Starting phenix.real_space_refine on Fri Jul 3 01:35:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xuh_33469/07_2026/7xuh_33469.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xuh_33469/07_2026/7xuh_33469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xuh_33469/07_2026/7xuh_33469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xuh_33469/07_2026/7xuh_33469.map" model { file = "/net/cci-nas-00/data/ceres_data/7xuh_33469/07_2026/7xuh_33469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xuh_33469/07_2026/7xuh_33469.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7xuh_33469/07_2026/7xuh_33469.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xuh_33469/07_2026/7xuh_33469.cif" } resolution = 2.76 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 40 5.16 5 C 7526 2.51 5 N 1812 2.21 5 O 1996 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11380 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 5519 Classifications: {'peptide': 707} Link IDs: {'PTRANS': 31, 'TRANS': 675} Chain breaks: 1 Chain: "B" Number of atoms: 5519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 5519 Classifications: {'peptide': 707} Link IDs: {'PTRANS': 31, 'TRANS': 675} Chain breaks: 1 Chain: "A" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 169 Unusual residues: {'I2L': 1, 'Y01': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 169 Unusual residues: {'I2L': 1, 'Y01': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.46, per 1000 atoms: 0.22 Number of scatterers: 11380 At special positions: 0 Unit cell: (98.917, 122.831, 115.222, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 F 6 9.00 O 1996 8.00 N 1812 7.00 C 7526 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: 0.86 Conformation dependent library (CDL) restraints added in 470.7 milliseconds 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2648 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 3 sheets defined 62.1% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 removed outlier: 3.711A pdb=" N ASN A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 43 removed outlier: 4.177A pdb=" N HIS A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 39 " --> pdb=" O PHE A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 58 removed outlier: 3.950A pdb=" N LEU A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 68 through 95 removed outlier: 5.912A pdb=" N LEU A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N SER A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 110 through 120 removed outlier: 3.682A pdb=" N LEU A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 145 Processing helix chain 'A' and resid 170 through 196 removed outlier: 3.655A pdb=" N VAL A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.563A pdb=" N TYR A 204 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 205 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.535A pdb=" N ILE A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 225 through 230' Processing helix chain 'A' and resid 241 through 252 Processing helix chain 'A' and resid 253 through 257 removed outlier: 3.717A pdb=" N THR A 257 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 276 removed outlier: 3.738A pdb=" N THR A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 291 through 305 removed outlier: 3.552A pdb=" N ILE A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.564A pdb=" N PHE A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 removed outlier: 3.797A pdb=" N ASN A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 366 removed outlier: 3.714A pdb=" N GLY A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 removed outlier: 3.919A pdb=" N LEU A 375 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 376 " --> pdb=" O ASN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 406 Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'A' and resid 438 through 445 removed outlier: 3.599A pdb=" N ALA A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' Processing helix chain 'A' and resid 457 through 463 removed outlier: 3.838A pdb=" N ARG A 463 " --> pdb=" O GLY A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 483 removed outlier: 3.561A pdb=" N ILE A 471 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 503 removed outlier: 3.919A pdb=" N LEU A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 493 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE A 499 " --> pdb=" O GLN A 495 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A 503 " --> pdb=" O ILE A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 560 Processing helix chain 