Starting phenix.real_space_refine on Wed Mar 4 06:31:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t57_25697/03_2026/7t57_25697.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t57_25697/03_2026/7t57_25697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t57_25697/03_2026/7t57_25697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t57_25697/03_2026/7t57_25697.map" model { file = "/net/cci-nas-00/data/ceres_data/7t57_25697/03_2026/7t57_25697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t57_25697/03_2026/7t57_25697.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.032 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 60 5.16 5 C 7382 2.51 5 N 1870 2.21 5 O 2140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11460 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5581 Classifications: {'peptide': 715} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 701} Chain: "C" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 117 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5581 Classifications: {'peptide': 715} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 701} Chain: "D" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 117 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.55, per 1000 atoms: 0.22 Number of scatterers: 11460 At special positions: 0 Unit cell: (106.09, 98.88, 143.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 6 15.00 Mg 2 11.99 O 2140 8.00 N 1870 7.00 C 7382 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: 0.90 Conformation dependent library (CDL) restraints added in 561.8 milliseconds 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2712 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 8 sheets defined 63.0% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 20 through 34 Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 54 through 66 Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 153 through 160 removed outlier: 3.875A pdb=" N LYS A 157 " --> pdb=" O ASN A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 164 Proline residue: A 164 - end of helix No H-bonds generated for 'chain 'A' and resid 161 through 164' Processing helix chain 'A' and resid 165 through 196 removed outlier: 3.720A pdb=" N VAL A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE A 190 " --> pdb=" O GLY A 186 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 213 Processing helix chain 'A' and resid 214 through 251 Processing helix chain 'A' and resid 254 through 261 removed outlier: 3.871A pdb=" N PHE A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 281 removed outlier: 4.155A pdb=" N ARG A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS A 275 " --> pdb=" O MET A 271 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 305 removed outlier: 3.712A pdb=" N LEU A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 354 removed outlier: 4.569A pdb=" N LYS A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Proline residue: A 329 - end of helix removed outlier: 3.601A pdb=" N ALA A 342 " --> pdb=" O MET A 338 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS A 343 " --> pdb=" O GLU A 339 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR A 345 " --> pdb=" O ASN A 341 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 363 through 418 removed outlier: 3.588A pdb=" N THR A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 374 " --> pdb=" O SER A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 460 removed outlier: 4.418A pdb=" N LEU A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A 433 " --> pdb=" O ASN A 429 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Proline residue: A 438 - end of helix removed outlier: 4.122A pdb=" N GLN A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Proline residue: A 447 - end of helix Processing helix chain 'A' and resid 461 through 465 removed outlier: 3.615A pdb=" N GLU A 464 " --> pdb=" O GLU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 472 removed outlier: 3.696A pdb=" N LEU A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 533 Processing helix chain 'A' and resid 549 through 553 Processing helix chain 'A' and resid 554 through 561 Processing helix chain 'A' and resid 576 through 581 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.985A pdb=" N ILE A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 606 removed outlier: 3.666A pdb=" N GLU A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 621 Processing helix chain 'A' and resid 624 