Starting phenix.real_space_refine on Thu Dec 7 18:41:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2j_18109/12_2023/8q2j_18109.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2j_18109/12_2023/8q2j_18109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2j_18109/12_2023/8q2j_18109.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2j_18109/12_2023/8q2j_18109.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2j_18109/12_2023/8q2j_18109.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2j_18109/12_2023/8q2j_18109.pdb" } resolution = 2.23 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: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2193 2.51 5 N 648 2.21 5 O 660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 348": "OD1" <-> "OD2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 348": "OD1" <-> "OD2" Residue "D ASP 358": "OD1" <-> "OD2" Residue "D GLU 380": "OE1" <-> "OE2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 348": "OD1" <-> "OD2" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3507 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 582 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "C" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 582 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "D" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "E" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 582 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "F" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Time building chain proxies: 2.36, per 1000 atoms: 0.67 Number of scatterers: 3507 At special positions: 0 Unit cell: (117.047, 119.228, 37.804, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 660 8.00 N 648 7.00 C 2193 6.00 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: 1.15 Conformation dependent library (CDL) restraints added in 637.6 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 798 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 51.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.518A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.781A 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 322 removed outlier: 6.543A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 325 through 330 removed outlier: 6.872A pdb=" N GLY C 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN A 327 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLY A 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN E 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 342 removed outlier: 6.537A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.504A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.261A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.577A 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: 6.419A pdb=" N LEU A 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ILE E 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASN A 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N HIS E 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 378 removed outlier: 6.423A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N PHE C 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.521A 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: 6.580A pdb=" N SER B 305 " --> pdb=" O VAL D 306 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE D 308 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.643A 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: 6.935A 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: 6.525A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 5.910A 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: 6.720A 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: 6.684A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LYS F 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL B 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLU F 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.570A 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: 6.358A 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: 6.190A pdb=" N VAL B 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N LYS F 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N SER B 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 357 through 362 removed outlier: 6.733A pdb=" N ASP B 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR D 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE B 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU B 357 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE F 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN B 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N HIS F 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 368 through 378 removed outlier: 6.486A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE D 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR B 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) 76 hydrogen bonds defined for protein. 228 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: 0.81 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1074 1.33 - 1.45: 374 1.45 - 1.57: 2107 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3561 Sorted by residual: bond pdb=" CA LYS F 331 " pdb=" C LYS F 331 " ideal model delta sigma weight residual 1.532 1.555 -0.023 6.50e-03 2.37e+04 1.26e+01 bond pdb=" CZ ARG F 349 " pdb=" NH2 ARG F 349 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.64e+00 bond pdb=" CA LYS F 331 " pdb=" CB LYS F 331 " ideal model delta sigma weight residual 1.522 1.548 -0.026 8.90e-03 1.26e+04 8.32e+00 bond pdb=" CA LYS D 331 " pdb=" CB LYS D 331 " ideal model delta sigma weight residual 1.522 1.547 -0.025 8.90e-03 1.26e+04 7.63e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.17e+00 ... (remaining 3556 not shown) Histogram of bond angle deviations from ideal: 101.88 - 107.35: 183 107.35 - 112.82: 1758 112.82 - 118.29: 920 118.29 - 123.75: 1526 123.75 - 129.22: 374 Bond angle restraints: 4761 Sorted by residual: angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.69 117.51 -6.82 1.33e+00 5.65e-01 2.63e+01 angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 117.65 -5.05 1.00e+00 1.00e+00 2.55e+01 angle pdb=" OE1 GLN B 336 " pdb=" CD GLN B 336 " pdb=" NE2 GLN B 336 " ideal model delta sigma weight residual 122.60 117.74 4.86 1.00e+00 1.00e+00 2.37e+01 angle pdb=" C ASP F 348 " pdb=" N ARG F 349 " pdb=" CA ARG F 349 " ideal model delta sigma weight residual 121.05 127.81 -6.76 1.43e+00 