowed : 12.98 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.36), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.03 (0.27), residues: 441 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5561.98 seconds wall clock time: 97 minutes 8.49 seconds (5828.49 seconds total)