Starting phenix.real_space_refine on Sat Aug 3 05:34:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8z_18266/08_2024/8q8z_18266.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8z_18266/08_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_18266/08_2024/8q8z_18266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8z_18266/08_2024/8q8z_18266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8z_18266/08_2024/8q8z_18266.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8z_18266/08_2024/8q8z_18266.cif" } 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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 4.65, per 1000 atoms: 0.66 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: 5.25 Conformation dependent library (CDL) restraints added in 871.1 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: 0.73 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: 2.37 Time building geometry restraints manager: 5.58 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 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.583 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.589 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.615 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.616 2.450 ... (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 Time spend for trying shortcut: 0.00 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: 5.110 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: 0.120 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.670 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.280 ------------------------------------------------------------------------------- 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 : 0.600 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: 0.6658 time to fit residues: 92.3337 Evaluate side-chains 87 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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: 5.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 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 B 327 ASN D 327 ASN F 327 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3498 Z= 0.283 Angle : 0.555 4.200 4680 Z= 0.285 Chirality : 0.052 0.132 528 Planarity : 0.004 0.036 594 Dihedral : 5.016 13.399 462 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 0.76 % Allowed : 4.29 % Favored : 94.95 % 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: -1.38 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.012 0.002 PHE F 346 TYR 0.013 0.003 TYR D 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 80 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7535 (tttt) cc_final: 0.6927 (ttmt) REVERT: A 342 GLU cc_start: 0.7168 (mp0) cc_final: 0.6907 (mp0) REVERT: A 375 LYS cc_start: 0.7748 (tttt) cc_final: 0.7365 (tttm) REVERT: C 311 LYS cc_start: 0.8680 (mttt) cc_final: 0.8245 (mtmt) REVERT: C 368 ASN cc_start: 0.8668 (m-40) cc_final: 0.8408 (m-40) REVERT: C 375 LYS cc_start: 0.8374 (tttt) cc_final: 0.8022 (tttp) REVERT: E 311 LYS cc_start: 0.8001 (mttt) cc_final: 0.7285 (tppt) REVERT: E 348 ASP cc_start: 0.7918 (t0) cc_final: 0.7655 (t0) REVERT: E 349 ARG cc_start: 0.6311 (mtm180) cc_final: 0.6061 (mmp-170) REVERT: B 348 ASP cc_start: 0.8493 (t0) cc_final: 0.8204 (t70) REVERT: B 351 GLN cc_start: 0.7329 (tt0) cc_final: 0.6923 (mt0) REVERT: B 375 LYS cc_start: 0.8117 (tttt) cc_final: 0.7735 (ttmt) REVERT: D 311 LYS cc_start: 0.8173 (mttt) cc_final: 0.7773 (pttp) REVERT: D 327 ASN cc_start: 0.7691 (m110) cc_final: 0.7337 (m110) REVERT: D 349 ARG cc_start: 0.7200 (mtm180) cc_final: 