Starting phenix.real_space_refine on Sat May 10 22:47:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q27_18070/05_2025/8q27_18070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q27_18070/05_2025/8q27_18070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q27_18070/05_2025/8q27_18070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q27_18070/05_2025/8q27_18070.map" model { file = "/net/cci-nas-00/data/ceres_data/8q27_18070/05_2025/8q27_18070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q27_18070/05_2025/8q27_18070.cif" } resolution = 2.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2154 2.51 5 N 630 2.21 5 O 645 1.98 5 H 3567 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7002 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1162 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1162 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1162 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 4.39, per 1000 atoms: 0.63 Number of scatterers: 7002 At special positions: 0 Unit cell: (135.222, 135.949, 59.614, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 645 8.00 N 630 7.00 C 2154 6.00 H 3567 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.70 Conformation dependent library (CDL) restraints added in 630.9 milliseconds 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 57.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.546A pdb=" N VAL A 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL C 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.877A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 325 removed outlier: 6.561A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLY C 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N CYS A 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU C 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER A 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.666A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 346 removed outlier: 6.774A pdb=" N LEU C 344 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASP A 345 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N PHE C 346 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 9.814A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 9.397A pdb=" N LEU E 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LYS A 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N PHE E 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 350 through 362 removed outlier: 8.982A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 10.260A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N SER C 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLY A 355 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ASP C 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 357 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE C 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N HIS C 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLN E 351 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N SER A 352 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS E 353 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE A 354 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLY E 355 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER A 356 " --> pdb=" O GLY E 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 368 through 378 removed outlier: 6.487A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU E 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LYS A 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE E 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR A 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.544A pdb=" N GLN B 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N TYR F 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.832A pdb=" N VAL B 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.295A pdb=" N LYS B 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N SER F 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR B 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N CYS F 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LYS B 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N SER F 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY B 323 " --> pdb=" O SER F 324 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.516A pdb=" N ILE B 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 336 through 340 removed outlier: 6.544A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 343 through 347 removed outlier: 6.419A pdb=" N LEU B 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LYS D 347 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE B 346 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.347A pdb=" N GLN B 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE F 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS B 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 357 through 362 Processing sheet with id=AB7, first strand: chain 'D' and resid 368 through 377 88 hydrogen bonds defined for protein. 