Starting phenix.real_space_refine (version: dev) on Sat Feb 18 03:36:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qki_14043/02_2023/7qki_14043.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qki_14043/02_2023/7qki_14043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qki_14043/02_2023/7qki_14043.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qki_14043/02_2023/7qki_14043.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qki_14043/02_2023/7qki_14043.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qki_14043/02_2023/7qki_14043.pdb" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "D GLU 342": "OE1" <-> "OE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "E GLU 342": "OE1" <-> "OE2" Residue "F GLU 342": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 7074 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "A" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "F" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 3.64, per 1000 atoms: 0.51 Number of scatterers: 7074 At special positions: 0 Unit cell: (127.72, 134.312, 41.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 648 8.00 N 642 7.00 C 2172 6.00 H 3606 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: 5.48 Conformation dependent library (CDL) restraints added in 582.0 milliseconds 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 44.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.548A pdb=" N VAL D 306 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL A 309 " --> pdb=" O VAL D 306 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE D 308 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN D 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N TYR B 310 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL D 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.522A pdb=" N VAL D 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 322 removed outlier: 6.429A pdb=" N LYS D 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N SER B 320 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR D 319 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N CYS B 322 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS D 321 " --> pdb=" O CYS B 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 330 removed outlier: 5.882A pdb=" N GLY D 326 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N HIS A 329 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE D 328 " --> pdb=" O HIS A 329 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY B 326 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN D 327 " --> pdb=" O GLY B 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 removed outlier: 6.461A pdb=" N VAL D 337 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N LYS A 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL D 339 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 353 through 354 removed outlier: 6.669A pdb=" N LYS D 353 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 362 removed outlier: 6.310A pdb=" N ASP D 358 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N THR B 361 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE D 360 " --> pdb=" O THR B 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 378 removed outlier: 6.517A pdb=" N LYS D 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N GLU B 372 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE D 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N HIS B 374 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR D 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N LEU B 376 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS D 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N PHE B 378 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N THR D 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 306 through 310 Processing sheet with id=AB1, first strand: chain 'E' and resid 317 through 318 Processing sheet with id=AB2, first strand: chain 'E' and resid 317 through 318 removed outlier: 6.441A pdb=" N LYS C 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N SER F 320 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR C 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N CYS F 322 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS C 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 325 through 330 removed outlier: 5.734A pdb=" N GLY C 326 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N HIS E 329 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE C 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLY F 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN C 327 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 336 through 340 removed outlier: 6.489A pdb=" N VAL C 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N LYS E 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL C 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 353 through 354 removed outlier: 6.681A pdb=" N LYS C 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 357 through 362 removed outlier: 6.532A pdb=" N LEU C 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE E 360 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASN C 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N HIS E 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR C 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASP C 358 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N THR F 361 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE C 360 " --> pdb=" O THR F 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 369 through 378 removed outlier: 7.657A pdb=" N GLU F 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE C 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N HIS F 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N THR C 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N LEU F 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS C 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N PHE F 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR C 377 " --> pdb=" O PHE F 378 " (cutoff:3.500A) 57 hydrogen bonds defined for protein. 168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 5.