Starting phenix.real_space_refine on Wed Sep 17 04:30:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p6a_13223/09_2025/7p6a_13223.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p6a_13223/09_2025/7p6a_13223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7p6a_13223/09_2025/7p6a_13223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p6a_13223/09_2025/7p6a_13223.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p6a_13223/09_2025/7p6a_13223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p6a_13223/09_2025/7p6a_13223.map" } resolution = 1.9 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 2555 2.51 5 N 765 2.21 5 O 836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4166 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Conformer: "B" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} bond proxies already assigned to first conformer: 816 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Restraints were copied for chains: B, C, D, E Time building chain proxies: 1.10, per 1000 atoms: 0.26 Number of scatterers: 4166 At special positions: 0 Unit cell: (105.415, 82.878, 39.985, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 836 8.00 N 765 7.00 C 2555 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.34 Conformation dependent library (CDL) restraints added in 323.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 51.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 275 through 292 removed outlier: 6.322A pdb=" N VAL B 275 " --> pdb=" O GLN C 276 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE C 278 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE B 277 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LYS C 280 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASN B 279 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU C 282 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LYS B 281 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N LEU C 284 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N ASP B 283 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 10.022A pdb=" N ASN C 286 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N SER B 285 " --> pdb=" O ASN C 286 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N GLN C 288 " --> pdb=" O SER B 285 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL B 287 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N LYS C 290 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N SER B 289 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N GLY C 292 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N CYS B 291 " --> pdb=" O GLY C 292 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL A 275 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ILE B 278 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 277 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N LYS B 280 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASN A 279 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU B 282 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LYS A 281 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N LEU B 284 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N ASP A 283 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 10.009A pdb=" N ASN B 286 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N SER A 285 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N GLN B 288 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 287 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LYS B 290 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N SER A 289 " --> pdb=" O LYS B 290 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N GLY B 292 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N CYS A 291 " --> pdb=" O GLY B 292 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 282 " --> pdb=" O LYS D 281 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASP D 283 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A 284 " --> pdb=" O ASP D 283 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER D 285 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASN A 286 " --> pdb=" O SER D 285 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU D 282 " --> pdb=" O LYS E 281 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASP E 283 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU D 284 " --> pdb=" O ASP E 283 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER E 285 " --> pdb=" O LEU D 284 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN D 286 " --> pdb=" O SER E 285 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 297 through 298 removed outlier: 6.329A pdb=" N ILE B 297 " --> pdb=" O LYS C 298 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE A 297 " --> pdb=" O LYS B 298 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 305 through 310 removed outlier: 6.623A pdb=" N SER A 305 " --> pdb=" O VAL D 306 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ILE D 308 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLN A 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N TYR D 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL A 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER D 305 " --> pdb=" O VAL E 306 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ILE E 308 " --> pdb=" O SER D 305 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLN D 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N TYR E 310 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL D 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.758A pdb=" N VAL A 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL D 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.263A pdb=" N VAL B 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LYS C 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N SER B 