'A' and resid 563 through 583 Processing helix chain 'A' and resid 612 through 616 removed outlier: 3.548A pdb=" N LEU A 616 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 677 removed outlier: 3.723A pdb=" N ILE A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 695 removed outlier: 3.620A pdb=" N ILE A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 724 removed outlier: 3.569A pdb=" N MET A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 25 removed outlier: 3.710A pdb=" N ASN B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 43 removed outlier: 4.178A pdb=" N HIS B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 58 removed outlier: 3.950A pdb=" N LEU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 64 Processing helix chain 'B' and resid 68 through 95 removed outlier: 5.912A pdb=" N LEU B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N SER B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 110 through 120 removed outlier: 3.681A pdb=" N LEU B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE B 118 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 145 Processing helix chain 'B' and resid 170 through 196 removed outlier: 3.656A pdb=" N VAL B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA B 177 " --> pdb=" O ARG B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 205 removed outlier: 3.563A pdb=" N TYR B 204 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 205 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 225 removed outlier: 3.500A pdb=" N VAL B 219 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 230 removed outlier: 3.535A pdb=" N ILE B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 225 through 230' Processing helix chain 'B' and resid 241 through 252 Processing helix chain 'B' and resid 253 through 257 removed outlier: 3.717A pdb=" N THR B 257 " --> pdb=" O ILE B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 276 removed outlier: 3.738A pdb=" N THR B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 265 " --> pdb=" O ASP B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.552A pdb=" N ILE B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.563A pdb=" N PHE B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 removed outlier: 3.797A pdb=" N ASN B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 366 removed outlier: 3.714A pdb=" N GLY B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 removed outlier: 3.919A pdb=" N LEU B 375 " --> pdb=" O GLY B 371 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 376 " --> pdb=" O ASN B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 406 Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 438 through 445 removed outlier: 3.599A pdb=" N ALA B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 454 through 456 No H-bonds generated for 'chain 'B' and resid 454 through 456' Processing helix chain 'B' and resid 457 through 463 removed outlier: 3.837A pdb=" N ARG B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 483 removed outlier: 3.561A pdb=" N ILE B 471 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 503 removed outlier: 3.919A pdb=" N LEU B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE B 499 " --> pdb=" O GLN B 495 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 503 " --> pdb=" O ILE B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 560 Processing helix chain 'B' and resid 563 through 583 Processing helix chain 'B' and resid 612 through 616 removed outlier: 3.548A pdb=" N LEU B 616 " --> pdb=" O ILE B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 677 removed outlier: 3.723A pdb=" N ILE B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 695 removed outlier: 3.619A pdb=" N ILE B 691 " --> pdb=" O ASP B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 724 removed outlier: 3.570A pdb=" N MET B 722 " --> pdb=" O LEU B 718 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.773A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N ASN A 513 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 13.002A pdb=" N VAL A 535 " --> pdb=" O ASN A 513 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS A 536 " --> pdb=" O ILE A 650 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ASP A 652 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE A 538 " --> pdb=" O ASP A 652 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N PHE A 710 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A 683 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.773A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N ASN B 513 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 13.002A pdb=" N VAL B 535 " --> pdb=" O ASN B 513 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS B 536 " --> pdb=" O ILE B 650 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASP B 652 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE B 538 " --> pdb=" O ASP B 652 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N PHE B 710 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE B 683 " --> pdb=" O PHE B 710 " (cutoff:3.500A) 543 hydrogen bonds defined for protein. 