0.6851 (mtt-85) REVERT: F 311 LYS cc_start: 0.7768 (mttt) cc_final: 0.7446 (mmtm) REVERT: F 351 GLN cc_start: 0.7414 (tt0) cc_final: 0.7098 (mt0) outliers start: 3 outliers final: 2 residues processed: 79 average time/residue: 0.7170 time to fit residues: 62.4693 Evaluate side-chains 66 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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: 0.9980 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 38 optimal weight: 0.1980 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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: 0.7542 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3498 Z= 0.157 Angle : 0.467 3.855 4680 Z= 0.234 Chirality : 0.051 0.130 528 Planarity : 0.004 0.039 594 Dihedral : 4.549 11.746 462 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: -1.27 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.96 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 374 PHE 0.006 0.001 PHE B 378 TYR 0.010 0.002 TYR F 310 ARG 0.007 0.001 ARG C 349 *********************** 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 72 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7381 (tttt) cc_final: 0.6798 (ttmt) REVERT: A 342 GLU cc_start: 0.7177 (mp0) cc_final: 0.6876 (mp0) REVERT: A 375 LYS cc_start: 0.7787 (tttt) cc_final: 0.7468 (tttm) REVERT: C 311 LYS cc_start: 0.8635 (mttt) cc_final: 0.8179 (ttpt) REVERT: C 349 ARG cc_start: 0.7652 (mtt90) cc_final: 0.7397 (mtt90) REVERT: C 368 ASN cc_start: 0.8721 (m-40) cc_final: 0.8476 (m-40) REVERT: C 375 LYS cc_start: 0.8372 (tttt) cc_final: 0.8049 (tttp) REVERT: E 311 LYS cc_start: 0.7937 (mttt) cc_final: 0.7221 (tppt) REVERT: E 347 LYS cc_start: 0.8277 (mppt) cc_final: 0.8045 (mmtp) REVERT: E 348 ASP cc_start: 0.7904 (t0) cc_final: 0.7627 (t0) REVERT: E 349 ARG cc_start: 0.6335 (mtm180) cc_final: 0.6109 (mmp-170) REVERT: B 351 GLN cc_start: 0.7424 (tt0) cc_final: 0.6976 (mt0) REVERT: B 375 LYS cc_start: 0.8120 (tttt) cc_final: 0.7731 (ttmt) REVERT: D 311 LYS cc_start: 0.8146 (mttt) cc_final: 0.7730 (pttp) REVERT: D 327 ASN cc_start: 0.7660 (m110) cc_final: 0.7285 (m110) REVERT: D 349 ARG cc_start: 0.7078 (mtm180) cc_final: 0.6780 (mtt-85) REVERT: F 311 LYS cc_start: 0.7660 (mttt) cc_final: 0.7376 (mmtm) REVERT: F 351 GLN cc_start: 0.7384 (tt0) cc_final: 0.7084 (mt0) REVERT: F 353 LYS cc_start: 0.7641 (tttp) cc_final: 0.7336 (tttm) REVERT: F 375 LYS cc_start: 0.8039 (tttt) cc_final: 0.7662 (ttmt) outliers start: 3 outliers final: 2 residues processed: 71 average time/residue: 0.8178 time to fit residues: 63.5366 Evaluate side-chains 66 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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: 1.9990 chunk 25 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 0.4980 chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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: 0.7564 moved from start: 0.4659 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= 0.201 Angle : 0.470 3.857 4680 Z= 0.234 Chirality : 0.051 0.125 528 Planarity : 0.003 0.025 594 Dihedral : 4.388 11.421 462 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.01 % Allowed : 6.31 % 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: -1.38 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 374 PHE 0.007 0.001 PHE F 346 TYR 0.010 0.002 TYR F 310 ARG 0.005 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 70 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7364 (tttt) cc_final: 0.6798 (ttmt) REVERT: A 342 GLU cc_start: 0.7123 (mp0) cc_final: 