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL A 318 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LYS B 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N SER A 320 " --> pdb=" O LYS B 321 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.414A pdb=" N ILE B 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 337 through 340 removed outlier: 6.339A pdb=" N VAL B 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LYS C 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL A 337 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LYS B 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL A 339 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 343 through 346 removed outlier: 6.441A pdb=" N LEU A 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU D 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 349 through 354 removed outlier: 6.525A pdb=" N VAL A 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LYS D 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N SER A 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL D 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LYS E 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N SER D 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 357 through 362 removed outlier: 8.704A pdb=" N LEU B 357 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 9.580A pdb=" N ILE C 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASN B 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N HIS C 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR B 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N LEU A 357 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 9.582A pdb=" N ILE B 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASN A 359 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N HIS B 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR A 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP A 358 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN D 359 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP D 358 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN E 359 " --> pdb=" O ASP D 358 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 369 through 378 removed outlier: 6.288A pdb=" N LYS B 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N GLU C 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE B 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N HIS C 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR B 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEU C 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LYS B 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N PHE C 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR B 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N PHE B 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LYS A 370 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS D 370 " --> pdb=" O LYS E 369 " (cutoff:3.500A) 96 hydrogen bonds defined for protein. 288 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.69 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1354 1.34 - 1.46: 678 1.46 - 1.58: 2108 1.58 - 1.69: 0 1.69 - 1.81: 10 Bond restraints: 4150 Sorted by residual: bond pdb=" N SER A 285 " pdb=" CA SER A 285 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.23e-02 6.61e+03 6.64e+00 bond pdb=" N LEU D 284 " pdb=" CA LEU D 284 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.21e-02 6.83e+03 6.40e+00 bond pdb=" N LEU E 284 " pdb=" CA LEU E 284 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.21e-02 6.83e+03 6.39e+00 bond pdb=" N LEU C 284 " pdb=" CA LEU C 284 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.21e-02 6.83e+03 6.25e+00 bond pdb=" N LEU B 284 " pdb=" CA LEU B 284 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.21e-02 6.83e+03 6.18e+00 ... (remaining 4145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 5187 1.26 - 2.52: 283 2.52 - 3.78: 49 3.78 - 5.04: 21 5.04 - 6.29: 5 Bond angle restraints: 5545 Sorted by residual: angle pdb=" N SER B 285 " pdb=" CA SER B 285 " pdb=" C SER B 285 " ideal model delta sigma weight residual 108.79 113.80 -5.01 1.53e+00 4.27e-01 1.07e+01 angle pdb=" N SER D 285 " pdb=" CA SER D 285 " pdb=" C SER D 285 " ideal model delta sigma weight residual 108.79 113.79 -5.00 1.53e+00 4.27e-01 1.07e+01 angle pdb=" N SER E 285 " pdb=" CA SER E 285 " pdb=" C SER E 285 " ideal model delta sigma weight residual 108.79 113.78 -4.99 1.53e+00 4.27e-01 1.06e+01 angle pdb=" N SER C 285 " pdb=" CA SER C 285 " pdb=" C SER C 285 " ideal model delta sigma weight residual 108.79 113.75 -4.96 1.53e+00 4.27e-01 1.05e+01 angle pdb=" N SER A 285 " pdb=" CA SER A 285 " pdb=" C SER A 285 " ideal model delta sigma weight residual 108.79 113.74 -4.95 1.53e+00 4.27e-01 1.05e+01 ... (remaining 5540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 2360 15.94 - 31.88: 155 31.88 - 47.82: 40 47.82 - 63.76: 5 63.76 - 79.70: 5 Dihedral angle restraints: 2565 sinusoidal: 1075 harmonic: 1490 Sorted by residual: dihedral pdb=" CB GLU D 372 " pdb=" CG GLU D 372 " pdb=" CD GLU D 372 " pdb=" OE1 GLU D 372 " ideal model delta sinusoidal sigma weight residual 0.00 -79.70 79.70 1 3.00e+01 1.11e-03 8.76e+00 dihedral pdb=" CB GLU B 372 " pdb=" CG GLU B 372 " pdb=" CD GLU B 372 " pdb=" OE1 GLU B 372 " ideal model delta sinusoidal sigma weight residual 0.00 -79.68 79.68 1 3.00e+01 1.11e-03 8.76e+00 dihedral pdb=" CB GLU A 372 " pdb=" CG GLU A 372 " pdb=" CD GLU A 372 " pdb=" OE1 GLU A 372 " ideal model delta sinusoidal sigma weight residual 0.00 -79.67 79.67 1 3.00e+01 1.11e-03 8.75e+00 ... (remaining 2562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 409 0.047 - 0.095: 108 0.095 - 0.142: 91 0.142 - 0.190: 7 0.190 - 0.237: 5 Chirality restraints: 620 Sorted by residual: chirality pdb=" CG