1581 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.26: 1782 1.26 - 1.40: 2762 1.40 - 1.54: 6601 1.54 - 1.67: 435 1.67 - 1.81: 62 Bond restraints: 11642 Sorted by residual: bond pdb=" C13 I2L A1001 " pdb=" C17 I2L A1001 " ideal model delta sigma weight residual 1.457 1.780 -0.323 2.00e-02 2.50e+03 2.60e+02 bond pdb=" C13 I2L B 803 " pdb=" C17 I2L B 803 " ideal model delta sigma weight residual 1.457 1.779 -0.322 2.00e-02 2.50e+03 2.60e+02 bond pdb=" C14 I2L B 803 " pdb=" C16 I2L B 803 " ideal model delta sigma weight residual 1.397 1.126 0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" C14 I2L A1001 " pdb=" C16 I2L A1001 " ideal model delta sigma weight residual 1.397 1.126 0.271 2.00e-02 2.50e+03 1.83e+02 bond pdb=" C10 I2L A1001 " pdb=" C12 I2L A1001 " ideal model delta sigma weight residual 1.397 1.602 -0.205 2.00e-02 2.50e+03 1.05e+02 ... (remaining 11637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 15313 2.25 - 4.50: 450 4.50 - 6.74: 59 6.74 - 8.99: 22 8.99 - 11.24: 8 Bond angle restraints: 15852 Sorted by residual: angle pdb=" CA VAL A 288 " pdb=" CB VAL A 288 " pdb=" CG1 VAL A 288 " ideal model delta sigma weight residual 110.40 117.60 -7.20 1.70e+00 3.46e-01 1.80e+01 angle pdb=" CA VAL B 288 " pdb=" CB VAL B 288 " pdb=" CG1 VAL B 288 " ideal model delta sigma weight residual 110.40 117.59 -7.19 1.70e+00 3.46e-01 1.79e+01 angle pdb=" C PRO A 150 " pdb=" N ASP A 151 " pdb=" CA ASP A 151 " ideal model delta sigma weight residual 121.54 129.14 -7.60 1.91e+00 2.74e-01 1.58e+01 angle pdb=" C PRO B 150 " pdb=" N ASP B 151 " pdb=" CA ASP B 151 " ideal model delta sigma weight residual 121.54 129.06 -7.52 1.91e+00 2.74e-01 1.55e+01 angle pdb=" C VAL A 241 " pdb=" N SER A 242 " pdb=" CA SER A 242 " ideal model delta sigma weight residual 120.38 126.01 -5.63 1.46e+00 4.69e-01 1.49e+01 ... (remaining 15847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 6520 23.98 - 47.96: 322 47.96 - 71.94: 38 71.94 - 95.92: 10 95.92 - 119.90: 2 Dihedral angle restraints: 6892 sinusoidal: 2794 harmonic: 4098 Sorted by residual: dihedral pdb=" CA PRO B 150 " pdb=" C PRO B 150 " pdb=" N ASP B 151 " pdb=" CA ASP B 151 " ideal model delta harmonic sigma weight residual 180.00 -139.35 -40.65 0 5.00e+00 4.00e-02 6.61e+01 dihedral pdb=" CA PRO A 150 " pdb=" C PRO A 150 " pdb=" N ASP A 151 " pdb=" CA ASP A 151 " ideal model delta harmonic sigma weight residual 180.00 -139.40 -40.60 0 5.00e+00 4.00e-02 6.59e+01 dihedral pdb=" CA ASP A 239 " pdb=" C ASP A 239 " pdb=" N PRO A 240 " pdb=" CA PRO A 240 " ideal model delta harmonic sigma weight residual 180.00 152.28 27.72 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 6889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1175 0.046 - 0.091: 535 0.091 - 0.136: 145 0.136 - 0.182: 19 0.182 - 0.227: 10 Chirality restraints: 1884 Sorted by residual: chirality pdb=" CB VAL A 560 " pdb=" CA VAL A 560 " pdb=" CG1 VAL A 560 " pdb=" CG2 VAL A 560 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB VAL B 560 " pdb=" CA VAL B 560 " pdb=" CG1 VAL B 560 " pdb=" CG2 VAL B 560 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE B 677 " pdb=" CA ILE B 677 " pdb=" CG1 ILE B 677 " pdb=" CG2 ILE B 677 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1881 not shown) Planarity restraints: 1934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 433 " 0.046 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO A 434 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 434 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 434 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 433 " 0.046 5.00e-02 4.00e+02 6.82e-02 7.44e+00 pdb=" N PRO B 434 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 434 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 434 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 18 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.19e+00 pdb=" C THR A 18 " 0.046 2.00e-02 2.50e+03 pdb=" O THR A 18 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN A 19 " -0.016 2.00e-02 2.50e+03 ... (remaining 1931 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2975 