264 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3561 1.12 - 1.29: 574 1.29 - 1.47: 1172 1.47 - 1.64: 1743 1.64 - 1.82: 6 Bond restraints: 7056 Sorted by residual: bond pdb=" N GLY C 367 " pdb=" H GLY C 367 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" NE2 GLN A 351 " pdb="HE21 GLN A 351 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N VAL E 318 " pdb=" H VAL E 318 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" NE2 GLN F 336 " pdb="HE21 GLN F 336 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N GLY A 367 " pdb=" H GLY A 367 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 7051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 11044 2.61 - 5.23: 1398 5.23 - 7.84: 409 7.84 - 10.45: 1 10.45 - 13.07: 6 Bond angle restraints: 12858 Sorted by residual: angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 118.92 -6.32 1.00e+00 1.00e+00 4.00e+01 angle pdb=" CA ASP F 358 " pdb=" CB ASP F 358 " pdb=" CG ASP F 358 " ideal model delta sigma weight residual 112.60 118.64 -6.04 1.00e+00 1.00e+00 3.65e+01 angle pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " ideal model delta sigma weight residual 112.60 118.53 -5.93 1.00e+00 1.00e+00 3.52e+01 angle pdb=" OE1 GLN A 336 " pdb=" CD GLN A 336 " pdb=" NE2 GLN A 336 " ideal model delta sigma weight residual 122.60 116.92 5.68 1.00e+00 1.00e+00 3.22e+01 angle pdb=" OE1 GLN C 336 " pdb=" CD GLN C 336 " pdb=" NE2 GLN C 336 " ideal model delta sigma weight residual 122.60 117.21 5.39 1.00e+00 1.00e+00 2.91e+01 ... (remaining 12853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 2931 17.68 - 35.36: 138 35.36 - 53.04: 78 53.04 - 70.73: 101 70.73 - 88.41: 4 Dihedral angle restraints: 3252 sinusoidal: 1857 harmonic: 1395 Sorted by residual: dihedral pdb=" CA LYS F 343 " pdb=" C LYS F 343 " pdb=" N LEU F 344 " pdb=" CA LEU F 344 " ideal model delta harmonic sigma weight residual 180.00 155.20 24.80 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA ASP E 358 " pdb=" C ASP E 358 " pdb=" N ASN E 359 " pdb=" CA ASN E 359 " ideal model delta harmonic sigma weight residual 180.00 155.71 24.29 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA SER B 341 " pdb=" C SER B 341 " pdb=" N GLU B 342 " pdb=" CA GLU B 342 " ideal model delta harmonic sigma weight residual 180.00 156.71 23.29 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 3249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 276 0.059 - 0.117: 185 0.117 - 0.176: 49 0.176 - 0.234: 13 0.234 - 0.293: 2 Chirality restraints: 525 Sorted by residual: chirality pdb=" CA THR A 319 " pdb=" N THR A 319 " pdb=" C THR A 319 " pdb=" CB THR A 319 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA THR E 319 " pdb=" N THR E 319 " pdb=" C THR E 319 " pdb=" CB THR E 319 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA GLU E 342 " pdb=" N GLU E 342 " pdb=" C GLU E 342 " pdb=" CB GLU E 342 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 522 not shown) Planarity restraints: 1023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.121 2.00e-02 2.50e+03 5.40e-02 8.75e+01 pdb=" CG TYR C 310 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " -0.022 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.114 2.00e-02 2.50e+03 pdb=" HD1 TYR C 310 " -0.006 2.00e-02 2.50e+03 pdb=" HD2 TYR C 310 " -0.036 2.00e-02 2.50e+03 pdb=" HE1 TYR C 310 " -0.026 2.00e-02 2.50e+03 pdb=" HE2 TYR C 310 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 327 " 0.034 2.00e-02 2.50e+03 7.06e-02 7.48e+01 pdb=" CG ASN C 327 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN C 327 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN C 327 " -0.140 2.00e-02 2.50e+03 pdb="HD21 ASN C 327 " 0.046 2.00e-02 2.50e+03 pdb="HD22 ASN C 327 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 368 " 0.073 2.00e-02 2.50e+03 6.82e-02 6.98e+01 pdb=" CG ASN A 368 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 368 " -0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN A 368 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN A 368 " -0.094 2.00e-02 2.50e+03 pdb="HD22 ASN A 368 " 0.097 2.00e-02 2.50e+03 ... (remaining 1020 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 567 2.17 - 2.77: 11740 2.77 - 3.38: 18325 3.38 - 3.99: 24870 3.99 - 4.60: 34541 Nonbonded interactions: 90043 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.558 