Starting phenix.real_space_refine on Fri Aug 22 17:59:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q8c_18250/08_2025/8q8c_18250.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q8c_18250/08_2025/8q8c_18250.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8q8c_18250/08_2025/8q8c_18250.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q8c_18250/08_2025/8q8c_18250.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q8c_18250/08_2025/8q8c_18250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q8c_18250/08_2025/8q8c_18250.map" } resolution = 1.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.003 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 2034 2.51 5 N 594 2.21 5 O 612 1.98 5 H 3372 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6618 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "B" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "D" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "F" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 1.29, per 1000 atoms: 0.19 Number of scatterers: 6618 At special positions: 0 Unit cell: (134.495, 126.498, 48.709, 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 612 8.00 N 594 7.00 C 2034 6.00 H 3372 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: 0.53 Conformation dependent library (CDL) restraints added in 264.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 57.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 309 through 310 removed outlier: 6.499A pdb=" N VAL C 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.720A pdb=" N VAL C 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 325 removed outlier: 6.488A pdb=" N VAL A 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LYS E 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N SER A 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N GLY E 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N CYS A 322 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU E 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER A 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330 removed outlier: 6.479A pdb=" N ILE C 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 346 removed outlier: 6.908A pdb=" N VAL E 337 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLU A 338 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL E 339 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LYS A 340 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N SER E 341 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLU A 342 " --> pdb=" O SER E 341 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LYS E 343 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N VAL C 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 10.369A pdb=" N LYS E 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N VAL C 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N GLU E 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 9.136A pdb=" N SER C 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 9.238A pdb=" N LEU E 344 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS C 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N PHE E 346 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASP C 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 354 removed outlier: 6.354A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 362 removed outlier: 6.395A pdb=" N ASP C 358 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR E 361 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE C 360 " --> pdb=" O THR E 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 368 through 374 removed outlier: 6.480A pdb=" N LYS C 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLU E 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE C 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N HIS E 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR C 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.488A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.860A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 317 through 325 Processing sheet with id=AB3, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.578A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 337 through 346 removed outlier: 6.569A pdb=" N GLU B 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N SER D 341 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LYS B 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N LYS D 343 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N GLU B 342 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ASP D 345 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N LEU B 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU F 344 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASP B 345 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE F 346 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 350 through 362 removed outlier: 6.898A