2.80 - 3.32: 9741 3.32 - 3.85: 17679 3.85 - 4.37: 21162 4.37 - 4.90: 36354 Nonbonded interactions: 87911 Sorted by model distance: nonbonded pdb=" OG1 THR A 121 " pdb=" OE2 GLU A 374 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR B 121 " pdb=" OE2 GLU B 374 " model vdw 2.275 3.040 nonbonded pdb=" NZ LYS B 245 " pdb=" OAH Y01 B 804 " model vdw 2.293 3.120 nonbonded pdb=" NZ LYS A 245 " pdb=" OAH Y01 A1002 " model vdw 2.294 3.120 nonbonded pdb=" OG1 THR B 712 " pdb=" OD2 ASP B 715 " model vdw 2.300 3.040 ... (remaining 87906 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 725 or resid 1002 or resid 1004 through 1005)) selection = (chain 'B' and (resid 8 through 725 or resid 802 or resid 804 through 805)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 9.940 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.323 11642 Z= 0.502 Angle : 0.962 11.241 15852 Z= 0.505 Chirality : 0.055 0.227 1884 Planarity : 0.008 0.068 1934 Dihedral : 14.338 119.898 4244 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.98 % Allowed : 5.74 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 are not related in a simple way. whole: -3.53 (0.17), residues: 1406 helix: -2.22 (0.13), residues: 828 sheet: 1.32 (0.72), residues: 34 loop : -2.61 (0.22), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 152 TYR 0.029 0.002 TYR B 9 PHE 0.031 0.002 PHE A 130 TRP 0.032 0.003 TRP B 63 HIS 0.004 0.001 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.01102 / 0.50 (11642) covalent geometry : angle 0.96195 / 0.51 (15852) hydrogen bonds : bond 0.17912 / 11.90 ( 543) hydrogen bonds : angle 6.33356 / 4.62 ( 1581) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.393 Fit side-chains REVERT: A 34 THR cc_start: 0.6038 (OUTLIER) cc_final: 0.5818 (m) REVERT: A 171 ASP cc_start: 0.8246 (p0) cc_final: 0.7971 (p0) REVERT: A 193 PHE cc_start: 0.8937 (m-80) cc_final: 0.8656 (m-80) REVERT: A 296 MET cc_start: 0.8812 (mmm) cc_final: 0.8603 (mmp) REVERT: A 558 ASP cc_start: 0.7041 (m-30) cc_final: 0.6824 (m-30) REVERT: B 34 THR cc_start: 0.6079 (OUTLIER) cc_final: 0.5846 (m) REVERT: B 171 ASP cc_start: 0.8232 (p0) cc_final: 0.7943 (p0) REVERT: B 193 PHE cc_start: 0.8939 (m-80) cc_final: 0.8668 (m-80) REVERT: B 296 MET cc_start: 0.8768 (mmm) cc_final: 0.8562 (mmp) REVERT: B 558 ASP cc_start: 0.6989 (m-30) cc_final: 0.6723 (m-30) outliers start: 12 outliers final: 6 residues processed: 145 average time/residue: 0.6012 time to fit residues: 94.1263 Evaluate side-chains 86 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 406 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.0980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 GLN A 495 GLN A 513 ASN B 337 GLN B 495 GLN B 504 GLN B 513 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.114727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.080223 restraints weight = 15488.869| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.18 r_work: 0.2774 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11642 Z= 0.119 Angle : 0.555 5.964 15852 Z= 0.293 Chirality : 0.041 0.140 1884 Planarity : 0.005 0.047 1934 Dihedral : 8.132 116.157 1682 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.48 % Allowed : 10.00 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 are not related in a simple way. whole: -1.25 (0.22), residues: 1406 helix: -0.23 (0.18), residues: 840 sheet: 2.58 (0.72), residues: 34 loop : -1.96 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 281 TYR 0.012 0.001 TYR A 9 PHE 0.018 0.001 PHE A 130 TRP 0.006 0.001 TRP B 472 HIS 0.003 0.001 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (11642) covalent geometry : angle 0.55547 / 0.29 (15852) hydrogen bonds : bond 0.04905 / 3.31 ( 543) hydrogen bonds : angle 4.34033 / 3.16 ( 1581) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.452 Fit side-chains REVERT: A 24 ASN cc_start: 0.9099 (m-40) cc_final: 0.8796 (m110) REVERT: A 58 PHE cc_start: 0.8300 (m-80) cc_final: 0.7667 (t80) REVERT: A 171 ASP cc_start: 0.8158 (p0) cc_final: 0.7863 (p0) REVERT: A 193 PHE cc_start: 0.8876 (m-80) cc_final: 0.8670 (m-80) REVERT: A 274 ILE cc_start: 0.8538 (pt) cc_final: 0.8308 (pp) REVERT: B 24 ASN cc_start: 0.9127 (m-40) cc_final: 0.8821 (m110) REVERT: B 58 PHE cc_start: 0.8273 (m-80) cc_final: 0.7695 (t80) REVERT: B 171 ASP cc_start: 0.8155 (p0) cc_final: 0.7864 (p0) REVERT: B 193 PHE cc_start: 0.8858 (m-80) cc_final: 0.8637 (m-80) REVERT: B 274 ILE cc_start: 0.8465 (pt) cc_final: 0.8215 (pp) REVERT: B 285 LYS cc_start: 0.7508 (tmtt) cc_final: 0.7081 (tptt) outliers start: 18 outliers final: 8 residues processed: 109 