LEU D 282 " pdb=" CB LEU D 282 " pdb=" CD1 LEU D 282 " pdb=" CD2 LEU D 282 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CG LEU B 282 " pdb=" CB LEU B 282 " pdb=" CD1 LEU B 282 " pdb=" CD2 LEU B 282 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CG LEU C 282 " pdb=" CB LEU C 282 " pdb=" CD1 LEU C 282 " pdb=" CD2 LEU C 282 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 617 not shown) Planarity restraints: 710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 349 " 0.121 9.50e-02 1.11e+02 5.44e-02 2.27e+00 pdb=" NE ARG C 349 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG C 349 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 349 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 349 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 349 " 0.122 9.50e-02 1.11e+02 5.48e-02 2.25e+00 pdb=" NE ARG B 349 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 349 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 349 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 349 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 349 " 0.121 9.50e-02 1.11e+02 5.44e-02 2.25e+00 pdb=" NE ARG E 349 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG E 349 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG E 349 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG E 349 " 0.001 2.00e-02 2.50e+03 ... (remaining 707 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 463 2.78 - 3.31: 3710 3.31 - 3.84: 7626 3.84 - 4.37: 8842 4.37 - 4.90: 16483 Nonbonded interactions: 37124 Sorted by model distance: nonbonded pdb=" O LEU B 357 " pdb=" O HOH B 501 " model vdw 2.247 3.040 nonbonded pdb=" OD1 ASP D 358 " pdb=" O HOH D 501 " model vdw 2.306 3.040 nonbonded pdb=" OD1 ASP B 358 " pdb=" O HOH B 502 " model vdw 2.358 3.040 nonbonded pdb=" O LEU C 357 " pdb=" O HOH B 502 " model vdw 2.360 3.040 nonbonded pdb=" O ASP D 295 " pdb=" OH TYR D 310 " model vdw 2.372 3.040 ... (remaining 37119 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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=0.50 max=1.00 mean=0.99 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: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.560 Find NCS groups from input model: 0.050 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:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 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 : 0.004 0.032 4150 Z= 0.206 Angle : 0.718 6.294 5545 Z= 0.415 Chirality : 0.059 0.237 620 Planarity : 0.006 0.055 710 Dihedral : 12.298 79.700 1625 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -3.07 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.19), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.003 ARG C 349 TYR 0.005 0.002 TYR B 310 PHE 0.006 0.001 PHE D 378 HIS 0.002 0.000 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 4150) covalent geometry : angle 0.71768 ( 5545) hydrogen bonds : bond 0.09167 ( 96) hydrogen bonds : angle 7.18755 ( 288) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.106 Fit side-chains REVERT: E 349 ARG cc_start: 0.7127 (mtt-85) cc_final: 0.6911 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.4142 time to fit residues: 49.2063 Evaluate side-chains 94 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS B 330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.136749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.119701 restraints weight = 16232.012| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.30 r_work: 0.3740 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4150 Z= 0.093 Angle : 0.535 6.534 5545 Z= 0.266 Chirality : 0.052 0.165 620 Planarity : 0.003 0.037 710 Dihedral : 5.150 14.918 560 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.43 % Allowed : 5.32 % Favored : 94.26 % 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: -3.00 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.20), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.008 0.002 TYR C 310 PHE 0.005 0.001 PHE E 378 HIS 0.008 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 4150) covalent geometry : angle 0.53475 ( 5545) hydrogen bonds : bond 0.02220 ( 96) hydrogen bonds : angle 5.18771 ( 288) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: C 349 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7498 (mtp180) outliers start: 2 outliers final: 0 residues processed: 105 average time/residue: 0.3920 time to fit residues: 42.9174 Evaluate side-chains 97 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 29 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN B 276 GLN D 276 GLN E 276 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.129198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.112018 restraints weight = 12939.892| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.08 r_work: 0.3627 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4150 Z= 0.212 Angle : 0.629 6.767 5545 Z= 0.323 Chirality : 0.054 0.187 620 Planarity : 0.004 0.026 710 Dihedral : 5.827 14.567 560 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.64 % Allowed : 7.87 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.74 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.20), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 349 TYR 0.005 0.002 TYR E 310 PHE 0.008 0.002 PHE E 378 HIS 0.003 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 4150) covalent geometry : angle 0.62892 ( 5545) hydrogen bonds : bond 0.02790 ( 96) hydrogen bonds : angle 5.47512 ( 288) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 356 SER cc_start: 0.8952 (t) cc_final: 0.8658 (p) REVERT: E 349 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7811 (mtm180) outliers start: 3 outliers final: 0 residues processed: 105 average time/residue: 0.4015 time to fit residues: 43.9630 Evaluate side-chains 99 