Starting phenix.real_space_refine on Tue Feb 11 04:54:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p6a_13223/02_2025/7p6a_13223.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p6a_13223/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7p6a_13223/02_2025/7p6a_13223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p6a_13223/02_2025/7p6a_13223.map" model { file = "/net/cci-nas-00/data/ceres_data/7p6a_13223/02_2025/7p6a_13223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p6a_13223/02_2025/7p6a_13223.cif" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: C, B, E, D Time building chain proxies: 2.98, per 1000 atoms: 0.72 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: 0.93 Conformation dependent library (CDL) restraints added in 946.3 milliseconds 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: 0.80 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: 1.13 Time building geometry restraints manager: 1.10 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 3.560 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 15.460 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.760 ------------------------------------------------------------------------------- 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= 0.245 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.002 0.000 HIS D 374 PHE 0.006 0.001 PHE D 378 TYR 0.005 0.002 TYR B 310 ARG 0.012 0.003 ARG C 349 *********************** 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 : 0.557 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: 0.9175 time to fit residues: 109.4252 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 : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 21 optimal weight: 0.3980 chunk 12 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 330 HIS B 276 GLN B 330 HIS 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 = 0.3987 r_free = 0.3987 target = 0.128316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.111148 restraints weight = 12933.091| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.08 r_work: 0.3611 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 4150 Z= 0.378 Angle : 0.662 7.217 5545 Z= 0.341 Chirality : 0.055 0.175 620 Planarity : 0.004 0.061 710 Dihedral : 6.025 15.000 560 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.85 % Allowed : 5.32 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.20), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS A 330 PHE 0.010 0.002 PHE E 378 TYR 0.006 0.002 TYR C 310 ARG 0.006 0.001 ARG D 349 *********************** 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 109 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.499 Fit side-chains REVERT: A 349 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7792 (mtm180) REVERT: A 356 SER cc_start: 0.8962 (t) cc_final: 0.8658 (p) REVERT: E 349 ARG cc_start: 0.8312 (mtt-85) cc_final: 0.8038 (mtm180) outliers start: 4 outliers final: 2 residues processed: 106 average time/residue: 0.9059 time to fit residues: 100.5450 Evaluate side-chains 101 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 HIS Chi-restraints excluded: chain A residue 349 ARG 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 10 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 A 330 HIS B 276 GLN D 276 GLN D 279 ASN E 276 GLN E 279 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.129672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.112061 restraints weight = 16587.082| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.33 r_work: 0.3626 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- 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 = 0.42 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 = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4150 Z= 0.252 Angle : 0.588 6.723 5545 Z= 0.302 Chirality : 0.053 0.143 620 Planarity : 0.003 0.038 710 Dihedral : 5.861 15.135 560 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.85 % Allowed : 7.02 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.20), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS A 330 PHE 0.007 0.001 PHE E 378 TYR 0.006 0.002 TYR C 310 ARG 0.003 0.001 ARG D 349 *********************** 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 105 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 356 SER cc_start: 0.8999 (t) cc_final: 0.8712 (p) REVERT: E 349 ARG cc_start: 0.8356 (mtt-85) cc_final: 0.8075 (mtm180) outliers start: 4 outliers final: 1 residues processed: 103 average time/residue: 0.9053 time to fit residues: 97.4946 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 : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 330 HIS B 276 GLN B 279 ASN D 276 GLN D 279 ASN E 276 GLN E 279 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.129073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.111441 restraints weight = 16595.653| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.34 r_work: 0.3615 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4150 Z= 0.284 Angle : 0.598 7.004 5545 Z= 0.309 Chirality : 0.053 0.154 620 Planarity : 0.003 0.032 710 Dihedral : 5.913 15.276 560 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.06 % Allowed : 7.02 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (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 HIS 0.009 0.001 HIS A 330 PHE 0.007 0.001 PHE E 378 TYR 0.005 0.002 TYR C 310 ARG 0.003 0.001 ARG D 349 *********************** 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 101 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.552 Fit side-chains REVERT: A 356 SER cc_start: 0.8991 (t) cc_final: 0.8699 (p) REVERT: E 349 ARG cc_start: 0.8375 (mtt-85) cc_final: 0.8087 (mtm180) outliers start: 5 outliers final: 1 residues processed: 98 average time/residue: 0.8994 time to fit residues: 92.2430 Evaluate side-chains 95 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 A 330 HIS B 276 GLN D 276 GLN E 276 GLN E 279 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.127369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.109756 restraints weight = 16744.330| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.34 r_work: 0.3593 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 4150 Z= 0.403 Angle : 0.658 7.399 5545 Z= 0.344 Chirality : 0.054 0.182 620 Planarity : 0.004 0.032 710 Dihedral : 6.166 15.953 560 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.85 % Allowed : 7.23 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (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 HIS 0.013 0.001 HIS A 330 PHE 0.009 0.002 PHE E 378 TYR 0.006 0.002 TYR E 310 ARG 0.003 0.001 ARG D 349 *********************** 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 103 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.549 Fit side-chains REVERT: A 356 SER cc_start: 0.9007 (t) cc_final: 0.8706 (p) REVERT: B 284 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8758 (mt) REVERT: E 349 ARG cc_start: 0.8415 (mtt-85) cc_final: 0.8108 (mmt180) outliers start: 4 outliers final: 2 residues processed: 101 average time/residue: 0.8958 time to fit residues: 94.8999 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 : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 HIS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 276 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 330 HIS B 276 GLN B 279 ASN D 276 GLN E 276 GLN E 279 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.127032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.109289 restraints weight = 18191.302| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.42 r_work: 0.3585 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 4150 Z= 0.405 Angle : 0.664 7.696 5545 Z= 0.346 Chirality : 0.054 0.181 620 Planarity : 0.004 0.028 710 Dihedral : 6.235 16.302 560 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.06 % Allowed : 8.30 