pdb=" N GLN D 351 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER B 352 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LYS D 353 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE B 354 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY D 355 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N SER B 356 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLN B 351 " --> pdb=" O VAL F 350 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER F 352 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS B 353 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE F 354 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLY B 355 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER F 356 " --> pdb=" O GLY B 355 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 368 through 377 removed outlier: 6.463A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) 80 hydrogen bonds defined for protein. 240 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: 1.38 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 3366 1.12 - 1.29: 546 1.29 - 1.47: 1092 1.47 - 1.64: 1659 1.64 - 1.82: 6 Bond restraints: 6669 Sorted by residual: bond pdb=" N ILE F 360 " pdb=" H ILE F 360 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CE1 HIS D 362 " pdb=" HE1 HIS D 362 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N LYS D 353 " pdb=" H LYS D 353 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CZ PHE F 378 " pdb=" HZ PHE F 378 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N ILE D 360 " pdb=" H ILE D 360 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 6664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 10468 2.56 - 5.11: 1308 5.11 - 7.67: 380 7.67 - 10.23: 6 10.23 - 12.79: 6 Bond angle restraints: 12168 Sorted by residual: angle pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " ideal model delta sigma weight residual 112.60 118.84 -6.24 1.00e+00 1.00e+00 3.89e+01 angle pdb=" CA ASP E 358 " pdb=" CB ASP E 358 " pdb=" CG ASP E 358 " ideal model delta sigma weight residual 112.60 118.43 -5.83 1.00e+00 1.00e+00 3.40e+01 angle pdb=" OE1 GLN B 336 " pdb=" CD GLN B 336 " pdb=" NE2 GLN B 336 " ideal model delta sigma weight residual 122.60 117.13 5.47 1.00e+00 1.00e+00 2.99e+01 angle pdb=" CA ASP C 358 " pdb=" CB ASP C 358 " pdb=" CG ASP C 358 " ideal model delta sigma weight residual 112.60 117.89 -5.29 1.00e+00 1.00e+00 2.80e+01 angle pdb=" N PRO F 312 " pdb=" CA PRO F 312 " pdb=" CB PRO F 312 " ideal model delta sigma weight residual 103.25 107.20 -3.95 8.80e-01 1.29e+00 2.01e+01 ... (remaining 12163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.64: 2739 15.64 - 31.29: 169 31.29 - 46.93: 48 46.93 - 62.57: 91 62.57 - 78.22: 25 Dihedral angle restraints: 3072 sinusoidal: 1758 harmonic: 1314 Sorted by residual: dihedral pdb=" CA GLU F 372 " pdb=" C GLU F 372 " pdb=" N THR F 373 " pdb=" CA THR F 373 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA THR E 319 " pdb=" C THR E 319 " pdb=" N SER E 320 " pdb=" CA SER E 320 " ideal model delta harmonic sigma weight residual 180.00 162.53 17.47 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA THR C 319 " pdb=" C THR C 319 " pdb=" N SER C 320 " pdb=" CA SER C 320 " ideal model delta harmonic sigma weight residual 180.00 162.74 17.26 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 3069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 235 0.059 - 0.118: 198 0.118 - 0.177: 58 0.177 - 0.236: 3 0.236 - 0.295: 1 Chirality restraints: 495 Sorted by residual: chirality pdb=" CA LYS F 347 " pdb=" N LYS F 347 " pdb=" C LYS F 347 " pdb=" CB LYS F 347 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA GLU B 342 " pdb=" N GLU B 342 " pdb=" C GLU B 342 " pdb=" CB GLU B 342 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA LYS C 311 " pdb=" N LYS C 311 " pdb=" C LYS C 311 " pdb=" CB LYS C 311 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.22e-01 ... (remaining 492 not shown) Planarity restraints: 966 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN C 336 " -0.062 2.00e-02 2.50e+03 5.63e-02 4.76e+01 pdb=" CD GLN C 336 " 0.029 2.00e-02 2.50e+03 pdb=" OE1 GLN C 336 " 0.038 2.00e-02 2.50e+03 pdb=" NE2 GLN C 336 " 0.045 2.00e-02 2.50e+03 pdb="HE21 GLN C 336 " 0.045 2.00e-02 2.50e+03 pdb="HE22 GLN C 336 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 330 " 0.070 2.00e-02 2.50e+03 4.53e-02 4.62e+01 pdb=" CG HIS E 330 " -0.020 2.00e-02 2.50e+03 pdb=" ND1 HIS E 330 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 HIS E 330 " -0.052 2.00e-02 2.50e+03 pdb=" CE1 HIS E 330 " -0.024 2.00e-02 2.50e+03 pdb=" NE2 HIS E 330 " -0.043 2.00e-02 2.50e+03 pdb=" HD2 HIS E 330 " -0.012 2.00e-02 2.50e+03 pdb=" HE1 HIS E 330 " 0.026 2.00e-02 2.50e+03 pdb=" HE2 HIS E 330 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 362 " -0.071 2.00e-02 2.50e+03 4.36e-02 4.27e+01 pdb=" CG HIS B 362 " 0.053 2.00e-02 2.50e+03 pdb=" ND1 HIS B 362 