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.566 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.570 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.577 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.578 2.450 ... (remaining 90038 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 305 through 378) selection = (chain 'B' and resid 305 through 378) selection = (chain 'C' and resid 305 through 378) selection = (chain 'D' and resid 305 through 378) selection = (chain 'E' and resid 305 through 378) selection = (chain 'F' and resid 305 through 378) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.720 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: 0.130 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 19.240 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.036 3489 Z= 0.679 Angle : 1.744 6.322 4668 Z= 1.165 Chirality : 0.079 0.293 525 Planarity : 0.009 0.063 594 Dihedral : 11.916 88.408 1332 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.27 % Allowed : 4.33 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.34), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS C 362 PHE 0.034 0.011 PHE E 346 TYR 0.111 0.022 TYR C 310 ARG 0.005 0.001 ARG F 349 Details of bonding type rmsd hydrogen bonds : bond 0.07334 ( 88) hydrogen bonds : angle 7.58708 ( 264) covalent geometry : bond 0.01104 ( 3489) covalent geometry : angle 1.74423 ( 4668) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 166 time to evaluate : 0.475 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: A 311 LYS cc_start: 0.7207 (ttmt) cc_final: 0.6941 (mttt) REVERT: A 314 ASP cc_start: 0.7168 (t0) cc_final: 0.6705 (t0) REVERT: A 324 SER cc_start: 0.8126 (m) cc_final: 0.7733 (t) REVERT: A 331 LYS cc_start: 0.7114 (mtpt) cc_final: 0.6740 (mttt) REVERT: A 336 GLN cc_start: 0.7075 (tt0) cc_final: 0.6662 (tt0) REVERT: A 338 GLU cc_start: 0.6818 (mt-10) cc_final: 0.6298 (mt-10) REVERT: A 340 LYS cc_start: 0.6516 (mttt) cc_final: 0.6098 (mtpm) REVERT: A 353 LYS cc_start: 0.5855 (mttt) cc_final: 0.5619 (tttm) REVERT: A 358 ASP cc_start: 0.6256 (m-30) cc_final: 0.6042 (m-30) REVERT: A 369 LYS cc_start: 0.6831 (ttmt) cc_final: 0.6531 (ttpt) REVERT: A 372 GLU cc_start: 0.7144 (tt0) cc_final: 0.6468 (mm-30) REVERT: A 375 LYS cc_start: 0.7108 (ttmt) cc_final: 0.6881 (ttmp) REVERT: B 315 LEU cc_start: 0.7881 (mt) cc_final: 0.7615 (mt) REVERT: B 340 LYS cc_start: 0.6897 (tttt) cc_final: 0.6639 (tttp) REVERT: B 342 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6367 (mm-30) REVERT: B 369 LYS cc_start: 0.6998 (tttt) cc_final: 0.6777 (tppt) REVERT: C 311 LYS cc_start: 0.7409 (ttmt) cc_final: 0.7127 (mttt) REVERT: C 317 LYS cc_start: 0.6710 (mttt) cc_final: 0.6487 (mtpt) REVERT: C 321 LYS cc_start: 0.6685 (mttt) cc_final: 0.6437 (mtpt) REVERT: C 331 LYS cc_start: 0.7068 (mtpt) cc_final: 0.6837 (mttt) REVERT: C 338 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6650 (mt-10) REVERT: C 345 ASP cc_start: 0.6667 (t0) cc_final: 0.6334 (t70) REVERT: C 353 LYS cc_start: 0.5917 (mttt) cc_final: 0.5652 (tttp) REVERT: C 356 SER cc_start: 0.7566 (m) cc_final: 0.7344 (t) REVERT: C 369 LYS cc_start: 0.7122 (ttmt) cc_final: 0.6598 (ttpt) REVERT: C 372 GLU cc_start: 0.7560 (tt0) cc_final: 0.6954 (mm-30) REVERT: C 375 LYS cc_start: 0.7212 (ttmt) cc_final: 0.7005 (ttmp) REVERT: D 315 LEU cc_start: 0.7874 (mp) cc_final: 0.7671 (mt) REVERT: D 340 LYS cc_start: 0.6688 (tttt) cc_final: 0.5987 (tptt) REVERT: D 343 LYS cc_start: 0.7005 (ttmt) cc_final: 0.6749 (ttmt) REVERT: D 369 LYS cc_start: 0.7132 (tttt) cc_final: 0.6907 (tttt) REVERT: D 375 LYS cc_start: 0.6900 (tttt) cc_final: 0.6570 (ttpt) REVERT: E 311 LYS cc_start: 0.7503 (ttmt) cc_final: 0.7181 (mttt) REVERT: E 314 ASP cc_start: 0.7355 (t0) cc_final: 0.6757 (t0) REVERT: E 320 SER cc_start: 0.8122 (m) cc_final: 0.7546 (p) REVERT: E 331 LYS cc_start: 0.7193 (mtpt) cc_final: 0.6902 (mttm) REVERT: E 338 GLU cc_start: 0.7336 (mt-10) cc_final: 0.6665 (tt0) REVERT: E 340 LYS cc_start: 0.7293 (mttt) cc_final: 0.6804 (mttp) REVERT: E 353 LYS cc_start: 0.6701 (mttt) cc_final: 0.6352 (tttm) REVERT: E 358 ASP cc_start: 0.6858 (m-30) cc_final: 0.6645 (m-30) REVERT: E 369 LYS cc_start: 0.7510 (ttmt) cc_final: 0.7237 (ttpt) REVERT: E 372 GLU cc_start: 0.7036 (tt0) cc_final: 0.6740 (mm-30) REVERT: F 338 GLU cc_start: 0.7215 (tt0) cc_final: 0.6989 (tt0) outliers start: 5 outliers final: 0 residues processed: 171 average time/residue: 2.8674 time to fit residues: 501.8798 Evaluate side-chains 126 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 307 GLN C 351 GLN E 336 GLN F 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.149216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.132564 