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 349 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 13 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 279 ASN B 276 GLN D 276 GLN D 279 ASN E 276 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.129345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.111944 restraints weight = 15040.872| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.22 r_work: 0.3624 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4150 Z= 0.192 Angle : 0.610 6.889 5545 Z= 0.314 Chirality : 0.053 0.170 620 Planarity : 0.003 0.024 710 Dihedral : 5.885 15.006 560 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.28 % Allowed : 8.72 % Favored : 90.00 % 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: -2.70 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.20), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.006 0.002 TYR C 310 PHE 0.008 0.002 PHE E 378 HIS 0.003 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 4150) covalent geometry : angle 0.61016 ( 5545) hydrogen bonds : bond 0.02607 ( 96) hydrogen bonds : angle 5.33192 ( 288) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.185 Fit side-chains REVERT: A 356 SER cc_start: 0.8980 (t) cc_final: 0.8699 (p) REVERT: E 349 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7837 (mtm180) outliers start: 6 outliers final: 0 residues processed: 102 average time/residue: 0.4463 time to fit residues: 47.5500 Evaluate side-chains 99 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 349 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 16 optimal weight: 10.0000 chunk 20 optimal weight: 0.0070 chunk 49 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 overall best weight: 3.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN B 276 GLN B 279 ASN C 276 GLN D 276 GLN E 276 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.127575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.111326 restraints weight = 9565.470| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 1.76 r_work: 0.3634 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 4150 Z= 0.258 Angle : 0.666 7.049 5545 Z= 0.345 Chirality : 0.056 0.231 620 Planarity : 0.004 0.032 710 Dihedral : 6.146 15.806 560 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.43 % Allowed : 9.79 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.60 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.20), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.005 0.002 TYR E 310 PHE 0.009 0.002 PHE E 378 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00582 ( 4150) covalent geometry : angle 0.66596 ( 5545) hydrogen bonds : bond 0.02814 ( 96) hydrogen bonds : angle 5.47839 ( 288) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.147 Fit side-chains REVERT: A 356 SER cc_start: 0.8945 (t) cc_final: 0.8665 (p) REVERT: E 349 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7778 (mtm180) outliers start: 2 outliers final: 0 residues processed: 103 average time/residue: 0.4257 time to fit residues: 45.7384 Evaluate side-chains 99 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 349 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN B 276 GLN C 276 GLN D 279 ASN E 276 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.128085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.110962 restraints weight = 14119.772| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.14 r_work: 0.3625 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4150 Z= 0.201 Angle : 0.624 6.830 5545 Z= 0.321 Chirality : 0.053 0.169 620 Planarity : 0.003 0.024 710 Dihedral : 6.046 15.870 560 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.64 % Allowed : 9.36 % Favored : 90.00 % 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: -2.62 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.20), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 379 TYR 0.006 0.002 TYR C 310 PHE 0.007 0.002 PHE B 378 HIS 0.003 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 4150) covalent geometry : angle 0.62371 ( 5545) hydrogen bonds : bond 0.02555 ( 96) hydrogen bonds : angle 5.35653 ( 288) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.192 Fit side-chains REVERT: A 356 SER cc_start: 0.8981 (t) cc_final: 0.8694 (p) REVERT: E 349 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7873 (mtm180) outliers start: 3 outliers final: 0 residues processed: 99 average time/residue: 0.4562 time to fit residues: 47.2082 Evaluate side-chains 98 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 349 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN B 276 GLN B 279 ASN E 276 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.128093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.110355 restraints weight = 18240.451| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.42 r_work: 0.3600 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4150 Z= 0.216 Angle : 0.640 7.430 5545 Z= 0.330 Chirality : 0.055 0.196 620 Planarity : 0.003 0.025 710 Dihedral : 6.093 15.971 560 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.43 % Allowed : 10.43 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.59 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.20), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 349 TYR 0.005 0.002 TYR C 310 PHE 0.008 0.002 PHE B 378 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 4150) covalent geometry : angle 0.64028 ( 5545) hydrogen bonds : bond 0.02621 ( 96) hydrogen bonds : angle 5.39956 ( 288) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.190 Fit side-chains REVERT: A 356 SER cc_start: 0.9015 (t) cc_final: 0.8723 (p) REVERT: C 349 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7819 (mtp180) outliers start: 2 outliers final: 0 residues processed: 98 average time/residue: 0.4291 time