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (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 HIS 0.010 0.001 HIS A 330 PHE 0.009 0.002 PHE E 378 TYR 0.005 0.002 TYR E 310 ARG 0.003 0.001 ARG D 349 *********************** 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 104 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.562 Fit side-chains REVERT: A 356 SER cc_start: 0.9011 (t) cc_final: 0.8706 (p) REVERT: B 284 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8770 (mt) REVERT: C 349 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7808 (mtp180) REVERT: E 349 ARG cc_start: 0.8432 (mtt-85) cc_final: 0.8210 (mtm180) outliers start: 5 outliers final: 2 residues processed: 101 average time/residue: 0.8739 time to fit residues: 92.4448 Evaluate side-chains 102 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 HIS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 349 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 30 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 330 HIS B 276 GLN D 276 GLN D 279 ASN E 276 GLN E 279 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.131788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.114628 restraints weight = 13970.629| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.15 r_work: 0.3675 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4150 Z= 0.188 Angle : 0.561 6.901 5545 Z= 0.287 Chirality : 0.052 0.137 620 Planarity : 0.003 0.025 710 Dihedral : 5.788 15.818 560 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.85 % Allowed : 9.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.20), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 330 PHE 0.005 0.001 PHE E 378 TYR 0.009 0.002 TYR C 310 ARG 0.002 0.001 ARG B 379 *********************** 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 106 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.483 Fit side-chains REVERT: A 356 SER cc_start: 0.8983 (t) cc_final: 0.8738 (p) REVERT: C 349 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7711 (mtp180) outliers start: 4 outliers final: 1 residues processed: 105 average time/residue: 0.8917 time to fit residues: 98.0860 Evaluate side-chains 98 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 HIS 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 23 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 8 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 330 HIS B 276 GLN B 279 ASN D 276 GLN D 279 ASN E 276 GLN E 279 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.131763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.114613 restraints weight = 13711.052| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.14 r_work: 0.3677 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4150 Z= 0.198 Angle : 0.575 7.210 5545 Z= 0.293 Chirality : 0.053 0.170 620 Planarity : 0.003 0.041 710 Dihedral : 5.715 15.298 560 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.28 % Allowed : 10.43 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.19), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 330 PHE 0.005 0.001 PHE E 378 TYR 0.008 0.002 TYR C 310 ARG 0.002 0.001 ARG A 379 *********************** 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 104 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.456 Fit side-chains REVERT: A 356 SER cc_start: 0.8999 (t) cc_final: 0.8748 (p) REVERT: C 349 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7708 (mtp180) outliers start: 6 outliers final: 1 residues processed: 100 average time/residue: 0.9120 time to fit residues: 95.3646 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 : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 HIS 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 17 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 330 HIS B 276 GLN D 279 ASN E 276 GLN E 279 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.128666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.111183 restraints weight = 15118.057| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.24 r_work: 0.3613 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 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 = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2097 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= 0.327 Angle : 0.635 7.039 5545 Z= 0.328 Chirality : 0.055 0.233 620 Planarity : 0.003 0.023 710 Dihedral : 6.001 15.463 560 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.85 % Allowed : 11.06 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.20), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS A 330 PHE 0.008 0.002 PHE E 378 TYR 0.005 0.002 TYR C 310 ARG 0.001 0.000 ARG B 349 *********************** 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 104 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.496 Fit side-chains REVERT: A 356 SER cc_start: 0.9017 (t) cc_final: 0.8719 (p) REVERT: C 349 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7802 (mtp180) REVERT: E 349 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7998 (mtm180) outliers start: 4 outliers final: 1 residues processed: 101 average time/residue: 0.9356 time to fit residues: 98.8998 Evaluate side-chains 103 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 HIS Chi-restraints excluded: chain C residue 349 ARG Chi-restraints excluded: chain E residue 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 3 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 330 HIS B 276 GLN B 279 ASN E 276 GLN E 279 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.127406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.109735 restraints weight = 16727.098| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.34 r_work: 0.3592 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 4150 Z= 0.416 Angle : 0.683 7.135 5545 Z= 0.356 Chirality : 0.057 0.270 620 Planarity : 0.004 0.024 710 Dihedral : 6.195 16.071 560 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.85 % Allowed : 11.06 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.010 0.001 HIS A 330 PHE 0.009 0.002 PHE B 378 TYR 0.006 0.002 TYR E 310 ARG 0.001 0.000 ARG A 379 ********************** 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 104 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.469 Fit side-chains REVERT: A 349 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8056 (mtm180) REVERT: A 356 SER cc_start: 0.9027 (t) cc_final: 0.8722 (p) REVERT: E 349 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8006 (mtm180) outliers start: 4 outliers final: 1 residues processed: 101 average time/residue: 0.9216 time to fit residues: 97.6368 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 : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 HIS Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain E residue 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 29 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 330 HIS B 276 GLN D 276 GLN D 279 ASN E 276 GLN E 279 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.129069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.111385 restraints weight = 16694.560| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.34 r_work: 0.3616 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3512 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4150 Z= 0.286 Angle : 0.622 7.376 5545 Z= 0.320 Chirality : 0.055 0.228 620 Planarity : 0.003 0.025 710 Dihedral : 6.039 15.851 560 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.43 % Allowed : 11.91 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.26), residues: 535 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.20), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS A 330 PHE 0.007 0.001 PHE E 378 TYR 0.006 0.002 TYR C 310 ARG 0.002 0.001 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4882.18 seconds wall clock time: 87 minutes 6.96 seconds (5226.96 seconds total)