restraints weight = 10315.194| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 1.10 r_work: 0.3872 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3806 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3489 Z= 0.201 Angle : 0.646 4.535 4668 Z= 0.335 Chirality : 0.051 0.135 525 Planarity : 0.005 0.031 594 Dihedral : 6.027 19.606 462 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.02 % Allowed : 7.89 % Favored : 91.09 % 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: -1.32 (0.35), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 374 PHE 0.010 0.002 PHE E 378 TYR 0.009 0.002 TYR A 310 ARG 0.002 0.000 ARG C 379 Details of bonding type rmsd hydrogen bonds : bond 0.03175 ( 88) hydrogen bonds : angle 5.47737 ( 264) covalent geometry : bond 0.00442 ( 3489) covalent geometry : angle 0.64641 ( 4668) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 343 LYS cc_start: 0.8339 (ttmt) cc_final: 0.8104 (ttpt) REVERT: E 314 ASP cc_start: 0.8525 (t0) cc_final: 0.8253 (t0) REVERT: F 338 GLU cc_start: 0.8241 (tt0) cc_final: 0.7975 (tt0) REVERT: F 343 LYS cc_start: 0.8345 (ttmt) cc_final: 0.8127 (ttmm) outliers start: 4 outliers final: 1 residues processed: 126 average time/residue: 3.2129 time to fit residues: 413.1260 Evaluate side-chains 96 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 35 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 351 GLN B 307 GLN C 336 GLN C 351 GLN D 307 GLN F 351 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.148783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.132581 restraints weight = 10531.621| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 1.05 r_work: 0.3868 rms_B_bonded: 1.10 restraints_weight: 0.5000 r_work: 0.3808 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3489 Z= 0.123 Angle : 0.543 4.887 4668 Z= 0.276 Chirality : 0.053 0.135 525 Planarity : 0.004 0.028 594 Dihedral : 5.565 17.505 462 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.25 % Allowed : 13.23 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.35), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.009 0.001 PHE E 378 TYR 0.010 0.002 TYR A 310 ARG 0.004 0.000 ARG C 379 Details of bonding type rmsd hydrogen bonds : bond 0.02445 ( 88) hydrogen bonds : angle 5.01682 ( 264) covalent geometry : bond 0.00257 ( 3489) covalent geometry : angle 0.54289 ( 4668) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 343 LYS cc_start: 0.8368 (ttmt) cc_final: 0.8167 (ttpt) REVERT: E 314 ASP cc_start: 0.8512 (t0) cc_final: 0.8266 (t0) REVERT: F 338 GLU cc_start: 0.8237 (tt0) cc_final: 0.8004 (tt0) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 2.8158 time to fit residues: 271.1345 Evaluate side-chains 84 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 16 optimal weight: 0.0970 chunk 37 optimal weight: 0.2980 overall best weight: 1.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 307 GLN C 351 GLN D 307 GLN F 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.148226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.132182 restraints weight = 10578.554| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 1.04 r_work: 0.3863 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.3804 rms_B_bonded: 1.90 restraints_weight: 0.2500 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3489 Z= 0.123 Angle : 0.514 4.990 4668 Z= 0.262 Chirality : 0.052 0.136 525 Planarity : 0.003 0.026 594 Dihedral : 5.302 16.386 462 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.27 % Allowed : 11.20 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.35), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.02 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.009 0.002 PHE E 378 TYR 0.009 0.002 TYR A 310 ARG 0.001 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.02260 ( 88) hydrogen bonds : angle 4.76433 ( 264) covalent geometry : bond 0.00268 ( 3489) covalent geometry : angle 0.51438 ( 4668) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 314 ASP cc_start: 0.8519 (t0) cc_final: 0.8260 (t0) REVERT: F 338 GLU cc_start: 0.8267 (tt0) cc_final: 0.8062 (tt0) outliers start: 5 outliers final: 1 residues processed: 90 average time/residue: 2.7001 time to fit residues: 249.1217 Evaluate side-chains 86 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 30 optimal weight: 0.0070 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 307 GLN D 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.149526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.133782 restraints weight = 10695.213| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 1.05 r_work: 0.3898 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.3839 