through 639 removed outlier: 3.827A pdb=" N LYS A 639 " --> pdb=" O ARG A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 652 removed outlier: 4.380A pdb=" N ASN A 652 " --> pdb=" O ALA A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 667 Processing helix chain 'A' and resid 703 through 711 removed outlier: 3.650A pdb=" N LEU A 707 " --> pdb=" O SER A 703 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 711 " --> pdb=" O LEU A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 722 Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'B' and resid 20 through 34 removed outlier: 3.509A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 47 Processing helix chain 'B' and resid 54 through 66 Processing helix chain 'B' and resid 125 through 132 Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 160 through 164 Proline residue: B 164 - end of helix Processing helix chain 'B' and resid 165 through 196 removed outlier: 3.694A pdb=" N VAL B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LYS B 191 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE B 192 " --> pdb=" O PHE B 188 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP B 196 " --> pdb=" O PHE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 213 Processing helix chain 'B' and resid 214 through 251 Processing helix chain 'B' and resid 254 through 261 removed outlier: 3.751A pdb=" N PHE B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 281 removed outlier: 4.077A pdb=" N ILE B 266 " --> pdb=" O LYS B 262 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER B 274 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS B 275 " --> pdb=" O MET B 271 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 305 removed outlier: 3.674A pdb=" N LEU B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 354 removed outlier: 4.645A pdb=" N LYS B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix removed outlier: 3.872A pdb=" N LYS B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR B 345 " --> pdb=" O ASN B 341 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER B 346 " --> pdb=" O ALA B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 363 through 418 removed outlier: 3.599A pdb=" N THR B 367 " --> pdb=" O ALA B 363 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 461 removed outlier: 4.074A pdb=" N LEU B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU B 426 " --> pdb=" O GLY B 422 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA B 433 " --> pdb=" O ASN B 429 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) Proline residue: B 438 - end of helix removed outlier: 4.000A pdb=" N GLN B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) Proline residue: B 447 - end of helix removed outlier: 3.579A pdb=" N GLU B 461 " --> pdb=" O ASN B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 465 Processing helix chain 'B' and resid 467 through 472 removed outlier: 4.069A pdb=" N LEU B 471 " --> pdb=" O THR B 467 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG B 472 " --> pdb=" O GLU B 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 467 through 472' Processing helix chain 'B' and resid 525 through 534 Processing helix chain 'B' and resid 554 through 561 removed outlier: 3.599A pdb=" N ILE B 558 " --> pdb=" O SER B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 581 Processing helix chain 'B' and resid 589 through 599 Processing helix chain 'B' and resid 603 through 608 removed outlier: 3.944A pdb=" N GLU B 606 " --> pdb=" O ASP B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 620 Processing helix chain 'B' and resid 624 through 639 removed outlier: 3.931A pdb=" N LYS B 639 " --> pdb=" O ARG B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 652 removed outlier: 4.380A pdb=" N ASN B 652 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 667 Processing helix chain 'B' and resid 703 through 711 removed outlier: 3.630A pdb=" N LYS B 711 " --> pdb=" O LEU B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 718 Processing helix chain 'D' and resid 14 through 21 removed outlier: 3.639A pdb=" N GLU D 20 " --> pdb=" O GLU D 16 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 72 removed outlier: 6.999A pdb=" N THR A 112 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ILE A 106 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 506 through 509 removed outlier: 4.240A pdb=" N VAL A 491 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LYS A 540 " --> pdb=" O VAL A 491 