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 HIS B 362 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 HIS B 362 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS B 362 " 0.040 2.00e-02 2.50e+03 pdb=" HD2 HIS B 362 " -0.016 2.00e-02 2.50e+03 pdb=" HE1 HIS B 362 " -0.038 2.00e-02 2.50e+03 pdb=" HE2 HIS B 362 " -0.054 2.00e-02 2.50e+03 ... (remaining 963 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 481 2.16 - 2.77: 10878 2.77 - 3.38: 17307 3.38 - 3.99: 23620 3.99 - 4.60: 32257 Nonbonded interactions: 84543 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.545 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.559 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.568 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.568 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.575 2.450 ... (remaining 84538 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 308 through 375) selection = chain 'C' selection = (chain 'D' and resid 308 through 375) selection = chain 'E' selection = (chain 'F' and resid 308 through 375) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.370 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: 0.040 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.040 Find NCS groups from input model: 0.080 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:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 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 0.039 3297 Z= 0.690 Angle : 1.664 6.272 4410 Z= 1.109 Chirality : 0.077 0.295 495 Planarity : 0.008 0.038 561 Dihedral : 10.695 78.218 1263 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.27 % Allowed : 1.61 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.34), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.26), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG B 349 TYR 0.035 0.012 TYR B 310 PHE 0.048 0.015 PHE D 378 HIS 0.011 0.003 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.01116 ( 3297) covalent geometry : angle 1.66370 ( 4410) hydrogen bonds : bond 0.09305 ( 80) hydrogen bonds : angle 8.26429 ( 240) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7342 (mtmt) cc_final: 0.6994 (mttt) REVERT: A 315 LEU cc_start: 0.7638 (mt) cc_final: 0.7382 (mt) REVERT: A 317 LYS cc_start: 0.7328 (mttt) cc_final: 0.6972 (mttp) REVERT: A 324 SER cc_start: 0.7139 (p) cc_final: 0.6938 (t) REVERT: A 342 GLU cc_start: 0.6579 (tt0) cc_final: 0.5870 (tm-30) REVERT: A 343 LYS cc_start: 0.7171 (mttt) cc_final: 0.6962 (mttt) REVERT: A 369 LYS cc_start: 0.6792 (ttmt) cc_final: 0.6313 (ttpt) REVERT: B 311 LYS cc_start: 0.7137 (mttt) cc_final: 0.6712 (mttp) REVERT: B 317 LYS cc_start: 0.6616 (mttt) cc_final: 0.6264 (mttm) REVERT: B 336 GLN cc_start: 0.6722 (tt0) cc_final: 0.6320 (tt0) REVERT: B 340 LYS cc_start: 0.6200 (mttt) cc_final: 0.5699 (mtpp) REVERT: B 345 ASP cc_start: 0.6847 (t0) cc_final: 0.6639 (t70) REVERT: B 369 LYS cc_start: 0.6862 (tttt) cc_final: 0.6602 (ttpt) REVERT: B 372 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6420 (mm-30) REVERT: C 311 LYS cc_start: 0.6874 (mtmt) cc_final: 0.6099 (mttm) REVERT: C 342 GLU cc_start: 0.6017 (tt0) cc_final: 0.5717 (tt0) REVERT: C 345 ASP cc_start: 0.6946 (m-30) cc_final: 0.6487 (t0) REVERT: C 351 GLN cc_start: 0.6850 (mt0) cc_final: 0.6647 (mt0) REVERT: C 369 LYS cc_start: 0.6336 (ttmt) cc_final: 0.5909 (ttpt) REVERT: C 372 GLU cc_start: 0.6975 (tt0) cc_final: 0.6673 (mm-30) REVERT: C 373 THR cc_start: 0.7260 (m) cc_final: 0.6743 (p) REVERT: D 311 LYS cc_start: 0.7440 (mttt) cc_final: 0.7176 (mttp) REVERT: D 338 GLU cc_start: 0.6827 (mt-10) cc_final: 0.6249 (mt-10) REVERT: D 340 LYS cc_start: 0.6745 (mttt) cc_final: 0.6160 (mtpt) REVERT: D 369 LYS cc_start: 0.7477 (tttt) cc_final: 0.7174 (ttpt) REVERT: D 375 LYS cc_start: 0.7491 (tttt) cc_final: 0.7034 (tppt) REVERT: E 317 LYS cc_start: 0.6681 (mttt) cc_final: 0.6346 (mttp) REVERT: E 324 SER cc_start: 0.7159 (p) cc_final: 0.6950 (t) REVERT: E 342 GLU cc_start: 0.6120 (tt0) cc_final: 0.5344 (tm-30) REVERT: E 343 LYS cc_start: 0.6946 (mttt) cc_final: 0.6641 (mttt) REVERT: E 345 ASP cc_start: 0.6993 (m-30) cc_final: 0.6620 (m-30) REVERT: E 347 LYS cc_start: 0.6949 (mttt) cc_final: 0.6723 (mmtt) REVERT: E 369 LYS cc_start: 0.6188 (ttmt) cc_final: 0.5803 (ttpt) REVERT: E 372 GLU cc_start: 0.6736 (tt0) cc_final: 0.6400 (tt0) REVERT: F 317 LYS cc_start: 0.6739 (mttt) cc_final: 0.6486 (mttm) REVERT: F 338 GLU cc_start: 0.5326 (mm-30) cc_final: 0.5124 (mt-10) REVERT: F 340 LYS cc_start: 0.6289 (mttt) cc_final: 0.5819 (mtpp) REVERT: F 342 GLU cc_start: 0.6299 (pt0) cc_final: 0.6019 (pt0) REVERT: F 349 ARG cc_start: 0.6240 (mtm110) cc_final: 0.5643 (mtt180) REVERT: F 353 LYS cc_start: 0.6663 (tttt) cc_final: 0.6309 (tttp) REVERT: F 356 SER cc_start: 0.7183 (m) cc_final: 0.6936 (t) REVERT: F 369 LYS cc_start: 0.6934 (tttt) cc_final: 0.6375 (ttpt) REVERT: F 371 ILE cc_start: 0.7214 (mt) cc_final: 0.6970 (mm) REVERT: F 372 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6670 (mm-30) outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 1.4674 time to fit residues: 220.0660 Evaluate side-chains 118 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 GLN D 327 ASN F 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.153904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.140455 restraints weight = 9082.324| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 0.88 r_work: 0.3903 rms_B_bonded: 0.92 restraints_weight: 0.5000 r_work: 0.3842 rms_B_bonded: 1.62 restraints_weight: 0.2500 r_work: 0.3693 rms_B_bonded: 4.54 restraints_weight: 0.1250 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3297 Z= 0.167 Angle : 0.572 4.123 4410 Z= 0.297 Chirality : 0.051 0.131 495 Planarity : 0.004 0.031 561 Dihedral : 5.697 14.494 435 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.66 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 349 TYR 0.007 0.002 TYR B 310 PHE 0.005 0.001 PHE D 346 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 3297) covalent geometry : angle 0.57245 ( 4410) hydrogen bonds : bond 0.03521 ( 80) hydrogen bonds : angle 5.82964 ( 240) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.8114 (mtp85) cc_final: 0.7863 (mtt180) REVERT: C 311 LYS cc_start: 0.8055 (mtmt) cc_final: 0.7829 (mttm) REVERT: C 349 ARG cc_start: 0.8313 (mtt180) cc_final: 0.6929 (mmp-170) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 1.6776 time to fit residues: 198.1431 Evaluate side-chains 97 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 chunk 14 optimal weight: 6.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN B 336 GLN D 307 GLN F 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.154248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.140806 restraints weight = 8780.664| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 0.87 r_work: 0.3900 rms_B_bonded: 0.91 restraints_weight: 0.5000 r_work: 0.3840 rms_B_bonded: 1.60 restraints_weight: 0.2500 r_work: 0.3690 rms_B_bonded: 4.50 restraints_weight: 0.1250 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3297 Z= 0.129 Angle : 0.542 4.330 4410 Z= 0.275 Chirality : 0.052 0.132 495 Planarity : 0.003 0.026 561 Dihedral : 5.207 13.055 435 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.34 % Allowed : 11.83 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.37), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.66 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 349 TYR 0.008 0.002 TYR B 310 PHE 0.007 0.001 PHE A 346 HIS 0.002 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 3297) covalent geometry : angle 0.54176 ( 4410) hydrogen bonds : bond 0.02861 ( 80) hydrogen bonds : angle 5.27118 ( 240) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7848 (tm-30) REVERT: A 349 ARG cc_start: 0.8194 (mtp85) cc_final: 0.7920 (mtt180) REVERT: C 311 LYS cc_start: 0.8103 (mtmt) cc_final: 0.7868 (mttm) REVERT: C 349 ARG cc_start: 0.8318 (mtt180) cc_final: 0.8085 (mtt180) outliers start: 5 outliers final: 0 residues processed: 103 average time/residue: 1.6370 time to fit residues: 171.7162 Evaluate side-chains 93 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 34 optimal weight: 4.9990 chunk 26 optimal weight: 0.0000 chunk 30 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN D 307 GLN F 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.152261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.138647 restraints weight = 8799.302| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 0.89 r_work: 0.3874 rms_B_bonded: 0.92 restraints_weight: 0.5000 r_work: 0.3812 rms_B_bonded: 1.62 restraints_weight: 0.2500 r_work: 0.3659 rms_B_bonded: 4.50 restraints_weight: 0.1250 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3297 Z= 0.141 Angle : 0.534 4.453 4410 Z= 0.272 Chirality : 0.052 0.132 495 Planarity : 0.003 0.024 561 Dihedral : 5.153 13.191 435 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.81 % Allowed : 12.10 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.68 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 349 TYR 0.008 0.002 TYR B 310 PHE 0.006 0.001 PHE E 346 HIS 0.002 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 3297) covalent geometry : angle 0.53403 ( 4410) hydrogen bonds : bond 0.02834 ( 80) hydrogen bonds : angle 5.15475 ( 240) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.8233 (mtp85) cc_final: 0.7981 (mtt180) REVERT: C 311 LYS cc_start: 0.8189 (mtmt) cc_final: 0.7939 (mttm) outliers start: 3 outliers final: 1 residues processed: 92 average time/residue: 1.5213 time to fit residues: 142.7443 Evaluate side-chains 91 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 375 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN D 307 GLN F 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.151845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.138124 restraints weight = 8877.503| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 0.88 r_work: 0.3868 rms_B_bonded: 0.92 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 1.62 restraints_weight: 0.2500 r_work: 0.3654 rms_B_bonded: 4.51 restraints_weight: 0.1250 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3297 Z= 0.133 Angle : 0.519 4.345 4410 Z= 0.266 Chirality : 0.052 0.133 495 Planarity : 0.003 0.024 561 Dihedral : 5.109 12.994 435 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.81 % Allowed : 11.83 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.73 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 349 TYR 0.008 0.002 TYR B 310 PHE 0.005 0.001 PHE E 346 HIS 0.002 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 3297) covalent geometry : angle 0.51875 ( 4410) hydrogen bonds : bond 0.02720 ( 80) hydrogen bonds : angle 5.00702 ( 240) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.8277 (mtp85) cc_final: 0.7949 (mtt180) REVERT: C 349 ARG cc_start: 0.8348 (mtt180) cc_final: 0.6994 (mmp-170) outliers start: 3 outliers final: 1 residues processed: 93 average time/residue: 1.5431 time to fit residues: 146.2678 Evaluate side-chains 90 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN F 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.151990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.138267 restraints weight = 8839.944| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 0.87 r_work: 0.3875 rms_B_bonded: 0.89 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 1.57 restraints_weight: 0.2500 r_work: 0.3665 rms_B_bonded: 4.42 restraints_weight: 0.1250 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3297 Z= 0.164 Angle : 0.546 4.232 4410 Z= 0.281 Chirality : 0.052 0.132 495 Planarity : 0.003 0.025 561 Dihedral : 5.222 12.911 435 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.34 % Allowed : 11.29 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.78 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 349 TYR 0.009 0.002 TYR B 310 PHE 0.006 0.001 PHE E 346 HIS 0.003 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 3297) covalent geometry : angle 0.54559 ( 4410) hydrogen bonds : bond 0.02966 ( 80) hydrogen bonds : angle 5.05650 ( 240) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8812 (mmtp) cc_final: 0.7679 (pmtt) REVERT: A 349 ARG cc_start: 0.8281 (mtp85) cc_final: 0.7930 (mtt180) REVERT: C 349 ARG cc_start: 0.8312 (mtt180) cc_final: 0.6977 (mmp-170) outliers start: 5 outliers final: 0 residues processed: 89 average time/residue: 1.4966 time to fit residues: 135.7790 Evaluate side-chains 88 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN F 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.150790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.137231 restraints weight = 8793.802| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 0.85 r_work: 0.3860 rms_B_bonded: 0.88 restraints_weight: 0.5000 r_work: 0.3800 rms_B_bonded: 1.56 restraints_weight: 0.2500 r_work: 0.3649 rms_B_bonded: 4.39 restraints_weight: 0.1250 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3297 Z= 0.208 Angle : 0.580 4.059 4410 Z= 0.302 Chirality : 0.051 0.136 495 Planarity : 0.003 0.026 561 Dihedral : 5.368 13.176 435 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.81 % Allowed : 12.37 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.86 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 349 TYR 0.010 0.002 TYR B 310 PHE 0.005 0.001 PHE E 346 HIS 0.004 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 3297) covalent geometry : angle 0.57997 ( 4410) hydrogen bonds : bond 0.03228 ( 80) hydrogen bonds : angle 5.18657 ( 240) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 LYS cc_start: 0.8808 (mmtp) cc_final: 0.7611 (pmtt) REVERT: A 349 ARG cc_start: 0.8292 (mtp85) cc_final: 0.8004 (mtt180) REVERT: C 349 ARG cc_start: 0.8287 (mtt180) cc_final: 0.7010 (mmp-170) outliers start: 3 outliers final: 0 residues processed: 86 average time/residue: 1.7068 time to fit residues: 149.6502 Evaluate side-chains 85 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN F 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.151533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.138045 restraints weight = 8903.680| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 0.86 r_work: 0.3872 rms_B_bonded: 0.88 restraints_weight: 0.5000 r_work: 0.3813 rms_B_bonded: 1.56 restraints_weight: 0.2500 r_work: 0.3663 rms_B_bonded: 4.39 restraints_weight: 0.1250 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3297 Z= 0.156 Angle : 0.537 3.892 4410 Z= 0.278 Chirality : 0.052 0.137 495 Planarity : 0.003 0.025 561 Dihedral : 5.248 12.884 435 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.81 % Allowed : 12.10 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.86 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 349 TYR 0.008 0.002 TYR B 310 PHE 0.005 0.001 PHE E 346 HIS 0.002 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 3297) covalent geometry : angle 0.53735 ( 4410) hydrogen bonds : bond 0.02905 ( 80) hydrogen bonds : angle 5.01442 ( 240) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.8290 (mtp85) cc_final: 0.7972 (mtt180) REVERT: C 349 ARG cc_start: 0.8288 (mtt180) cc_final: 0.6957 (mmp-170) outliers start: 3 outliers final: 1 residues processed: 86 average time/residue: 1.7676 time to fit residues: 154.9095 Evaluate side-chains 85 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 372 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.0170 chunk 13 optimal weight: 6.9990 overall best weight: 1.