average time/residue: 0.4552 time to fit residues: 55.3397 Evaluate side-chains 88 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 594 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 109 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 436 GLN A 504 GLN A 714 HIS B 436 GLN B 714 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.112566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.077954 restraints weight = 15670.773| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.20 r_work: 0.2728 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11642 Z= 0.158 Angle : 0.555 6.134 15852 Z= 0.290 Chirality : 0.042 0.128 1884 Planarity : 0.004 0.049 1934 Dihedral : 7.914 116.945 1674 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.21 % Allowed : 10.82 % Favored : 86.97 % 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 are not related in a simple way. whole: -0.49 (0.23), residues: 1406 helix: 0.40 (0.19), residues: 836 sheet: 3.13 (0.80), residues: 34 loop : -1.70 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 281 TYR 0.018 0.002 TYR B 9 PHE 0.020 0.001 PHE B 130 TRP 0.006 0.001 TRP A 472 HIS 0.005 0.001 HIS A 714 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (11642) covalent geometry : angle 0.55524 / 0.29 (15852) hydrogen bonds : bond 0.05137 / 3.49 ( 543) hydrogen bonds : angle 4.07949 / 2.97 ( 1581) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.367 Fit side-chains REVERT: A 24 ASN cc_start: 0.9089 (m-40) cc_final: 0.8776 (m110) REVERT: A 58 PHE cc_start: 0.8423 (m-80) cc_final: 0.7910 (t80) REVERT: A 193 PHE cc_start: 0.8937 (m-80) cc_final: 0.8700 (m-80) REVERT: A 285 LYS cc_start: 0.7599 (tmtt) cc_final: 0.7244 (tmtm) REVERT: B 24 ASN cc_start: 0.9093 (m-40) cc_final: 0.8785 (m110) REVERT: B 58 PHE cc_start: 0.8367 (m-80) cc_final: 0.7916 (t80) REVERT: B 193 PHE cc_start: 0.8933 (m-80) cc_final: 0.8715 (m-80) REVERT: B 285 LYS cc_start: 0.7584 (tmtt) cc_final: 0.7214 (tmtm) outliers start: 27 outliers final: 19 residues processed: 107 average time/residue: 0.4987 time to fit residues: 58.9574 Evaluate side-chains 97 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 558 ASP Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 55 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.110663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.075870 restraints weight = 15714.667| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.21 r_work: 0.2676 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11642 Z= 0.218 Angle : 0.595 6.490 15852 Z= 0.312 Chirality : 0.044 0.133 1884 Planarity : 0.005 0.054 1934 Dihedral : 8.032 117.746 1672 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.54 % Allowed : 11.89 % Favored : 85.57 % 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 are not related in a simple way. whole: -0.33 (0.23), residues: 1406 helix: 0.55 (0.19), residues: 844 sheet: 2.90 (0.80), residues: 34 loop : -1.68 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 281 TYR 0.023 0.002 TYR A 9 PHE 0.018 0.002 PHE B 130 TRP 0.009 0.001 TRP A 63 HIS 0.006 0.001 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.22 (11642) covalent geometry : angle 0.59543 / 0.31 (15852) hydrogen bonds : bond 0.05755 / 3.91 ( 543) hydrogen bonds : angle 4.10898 / 2.98 ( 1581) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.468 Fit side-chains REVERT: A 58 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.7973 (t80) REVERT: A 171 ASP cc_start: 0.8214 (p0) cc_final: 0.7847 (p0) REVERT: A 193 PHE cc_start: 0.8938 (m-80) cc_final: 0.8718 (m-80) REVERT: A 285 LYS cc_start: 0.7706 (tmtt) cc_final: 0.7365 (tmtm) REVERT: B 58 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7966 (t80) REVERT: B 171 ASP cc_start: 0.8231 (p0) cc_final: 0.7846 (p0) REVERT: B 193 PHE cc_start: 0.8929 (m-80) cc_final: 0.8710 (m-80) REVERT: B 281 ARG cc_start: 0.7538 (ttm110) cc_final: 0.6784 (ttm170) REVERT: B 285 LYS cc_start: 0.7710 (tmtt) cc_final: 0.7353 (tmtm) outliers start: 31 outliers final: 26 residues processed: 106 average time/residue: 0.4953 time to fit residues: 58.0499 Evaluate side-chains 103 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 74 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.114093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.079378 restraints weight = 15595.831| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.21 r_work: 0.2747 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11642 Z= 0.110 Angle : 0.526 8.147 15852 Z= 0.271 Chirality : 0.040 0.137 1884 Planarity : 0.004 0.049 1934 Dihedral : 7.527 116.630 1672 