4.89e-01 2.24e+01 angle pdb=" CB HIS B 374 " pdb=" CG HIS B 374 " pdb=" CD2 HIS B 374 " ideal model delta sigma weight residual 131.20 125.06 6.14 1.30e+00 5.92e-01 2.23e+01 ... (remaining 4756 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.74: 2053 17.74 - 35.48: 92 35.48 - 53.22: 13 53.22 - 70.96: 3 70.96 - 88.69: 2 Dihedral angle restraints: 2163 sinusoidal: 903 harmonic: 1260 Sorted by residual: dihedral pdb=" CA GLY A 355 " pdb=" C GLY A 355 " pdb=" N SER A 356 " pdb=" CA SER A 356 " ideal model delta harmonic sigma weight residual 180.00 151.73 28.27 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA LEU E 357 " pdb=" C LEU E 357 " pdb=" N ASP E 358 " pdb=" CA ASP E 358 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA GLY B 355 " pdb=" C GLY B 355 " pdb=" N SER B 356 " pdb=" CA SER B 356 " ideal model delta harmonic sigma weight residual 180.00 154.81 25.19 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 2160 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 301 0.062 - 0.124: 175 0.124 - 0.186: 42 0.186 - 0.248: 9 0.248 - 0.311: 4 Chirality restraints: 531 Sorted by residual: chirality pdb=" CA GLU A 372 " pdb=" N GLU A 372 " pdb=" C GLU A 372 " pdb=" CB GLU A 372 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA GLU E 372 " pdb=" N GLU E 372 " pdb=" C GLU E 372 " pdb=" CB GLU E 372 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA THR B 319 " pdb=" N THR B 319 " pdb=" C THR B 319 " pdb=" CB THR B 319 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 528 not shown) Planarity restraints: 609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.091 2.00e-02 2.50e+03 5.23e-02 5.48e+01 pdb=" CG TYR F 310 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " -0.029 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.083 2.00e-02 2.50e+03 4.63e-02 4.29e+01 pdb=" CG TYR E 310 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.072 2.00e-02 2.50e+03 4.13e-02 3.41e+01 pdb=" CG TYR A 310 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " 0.070 2.00e-02 2.50e+03 ... (remaining 606 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 1505 2.97 - 3.45: 2687 3.45 - 3.94: 5705 3.94 - 4.42: 5591 4.42 - 4.90: 10696 Nonbonded interactions: 26184 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.490 2.440 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.499 2.440 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.519 2.440 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.535 2.440 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.535 2.440 ... (remaining 26179 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 304 through 379) selection = (chain 'B' and resid 304 through 379) selection = (chain 'C' and resid 304 through 379) selection = (chain 'D' and resid 304 through 379) selection = (chain 'E' and resid 304 through 379) selection = (chain 'F' and resid 304 through 379) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 11.420 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.170 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.010 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:14.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 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 0.038 3561 Z= 0.737 Angle : 1.720 6.824 4761 Z= 1.160 Chirality : 0.079 0.311 531 Planarity : 0.010 0.071 609 Dihedral : 11.078 88.693 1365 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 0.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % 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: -1.62 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.004 HIS A 330 PHE 0.035 0.012 PHE A 346 TYR 0.091 0.026 TYR F 310 ARG 0.008 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 0.419 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 1.2633 time to fit residues: 263.8521 Evaluate side-chains 151 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 0.455 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6471 ------------------------------------------------------------------------------- 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: 4.9990 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 351 GLN D 307 GLN D 327 ASN F 336 GLN F 351 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3561 Z= 0.171 Angle : 0.581 5.574 4761 Z= 0.293 Chirality : 0.049 0.136 531 Planarity : 0.003 0.022 609 Dihedral : 5.201 18.134 474 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.75 % Allowed : 17.54 % Favored : 80.70 % 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: -1.47 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 PHE 0.013 0.002 PHE B 346 TYR 0.010 0.002 TYR A 310 ARG 0.003 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 156 time to evaluate : 0.402 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 158 average time/residue: 1.1328 time to fit residues: 183.9074 Evaluate side-chains 142 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.7553 time to fit residues: 2.4441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN C 307 GLN D 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 3561 Z= 0.399 Angle : 0.658 4.858 4761 Z= 0.334 Chirality : 0.051 0.131 531 Planarity : 0.004 0.028 609 Dihedral : 5.185 17.299 474 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 3.26 % Allowed : 18.80 % Favored : 77.94 % 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: -1.72 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 329 PHE 0.016 0.003 PHE B 346 TYR 0.015 0.003 TYR E 310 ARG 0.003 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 0.445 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 130 average time/residue: 1.2476 time to fit residues: 166.3296 Evaluate side-chains 126 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 123 time to evaluate : 0.340 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.4532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN C 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3561 Z= 0.209 Angle : 0.555 6.372 4761 Z= 0.277 Chirality : 0.049 0.122 531 Planarity : 0.003 0.024 609 Dihedral : 4.798 17.212 474 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.01 % Allowed : 19.05 % Favored : 78.95 % 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: -1.80 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 PHE 0.013 0.002 PHE C 378 TYR 0.010 0.002 TYR E 310 ARG 0.002 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 0.444 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 