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 3600 1.11 - 1.29: 576 1.29 - 1.46: 950 1.46 - 1.63: 1996 1.63 - 1.81: 6 Bond restraints: 7128 Sorted by residual: bond pdb=" ND2 ASN A 359 " pdb="HD22 ASN A 359 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N LYS E 369 " pdb=" H LYS E 369 " 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 E 355 " pdb=" H GLY E 355 " 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 355 " pdb=" H GLY A 355 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ASP C 358 " pdb=" H ASP C 358 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 7123 not shown) Histogram of bond angle deviations from ideal: 75.75 - 86.62: 3 86.62 - 97.50: 5 97.50 - 108.37: 2675 108.37 - 119.24: 8088 119.24 - 130.11: 2213 Bond angle restraints: 12984 Sorted by residual: angle pdb=" CB HIS E 362 " pdb=" CA HIS E 362 " pdb=" HA HIS E 362 " ideal model delta sigma weight residual 109.00 75.75 33.25 3.00e+00 1.11e-01 1.23e+02 angle pdb=" C HIS E 362 " pdb=" CA HIS E 362 " pdb=" HA HIS E 362 " ideal model delta sigma weight residual 109.00 76.95 32.05 3.00e+00 1.11e-01 1.14e+02 angle pdb=" N HIS E 362 " pdb=" CA HIS E 362 " pdb=" HA HIS E 362 " ideal model delta sigma weight residual 110.00 78.83 31.17 3.00e+00 1.11e-01 1.08e+02 angle pdb=" C HIS E 362 " pdb=" CA HIS E 362 " pdb=" CB HIS E 362 " ideal model delta sigma weight residual 110.79 122.32 -11.53 1.63e+00 3.76e-01 5.00e+01 angle pdb=" N LYS F 369 " pdb=" CA LYS F 369 " pdb=" C LYS F 369 " ideal model delta sigma weight residual 108.76 119.82 -11.06 1.69e+00 3.50e-01 4.28e+01 ... (remaining 12979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 2506 15.26 - 30.52: 147 30.52 - 45.79: 16 45.79 - 61.05: 34 61.05 - 76.31: 39 Dihedral angle restraints: 2742 sinusoidal: 1338 harmonic: 1404 Sorted by residual: dihedral pdb=" C HIS E 362 " pdb=" N HIS E 362 " pdb=" CA HIS E 362 " pdb=" CB HIS E 362 " ideal model delta harmonic sigma weight residual -122.60 -140.63 18.03 0 2.50e+00 1.60e-01 5.20e+01 dihedral pdb=" N HIS E 362 " pdb=" C HIS E 362 " pdb=" CA HIS E 362 " pdb=" CB HIS E 362 " ideal model delta harmonic sigma weight residual 122.80 134.70 -11.90 0 2.50e+00 1.60e-01 2.27e+01 dihedral pdb=" CA LEU B 344 " pdb=" C LEU B 344 " pdb=" N ASP B 345 " pdb=" CA ASP B 345 " ideal model delta harmonic sigma weight residual -180.00 -157.23 -22.77 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 2739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 432 0.117 - 0.233: 78 0.233 - 0.349: 16 0.349 - 0.466: 1 0.466 - 0.582: 1 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA HIS E 362 " pdb=" N HIS E 362 " pdb=" C HIS E 362 " pdb=" CB HIS E 362 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.48e+00 chirality pdb=" CA LYS D 347 " pdb=" N LYS D 347 " pdb=" C LYS D 347 " pdb=" CB LYS D 347 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" CA ASN C 368 " pdb=" N ASN C 368 " pdb=" C ASN C 368 " pdb=" CB ASN C 368 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 525 not shown) Planarity restraints: 1032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " -0.111 2.00e-02 2.50e+03 4.55e-02 6.21e+01 pdb=" CG TYR F 310 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " -0.079 2.00e-02 2.50e+03 pdb=" HD1 TYR F 310 " 0.007 2.00e-02 2.50e+03 pdb=" HD2 TYR F 310 " 0.017 2.00e-02 2.50e+03 pdb=" HE1 TYR F 310 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR F 310 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 368 " -0.056 2.00e-02 2.50e+03 5.49e-02 4.52e+01 pdb=" CG ASN D 368 " 0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN D 368 " 0.057 2.00e-02 2.50e+03 pdb=" ND2 ASN D 368 " 0.011 2.00e-02 2.50e+03 pdb="HD21 ASN D 368 " 0.069 2.00e-02 2.50e+03 pdb="HD22 ASN D 368 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 346 " 0.098 2.00e-02 2.50e+03 3.84e-02 4.43e+01 pdb=" CG PHE B 346 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE B 346 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE B 346 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 PHE B 346 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 346 " -0.021 2.00e-02 2.50e+03 pdb=" CZ PHE B 346 " 0.011 2.00e-02 2.50e+03 pdb=" HD1 PHE B 346 " -0.048 2.00e-02 2.50e+03 pdb=" HD2 PHE B 346 " -0.020 2.00e-02 2.50e+03 pdb=" HE1 PHE B 346 " 0.014 2.00e-02 2.50e+03 pdb=" HE2 PHE B 346 " 0.001 2.00e-02 2.50e+03 pdb=" HZ PHE B 346 " 0.046 2.00e-02 2.50e+03 ... (remaining 1029 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 458 2.16 - 2.77: 11758 2.77 - 3.38: 18729 3.38 - 3.99: 24357 3.99 - 4.60: 34752 Nonbonded interactions: 90054 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.551 1.850 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.552 1.850 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.554 1.850 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.555 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.577 1.850 ... (remaining 90049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2172 2.51 5 N 642 2.21 5 O 648 1.98 5 H 3606 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.870 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: 10.730 Check model and map are aligned: 0.100 Process input model: 25.690 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.060 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 0.041 3522 Z= 0.772 Angle : 1.990 11.529 4710 Z= 1.333 Chirality : 0.096 0.582 528 Planarity : 0.010 0.055 600 Dihedral : 9.181 52.222 1350 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.76 % 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: -1.50 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.25), residues: 444 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.5634 time to fit residues: 29.7173 Evaluate side-chains 25 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.598 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 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: 2.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 3522 Z= 0.235 Angle : 0.640 5.332 4710 Z= 0.354 Chirality : 0.053 0.326 528 Planarity : 0.003 0.035 600 Dihedral : 6.434 19.648 468 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 0.51 % 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: -1.92 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.24), residues: 444 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 25 time to evaluate : 0.618 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 26 average time/residue: 0.7861 time to fit residues: 23.0426 Evaluate side-chains 19 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 0.628 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0994 time to fit residues: 0.9935 ------------------------------------------------------------------------------- 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: 5.