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 562 through 565 removed outlier: 6.483A pdb=" N ALA A 563 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL A 515 " --> pdb=" O ILE A 676 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ALA A 678 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 517 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE A 690 " --> pdb=" O SER A 701 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER A 701 " --> pdb=" O ILE A 690 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU A 692 " --> pdb=" O VAL A 699 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 574 through 575 Processing sheet with id=AA5, first strand: chain 'B' and resid 67 through 72 removed outlier: 7.049A pdb=" N THR B 112 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ILE B 106 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 506 through 509 removed outlier: 4.198A pdb=" N VAL B 491 " --> pdb=" O LYS B 540 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS B 540 " --> pdb=" O VAL B 491 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 562 through 564 removed outlier: 6.609A pdb=" N LEU B 644 " --> pdb=" O ILE B 675 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE B 677 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU B 646 " --> pdb=" O ILE B 677 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL B 515 " --> pdb=" O ILE B 676 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ALA B 678 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE B 517 " --> pdb=" O ALA B 678 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE B 690 " --> pdb=" O SER B 701 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER B 701 " --> pdb=" O ILE B 690 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 692 " --> pdb=" O VAL B 699 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 574 through 575 removed outlier: 3.733A pdb=" N GLY B 574 " --> pdb=" O LEU B 616 " (cutoff:3.500A) 681 hydrogen bonds defined for protein. 1971 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: 1.58 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3592 1.34 - 1.46: 1450 1.46 - 1.57: 6482 1.57 - 1.69: 8 1.69 - 1.81: 104 Bond restraints: 11636 Sorted by residual: bond pdb=" O2B ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 1.529 1.459 0.070 2.20e-02 2.07e+03 1.01e+01 bond pdb=" N ARG A 84 " pdb=" CA ARG A 84 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 6.94e+00 bond pdb=" N LEU A 80 " pdb=" CA LEU A 80 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.25e-02 6.40e+03 6.72e+00 bond pdb=" N PHE A 83 " pdb=" CA PHE A 83 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.18e-02 7.18e+03 6.25e+00 bond pdb=" O2A ATP B 801 " pdb=" PA ATP B 801 " ideal model delta sigma weight residual 1.529 1.474 0.055 2.20e-02 2.07e+03 6.20e+00 ... (remaining 11631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.84: 15664 4.84 - 9.68: 27 9.68 - 14.52: 2 14.52 - 19.37: 2 19.37 - 24.21: 1 Bond angle restraints: 15696 Sorted by residual: angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 115.66 24.21 1.00e+00 1.00e+00 5.86e+02 angle pdb=" PA ATP B 801 " pdb=" O3A ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 136.83 117.68 19.15 1.00e+00 1.00e+00 3.67e+02 angle pdb=" C5' ATP B 801 " pdb=" O5' ATP B 801 " pdb=" PA ATP B 801 " ideal model delta sigma weight residual 121.27 103.55 17.72 1.00e+00 1.00e+00 3.14e+02 angle pdb=" N VAL B 479 " pdb=" CA VAL B 479 " pdb=" C VAL B 479 " ideal model delta sigma weight residual 108.11 115.53 -7.42 1.40e+00 5.10e-01 2.81e+01 angle pdb=" N SER A 549 " pdb=" CA SER A 549 " pdb=" C SER A 549 " ideal model delta sigma weight residual 110.19 116.71 -6.52 1.24e+00 6.50e-01 2.77e+01 ... (remaining 15691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 6311 16.69 - 33.38: 566 33.38 - 50.06: 147 50.06 - 66.75: 31 66.75 - 83.44: 13 Dihedral angle restraints: 7068 sinusoidal: 2846 harmonic: 4222 Sorted by residual: dihedral pdb=" CA ILE B 110 " pdb=" C ILE B 110 " pdb=" N ILE B 111 " pdb=" CA ILE B 111 " ideal model delta harmonic sigma weight residual -180.00 -160.75 -19.25 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ILE A 110 " pdb=" C ILE A 110 " pdb=" N ILE A 111 " pdb=" CA ILE A 111 " ideal model delta harmonic sigma weight residual -180.00 -161.39 -18.61 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA ASP B 94 " pdb=" CB ASP B 94 " pdb=" CG ASP B 94 " pdb=" OD1 ASP B 94 " ideal model delta sinusoidal sigma weight residual -30.00 -89.94 59.94 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 7065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1580 0.061 - 0.122: 238 0.122 - 0.182: 27 0.182 - 0.243: 6 0.243 - 0.304: 1 Chirality restraints: 1852 Sorted by residual: chirality pdb=" CA TYR A 150 " pdb=" N TYR A 150 " pdb=" C TYR A 150 " pdb=" CB TYR A 150 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA PHE B 478 " pdb=" N PHE B 478 " pdb=" C PHE B 478 " pdb=" CB PHE B 478 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ASN A 552 " pdb=" N ASN A 552 " pdb=" C ASN A 552 " pdb=" CB ASN A 552 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1849 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 548 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C HIS A 548 " -0.049 2.00e-02 2.50e+03 pdb=" O HIS A 548 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 549 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 550 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C ILE A 550 " -0.044 2.00e-02 2.50e+03 pdb=" O ILE A 550 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS A 551 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 551 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" C LYS A 551 " -0.034 2.00e-02 2.50e+03 pdb=" O LYS A 551 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN A 552 " 0.011 2.00e-02 2.50e+03 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 32 2.44 - 3.06: 7549 3.06 - 3.67: 16710 3.67 - 4.29: 24004 4.29 - 4.90: 39867 Nonbonded interactions: 88162 Sorted by model distance: nonbonded pdb=" O2G ATP B 801 " pdb="MG MG B 802 " model vdw 1.826 2.170 nonbonded pdb=" O2B ATP B 801 " pdb="MG MG B 802 " model vdw 1.923 2.170 nonbonded pdb=" O1B ATP A 801 " pdb="MG MG A 802 " model vdw 2.108 2.170 nonbonded pdb=" O GLY B 282 " pdb=" OG1 THR B 286 " model vdw 2.212 3.040 nonbonded pdb=" O ASP A 476 " pdb=" OD1 ASP A 476 " model vdw 2.226 3.040 ... (remaining 88157 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.830 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 10.550 Find NCS groups from input model: 0.130 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 : 0.003 0.070 11636 Z= 0.193 Angle : 0.735 24.206 15696 Z= 0.500 Chirality : 0.045 0.304 1852 Planarity : 0.003 0.029 1944 Dihedral : 14.109 83.440 4356 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.75 % Favored : 97.12 % Rotamer: Outliers : 0.72 % Allowed : 0.64 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.90 (0.23), residues: 1456 helix: 1.80 (0.19), residues: 832 sheet: -0.21 (0.42), residues: 132 loop : -1.30 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 122 TYR 0.012 0.001 TYR A 413 PHE 0.011 0.001 PHE B 615 TRP 0.012 0.001 TRP A 132 HIS 0.006 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00313 (11636) covalent geometry : angle 0.73498 (15696) hydrogen bonds : bond 0.12793 ( 681) hydrogen bonds : angle 4.81229 ( 1971) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 433 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 MET cc_start: 0.8303 (mmm) cc_final: 0.8025 (tpp) REVERT: B 266 ILE cc_start: 0.8480 (mm) cc_final: 0.8122 (mm) REVERT: B 373 ASP cc_start: 0.7239 (m-30) cc_final: 0.6906 (m-30) REVERT: D 19 MET cc_start: 0.7726 (mmt) cc_final: 0.7197 (mmp) outliers start: 9 outliers final: 4 residues processed: 441 average time/residue: 0.1080 time to fit residues: 66.4401 Evaluate side-chains 268 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 264 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 471 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 ASN B 54 ASN B 90 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.131722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.110213 restraints weight = 28357.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.112981 restraints weight = 14941.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.114829 restraints weight = 9578.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.116080 restraints weight = 6881.