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3489 Z= 0.089 Angle : 0.490 4.826 4668 Z= 0.245 Chirality : 0.053 0.133 525 Planarity : 0.003 0.022 594 Dihedral : 5.006 15.056 462 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.76 % Allowed : 11.96 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.35), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.98 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.008 0.001 PHE E 378 TYR 0.007 0.002 TYR A 310 ARG 0.001 0.000 ARG C 379 Details of bonding type rmsd hydrogen bonds : bond 0.01894 ( 88) hydrogen bonds : angle 4.49623 ( 264) covalent geometry : bond 0.00201 ( 3489) covalent geometry : angle 0.48996 ( 4668) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 91 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 LYS cc_start: 0.8279 (ttmt) cc_final: 0.8063 (ttmm) REVERT: C 319 THR cc_start: 0.8624 (p) cc_final: 0.8346 (t) REVERT: C 375 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.8029 (ttmt) outliers start: 3 outliers final: 1 residues processed: 93 average time/residue: 2.8483 time to fit residues: 271.7829 Evaluate side-chains 88 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 375 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 307 GLN D 307 GLN E 351 GLN F 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.145630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.129558 restraints weight = 10641.725| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 1.05 r_work: 0.3844 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 1.89 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3489 Z= 0.175 Angle : 0.542 4.800 4668 Z= 0.278 Chirality : 0.052 0.135 525 Planarity : 0.003 0.025 594 Dihedral : 5.217 15.439 462 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.51 % Allowed : 10.94 % Favored : 88.55 % 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: -1.43 (0.35), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.010 0.002 PHE C 346 TYR 0.011 0.003 TYR A 310 ARG 0.001 0.000 ARG C 379 Details of bonding type rmsd hydrogen bonds : bond 0.02452 ( 88) hydrogen bonds : angle 4.69239 ( 264) covalent geometry : bond 0.00372 ( 3489) covalent geometry : angle 0.54225 ( 4668) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 LYS cc_start: 0.8308 (ttmt) cc_final: 0.8077 (ttmm) REVERT: E 314 ASP cc_start: 0.8564 (t0) cc_final: 0.8277 (t0) outliers start: 2 outliers final: 1 residues processed: 85 average time/residue: 2.8013 time to fit residues: 243.9582 Evaluate side-chains 85 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 351 GLN D 307 GLN E 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.145133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.129173 restraints weight = 10599.561| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 1.04 r_work: 0.3840 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3489 Z= 0.178 Angle : 0.550 4.731 4668 Z= 0.282 Chirality : 0.052 0.129 525 Planarity : 0.004 0.027 594 Dihedral : 5.240 15.516 462 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.02 % Allowed : 11.20 % Favored : 87.79 % 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: -1.53 (0.34), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.009 0.002 PHE C 346 TYR 0.011 0.003 TYR C 310 ARG 0.001 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.02503 ( 88) hydrogen bonds : angle 4.73876 ( 264) covalent geometry : bond 0.00373 ( 3489) covalent geometry : angle 0.55004 ( 4668) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 LYS cc_start: 0.8304 (ttmt) cc_final: 0.8080 (ttmm) REVERT: E 314 ASP cc_start: 0.8551 (t0) cc_final: 0.8259 (t0) outliers start: 4 outliers final: 1 residues processed: 86 average time/residue: 2.7451 time to fit residues: 242.0461 Evaluate side-chains 85 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN D 307 GLN E 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.143898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.127839 restraints weight = 10702.546| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.05 r_work: 0.3822 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3489 Z= 0.228 Angle : 0.589 4.982 4668 Z= 0.303 Chirality : 0.052 0.132 525 Planarity : 0.004 0.030 594 Dihedral : 5.321 15.350 462 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.76 % Allowed : 13.23 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.34), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 362 PHE 0.011 0.002 PHE C 346 TYR 0.013 0.003 TYR C 310 ARG 0.001 0.000 ARG E 379 Details of bonding type rmsd hydrogen bonds : bond 0.02759 ( 88) hydrogen bonds : angle 4.86646 ( 264) covalent geometry : bond 0.00487 ( 