0.6820 (mp0) REVERT: A 347 LYS cc_start: 0.8414 (mttt) cc_final: 0.7911 (mtpp) REVERT: A 375 LYS cc_start: 0.7931 (tttt) cc_final: 0.7596 (tttm) REVERT: C 311 LYS cc_start: 0.8631 (mttt) cc_final: 0.8229 (ttpt) REVERT: C 347 LYS cc_start: 0.8490 (mppt) cc_final: 0.8255 (mppt) REVERT: C 349 ARG cc_start: 0.7644 (mtt90) cc_final: 0.7422 (mtt90) REVERT: C 368 ASN cc_start: 0.8645 (m-40) cc_final: 0.8438 (m-40) REVERT: E 311 LYS cc_start: 0.7980 (mttt) cc_final: 0.7448 (tppt) REVERT: E 347 LYS cc_start: 0.8370 (mppt) cc_final: 0.8046 (mmtp) REVERT: E 348 ASP cc_start: 0.7875 (t0) cc_final: 0.7635 (t0) REVERT: E 349 ARG cc_start: 0.6412 (mtm180) cc_final: 0.6155 (mmp-170) REVERT: B 351 GLN cc_start: 0.7439 (tt0) cc_final: 0.7015 (mt0) REVERT: B 358 ASP cc_start: 0.7189 (m-30) cc_final: 0.6855 (t0) REVERT: B 375 LYS cc_start: 0.8241 (tttt) cc_final: 0.7861 (ttmt) REVERT: D 311 LYS cc_start: 0.8155 (mttt) cc_final: 0.7738 (pttp) REVERT: D 327 ASN cc_start: 0.7611 (m110) cc_final: 0.7190 (m110) REVERT: F 311 LYS cc_start: 0.7749 (mttt) cc_final: 0.7313 (mmtm) REVERT: F 351 GLN cc_start: 0.7416 (tt0) cc_final: 0.7087 (mt0) REVERT: F 375 LYS cc_start: 0.8077 (tttt) cc_final: 0.7711 (ttmt) outliers start: 4 outliers final: 3 residues processed: 69 average time/residue: 0.7892 time to fit residues: 59.8350 Evaluate side-chains 69 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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: 2.9990 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 0.3980 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 overall best weight: 2.6586 ------------------------------------------------------------------------------- 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: 0.7583 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3498 Z= 0.259 Angle : 0.477 3.891 4680 Z= 0.242 Chirality : 0.051 0.122 528 Planarity : 0.003 0.025 594 Dihedral : 4.467 10.689 462 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.01 % Allowed : 6.06 % Favored : 92.93 % 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: -1.60 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 374 PHE 0.007 0.001 PHE B 346 TYR 0.011 0.002 TYR F 310 ARG 0.004 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 85 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7445 (tttt) cc_final: 0.6804 (ttmt) REVERT: A 342 GLU cc_start: 0.7078 (mp0) cc_final: 0.6757 (mp0) REVERT: A 375 LYS cc_start: 0.7927 (tttt) cc_final: 0.7614 (tttm) REVERT: C 311 LYS cc_start: 0.8637 (mttt) cc_final: 0.8228 (ttpt) REVERT: C 340 LYS cc_start: 0.8117 (tttt) cc_final: 0.7490 (ttmt) REVERT: C 347 LYS cc_start: 0.8478 (mppt) cc_final: 0.8208 (mppt) REVERT: C 349 ARG cc_start: 0.7662 (mtt90) cc_final: 0.7411 (mtt90) REVERT: E 311 LYS cc_start: 0.7976 (mttt) cc_final: 0.7312 (tppt) REVERT: E 348 ASP cc_start: 0.7918 (t0) cc_final: 0.7677 (t0) REVERT: E 349 ARG cc_start: 0.6289 (mtm180) cc_final: 0.5935 (mmm160) REVERT: B 317 LYS cc_start: 0.7186 (mttt) cc_final: 0.6947 (mtmt) REVERT: B 321 LYS cc_start: 0.7156 (mttt) cc_final: 0.6593 (mtpt) REVERT: B 349 ARG cc_start: 0.7389 (mtt180) cc_final: 0.7117 (mtp180) REVERT: B 351 GLN cc_start: 0.7512 (tt0) cc_final: 0.7154 (mt0) REVERT: B 358 ASP cc_start: 0.7377 (m-30) cc_final: 0.7007 (t0) REVERT: B 375 LYS cc_start: 0.8206 (tttt) cc_final: 0.7809 (ttmt) REVERT: D 311 LYS cc_start: 0.8131 (mttt) cc_final: 0.7699 (pttp) REVERT: D 321 LYS cc_start: 0.8175 (mttt) cc_final: 0.7381 (mtpt) REVERT: D 327 ASN cc_start: 0.7660 (m110) cc_final: 0.7262 (m110) REVERT: D 340 LYS cc_start: 0.8059 (tttt) cc_final: 0.7540 (mtpt) REVERT: D 351 GLN cc_start: 0.8130 (tt0) cc_final: 0.7783 (mt0) REVERT: D 375 LYS cc_start: 0.8412 (tttt) cc_final: 0.8105 (ttmt) REVERT: F 311 LYS cc_start: 0.7819 (mttt) cc_final: 0.7449 (mmtt) REVERT: F 340 LYS cc_start: 0.7499 (tttt) cc_final: 0.7110 (mtpt) REVERT: F 351 GLN cc_start: 0.7414 (tt0) cc_final: 0.7026 (mt0) REVERT: F 353 LYS cc_start: 0.7568 (tttp) cc_final: 0.7363 (tttm) REVERT: F 375 LYS cc_start: 0.8027 (tttt) cc_final: 0.7662 (ttmt) outliers start: 4 outliers final: 4 residues processed: 84 average time/residue: 0.8698 time to fit residues: 79.1929 Evaluate side-chains 82 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- 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: 0.7598 moved from start: 0.5234 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= 0.224 Angle : 0.461 3.760 4680 Z= 0.232 Chirality : 0.050 0.123 528 Planarity : 0.003 0.019 594 Dihedral : 4.366 10.656 462 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.52 % Allowed : 6.06 % Favored : 92.42 % 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 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (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 B 378 TYR 0.009 0.002 TYR F 310 ARG 0.003 0.000 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 79 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7421 (tttt) cc_final: 0.6796 (ttmt) REVERT: A 342 GLU cc_start: 0.7001 (mp0) cc_final: 0.6633 (mp0) REVERT: A 375 LYS cc_start: 0.7949 (tttt) cc_final: 0.7640 (tttm) REVERT: C 311 LYS cc_start: 0.8614 (mttt) cc_final: 0.8211 (ttpt) REVERT: C 340 LYS cc_start: 0.8076 (tttt) cc_final: 0.7467 (ttmt) REVERT: C 347 LYS cc_start: 0.8498 (mppt) cc_final: 0.8246 (mppt) REVERT: E 311 LYS cc_start: 0.7982 (mttt) cc_final: 0.7315 (tppt) REVERT: E 349 ARG cc_start: 0.6340 (mtm180) cc_final: 0.6109 (mmp-170) REVERT: B 315 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8320 (mt) REVERT: B 317 LYS cc_start: 0.7250 (mttt) cc_final: 0.6979 (mtmt) REVERT: B 321 LYS cc_start: 0.7193 (mttt) cc_final: 0.6627 (mtpt) REVERT: B 340 LYS cc_start: 0.7111 (tttt) cc_final: 0.6680 (mtpt) REVERT: B 349 ARG cc_start: 0.7356 (mtt180) cc_final: 0.7063 (mtp180) REVERT: B 351 GLN cc_start: 0.7539 (tt0) cc_final: 0.7169 (mt0) REVERT: B 358 ASP cc_start: 0.7445 (m-30) cc_final: 0.7022 (t0) REVERT: B 375 LYS cc_start: 0.8197 (tttt) cc_final: 0.7771 (ttmt) REVERT: D 311 LYS cc_start: 0.8127 (mttt) cc_final: 0.7744 (pttp) REVERT: D 327 ASN cc_start: 0.7663 (m110) cc_final: 0.7254 (m110) REVERT: D 351 GLN cc_start: 0.8178 (tt0) cc_final: 0.7919 (mt0) REVERT: F 311 LYS cc_start: 0.7843 (mttt) cc_final: 0.7461 (mmtt) REVERT: F 340 LYS cc_start: 0.7514 (tttt) cc_final: 0.7169 (mtpt) REVERT: F 351 GLN cc_start: 0.7399 (tt0) cc_final: 0.7125 (mt0) REVERT: F 353 LYS cc_start: 0.7526 (tttp) cc_final: 0.7281 (tttp) REVERT: F 375 LYS cc_start: 0.8019 (tttt) cc_final: 0.7656 (ttmt) outliers start: 6 outliers final: 3 residues processed: 77 average time/residue: 0.8412 time to fit residues: 70.5400 Evaluate side-chains 77 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 315 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 5.9990 chunk 34 optimal weight: 0.3980 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- 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: 0.7619 moved from start: 0.5356 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= 0.321 Angle : 0.499 3.902 4680 Z= 0.257 Chirality : 0.050 0.122 528 Planarity : 0.004 0.047 594 Dihedral : 4.559 11.287 462 