Starting phenix.real_space_refine on Sat Apr 6 04:33:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8z_18266/04_2024/8q8z_18266.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8z_18266/04_2024/8q8z_18266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8z_18266/04_2024/8q8z_18266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8z_18266/04_2024/8q8z_18266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8z_18266/04_2024/8q8z_18266.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8z_18266/04_2024/8q8z_18266.pdb" } resolution = 3.16 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 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 H 3588 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 PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7032 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: "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: "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: "B" 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: 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: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 3.48, per 1000 atoms: 0.49 Number of scatterers: 7032 At special positions: 0 Unit cell: (146.672, 113.712, 50.264, 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 642 8.00 N 636 7.00 C 2160 6.00 H 3588 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: 4.95 Conformation dependent library (CDL) restraints added in 714.6 milliseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 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 18 sheets defined 0.0% alpha, 51.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.485A pdb=" N VAL A 306 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL E 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.855A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 325 removed outlier: 6.288A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N SER C 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLY A 323 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL A 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N LYS E 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER A 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N GLY E 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N CYS A 322 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU E 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N SER A 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.850A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 333 through 334 removed outlier: 6.730A pdb=" N GLY A 333 " --> pdb=" O GLY C 334 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 337 through 342 removed outlier: 6.576A pdb=" N GLU A 338 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N SER C 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS A 340 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.375A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.226A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 368 through 378 removed outlier: 6.672A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N PHE C 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.508A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.861A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.177A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLY B 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.745A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.542A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LYS F 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL B 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N GLU F 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER B 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.667A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.469A pdb=" N GLN B 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE D 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LYS B 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 359 through 362 Processing sheet with id=AB9, first strand: chain 'D' and resid 369 through 378 removed outlier: 6.473A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N PHE D 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR B 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) 67 hydrogen bonds defined for protein. 