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.117024 restraints weight = 5483.764| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 11636 Z= 0.209 Angle : 0.673 9.504 15696 Z= 0.350 Chirality : 0.043 0.221 1852 Planarity : 0.004 0.042 1944 Dihedral : 7.365 63.632 1626 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.77 % Allowed : 12.68 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.87 (0.22), residues: 1456 helix: 1.68 (0.18), residues: 848 sheet: -0.19 (0.39), residues: 150 loop : -1.25 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 96 TYR 0.022 0.001 TYR A 413 PHE 0.012 0.002 PHE A 564 TRP 0.015 0.002 TRP B 132 HIS 0.006 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00476 (11636) covalent geometry : angle 0.67320 (15696) hydrogen bonds : bond 0.04567 ( 681) hydrogen bonds : angle 4.30753 ( 1971) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 276 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8545 (pmm) cc_final: 0.8155 (pmm) REVERT: A 224 ASN cc_start: 0.8673 (t0) cc_final: 0.8388 (t0) REVERT: A 274 SER cc_start: 0.9000 (m) cc_final: 0.8679 (p) REVERT: B 41 LYS cc_start: 0.8724 (mtpt) cc_final: 0.8411 (mtpt) REVERT: B 125 MET cc_start: 0.7103 (tmm) cc_final: 0.6760 (tmm) REVERT: B 286 THR cc_start: 0.9031 (m) cc_final: 0.8780 (m) REVERT: B 350 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8282 (tt0) REVERT: B 615 PHE cc_start: 0.8193 (t80) cc_final: 0.7985 (t80) REVERT: D 19 MET cc_start: 0.8231 (mmt) cc_final: 0.7905 (mmp) outliers start: 47 outliers final: 31 residues processed: 308 average time/residue: 0.0939 time to fit residues: 41.9554 Evaluate side-chains 274 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 242 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain B residue 684 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 97 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 60 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.129149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.107566 restraints weight = 28496.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.110427 restraints weight = 14280.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.112294 restraints weight = 8811.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.113532 restraints weight = 6286.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.114248 restraints weight = 4985.717| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11636 Z= 0.130 Angle : 0.588 11.561 15696 Z= 0.304 Chirality : 0.041 0.209 1852 Planarity : 0.003 0.054 1944 Dihedral : 6.947 59.573 1623 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.05 % Allowed : 16.13 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.00 (0.22), residues: 1456 helix: 1.80 (0.18), residues: 848 sheet: 0.00 (0.40), residues: 150 loop : -1.29 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 122 TYR 0.017 0.001 TYR A 413 PHE 0.017 0.001 PHE A 428 TRP 0.013 0.001 TRP B 132 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00277 (11636) covalent geometry : angle 0.58783 (15696) hydrogen bonds : bond 0.04204 ( 681) hydrogen bonds : angle 4.04400 ( 1971) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 269 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8559 (pmm) cc_final: 0.8315 (pmm) REVERT: A 194 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7849 (t80) REVERT: A 224 ASN cc_start: 0.8690 (t0) cc_final: 0.8427 (t0) REVERT: A 274 SER cc_start: 0.8952 (m) cc_final: 0.8588 (p) REVERT: A 335 ARG cc_start: 0.8618 (ttp80) cc_final: 0.7600 (ttp80) REVERT: B 41 LYS cc_start: 0.8771 (mtpt) cc_final: 0.8423 (mtpt) REVERT: B 290 ASP cc_start: 0.8637 (m-30) cc_final: 0.8402 (m-30) REVERT: B 385 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8027 (tm-30) REVERT: B 615 PHE cc_start: 0.7999 (t80) cc_final: 0.7738 (t80) REVERT: D 19 MET cc_start: 0.8099 (mmt) cc_final: 0.7806 (mmp) outliers start: 38 outliers final: 26 residues processed: 287 average time/residue: 0.0994 time to fit residues: 41.4143 Evaluate side-chains 270 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 243 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 679 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN B 331 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.126295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.104405 restraints weight = 29034.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.107204 restraints weight = 15043.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.109053 restraints weight = 9439.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.110281 restraints weight = 6824.