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.26 % Allowed : 6.57 % Favored : 92.17 % 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: -1.99 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.007 0.001 PHE B 346 TYR 0.013 0.003 TYR F 310 ARG 0.010 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: 5 poor density : 79 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7426 (tttt) cc_final: 0.6810 (ttmt) REVERT: A 342 GLU cc_start: 0.6938 (mp0) cc_final: 0.6640 (mp0) REVERT: A 349 ARG cc_start: 0.7324 (mtp85) cc_final: 0.7026 (mtp85) REVERT: A 375 LYS cc_start: 0.7926 (tttt) cc_final: 0.7601 (tttm) REVERT: C 311 LYS cc_start: 0.8628 (mttt) cc_final: 0.8199 (ttpt) REVERT: C 340 LYS cc_start: 0.8116 (tttt) cc_final: 0.7510 (ttmt) REVERT: C 347 LYS cc_start: 0.8492 (mppt) cc_final: 0.8233 (mppt) REVERT: C 349 ARG cc_start: 0.7648 (mtt90) cc_final: 0.7398 (mtt90) REVERT: E 311 LYS cc_start: 0.7925 (mttt) cc_final: 0.7317 (tppt) REVERT: E 349 ARG cc_start: 0.6245 (mtm180) cc_final: 0.5922 (mmm160) REVERT: B 317 LYS cc_start: 0.7254 (mttt) cc_final: 0.6984 (mtmt) REVERT: B 321 LYS cc_start: 0.7217 (mttt) cc_final: 0.6630 (mtpt) REVERT: B 340 LYS cc_start: 0.7147 (tttt) cc_final: 0.6675 (mtpt) REVERT: B 349 ARG cc_start: 0.7390 (mtt180) cc_final: 0.7084 (mtp180) REVERT: B 351 GLN cc_start: 0.7647 (tt0) cc_final: 0.7217 (mt0) REVERT: B 375 LYS cc_start: 0.8205 (tttt) cc_final: 0.7768 (ttmt) REVERT: D 311 LYS cc_start: 0.8161 (mttt) cc_final: 0.7793 (pttp) REVERT: D 321 LYS cc_start: 0.8151 (mttt) cc_final: 0.7414 (mtpt) REVERT: D 327 ASN cc_start: 0.7816 (m110) cc_final: 0.7424 (m110) REVERT: D 340 LYS cc_start: 0.8080 (tttt) cc_final: 0.7420 (mttt) REVERT: D 351 GLN cc_start: 0.8416 (tt0) cc_final: 0.8062 (mt0) REVERT: D 375 LYS cc_start: 0.8431 (tttt) cc_final: 0.8112 (ttmt) REVERT: F 311 LYS cc_start: 0.7885 (mttt) cc_final: 0.7483 (mmtt) REVERT: F 340 LYS cc_start: 0.7607 (tttt) cc_final: 0.7236 (mtpt) REVERT: F 351 GLN cc_start: 0.7383 (tt0) cc_final: 0.6976 (mt0) REVERT: F 375 LYS cc_start: 0.8053 (tttt) cc_final: 0.7655 (ttmt) outliers start: 5 outliers final: 3 residues processed: 84 average time/residue: 0.8801 time to fit residues: 80.0636 Evaluate side-chains 78 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 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 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: 3.9990 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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: 0.7626 moved from start: 0.5563 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= 0.289 Angle : 0.489 4.013 4680 Z= 0.250 Chirality : 0.050 0.124 528 Planarity : 0.004 0.046 594 Dihedral : 4.510 11.536 462 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.01 % Allowed : 7.32 % Favored : 91.67 % 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: -2.07 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 374 PHE 0.006 0.001 PHE B 378 TYR 0.010 0.002 TYR F 310 ARG 0.007 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 80 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8092 (mttm) cc_final: 0.7878 (mtpp) REVERT: A 340 LYS cc_start: 0.7435 (tttt) cc_final: 0.6817 (ttmt) REVERT: A 342 GLU cc_start: 0.6925 (mp0) cc_final: 0.6626 (mp0) REVERT: A 349 ARG cc_start: 0.7276 (mtp85) cc_final: 0.7069 (mtp85) REVERT: A 375 LYS cc_start: 0.7940 (tttt) cc_final: 0.7581 (tttp) REVERT: C 311 LYS cc_start: 0.8642 (mttt) cc_final: 0.8229 (ttpt) REVERT: C 340 LYS cc_start: 0.8071 (tttt) cc_final: 0.7498 (ttmt) REVERT: C 347 LYS cc_start: 0.8503 (mppt) cc_final: 0.8214 (mppt) REVERT: C 375 LYS cc_start: 0.8396 (tttt) cc_final: 0.8030 (tttp) REVERT: E 311 LYS cc_start: 0.7984 (mttt) cc_final: 0.7304 (tppt) REVERT: E 349 ARG cc_start: 0.6315 (mtm180) cc_final: 0.5938 (mmm160) REVERT: B 317 LYS cc_start: 0.7260 (mttt) cc_final: 0.7015 (mtmt) REVERT: B 321 LYS cc_start: 0.7202 (mttt) cc_final: 0.6618 (mtpt) REVERT: B 340 LYS cc_start: 0.7087 (tttt) cc_final: 0.6630 (mtpt) REVERT: B 349 ARG cc_start: 0.7375 (mtt180) cc_final: 0.7146 (mtp180) REVERT: B 351 GLN cc_start: 0.7754 (tt0) cc_final: 0.7314 (mt0) REVERT: B 358 ASP cc_start: 0.7348 (m-30) cc_final: 0.6835 (t0) REVERT: B 375 LYS cc_start: 0.8173 (tttt) cc_final: 0.7746 (ttmt) REVERT: D 311 LYS cc_start: 0.8161 (mttt) cc_final: 0.7799 (pttp) REVERT: D 321 LYS cc_start: 0.8147 (mttt) cc_final: 0.7421 (mtpt) REVERT: D 327 ASN cc_start: 0.7778 (m110) cc_final: 0.7392 (m110) REVERT: D 340 LYS cc_start: 0.8105 (tttt) cc_final: 0.7430 (mttt) REVERT: D 351 GLN cc_start: 0.8427 (tt0) cc_final: 0.8080 (mt0) REVERT: D 375 LYS cc_start: 0.8443 (tttt) cc_final: 0.8126 (ttmt) REVERT: F 311 LYS cc_start: 0.7891 (mttt) cc_final: 0.7481 (mmtt) REVERT: F 340 LYS cc_start: 0.7700 (tttt) cc_final: 0.7313 (mtpt) REVERT: F 351 GLN cc_start: 0.7457 (tt0) cc_final: 0.7042 (mt0) REVERT: F 375 LYS cc_start: 0.8042 (tttt) cc_final: 0.7646 (ttmt) outliers start: 4 outliers final: 3 residues processed: 79 average time/residue: 0.8666 time to fit residues: 74.2359 Evaluate side-chains 77 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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: 0.7616 moved from start: 0.5611 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= 0.208 Angle : 0.463 4.324 4680 Z= 0.234 Chirality : 0.051 0.124 528 Planarity : 0.004 0.051 594 Dihedral : 4.341 10.978 462 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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: -2.01 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.006 0.001 PHE B 378 TYR 0.008 0.002 TYR F 310 ARG 0.010 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 80 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7450 (tttt) cc_final: 0.6856 (ttmt) REVERT: A 342 GLU cc_start: 0.6907 (mp0) cc_final: 0.6607 (mp0) REVERT: A 375 LYS cc_start: 0.7958 (tttt) cc_final: 0.7404 (ttmm) REVERT: C 311 LYS cc_start: 0.8538 (mttt) cc_final: 0.8142 (ttpt) REVERT: C 340 LYS cc_start: 0.8072 (tttt) cc_final: 0.7493 (ttmt) REVERT: C 347 LYS cc_start: 0.8513 (mppt) cc_final: 0.8256 (mppt) REVERT: C 349 ARG cc_start: 0.7605 (mtt90) cc_final: 0.7395 (mtt90) REVERT: E 311 LYS cc_start: 0.7938 (mttt) cc_final: 0.7240 (tppt) REVERT: E 349 ARG cc_start: 0.6339 (mtm180) cc_final: 0.5938 (mmm160) REVERT: B 317 LYS cc_start: 0.7242 (mttt) cc_final: 0.7007 (mtmt) REVERT: B 321 LYS cc_start: 0.7218 (mttt) cc_final: 0.6606 (mtpt) REVERT: B 340 LYS cc_start: 0.7079 (tttt) cc_final: 0.6629 (mtpt) REVERT: B 349 ARG cc_start: 0.7381 (mtt180) cc_final: 0.7155 (mtp180) REVERT: B 351 GLN cc_start: 0.7614 (tt0) cc_final: 0.7197 (mt0) REVERT: B 358 ASP cc_start: 0.7380 (m-30) cc_final: 0.6850 (t0) REVERT: B 375 LYS cc_start: 0.8123 (tttt) cc_final: 0.7738 (ttmt) REVERT: D 311 LYS cc_start: 0.8168 (mttt) cc_final: 0.7803 (pttp) REVERT: D 321 LYS cc_start: 0.8119 (mttt) cc_final: 0.7371 (mtpt) REVERT: D 327 ASN cc_start: 0.7768 (m110) cc_final: 0.7347 (m110) REVERT: D 340 LYS cc_start: 0.8110 (tttt) cc_final: 0.7459 (mttt) REVERT: D 351 GLN cc_start: 0.8311 (tt0) cc_final: 0.8016 (mt0) REVERT: D 375 LYS cc_start: 0.8439 (tttt) cc_final: 0.8121 (ttmt) REVERT: F 311 LYS cc_start: 