201 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: 2.19 Time building geometry restraints manager: 5.17 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: 3582 1.12 - 1.29: 570 1.29 - 1.47: 1140 1.47 - 1.64: 1788 1.64 - 1.81: 6 Bond restraints: 7086 Sorted by residual: bond pdb=" N SER A 305 " pdb=" H SER A 305 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N SER E 305 " pdb=" H SER E 305 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NE2 HIS D 330 " pdb=" HE2 HIS D 330 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CD2 HIS E 362 " pdb=" HD2 HIS E 362 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LYS C 311 " pdb=" H LYS C 311 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 7081 not shown) Histogram of bond angle deviations from ideal: 97.22 - 103.65: 53 103.65 - 110.08: 6607 110.08 - 116.52: 2658 116.52 - 122.95: 2984 122.95 - 129.38: 610 Bond angle restraints: 12912 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 112.60 118.37 -5.77 1.00e+00 1.00e+00 3.33e+01 angle pdb=" CA ASP E 358 " pdb=" CB ASP E 358 " pdb=" CG ASP E 358 " ideal model delta sigma weight residual 112.60 117.10 -4.50 1.00e+00 1.00e+00 2.03e+01 angle pdb=" CA ASP C 358 " pdb=" CB ASP C 358 " pdb=" CG ASP C 358 " ideal model delta sigma weight residual 112.60 117.06 -4.46 1.00e+00 1.00e+00 1.99e+01 angle pdb=" CB HIS E 329 " pdb=" CG HIS E 329 " pdb=" CD2 HIS E 329 " ideal model delta sigma weight residual 131.20 125.44 5.76 1.30e+00 5.92e-01 1.96e+01 angle pdb=" CA ASP F 358 " pdb=" CB ASP F 358 " pdb=" CG ASP F 358 " ideal model delta sigma weight residual 112.60 117.03 -4.43 1.00e+00 1.00e+00 1.96e+01 ... (remaining 12907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 2936 17.39 - 34.77: 164 34.77 - 52.16: 71 52.16 - 69.54: 87 69.54 - 86.93: 6 Dihedral angle restraints: 3264 sinusoidal: 1866 harmonic: 1398 Sorted by residual: dihedral pdb=" C LYS F 331 " pdb=" N LYS F 331 " pdb=" CA LYS F 331 " pdb=" CB LYS F 331 " ideal model delta harmonic sigma weight residual -122.60 -132.47 9.87 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" C LYS B 331 " pdb=" N LYS B 331 " pdb=" CA LYS B 331 " pdb=" CB LYS B 331 " ideal model delta harmonic sigma weight residual -122.60 -131.81 9.21 0 2.50e+00 1.60e-01 1.36e+01 dihedral pdb=" C LYS E 331 " pdb=" N LYS E 331 " pdb=" CA LYS E 331 " pdb=" CB LYS E 331 " ideal model delta harmonic sigma weight residual -122.60 -131.71 9.11 0 2.50e+00 1.60e-01 1.33e+01 ... (remaining 3261 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.067: 314 0.067 - 0.133: 173 0.133 - 0.199: 29 0.199 - 0.265: 5 0.265 - 0.332: 7 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS F 331 " pdb=" N LYS F 331 " pdb=" C LYS F 331 " pdb=" CB LYS F 331 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA LYS B 331 " pdb=" N LYS B 331 " pdb=" C LYS B 331 " pdb=" CB LYS B 331 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA LYS E 331 " pdb=" N LYS E 331 " pdb=" C LYS E 331 " pdb=" CB LYS E 331 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 525 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.141 2.00e-02 2.50e+03 6.19e-02 1.15e+02 pdb=" CG TYR F 310 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " -0.043 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " -0.027 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.129 2.00e-02 2.50e+03 pdb=" HD1 TYR F 310 " -0.013 2.00e-02 2.50e+03 pdb=" HD2 TYR F 310 " -0.040 2.00e-02 2.50e+03 pdb=" HE1 TYR F 310 " -0.027 2.00e-02 2.50e+03 pdb=" HE2 TYR F 310 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " 0.123 2.00e-02 2.50e+03 5.16e-02 