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.110999 restraints weight = 5453.968| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11636 Z= 0.184 Angle : 0.621 11.863 15696 Z= 0.318 Chirality : 0.041 0.160 1852 Planarity : 0.003 0.054 1944 Dihedral : 6.831 62.358 1621 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.57 % Allowed : 18.06 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.06 (0.22), residues: 1456 helix: 1.81 (0.18), residues: 838 sheet: 0.10 (0.40), residues: 150 loop : -1.15 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 335 TYR 0.014 0.001 TYR B 247 PHE 0.013 0.002 PHE A 257 TRP 0.009 0.001 TRP B 132 HIS 0.005 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00414 (11636) covalent geometry : angle 0.62107 (15696) hydrogen bonds : bond 0.04453 ( 681) hydrogen bonds : angle 4.20031 ( 1971) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 250 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7627 (m-30) cc_final: 0.7398 (m-30) REVERT: A 154 MET cc_start: 0.8633 (pmm) cc_final: 0.8424 (pmm) REVERT: A 194 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7860 (t80) REVERT: A 224 ASN cc_start: 0.8698 (t0) cc_final: 0.8422 (t0) REVERT: A 274 SER cc_start: 0.9052 (m) cc_final: 0.8656 (p) REVERT: A 461 GLU cc_start: 0.8374 (tp30) cc_final: 0.8149 (tp30) REVERT: A 647 ASP cc_start: 0.7963 (t0) cc_final: 0.7254 (t0) REVERT: A 648 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7929 (mm-30) REVERT: A 717 MET cc_start: 0.9191 (mmm) cc_final: 0.8949 (mmm) REVERT: B 37 MET cc_start: 0.8646 (mmm) cc_final: 0.8382 (mmp) REVERT: B 41 LYS cc_start: 0.8737 (mtpt) cc_final: 0.8453 (mtpt) REVERT: B 125 MET cc_start: 0.7637 (tmm) cc_final: 0.7315 (tmm) REVERT: B 154 MET cc_start: 0.8526 (mmp) cc_final: 0.8300 (mmp) REVERT: B 194 PHE cc_start: 0.7952 (t80) cc_final: 0.7578 (t80) REVERT: B 250 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8553 (t) REVERT: B 290 ASP cc_start: 0.8759 (m-30) cc_final: 0.8259 (m-30) REVERT: B 385 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8011 (tm-30) REVERT: B 428 PHE cc_start: 0.8239 (t80) cc_final: 0.7781 (t80) REVERT: D 21 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7901 (ttm) outliers start: 57 outliers final: 38 residues processed: 283 average time/residue: 0.0980 time to fit residues: 40.7312 Evaluate side-chains 277 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 236 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain D residue 21 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 97 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.126507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.104649 restraints weight = 29012.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.107436 restraints weight = 14882.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.109302 restraints weight = 9317.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.110441 restraints weight = 6693.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.111309 restraints weight = 5385.194| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11636 Z= 0.131 Angle : 0.582 14.363 15696 Z= 0.300 Chirality : 0.040 0.157 1852 Planarity : 0.003 0.051 1944 Dihedral : 6.742 63.369 1621 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.53 % Allowed : 20.47 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.17 (0.22), residues: 1456 helix: 1.89 (0.18), residues: 840 sheet: 0.22 (0.41), residues: 146 loop : -1.12 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 335 TYR 0.018 0.001 TYR B 56 PHE 0.018 0.001 PHE A 715 TRP 0.014 0.001 TRP A 718 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00287 (11636) covalent geometry : angle 0.58175 (15696) hydrogen bonds : bond 0.04153 ( 681) hydrogen bonds : angle 4.05122 ( 1971) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 253 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7498 (m-30) cc_final: 0.7252 (m-30) REVERT: A 45 MET cc_start: 0.9059 (mmm) cc_final: 0.7802 (tmm) REVERT: A 154 MET cc_start: 0.8548 (pmm) cc_final: 0.8345 (pmm) REVERT: A 194 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7802 (t80) REVERT: A 197 LEU cc_start: 0.8854 (mt) cc_final: 0.8615 (mt) REVERT: A 224 ASN cc_start: 0.8702 (t0) cc_final: 0.8430 (t0) REVERT: A 239 ASP cc_start: 0.9027 (m-30) cc_final: 0.8782 (m-30) REVERT: A 274 SER cc_start: 0.9025 (m) cc_final: 0.8619 (p) REVERT: A 335 ARG cc_start: 0.8724 (tmm160) cc_final: 0.8423 (tmm160) REVERT: A 387 MET cc_start: 0.9085 (mmp) cc_final: 0.8809 (tpp) REVERT: A 647 ASP cc_start: 0.7886 (t0) cc_final: 0.7278 (t0) REVERT: B 125 MET cc_start: 0.7551 (tmm) cc_final: 0.7213 (tmm) REVERT: B 194 PHE cc_start: 0.7949 (t80) cc_final: 0.7630 (t80) REVERT: B 250 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8481 (t) REVERT: B 290 ASP cc_start: 0.8782 (m-30) cc_final: 0.8357 (m-30) REVERT: B 428 PHE cc_start: 0.8170 (t80) cc_final: 0.7838 (t80) REVERT: B 495 TYR cc_start: 0.8629 (t80) cc_final: 0.8239 (t80) outliers start: 44 outliers final: 31 residues processed: 278 average time/residue: 0.0935 time to fit residues: 38.0206 Evaluate side-chains 263 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 230 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 679 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 84 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.123037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.101848 restraints weight = 28839.