to fit residues: 43.9652 Evaluate side-chains 99 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 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 276 GLN B 276 GLN D 279 ASN E 276 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.128029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.110791 restraints weight = 13973.898| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.13 r_work: 0.3618 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4150 Z= 0.217 Angle : 0.643 7.310 5545 Z= 0.331 Chirality : 0.055 0.214 620 Planarity : 0.003 0.025 710 Dihedral : 6.108 15.945 560 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.64 % Allowed : 10.21 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.58 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.20), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 349 TYR 0.005 0.002 TYR C 310 PHE 0.008 0.002 PHE E 378 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 4150) covalent geometry : angle 0.64337 ( 5545) hydrogen bonds : bond 0.02632 ( 96) hydrogen bonds : angle 5.40301 ( 288) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.183 Fit side-chains REVERT: A 349 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7952 (mtm180) REVERT: A 356 SER cc_start: 0.8986 (t) cc_final: 0.8694 (p) REVERT: C 349 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7794 (mtp180) outliers start: 3 outliers final: 0 residues processed: 97 average time/residue: 0.4361 time to fit residues: 44.2551 Evaluate side-chains 99 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain C residue 349 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN B 276 GLN B 279 ASN E 276 GLN E 279 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.129832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.112460 restraints weight = 14603.815| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.18 r_work: 0.3639 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4150 Z= 0.165 Angle : 0.608 7.325 5545 Z= 0.311 Chirality : 0.054 0.189 620 Planarity : 0.003 0.023 710 Dihedral : 5.946 15.407 560 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.43 % Allowed : 10.64 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.62 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.20), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 349 TYR 0.007 0.002 TYR C 310 PHE 0.006 0.001 PHE B 378 HIS 0.003 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 4150) covalent geometry : angle 0.60801 ( 5545) hydrogen bonds : bond 0.02400 ( 96) hydrogen bonds : angle 5.24093 ( 288) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.165 Fit side-chains REVERT: A 349 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7925 (mtm180) REVERT: A 356 SER cc_start: 0.8990 (t) cc_final: 0.8720 (p) REVERT: C 349 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7764 (mtp180) outliers start: 2 outliers final: 0 residues processed: 99 average time/residue: 0.4307 time to fit residues: 44.4146 Evaluate side-chains 100 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain C residue 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 0.0010 chunk 2 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 26 optimal weight: 0.0010 chunk 35 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN B 276 GLN D 279 ASN E 276 GLN E 279 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.128869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.111268 restraints weight = 15982.878| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.28 r_work: 0.3616 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4150 Z= 0.198 Angle : 0.634 7.400 5545 Z= 0.326 Chirality : 0.055 0.227 620 Planarity : 0.003 0.023 710 Dihedral : 6.038 15.737 560 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.64 % Allowed : 10.85 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.58 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.20), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 349 TYR 0.006 0.002 TYR C 310 PHE 0.007 0.002 PHE E 378 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 4150) covalent geometry : angle 0.63408 ( 5545) hydrogen bonds : bond 0.02534 ( 96) hydrogen bonds : angle 5.31609 ( 288) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.219 Fit side-chains REVERT: A 349 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7966 (mtm180) REVERT: A 356 SER cc_start: 0.8994 (t) cc_final: 0.8704 (p) REVERT: C 349 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7836 (mtp180) outliers start: 3 outliers final: 0 residues processed: 99 average time/residue: 0.4456 time to fit residues: 45.9818 Evaluate side-chains 101 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain C residue 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN B 276 GLN B 279 ASN E 276 GLN E 279 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.128313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.111295 restraints weight = 12486.389| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.02 r_work: 0.3626 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4150 Z= 0.218 Angle : 0.648 7.405 5545 Z= 0.334 Chirality : 0.055 0.239 620 Planarity : 0.003 0.024 710 Dihedral : 6.084 15.859 560 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.64 % Allowed : 10.85 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.57 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.20), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 349 TYR 0.005 0.002 TYR C 310 PHE 0.008 0.002 PHE B 378 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 4150) covalent geometry : angle 0.64759 ( 5545) hydrogen bonds : bond 0.02646 ( 96) hydrogen bonds : angle 5.37130 ( 288) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2651.36 seconds wall clock time: 46 minutes 12.23 seconds (2772.23 seconds total)