7.98e+01 pdb=" CG TYR D 310 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " 0.096 2.00e-02 2.50e+03 pdb=" HD1 TYR D 310 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR D 310 " -0.030 2.00e-02 2.50e+03 pdb=" HE1 TYR D 310 " -0.014 2.00e-02 2.50e+03 pdb=" HE2 TYR D 310 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 336 " 0.071 2.00e-02 2.50e+03 6.87e-02 7.08e+01 pdb=" CD GLN A 336 " -0.018 2.00e-02 2.50e+03 pdb=" OE1 GLN A 336 " -0.053 2.00e-02 2.50e+03 pdb=" NE2 GLN A 336 " -0.061 2.00e-02 2.50e+03 pdb="HE21 GLN A 336 " -0.056 2.00e-02 2.50e+03 pdb="HE22 GLN A 336 " 0.116 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 597 2.17 - 2.78: 12050 2.78 - 3.39: 18264 3.39 - 3.99: 25160 3.99 - 4.60: 34497 Nonbonded interactions: 90568 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.565 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.583 1.850 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.589 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.615 1.850 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.616 1.850 ... (remaining 90563 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 11.730 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 24.850 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 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 3498 Z= 0.732 Angle : 1.876 7.705 4680 Z= 1.233 Chirality : 0.083 0.332 528 Planarity : 0.010 0.072 594 Dihedral : 10.800 86.926 1344 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.003 HIS B 362 PHE 0.033 0.009 PHE B 346 TYR 0.127 0.043 TYR F 310 ARG 0.006 0.002 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7490 (tttt) cc_final: 0.7017 (ttmt) REVERT: A 375 LYS cc_start: 0.7480 (tttt) cc_final: 0.7117 (tttm) REVERT: C 311 LYS cc_start: 0.8435 (mttt) cc_final: 0.8036 (mtmt) REVERT: C 317 LYS cc_start: 0.7723 (mttt) cc_final: 0.7465 (mtpt) REVERT: C 327 ASN cc_start: 0.8060 (m-40) cc_final: 0.7756 (m110) REVERT: C 340 LYS cc_start: 0.8217 (tttt) cc_final: 0.7634 (ttmt) REVERT: C 370 LYS cc_start: 0.7845 (tttm) cc_final: 0.7622 (tttt) REVERT: C 372 GLU cc_start: 0.7660 (tt0) cc_final: 0.7373 (tt0) REVERT: C 375 LYS cc_start: 0.8195 (tttt) cc_final: 0.7866 (tttp) REVERT: E 311 LYS cc_start: 0.7968 (mttt) cc_final: 0.7280 (tppt) REVERT: E 349 ARG cc_start: 0.6304 (mtm180) cc_final: 0.5911 (mmm160) REVERT: B 348 ASP cc_start: 0.8291 (t0) cc_final: 0.8003 (t0) REVERT: B 351 GLN cc_start: 0.7106 (tt0) cc_final: 0.6608 (mt0) REVERT: B 375 LYS cc_start: 0.7659 (tttt) cc_final: 0.7363 (ttmt) REVERT: D 311 LYS cc_start: 0.8023 (mttt) cc_final: 0.7754 (pttp) REVERT: D 317 LYS cc_start: 0.7895 (mttt) cc_final: 0.7331 (mtmt) REVERT: D 340 LYS cc_start: 0.7997 (tttt) cc_final: 0.7583 (mtpt) REVERT: D 351 GLN cc_start: 0.8048 (tt0) cc_final: 0.7480 (mt0) REVERT: D 375 LYS cc_start: 0.8017 (tttt) cc_final: 0.7771 (ttmt) REVERT: F 311 LYS cc_start: 0.7765 (mttt) cc_final: 0.7268 (mmtm) REVERT: F 351 GLN cc_start: 0.7375 (tt0) cc_final: 0.6880 (mt0) REVERT: F 375 LYS cc_start: 0.7960 (tttt) cc_final: 0.7660 (ttmt) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.6586 time to fit residues: 91.4858 Evaluate side-chains 87 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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: 2.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 HIS B 327 ASN D 327 ASN ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3498 Z= 0.235 Angle : 0.532 3.989 4680 Z= 0.273 Chirality : 0.050 0.132 528 Planarity : 0.004 0.037 594 Dihedral : 4.943 13.006 462 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.51 % Allowed : 5.30 % Favored : 94.19 % 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: -1.31 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.99 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 330 PHE 0.011 0.001 PHE F 346 TYR 0.013 0.003 TYR F 310 ARG 0.005 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.7138 (mp0) cc_final: 0.6825 (mp0) REVERT: A 375 LYS cc_start: 0.7623 (tttt) cc_final: 0.7251 (tttm) REVERT: C 311 LYS cc_start: 0.8647 (mttt) cc_final: 0.8245 (mtmt) REVERT: C 317 LYS cc_start: 0.7777 (mttt) cc_final: 0.7521 (mtpt) REVERT: C 340 LYS cc_start: 0.8163 (tttt) cc_final: 0.7615 (ttmt) REVERT: C 343 LYS cc_start: 0.8159 (mttt) cc_final: 0.7935 (mtpt) REVERT: C 349 ARG cc_start: 0.7642 (mtt90) cc_final: 0.7412 (mtt90) REVERT: C 368 ASN cc_start: 0.8668 (m-40) cc_final: 0.8372 (m-40) REVERT: C 375 LYS cc_start: 0.8352 (tttt) cc_final: 0.8017 (tttp) REVERT: E 311 LYS cc_start: 0.8028 (mttt) cc_final: 0.7304 (tppt) REVERT: B 351 GLN cc_start: 0.7160 (tt0) cc_final: 0.6739 (mt0) REVERT: B 375 LYS cc_start: 0.8067 (tttt) cc_final: 0.7719 (ttmt) REVERT: D 311 LYS cc_start: 0.8084 (mttt) cc_final: 0.7744 (pttp) REVERT: D 317 LYS cc_start: 0.7853 (mttt) cc_final: 0.7340 (mtmt) REVERT: D 340 LYS cc_start: 0.8057 (tttt) cc_final: 0.7506 (mtpt) REVERT: D 349 ARG cc_start: 0.7081 (mtm180) cc_final: 0.6876 (mtt-85) REVERT: D 351 GLN cc_start: 0.8024 (tt0) cc_final: 0.7678 (mt0) REVERT: D 375 LYS cc_start: 0.8292 (tttt) cc_final: 0.8047 (ttmt) REVERT: F 311 LYS cc_start: 0.7791 (mttt) cc_final: 0.7461 (mmtm) REVERT: F 351 GLN cc_start: 0.7370 (tt0) cc_final: 0.7070 (mt0) outliers start: 2 outliers final: 2 residues processed: 84 average time/residue: 0.8308 time to fit residues: 76.9022 Evaluate side-chains 76 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain C residue 324 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3498 Z= 0.133 Angle : 0.449 3.850 4680 Z= 0.224 Chirality : 0.051 0.125 528 Planarity : 0.003 0.029 594 Dihedral : 4.334 11.518 462 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.76 % Allowed : 6.57 % Favored : 92.68 % 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: -1.06 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.80 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 374 PHE 0.005 0.001 PHE F 346 TYR 0.009 0.002 TYR F 310 ARG 0.006 0.001 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.7050 (mp0) cc_final: 0.6780 (mp0) REVERT: A 349 ARG cc_start: 0.7240 (mtp85) cc_final: 0.6509 (mtt90) REVERT: A 375 LYS cc_start: 0.7686 (tttt) cc_final: 0.7380 (tttm) REVERT: C 311 LYS cc_start: 0.8589 (mttt) cc_final: 0.8188 (ttpt) REVERT: C 317 LYS cc_start: 0.7703 (mttt) cc_final: 0.7487 (mtpt) REVERT: C 340 LYS cc_start: 0.8206 (tttt) cc_final: 0.7601 (ttmt) REVERT: C 343 LYS cc_start: 0.8192 (mttt) cc_final: 0.7908 (mtpt) REVERT: C 368 ASN cc_start: 0.8637 (m-40) cc_final: 0.8369 (m-40) REVERT: C 375 LYS cc_start: 0.8358 (tttt) cc_final: 0.8006 (tttp) REVERT: E 311 LYS cc_start: 0.7929 (mttt) cc_final: 0.7211 (tppt) REVERT: B 351 GLN cc_start: 0.7200 (tt0) cc_final: 0.6762 (mt0) REVERT: B 375 LYS cc_start: 0.8104 (tttt) cc_final: 0.7722 (ttmt) REVERT: D 311 LYS cc_start: 0.8064 (mttt) cc_final: 0.7762 (pttp) REVERT: D 349 ARG cc_start: 0.7031 (mtm180) cc_final: 0.6788 (mtt-85) REVERT: F 311 LYS cc_start: 0.7671 (mttt) cc_final: 0.7368 (mmtm) REVERT: F 351 GLN cc_start: 0.7333 (tt0) cc_final: 0.7047 (mt0) REVERT: F 375 LYS cc_start: 0.8048 (tttt) cc_final: 0.7706 (ttmt) outliers start: 3 outliers final: 2 residues processed: 74 average time/residue: 0.8377 time to fit residues: 68.1041 Evaluate side-chains 69 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 324 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 0.0980 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3498 Z= 0.313 Angle : 0.505 4.071 4680 Z= 0.257 Chirality : 0.050 0.122 528 Planarity : 0.003 0.027 594 Dihedral : 4.546 12.009 462 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.01 % Allowed : 7.58 % Favored : 91.41 % 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: -1.24 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 PHE 0.009 0.001 PHE B 346 TYR 0.013 0.003 TYR D 310 ARG 0.007 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.7016 (mp0) cc_final: 0.6737 (mp0) REVERT: A 347 LYS cc_start: 0.8402 (mttt) cc_final: 0.8163 (mmtt) REVERT: A 349 ARG cc_start: 0.7222 (mtp85) cc_final: 0.6446 (mtt90) REVERT: A 375 LYS cc_start: 0.7721 (tttt) cc_final: 0.7428 (tttm) REVERT: C 311 LYS cc_start: 0.8629 (mttt) cc_final: 0.8180 (ttpt) REVERT: C 317 LYS cc_start: 0.7767 (mttt) cc_final: 0.7547 (mtpt) REVERT: C 340 LYS cc_start: 0.8143 (tttt) cc_final: 0.7589 (ttmt) REVERT: E 311 LYS cc_start: 0.8051 (mttt) cc_final: 0.7311 (tppt) REVERT: B 348 ASP cc_start: 0.8278 (t70) cc_final: 0.8074 (t0) REVERT: B 351 GLN cc_start: 0.7397 (tt0) cc_final: 0.7063 (mt0) REVERT: B 358 ASP cc_start: 0.7474 (m-30) cc_final: 0.6854 (t0) REVERT: B 375 LYS cc_start: 0.8139 (tttt) cc_final: 0.7736 (ttmt) REVERT: D 311 LYS cc_start: 0.8053 (mttt) cc_final: 0.7740 (pttp) REVERT: D 317 LYS cc_start: 0.7824 (mttt) cc_final: 0.7330 (mtmt) REVERT: D 321 LYS cc_start: 0.8183 (mttt) cc_final: 0.7428 (mtpt) REVERT: D 340 LYS cc_start: 0.8057 (tttt) cc_final: 0.7564 (mtpt) REVERT: D 349 ARG cc_start: 0.6948 (mtm180) cc_final: 0.6742 (mtt-85) REVERT: D 351 GLN cc_start: 0.8168 (tt0) cc_final: 0.7830 (mt0) REVERT: D 375 LYS cc_start: 0.8426 (tttt) cc_final: 0.8095 (ttmt) REVERT: F 311 LYS cc_start: 0.7843 (mttt) cc_final: 0.7532 (mmtm) REVERT: F 351 GLN cc_start: 0.7450 (tt0) cc_final: 0.7093 (mt0) REVERT: F 375 LYS cc_start: 0.8063 (tttt) cc_final: 0.7720 (ttmt) outliers start: 4 outliers final: 3 residues processed: 75 average time/residue: 0.7984 time to fit residues: 65.4294 Evaluate side-chains 72 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 324 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 0.0060 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3498 Z= 0.114 Angle : 0.425 3.766 4680 Z= 0.210 Chirality : 0.051 0.125 528 Planarity : 0.003 0.036 594 Dihedral : 4.098 10.703 462 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.51 % Allowed : 8.59 % Favored : 90.91 % 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: -1.11 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.84 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 362 PHE 0.004 0.001 PHE B 378 TYR 0.005 0.001 TYR A 310 ARG 0.006 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.6943 (mp0) cc_final: 0.6651 (mp0) REVERT: A 349 ARG cc_start: 0.7203 (mtp85) cc_final: 0.6385 (mtt90) REVERT: A 375 LYS cc_start: 0.7719 (tttt) cc_final: 0.7409 (tttm) REVERT: C 311 LYS cc_start: 0.8548 (mttt) cc_final: 0.8192 (ttpt) REVERT: C 317 LYS cc_start: 0.7724 (mttt) cc_final: 0.7436 (mtpt) REVERT: C 340 LYS cc_start: 0.8180 (tttt) cc_final: 0.7586 (ttmt) REVERT: C 368 ASN cc_start: 0.8607 (m-40) cc_final: 0.8384 (m-40) REVERT: C 375 LYS cc_start: 0.8447 (tttt) cc_final: 0.7952 (ttmm) REVERT: E 311 LYS cc_start: 0.8036 (mttt) cc_final: 0.7468 (tppt) REVERT: B 351 GLN cc_start: 0.7338 (tt0) cc_final: 0.6974 (mt0) REVERT: B 375 LYS cc_start: 0.8108 (tttt) cc_final: 0.7673 (ttmt) REVERT: D 311 LYS cc_start: 0.8026 (mttt) cc_final: 0.7758 (pttp) REVERT: D 317 LYS cc_start: 0.7759 (mttt) cc_final: 0.7287 (mtmt) REVERT: D 321 LYS cc_start: 0.8101 (mttt) cc_final: 0.7320 (mtpt) REVERT: D 340 LYS cc_start: 0.8008 (tttt) cc_final: 0.7521 (mtpt) REVERT: D 375 LYS cc_start: 0.8378 (tttt) cc_final: 0.8075 (ttmt) REVERT: F 311 LYS cc_start: 0.7713 (mttt) cc_final: 0.7428 (mmtm) REVERT: F 351 GLN cc_start: 0.7331 (tt0) cc_final: 0.7018 (mt0) REVERT: F 353 LYS cc_start: 0.7615 (tttp) cc_final: 0.7298 (tttp) REVERT: F 375 LYS cc_start: 0.7950 (tttt) cc_final: 0.7581 (ttmt) outliers start: 2 outliers final: 2 residues processed: 73 average time/residue: 0.9050 time to fit residues: 71.9517 Evaluate side-chains 71 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 324 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3498 Z= 0.157 Angle : 0.433 3.770 4680 Z= 0.215 Chirality : 0.050 0.123 528 Planarity : 0.003 0.037 594 Dihedral : 4.053 10.785 462 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.01 % Allowed : 7.83 % Favored : 91.16 % 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: -1.12 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.85 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 374 PHE 0.005 0.001 PHE F 346 TYR 0.008 0.002 TYR F 310 ARG 0.007 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.6872 (mp0) cc_final: 0.6644 (mp0) REVERT: A 349 ARG cc_start: 0.7154 (mtp85) cc_final: 0.6383 (mtt90) REVERT: A 375 LYS cc_start: 0.7719 (tttt) cc_final: 0.7407 (tttm) REVERT: C 311 LYS cc_start: 0.8554 (mttt) cc_final: 0.8188 (ttpt) REVERT: C 317 LYS cc_start: 0.7748 (mttt) cc_final: 0.7465 (mtpt) REVERT: C 340 LYS cc_start: 0.8162 (tttt) cc_final: 0.7587 (ttmt) REVERT: C 375 LYS cc_start: 0.8467 (tttt) cc_final: 0.7967 (ttmm) REVERT: E 311 LYS cc_start: 0.8003 (mttt) cc_final: 0.7432 (tppt) REVERT: B 351 GLN cc_start: 0.7435 (tt0) cc_final: 0.7072 (mt0) REVERT: B 358 ASP cc_start: 0.7415 (m-30) cc_final: 0.6685 (t0) REVERT: B 375 LYS cc_start: 0.8134 (tttt) cc_final: 0.7713 (ttmt) REVERT: D 311 LYS cc_start: 0.8030 (mttt) cc_final: 0.7766 (pttp) REVERT: D 317 LYS cc_start: 0.7785 (mttt) cc_final: 0.7312 (mtmt) REVERT: D 321 LYS cc_start: 0.8130 (mttt) cc_final: 0.7353 (mtpt) REVERT: D 340 LYS cc_start: 0.8010 (tttt) cc_final: 0.7511 (mtpt) REVERT: D 351 GLN cc_start: 0.8140 (tt0) cc_final: 0.7815 (mt0) REVERT: D 375 LYS cc_start: 0.8388 (tttt) cc_final: 0.8075 (ttmt) REVERT: F 311 LYS cc_start: 0.7831 (mttt) cc_final: 0.7476 (mmtt) REVERT: F 351 GLN cc_start: 0.7368 (tt0) cc_final: 0.7089 (mt0) REVERT: F 375 LYS cc_start: 0.8000 (tttt) cc_final: 0.7644 (ttmt) outliers start: 4 outliers final: 4 residues processed: 76 average time/residue: 0.8393 time to fit residues: 69.6240 Evaluate side-chains 76 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain C residue 324 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.1980 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3498 Z= 0.256 Angle : 0.472 3.935 4680 Z= 0.238 Chirality : 0.050 0.122 528 Planarity : 0.003 0.036 594 Dihedral : 4.323 12.237 462 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.01 % Allowed : 7.58 % Favored : 91.41 % 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: -1.34 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 362 PHE 0.007 0.001 PHE B 346 TYR 0.011 0.002 TYR F 310 ARG 0.006 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7388 (tttt) cc_final: 0.6782 (ttmt) REVERT: A 342 GLU cc_start: 0.6866 (mp0) cc_final: 0.6549 (mp0) REVERT: A 349 ARG cc_start: 0.7147 (mtp85) cc_final: 0.6413 (mtt90) REVERT: A 375 LYS cc_start: 0.7782 (tttt) cc_final: 0.7462 (tttm) REVERT: C 311 LYS cc_start: 0.8583 (mttt) cc_final: 0.8181 (ttpt) REVERT: C 317 LYS cc_start: 0.7768 (mttt) cc_final: 0.7521 (mtpt) REVERT: C 340 LYS cc_start: 0.8167 (tttt) cc_final: 0.7635 (ttmt) REVERT: C 375 LYS cc_start: 0.8439 (tttt) cc_final: 0.7959 (ttmm) REVERT: E 311 LYS cc_start: 0.7994 (mttt) cc_final: 0.7384 (tppt) REVERT: B 317 LYS cc_start: 0.7066 (mttt) cc_final: 0.6858 (mtmt) REVERT: B 321 LYS cc_start: 0.6957 (mttt) cc_final: 0.6421 (mtpt) REVERT: B 340 LYS cc_start: 0.7066 (tttt) cc_final: 0.6665 (mtpt) REVERT: B 351 GLN cc_start: 0.7500 (tt0) cc_final: 0.7151 (mt0) REVERT: B 375 LYS cc_start: 0.8130 (tttt) cc_final: 0.7724 (ttmt) REVERT: D 311 LYS cc_start: 0.8018 (mttt) cc_final: 0.7718 (pttp) REVERT: D 317 LYS cc_start: 0.7829 (mttt) cc_final: 0.7381 (mtmt) REVERT: D 321 LYS cc_start: 0.8194 (mttt) cc_final: 0.7434 (mtpt) REVERT: D 340 LYS cc_start: 0.8091 (tttt) cc_final: 0.7594 (mtpt) REVERT: D 351 GLN cc_start: 0.8287 (tt0) cc_final: 0.8037 (mt0) REVERT: D 375 LYS cc_start: 0.8418 (tttt) cc_final: 0.8098 (ttmt) REVERT: F 311 LYS cc_start: 0.7859 (mttt) cc_final: 0.7454 (mmtt) REVERT: F 321 LYS cc_start: 0.6932 (mttt) cc_final: 0.6386 (mtpt) REVERT: F 351 GLN cc_start: 0.7445 (tt0) cc_final: 0.7066 (mt0) REVERT: F 375 LYS cc_start: 0.8031 (tttt) cc_final: 0.7641 (ttmt) outliers start: 4 outliers final: 3 residues processed: 83 average time/residue: 0.9120 time to