129 average time/residue: 1.1901 time to fit residues: 157.6042 Evaluate side-chains 125 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 0.399 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1590 time to fit residues: 0.7202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN C 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3561 Z= 0.246 Angle : 0.555 4.533 4761 Z= 0.282 Chirality : 0.049 0.122 531 Planarity : 0.003 0.026 609 Dihedral : 4.795 17.271 474 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.51 % Allowed : 17.54 % Favored : 79.95 % 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: -1.84 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 329 PHE 0.012 0.002 PHE B 346 TYR 0.012 0.003 TYR F 310 ARG 0.003 0.001 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 0.408 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 125 average time/residue: 1.2662 time to fit residues: 162.3189 Evaluate side-chains 127 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 123 time to evaluate : 0.416 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 1 average time/residue: 0.1851 time to fit residues: 0.8441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 0.0470 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 overall best weight: 3.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN C 307 GLN C 330 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3561 Z= 0.261 Angle : 0.572 7.791 4761 Z= 0.288 Chirality : 0.049 0.123 531 Planarity : 0.003 0.026 609 Dihedral : 4.823 17.133 474 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.51 % Allowed : 18.55 % Favored : 78.95 % 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: -1.89 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 329 PHE 0.011 0.002 PHE B 346 TYR 0.012 0.003 TYR E 310 ARG 0.002 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 0.459 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 125 average time/residue: 1.3132 time to fit residues: 168.1871 Evaluate side-chains 122 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.6456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN C 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3561 Z= 0.256 Angle : 0.553 4.490 4761 Z= 0.282 Chirality : 0.049 0.124 531 Planarity : 0.003 0.024 609 Dihedral : 4.769 17.201 474 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 2.01 % Allowed : 19.30 % Favored : 78.70 % 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 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 329 PHE 0.011 0.002 PHE B 346 TYR 0.012 0.003 TYR A 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 0.469 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 124 average time/residue: 1.2333 time to fit residues: 156.8786 Evaluate side-chains 114 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 0.438 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.5834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN C 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3561 Z= 0.288 Angle : 0.575 4.522 4761 Z= 0.294 Chirality : 0.049 0.124 531 Planarity : 0.003 0.026 609 Dihedral : 4.856 17.246 474 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.75 % Allowed : 19.05 % Favored : 79.20 % 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: -1.95 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 329 PHE 0.014 0.002 PHE B 346 TYR 0.012 0.003 TYR E 310 ARG 0.004 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 113 time to evaluate : 0.398 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 116 average time/residue: 1.1697 time to fit residues: 139.3460 Evaluate side-chains 115 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 0.406 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.5470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0020 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 overall best weight: 2.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN C 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3561 Z= 0.225 Angle : 0.555 8.257 4761 Z= 0.278 Chirality : 0.049 0.123 531 Planarity : 0.003 0.024 609 Dihedral : 4.728 17.242 474 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.00 % Allowed : 21.05 % Favored : 77.94 % 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: -1.93 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 PHE 0.010 0.002 PHE B 346 TYR 0.010 0.002 TYR F 310 ARG 0.003 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 0.409 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 117 average time/residue: 1.1986 time to fit residues: 144.3172 Evaluate side-chains 116 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 113 time to evaluate : 0.629 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.8250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.0980 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN C 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3561 Z= 0.135 Angle : 0.490 4.224 4761 Z= 0.247 Chirality : 0.048 0.121 531 Planarity : 0.002 0.023 609 Dihedral : 4.375 16.744 474 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.00 % Allowed : 20.55 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 329 PHE 0.008 0.001 PHE B 346 TYR 0.009 0.002 TYR F 310 ARG 0.002 0.000 ARG A 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 0.461 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 122 average time/residue: 1.1363 time to fit residues: 142.7077 Evaluate side-chains 118 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 0.411 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.5526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN C 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.122812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.108207 restraints weight = 3812.161| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.42 r_work: 0.3484 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3561 Z= 0.251 Angle : 0.560 5.508 4761 Z= 0.284 Chirality : 0.049 0.123 531 Planarity : 0.003 0.023 609 Dihedral : 4.678 16.592 474 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.25 % Allowed : 21.55 % Favored : 77.19 % 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: -1.89 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 329 PHE 0.010 0.002 PHE B 346 TYR 0.011 0.003 TYR A 310 ARG 0.004 0.001 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2875.72 seconds wall clock time: 51 minutes 17.22 seconds (3077.22 seconds total)