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.30 % Allowed : 13.28 % Favored : 84.43 % 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 are not related in a simple way. whole: 0.18 (0.23), residues: 1406 helix: 0.98 (0.19), residues: 834 sheet: 3.11 (0.81), residues: 34 loop : -1.46 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 281 TYR 0.011 0.001 TYR A 9 PHE 0.017 0.001 PHE A 130 TRP 0.013 0.001 TRP A 63 HIS 0.002 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (11642) covalent geometry : angle 0.52630 / 0.27 (15852) hydrogen bonds : bond 0.04161 / 2.83 ( 543) hydrogen bonds : angle 3.89749 / 2.83 ( 1581) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.540 Fit side-chains REVERT: A 24 ASN cc_start: 0.9000 (m-40) cc_final: 0.8665 (m110) REVERT: A 58 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7866 (t80) REVERT: A 169 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7731 (tp) REVERT: A 171 ASP cc_start: 0.8193 (p0) cc_final: 0.7880 (p0) REVERT: A 193 PHE cc_start: 0.8917 (m-80) cc_final: 0.8709 (m-80) REVERT: A 281 ARG cc_start: 0.7628 (ttm110) cc_final: 0.6862 (ttm170) REVERT: A 285 LYS cc_start: 0.7635 (tmtt) cc_final: 0.7344 (tmtm) REVERT: B 24 ASN cc_start: 0.8991 (m-40) cc_final: 0.8653 (m110) REVERT: B 58 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7851 (t80) REVERT: B 169 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7750 (tp) REVERT: B 171 ASP cc_start: 0.8203 (p0) cc_final: 0.7882 (p0) REVERT: B 193 PHE cc_start: 0.8911 (m-80) cc_final: 0.8704 (m-80) REVERT: B 281 ARG cc_start: 0.7627 (ttm110) cc_final: 0.6897 (ttm170) REVERT: B 285 LYS cc_start: 0.7689 (tmtt) cc_final: 0.7374 (tmtm) REVERT: B 637 LEU cc_start: 0.7852 (mm) cc_final: 0.7549 (tp) outliers start: 28 outliers final: 16 residues processed: 107 average time/residue: 0.5067 time to fit residues: 59.8538 Evaluate side-chains 99 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 57 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 137 optimal weight: 0.1980 chunk 69 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.114465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.079873 restraints weight = 15731.020| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.20 r_work: 0.2743 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11642 Z= 0.115 Angle : 0.524 6.976 15852 Z= 0.270 Chirality : 0.040 0.124 1884 Planarity : 0.004 0.046 1934 Dihedral : 7.244 116.304 1672 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.54 % Allowed : 12.79 % Favored : 84.67 % 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 are not related in a simple way. whole: 0.47 (0.23), residues: 1406 helix: 1.19 (0.19), residues: 836 sheet: 3.27 (0.81), residues: 34 loop : -1.31 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 281 TYR 0.012 0.001 TYR A 9 PHE 0.017 0.001 PHE A 130 TRP 0.012 0.001 TRP A 63 HIS 0.003 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (11642) covalent geometry : angle 0.52411 / 0.27 (15852) hydrogen bonds : bond 0.04012 / 2.73 ( 543) hydrogen bonds : angle 3.80745 / 2.77 ( 1581) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 90 time to evaluate : 0.475 Fit side-chains REVERT: A 24 ASN cc_start: 0.8966 (m-40) cc_final: 0.8617 (m110) REVERT: A 58 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7873 (t80) REVERT: A 281 ARG cc_start: 0.7493 (ttm110) cc_final: 0.6807 (ttm170) REVERT: B 24 ASN cc_start: 0.8970 (m-40) cc_final: 0.8618 (m110) REVERT: B 58 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7863 (t80) REVERT: B 193 PHE cc_start: 0.8880 (m-80) cc_final: 0.8671 (m-80) outliers start: 31 outliers final: 21 residues processed: 109 average time/residue: 0.4759 time to fit residues: 57.5694 Evaluate side-chains 103 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 46 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 131 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.115224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.080639 restraints weight = 15546.943| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.21 r_work: 0.2755 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11642 Z= 0.110 Angle : 0.515 6.627 15852 Z= 0.266 Chirality : 0.040 0.124 1884 Planarity : 0.004 0.045 1934 Dihedral : 7.056 116.166 1672 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.70 % Allowed : 13.93 % Favored : 83.36 % 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 are not related in a simple way. whole: 0.69 (0.23), residues: 1406 helix: 1.37 (0.19), residues: 834 sheet: 3.27 (0.81), residues: 34 loop : -1.20 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 281 TYR 0.011 0.001 