0.7866 (mttt) cc_final: 0.7470 (mmtt) REVERT: F 340 LYS cc_start: 0.7691 (tttt) cc_final: 0.7313 (mtpt) REVERT: F 351 GLN cc_start: 0.7402 (tt0) cc_final: 0.7132 (mt0) REVERT: F 375 LYS cc_start: 0.8027 (tttt) cc_final: 0.7645 (ttmt) outliers start: 4 outliers final: 4 residues processed: 79 average time/residue: 0.8568 time to fit residues: 73.4906 Evaluate side-chains 78 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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: 0.7604 moved from start: 0.5690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3498 Z= 0.171 Angle : 0.453 3.899 4680 Z= 0.226 Chirality : 0.051 0.123 528 Planarity : 0.003 0.057 594 Dihedral : 4.173 10.450 462 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.76 % Allowed : 8.08 % 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: -1.90 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 362 PHE 0.007 0.001 PHE B 378 TYR 0.006 0.001 TYR D 310 ARG 0.009 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 73 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7477 (tttt) cc_final: 0.6883 (ttmt) REVERT: A 342 GLU cc_start: 0.6844 (mp0) cc_final: 0.6562 (mp0) REVERT: A 375 LYS cc_start: 0.7973 (tttt) cc_final: 0.7424 (ttmm) REVERT: C 311 LYS cc_start: 0.8513 (mttt) cc_final: 0.8116 (ttpt) REVERT: C 340 LYS cc_start: 0.8108 (tttt) cc_final: 0.7501 (ttmt) REVERT: C 347 LYS cc_start: 0.8516 (mppt) cc_final: 0.8263 (mppt) REVERT: E 311 LYS cc_start: 0.7971 (mttt) cc_final: 0.7280 (tppt) REVERT: E 349 ARG cc_start: 0.6440 (mtm180) cc_final: 0.6109 (mmp-170) REVERT: B 349 ARG cc_start: 0.7381 (mtt180) cc_final: 0.7153 (mtp180) REVERT: B 351 GLN cc_start: 0.7543 (tt0) cc_final: 0.7187 (mt0) REVERT: B 358 ASP cc_start: 0.7408 (m-30) cc_final: 0.6840 (t0) REVERT: B 375 LYS cc_start: 0.8118 (tttt) cc_final: 0.7730 (ttmt) REVERT: D 311 LYS cc_start: 0.8145 (mttt) cc_final: 0.7746 (pttp) REVERT: D 321 LYS cc_start: 0.8103 (mttt) cc_final: 0.7354 (mtpt) REVERT: D 327 ASN cc_start: 0.7658 (m110) cc_final: 0.7201 (m110) REVERT: D 340 LYS cc_start: 0.8074 (tttt) cc_final: 0.7458 (mttt) REVERT: D 351 GLN cc_start: 0.8254 (tt0) cc_final: 0.8001 (mt0) REVERT: D 375 LYS cc_start: 0.8432 (tttt) cc_final: 0.8110 (ttmt) REVERT: F 311 LYS cc_start: 0.7863 (mttt) cc_final: 0.7481 (mmtt) REVERT: F 340 LYS cc_start: 0.7671 (tttt) cc_final: 0.7290 (mtpt) REVERT: F 351 GLN cc_start: 0.7360 (tt0) cc_final: 0.6923 (mt0) REVERT: F 375 LYS cc_start: 0.8027 (tttt) cc_final: 0.7647 (ttmt) outliers start: 3 outliers final: 2 residues processed: 72 average time/residue: 0.8319 time to fit residues: 65.1720 Evaluate side-chains 71 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 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 29 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.128452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.112491 restraints weight = 13628.901| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.90 r_work: 0.3734 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3498 Z= 0.182 Angle : 0.456 3.925 4680 Z= 0.228 Chirality : 0.051 0.122 528 Planarity : 0.003 0.052 594 Dihedral : 4.149 9.997 462 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.01 % Allowed : 7.32 % Favored : 91.67 % 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: -1.87 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 362 PHE 0.006 0.001 PHE B 378 TYR 0.007 0.002 TYR B 310 ARG 0.010 0.001 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3212.99 seconds wall clock time: 56 minutes 35.98 seconds (3395.98 seconds total)