fit residues: 81.7807 Evaluate side-chains 81 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 324 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.0060 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3498 Z= 0.113 Angle : 0.422 3.696 4680 Z= 0.207 Chirality : 0.051 0.125 528 Planarity : 0.003 0.046 594 Dihedral : 4.001 11.862 462 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 0.51 % Allowed : 8.59 % Favored : 90.91 % 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: -1.19 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.90 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 362 PHE 0.003 0.000 PHE B 378 TYR 0.005 0.001 TYR A 310 ARG 0.008 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.6843 (mp0) cc_final: 0.6588 (mp0) REVERT: A 349 ARG cc_start: 0.7060 (mtp85) cc_final: 0.6313 (mtt90) REVERT: A 375 LYS cc_start: 0.7790 (tttt) cc_final: 0.7489 (tttm) REVERT: C 311 LYS cc_start: 0.8516 (mttt) cc_final: 0.8181 (ttpt) REVERT: C 317 LYS cc_start: 0.7697 (mttt) cc_final: 0.7445 (mtpt) REVERT: C 340 LYS cc_start: 0.8193 (tttt) cc_final: 0.7648 (ttmt) REVERT: C 375 LYS cc_start: 0.8431 (tttt) cc_final: 0.7939 (ttmm) REVERT: E 311 LYS cc_start: 0.7934 (mttt) cc_final: 0.7291 (tppt) REVERT: B 321 LYS cc_start: 0.6885 (mttt) cc_final: 0.6353 (mtpt) REVERT: B 340 LYS cc_start: 0.7111 (tttt) cc_final: 0.6659 (mtpt) REVERT: B 349 ARG cc_start: 0.7243 (mtt180) cc_final: 0.6953 (mtp180) REVERT: B 351 GLN cc_start: 0.7368 (tt0) cc_final: 0.7050 (mt0) REVERT: B 358 ASP cc_start: 0.7300 (m-30) cc_final: 0.6539 (t0) REVERT: B 375 LYS cc_start: 0.8039 (tttt) cc_final: 0.7686 (ttmt) REVERT: D 311 LYS cc_start: 0.7994 (mttt) cc_final: 0.7737 (pttp) REVERT: D 317 LYS cc_start: 0.7738 (mttt) cc_final: 0.7321 (mtmt) REVERT: D 321 LYS cc_start: 0.8118 (mttt) cc_final: 0.7349 (mtpt) REVERT: D 340 LYS cc_start: 0.8041 (tttt) cc_final: 0.7553 (mtpt) REVERT: D 351 GLN cc_start: 0.8165 (tt0) cc_final: 0.7836 (mt0) REVERT: D 375 LYS cc_start: 0.8414 (tttt) cc_final: 0.8089 (ttmt) REVERT: F 311 LYS cc_start: 0.7850 (mttt) cc_final: 0.7459 (mmtt) REVERT: F 351 GLN cc_start: 0.7328 (tt0) cc_final: 0.6927 (mt0) REVERT: F 375 LYS cc_start: 0.7983 (tttt) cc_final: 0.7639 (ttmt) outliers start: 2 outliers final: 2 residues processed: 81 average time/residue: 0.9097 time to fit residues: 80.0595 Evaluate side-chains 79 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 324 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3498 Z= 0.165 Angle : 0.434 3.819 4680 Z= 0.215 Chirality : 0.050 0.122 528 Planarity : 0.003 0.043 594 Dihedral : 4.030 11.912 462 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.51 % Allowed : 9.34 % Favored : 90.15 % 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: -1.19 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.89 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 374 PHE 0.004 0.001 PHE A 378 TYR 0.007 0.002 TYR B 310 ARG 0.008 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7371 (tttt) cc_final: 0.6748 (ttmt) REVERT: A 342 GLU cc_start: 0.6838 (mp0) cc_final: 0.6481 (mp0) REVERT: A 349 ARG cc_start: 0.7078 (mtp85) cc_final: 0.6333 (mtt90) REVERT: A 375 LYS cc_start: 0.7814 (tttt) cc_final: 0.7509 (tttm) REVERT: C 311 LYS cc_start: 0.8539 (mttt) cc_final: 0.8194 (ttpt) REVERT: C 317 LYS cc_start: 0.7726 (mttt) cc_final: 0.7477 (mtpt) REVERT: C 340 LYS cc_start: 0.8187 (tttt) cc_final: 0.7635 (ttmt) REVERT: C 375 LYS cc_start: 0.8441 (tttt) cc_final: 0.7971 (ttmm) REVERT: E 311 LYS cc_start: 0.7981 (mttt) cc_final: 0.7297 (tppt) REVERT: B 321 LYS cc_start: 0.6900 (mttt) cc_final: 0.6365 (mtpt) REVERT: B 340 LYS cc_start: 0.7047 (tttt) cc_final: 0.6602 (mtpt) REVERT: B 349 ARG cc_start: 0.7299 (mtt180) cc_final: 0.6948 (mtp180) REVERT: B 351 GLN cc_start: 0.7434 (tt0) cc_final: 0.7113 (mt0) REVERT: B 358 ASP cc_start: 0.7346 (m-30) cc_final: 0.6535 (t0) REVERT: B 375 LYS cc_start: 0.8042 (tttt) cc_final: 0.7693 (ttmt) REVERT: D 311 LYS