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN F 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.152040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.138688 restraints weight = 8805.030| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 0.85 r_work: 0.3883 rms_B_bonded: 0.87 restraints_weight: 0.5000 r_work: 0.3824 rms_B_bonded: 1.54 restraints_weight: 0.2500 r_work: 0.3675 rms_B_bonded: 4.36 restraints_weight: 0.1250 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3297 Z= 0.127 Angle : 0.516 3.827 4410 Z= 0.266 Chirality : 0.052 0.135 495 Planarity : 0.003 0.024 561 Dihedral : 5.159 12.565 435 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.54 % Allowed : 12.90 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.84 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 349 TYR 0.007 0.002 TYR B 310 PHE 0.004 0.001 PHE E 346 HIS 0.002 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 3297) covalent geometry : angle 0.51610 ( 4410) hydrogen bonds : bond 0.02679 ( 80) hydrogen bonds : angle 4.82459 ( 240) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.8255 (mtp85) cc_final: 0.7952 (mtt180) REVERT: C 349 ARG cc_start: 0.8272 (mtt180) cc_final: 0.6936 (mmp-170) outliers start: 2 outliers final: 1 residues processed: 88 average time/residue: 1.7466 time to fit residues: 156.6802 Evaluate side-chains 86 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 372 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 5 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN F 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.154075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.140726 restraints weight = 8851.236| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 0.86 r_work: 0.3911 rms_B_bonded: 0.89 restraints_weight: 0.5000 r_work: 0.3852 rms_B_bonded: 1.57 restraints_weight: 0.2500 r_work: 0.3703 rms_B_bonded: 4.42 restraints_weight: 0.1250 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3297 Z= 0.097 Angle : 0.506 5.788 4410 Z= 0.255 Chirality : 0.052 0.133 495 Planarity : 0.003 0.023 561 Dihedral : 4.949 11.960 435 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.54 % Allowed : 13.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.80 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 349 TYR 0.006 0.001 TYR A 310 PHE 0.003 0.001 PHE A 346 HIS 0.002 0.000 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 3297) covalent geometry : angle 0.50614 ( 4410) hydrogen bonds : bond 0.02353 ( 80) hydrogen bonds : angle 4.55814 ( 240) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.8242 (tt0) cc_final: 0.7923 (tm-30) REVERT: A 349 ARG cc_start: 0.8248 (mtp85) cc_final: 0.7939 (mtt180) REVERT: C 349 ARG cc_start: 0.8270 (mtt180) cc_final: 0.6952 (mmp-170) outliers start: 2 outliers final: 1 residues processed: 90 average time/residue: 1.7084 time to fit residues: 156.7393 Evaluate side-chains 88 residues out of total 372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 372 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 2 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN D 307 GLN F 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.152482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.139481 restraints weight = 8903.380| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 0.82 r_work: 0.3896 rms_B_bonded: 0.87 restraints_weight: 0.5000 r_work: 0.3837 rms_B_bonded: 1.53 restraints_weight: 0.2500 r_work: 0.3690 rms_B_bonded: 4.32 restraints_weight: 0.1250 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3297 Z= 0.114 Angle : 0.515 4.933 4410 Z= 0.262 Chirality : 0.052 0.133 495 Planarity : 0.003 0.023 561 Dihedral : 5.014 12.260 435 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.54 % Allowed : 14.25 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.81 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 349 TYR 0.007 0.002 TYR B 310 PHE 0.004 0.001 PHE E 346 HIS 0.002 0.000 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 3297) covalent geometry : angle 0.51506 ( 4410) hydrogen bonds : bond 0.02445 ( 80) hydrogen bonds : angle 4.57031 ( 240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5430.40 seconds wall clock time: 92 minutes 29.97 seconds (5549.97 seconds total)