TYR A 9 PHE 0.016 0.001 PHE A 130 TRP 0.013 0.001 TRP A 63 HIS 0.002 0.001 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (11642) covalent geometry : angle 0.51479 / 0.27 (15852) hydrogen bonds : bond 0.03823 / 2.61 ( 543) hydrogen bonds : angle 3.75642 / 2.74 ( 1581) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 86 time to evaluate : 0.451 Fit side-chains REVERT: A 24 ASN cc_start: 0.8949 (m-40) cc_final: 0.8594 (m110) REVERT: A 58 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7840 (t80) REVERT: A 171 ASP cc_start: 0.8249 (p0) cc_final: 0.7916 (p0) REVERT: A 609 ASP cc_start: 0.8501 (p0) cc_final: 0.8286 (p0) REVERT: B 24 ASN cc_start: 0.8961 (m-40) cc_final: 0.8599 (m110) REVERT: B 58 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7828 (t80) REVERT: B 171 ASP cc_start: 0.8241 (p0) cc_final: 0.7908 (p0) REVERT: B 281 ARG cc_start: 0.7560 (ttm110) cc_final: 0.6809 (ttm170) outliers start: 33 outliers final: 19 residues processed: 107 average time/residue: 0.4547 time to fit residues: 54.1118 Evaluate side-chains 105 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 105 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 108 optimal weight: 9.9990 chunk 129 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.114518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.079859 restraints weight = 15525.885| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.21 r_work: 0.2741 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11642 Z= 0.125 Angle : 0.526 6.642 15852 Z= 0.274 Chirality : 0.041 0.127 1884 Planarity : 0.004 0.045 1934 Dihedral : 7.041 116.256 1672 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.46 % Allowed : 14.26 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.23), residues: 1406 helix: 1.38 (0.19), residues: 840 sheet: 3.22 (0.80), residues: 34 loop : -1.16 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 281 TYR 0.013 0.001 TYR A 9 PHE 0.017 0.001 PHE A 130 TRP 0.012 0.001 TRP A 63 HIS 0.003 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (11642) covalent geometry : angle 0.52648 / 0.27 (15852) hydrogen bonds : bond 0.04116 / 2.81 ( 543) hydrogen bonds : angle 3.76420 / 2.74 ( 1581) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.399 Fit side-chains REVERT: A 24 ASN cc_start: 0.8960 (m-40) cc_final: 0.8613 (m110) REVERT: A 58 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7862 (t80) REVERT: A 241 VAL cc_start: 0.7980 (OUTLIER) cc_final: 0.7716 (t) REVERT: A 277 GLU cc_start: 0.6713 (pp20) cc_final: 0.6428 (pp20) REVERT: A 281 ARG cc_start: 0.7581 (ttm110) cc_final: 0.6837 (ttm170) REVERT: A 609 ASP cc_start: 0.8515 (p0) cc_final: 0.8302 (p0) REVERT: B 24 ASN cc_start: 0.8971 (m-40) cc_final: 0.8613 (m110) REVERT: B 58 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7851 (t80) REVERT: B 241 VAL cc_start: 0.8039 (OUTLIER) cc_final: 0.7775 (t) REVERT: B 281 ARG cc_start: 0.7613 (ttm110) cc_final: 0.6887 (ttm170) REVERT: B 609 ASP cc_start: 0.8446 (p0) cc_final: 0.8243 (p0) outliers start: 30 outliers final: 21 residues processed: 105 average time/residue: 0.4515 time to fit residues: 52.7656 Evaluate side-chains 111 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 132 optimal weight: 0.0870 chunk 98 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.115602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.081031 restraints weight = 15422.249| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.20 r_work: 0.2752 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11642 Z= 0.109 Angle : 0.511 7.122 15852 Z= 0.266 Chirality : 0.040 0.126 1884 Planarity : 0.004 0.043 1934 Dihedral : 6.850 116.014 1672 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.30 % Allowed : 14.67 % Favored : 83.03 % 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 are not related in a simple way. whole: 0.89 (0.23), residues: 1406 helix: 1.49 (0.19), residues: 840 sheet: 3.35 (0.81), residues: 34 loop : -1.08 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 281 TYR 0.010 0.001 TYR A 9 PHE 0.016 0.001 PHE A 130 TRP 0.013 0.001 TRP A 63 HIS 0.002 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (11642) covalent geometry : angle 0.51125 / 0.27 (15852) hydrogen bonds : bond 0.03742 / 2.55 ( 543) hydrogen bonds : angle 3.72534 / 2.71 ( 1581) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.517 Fit side-chains REVERT: A 24 ASN cc_start: 0.8980 (m-40) cc_final: 0.8625 (m110) REVERT: A 58 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7807 (t80) REVERT: A 241 VAL cc_start: 0.7967 (OUTLIER) cc_final: 0.7704 (t) REVERT: A 277 GLU cc_start: 0.6741 (pp20) cc_final: 0.6456 (pp20) REVERT: A 281 ARG cc_start: 0.7546 (ttm110) cc_final: 0.6789 (ttm170) REVERT: A 609 ASP cc_start: 0.8444 (p0) cc_final: 0.8225 (p0) REVERT: B 24 ASN cc_start: 0.8989 (m-40) cc_final: 0.8619 (m110) REVERT: B 58 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7833 (t80) REVERT: B 241 VAL cc_start: 0.7958 (OUTLIER) cc_final: 0.7701 (t) REVERT: B 277 GLU cc_start: 0.6721 (pp20) cc_final: 0.6489 (pp20) REVERT: B 281 ARG cc_start: 0.7542 (ttm110) cc_final: 0.7025 (mtp-110) outliers start: 28 outliers final: 19 residues processed: 107 average time/residue: 0.4842 time to fit residues: 57.5512 Evaluate side-chains 111 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 47 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 ASN B 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.115972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.081374 restraints weight = 15555.601| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.21 r_work: 0.2763 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11642 Z= 0.108 Angle : 0.518 9.931 15852 Z= 0.267 Chirality : 0.040 0.129 1884 Planarity : 0.004 0.042 1934 Dihedral : 6.728 115.950 1672 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.30 % Allowed : 14.92 % Favored : 82.79 % 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 are not related in a simple way. whole: 0.98 (0.23), residues: 1406 helix: 1.56 (0.19), residues: 840 sheet: 3.34 (0.81), residues: 34 loop : -1.04 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 281 TYR 0.010 0.001 TYR B 9 PHE 0.016 0.001 PHE A 130 TRP 0.013 0.001 TRP A 63 HIS 0.003 0.001 HIS B 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (11642) covalent geometry : angle 0.51782 / 0.27 (15852) hydrogen bonds : bond 0.03682 / 2.52 ( 543) hydrogen bonds : angle 3.69440 / 2.70 ( 1581) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.490 Fit side-chains REVERT: A 24 ASN cc_start: 0.8956 (m-40) cc_final: 0.8593 (m110) REVERT: A 58 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7783 (t80) REVERT: A 241 VAL cc_start: 0.7912 (OUTLIER) cc_final: 0.7645 (t) REVERT: A 277 GLU cc_start: 0.6709 (pp20) cc_final: 0.6412 (pp20) REVERT: A 281 ARG cc_start: 0.7501 (ttm110) cc_final: 0.6778 (ttm170) REVERT: A 285 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7731 (pptt) REVERT: A 609 ASP cc_start: 0.8417 (p0) cc_final: 0.8216 (p0) REVERT: B 24 ASN cc_start: 0.8958 (m-40) cc_final: 0.8582 (m110) REVERT: B 58 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7743 (t80) REVERT: B 241 VAL cc_start: 0.7909 (OUTLIER) cc_final: 0.7648 (t) REVERT: B 277 GLU cc_start: 0.6683 (pp20) cc_final: 0.6440 (pp20) REVERT: B 281 ARG cc_start: 0.7569 (ttm110) cc_final: 0.7027 (mtp-110) REVERT: B 285 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7784 (pptt) REVERT: B 558 ASP cc_start: 0.8396 (t0) cc_final: 0.8051 (m-30) REVERT: B 609 ASP cc_start: 0.8285 (p0) cc_final: 0.8073 (p0) outliers start: 28 outliers final: 16 residues processed: 106 average time/residue: 0.4895 time to fit residues: 57.5624 Evaluate side-chains 109 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 594 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 528 ASP Chi-restraints excluded: chain B residue 594 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 684 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 32 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 ASN B 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.116022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.081405 restraints weight = 15551.112| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.21 r_work: 0.2746 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11642 Z= 0.107 Angle : 0.515 9.693 15852 Z= 0.264 Chirality : 0.040 0.190 1884 Planarity : 0.004 0.042 1934 Dihedral : 6.644 115.978 1672 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.97 % Allowed : 15.16 % Favored : 82.87 % 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 are not related in a simple way. whole: 1.03 (0.23), residues: 1406 helix: 1.60 (0.19), residues: 840 sheet: 3.34 (0.81), residues: 34 loop : -1.01 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 281 TYR 0.010 0.001 TYR A 9 PHE 0.016 0.001 PHE A 130 TRP 0.013 0.001 TRP A 63 HIS 0.002 0.000 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (11642) covalent geometry : angle 0.51511 / 0.26 (15852) hydrogen bonds : bond 0.03678 / 2.51 ( 543) hydrogen bonds : angle 3.68637 / 2.69 ( 1581) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3846.58 seconds wall clock time: 66 minutes 27.48 seconds (3987.48 seconds total)