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 3522 Z= 0.155 Angle : 0.539 4.400 4710 Z= 0.296 Chirality : 0.053 0.322 528 Planarity : 0.004 0.048 600 Dihedral : 5.568 17.273 468 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.25), residues: 444 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 0.598 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 1.0223 time to fit residues: 21.6529 Evaluate side-chains 18 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.639 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0825 time to fit residues: 0.9267 ------------------------------------------------------------------------------- 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: 6.9990 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 3522 Z= 0.147 Angle : 0.503 4.501 4710 Z= 0.273 Chirality : 0.053 0.324 528 Planarity : 0.005 0.058 600 Dihedral : 5.267 16.518 468 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 0.00 % 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: -1.81 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.26), residues: 444 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.635 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 1.0599 time to fit residues: 21.2216 Evaluate side-chains 18 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.618 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7593 ------------------------------------------------------------------------------- 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: 0.9980 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 0.3980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 3522 Z= 0.122 Angle : 0.462 4.633 4710 Z= 0.249 Chirality : 0.053 0.327 528 Planarity : 0.004 0.037 600 Dihedral : 4.924 14.948 468 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 0.00 % 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: -1.70 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.27), residues: 444 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.553 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.9145 time to fit residues: 18.5424 Evaluate side-chains 15 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.574 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7278 ------------------------------------------------------------------------------- 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: 5.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 3522 Z= 0.254 Angle : 0.542 4.759 4710 Z= 0.301 Chirality : 0.053 0.327 528 Planarity : 0.004 0.027 600 Dihedral : 5.278 17.748 468 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.27), residues: 444 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.580 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 1.0840 time to fit residues: 20.4490 Evaluate side-chains 17 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.622 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7931 ------------------------------------------------------------------------------- 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: 10.0000 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 3522 Z= 0.184 Angle : 0.500 4.715 4710 Z= 0.275 Chirality : 0.052 0.325 528 Planarity : 0.003 0.027 600 Dihedral : 5.207 16.592 468 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.27), residues: 444 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.574 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 17 average time/residue: 1.1869 time to fit residues: 22.2106 Evaluate side-chains 15 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.653 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7546 ------------------------------------------------------------------------------- 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: 5.9990 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 3522 Z= 0.264 Angle : 0.544 4.869 4710 Z= 0.301 Chirality : 0.053 0.328 528 Planarity : 0.003 0.028 600 Dihedral : 5.405 18.301 468 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.28), residues: 444 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.548 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 1.2021 time to fit residues: 21.2506 Evaluate side-chains 15 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.613 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7717 ------------------------------------------------------------------------------- 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: 1.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 3522 Z= 0.137 Angle : 0.472 4.705 4710 Z= 0.256 Chirality : 0.052 0.323 528 Planarity : 0.003 0.029 600 Dihedral : 5.107 15.792 468 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.28), residues: 444 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.643 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 1.1420 time to fit residues: 17.8281 Evaluate side-chains 14 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7060 ------------------------------------------------------------------------------- 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: 5.9990 chunk 26 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 3522 Z= 0.126 Angle : 0.451 4.815 4710 Z= 0.244 Chirality : 0.052 0.324 528 Planarity : 0.003 0.031 600 Dihedral : 4.811 14.356 468 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 0.00 % 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: -1.71 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.28), residues: 444 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.617 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 1.2022 time to fit residues: 17.4228 Evaluate side-chains 13 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.614 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7773 ------------------------------------------------------------------------------- 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: 5.9990 chunk 1 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.146856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.129793 restraints weight = 15526.941| |-----------------------------------------------------------------------------| r_work (start): 0.4541 rms_B_bonded: 2.88 r_work: 0.4467 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.4374 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 3522 Z= 0.234 Angle : 0.512 4.893 4710 Z= 0.283 Chirality : 0.053 0.329 528 Planarity : 0.004 0.028 600 Dihedral : 5.136 16.533 468 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.29), residues: 444 =============================================================================== Job complete usr+sys time: 2523.57 seconds wall clock time: 45 minutes 35.35 seconds (2735.35 seconds total)