cc_start: 0.7997 (mttt) cc_final: 0.7731 (pttp) REVERT: D 317 LYS cc_start: 0.7731 (mttt) cc_final: 0.7337 (mtmt) REVERT: D 321 LYS cc_start: 0.8125 (mttt) cc_final: 0.7364 (mtpt) REVERT: D 340 LYS cc_start: 0.8064 (tttt) cc_final: 0.7571 (mtpt) REVERT: D 351 GLN cc_start: 0.8201 (tt0) cc_final: 0.7899 (mt0) REVERT: D 375 LYS cc_start: 0.8422 (tttt) cc_final: 0.8096 (ttmt) REVERT: F 311 LYS cc_start: 0.7852 (mttt) cc_final: 0.7446 (mmtt) REVERT: F 351 GLN cc_start: 0.7357 (tt0) cc_final: 0.7044 (mt0) REVERT: F 375 LYS cc_start: 0.8018 (tttt) cc_final: 0.7638 (ttmt) outliers start: 2 outliers final: 2 residues processed: 81 average time/residue: 0.9143 time to fit residues: 81.0015 Evaluate side-chains 81 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3498 Z= 0.177 Angle : 0.438 3.746 4680 Z= 0.218 Chirality : 0.050 0.122 528 Planarity : 0.003 0.048 594 Dihedral : 4.088 11.580 462 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.25 % Allowed : 9.60 % Favored : 90.15 % 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: -1.24 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.93 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 374 PHE 0.004 0.001 PHE F 378 TYR 0.008 0.002 TYR B 310 ARG 0.008 0.001 ARG C 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7406 (tttt) cc_final: 0.6801 (ttmt) REVERT: A 342 GLU cc_start: 0.6829 (mp0) cc_final: 0.6513 (mp0) REVERT: A 349 ARG cc_start: 0.7111 (mtp85) cc_final: 0.6368 (mtt90) REVERT: A 375 LYS cc_start: 0.7803 (tttt) cc_final: 0.7499 (tttm) REVERT: C 311 LYS cc_start: 0.8550 (mttt) cc_final: 0.8204 (ttpt) REVERT: C 340 LYS cc_start: 0.8191 (tttt) cc_final: 0.7633 (ttmt) REVERT: C 375 LYS cc_start: 0.8416 (tttt) cc_final: 0.7964 (ttmm) REVERT: E 311 LYS cc_start: 0.7990 (mttt) cc_final: 0.7292 (tppt) REVERT: B 321 LYS cc_start: 0.6873 (mttt) cc_final: 0.6341 (mtpt) REVERT: B 340 LYS cc_start: 0.7078 (tttt) cc_final: 0.6617 (mtpt) REVERT: B 349 ARG cc_start: 0.7326 (mtt180) cc_final: 0.6960 (mtp180) REVERT: B 351 GLN cc_start: 0.7434 (tt0) cc_final: 0.7128 (mt0) REVERT: B 375 LYS cc_start: 0.8042 (tttt) cc_final: 0.7679 (ttmt) REVERT: D 311 LYS cc_start: 0.7991 (mttt) cc_final: 0.7746 (pttp) REVERT: D 317 LYS cc_start: 0.7713 (mttt) cc_final: 0.7341 (mtmt) REVERT: D 321 LYS cc_start: 0.8189 (mttt) cc_final: 0.7452 (mtpt) REVERT: D 340 LYS cc_start: 0.8059 (tttt) cc_final: 0.7563 (mtpt) REVERT: D 351 GLN cc_start: 0.8261 (tt0) cc_final: 0.7951 (mt0) REVERT: D 375 LYS cc_start: 0.8455 (tttt) cc_final: 0.8134 (ttmt) REVERT: F 311 LYS cc_start: 0.7828 (mttt) cc_final: 0.7432 (mmtt) REVERT: F 321 LYS cc_start: 0.6915 (mttt) cc_final: 0.6363 (mtpp) REVERT: F 340 LYS cc_start: 0.7409 (tttt) cc_final: 0.6921 (mtpt) REVERT: F 351 GLN cc_start: 0.7369 (tt0) cc_final: 0.6949 (mt0) REVERT: F 375 LYS cc_start: 0.8004 (tttt) cc_final: 0.7626 (ttmt) outliers start: 1 outliers final: 1 residues processed: 81 average time/residue: 0.9434 time to fit residues: 82.6266 Evaluate side-chains 80 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 0.0870 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 327 ASN ** 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 = 0.4016 r_free = 0.4016 target = 0.125276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.110029 restraints weight = 13723.500| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.84 r_work: 0.3715 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3498 Z= 0.199 Angle : 0.449 3.877 4680 Z= 0.224 Chirality : 0.050 0.120 528 Planarity : 0.003 0.047 594 Dihedral : 4.145 11.855 462 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.25 % Allowed : 9.34 % Favored : 90.40 % 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: -1.26 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 374 PHE 0.004 0.001 PHE F 378 TYR 0.008 0.002 TYR B 310 ARG 0.009 0.001 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3325.00 seconds wall clock time: 59 minutes 28.01 seconds (3568.01 seconds total)