3489) covalent geometry : angle 0.58936 ( 4668) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 LYS cc_start: 0.8339 (ttmt) cc_final: 0.8110 (ttmm) REVERT: E 314 ASP cc_start: 0.8583 (t0) cc_final: 0.8366 (t0) REVERT: F 343 LYS cc_start: 0.8369 (ttmt) cc_final: 0.8161 (ttmm) outliers start: 3 outliers final: 2 residues processed: 86 average time/residue: 2.7752 time to fit residues: 244.5694 Evaluate side-chains 84 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain C residue 348 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN D 307 GLN E 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.146230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.130328 restraints weight = 10727.918| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 1.05 r_work: 0.3855 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.3793 rms_B_bonded: 1.89 restraints_weight: 0.2500 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3489 Z= 0.129 Angle : 0.525 4.666 4668 Z= 0.265 Chirality : 0.052 0.127 525 Planarity : 0.003 0.027 594 Dihedral : 5.104 15.599 462 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.76 % Allowed : 13.49 % Favored : 85.75 % 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: -1.55 (0.35), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.006 0.001 PHE E 378 TYR 0.009 0.002 TYR A 310 ARG 0.003 0.000 ARG C 379 Details of bonding type rmsd hydrogen bonds : bond 0.02289 ( 88) hydrogen bonds : angle 4.63984 ( 264) covalent geometry : bond 0.00274 ( 3489) covalent geometry : angle 0.52463 ( 4668) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 LYS cc_start: 0.8313 (ttmt) cc_final: 0.8081 (ttmm) REVERT: E 314 ASP cc_start: 0.8576 (t0) cc_final: 0.8258 (t0) REVERT: F 343 LYS cc_start: 0.8337 (ttmt) cc_final: 0.8128 (ttmm) outliers start: 3 outliers final: 2 residues processed: 86 average time/residue: 2.7853 time to fit residues: 245.6698 Evaluate side-chains 84 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain C residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 GLN E 351 GLN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.146850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.130824 restraints weight = 10863.823| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 1.06 r_work: 0.3858 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.3798 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3489 Z= 0.129 Angle : 0.516 4.647 4668 Z= 0.261 Chirality : 0.052 0.126 525 Planarity : 0.003 0.024 594 Dihedral : 5.025 15.385 462 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.51 % Allowed : 13.74 % Favored : 85.75 % 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: -1.55 (0.35), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.006 0.001 PHE C 346 TYR 0.009 0.002 TYR A 310 ARG 0.002 0.000 ARG C 379 Details of bonding type rmsd hydrogen bonds : bond 0.02249 ( 88) hydrogen bonds : angle 4.55715 ( 264) covalent geometry : bond 0.00278 ( 3489) covalent geometry : angle 0.51628 ( 4668) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 LYS cc_start: 0.8296 (ttmt) cc_final: 0.8067 (ttmm) REVERT: E 314 ASP cc_start: 0.8585 (t0) cc_final: 0.8274 (t0) REVERT: F 343 LYS cc_start: 0.8341 (ttmt) cc_final: 0.8133 (ttmm) outliers start: 2 outliers final: 2 residues processed: 86 average time/residue: 2.7183 time to fit residues: 239.7169 Evaluate side-chains 85 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain C residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 0.4980 chunk 1 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN D 307 GLN E 351 GLN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.145963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.129903 restraints weight = 10742.307| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 1.05 r_work: 0.3846 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.3785 rms_B_bonded: 1.89 restraints_weight: 0.2500 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3489 Z= 0.165 Angle : 0.539 4.656 4668 Z= 0.274 Chirality : 0.052 0.129 525 Planarity : 0.004 0.027 594 Dihedral : 5.106 15.332 462 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.51 % Allowed : 12.98 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.34), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 362 PHE 0.008 0.002 PHE C 346 TYR 0.011 0.003 TYR A 310 ARG 0.002 0.000 ARG C 379 Details of bonding type rmsd hydrogen bonds : bond 0.02395 ( 88) hydrogen bonds : angle 4.52981 ( 264) covalent geometry : bond 0.00353 ( 3489) covalent geometry : angle 0.53896 ( 4668) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9712.45 seconds wall clock time: 166 minutes 40.07 seconds (10000.07 seconds total)