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.104343 restraints weight = 15368.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.106045 restraints weight = 9891.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.107118 restraints weight = 7221.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.107893 restraints weight = 5849.594| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 11636 Z= 0.256 Angle : 0.706 13.737 15696 Z= 0.363 Chirality : 0.043 0.199 1852 Planarity : 0.004 0.046 1944 Dihedral : 6.903 70.946 1621 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.41 % Allowed : 20.71 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.87 (0.22), residues: 1456 helix: 1.56 (0.18), residues: 844 sheet: 0.08 (0.41), residues: 148 loop : -1.07 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 122 TYR 0.019 0.002 TYR B 413 PHE 0.020 0.002 PHE A 715 TRP 0.020 0.002 TRP B 132 HIS 0.006 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00584 (11636) covalent geometry : angle 0.70619 (15696) hydrogen bonds : bond 0.04993 ( 681) hydrogen bonds : angle 4.49571 ( 1971) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 244 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7614 (m-30) cc_final: 0.7393 (m-30) REVERT: A 224 ASN cc_start: 0.8766 (t0) cc_final: 0.8507 (t0) REVERT: A 274 SER cc_start: 0.9098 (m) cc_final: 0.8708 (p) REVERT: A 440 LYS cc_start: 0.9153 (tmtt) cc_final: 0.8893 (tptm) REVERT: A 647 ASP cc_start: 0.7957 (t0) cc_final: 0.7348 (t0) REVERT: A 648 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8027 (mm-30) REVERT: B 37 MET cc_start: 0.8597 (mmm) cc_final: 0.8373 (mmp) REVERT: B 125 MET cc_start: 0.7977 (tmm) cc_final: 0.7552 (tmm) REVERT: B 244 MET cc_start: 0.9026 (mmm) cc_final: 0.8470 (tpp) REVERT: B 266 ILE cc_start: 0.8923 (mm) cc_final: 0.8446 (mm) REVERT: B 350 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8601 (tm-30) REVERT: B 369 LYS cc_start: 0.8410 (tptt) cc_final: 0.7965 (tptt) REVERT: B 385 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8243 (tm-30) REVERT: B 428 PHE cc_start: 0.8457 (t80) cc_final: 0.8000 (t80) REVERT: B 531 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8740 (mm) REVERT: B 598 MET cc_start: 0.8283 (tpt) cc_final: 0.8064 (tpt) outliers start: 55 outliers final: 45 residues processed: 277 average time/residue: 0.1010 time to fit residues: 40.7669 Evaluate side-chains 278 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 232 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 679 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 0.0570 chunk 91 optimal weight: 0.3980 chunk 66 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 327 ASN ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.125707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.103943 restraints weight = 28703.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.106751 restraints weight = 14633.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.108572 restraints weight = 9127.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.109814 restraints weight = 6610.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.110537 restraints weight = 5250.791| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11636 Z= 0.129 Angle : 0.628 14.835 15696 Z= 0.323 Chirality : 0.041 0.203 1852 Planarity : 0.003 0.041 1944 Dihedral : 6.711 67.315 1621 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.69 % Allowed : 23.11 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.09 (0.22), residues: 1456 helix: 1.79 (0.18), residues: 842 sheet: 0.17 (0.42), residues: 148 loop : -1.09 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 122 TYR 0.010 0.001 TYR B 179 PHE 0.015 0.001 PHE A 715 TRP 0.020 0.001 TRP B 132 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00280 (11636) covalent geometry : angle 0.62831 (15696) hydrogen bonds : bond 0.04235 ( 681) hydrogen bonds : angle 4.12314 ( 1971) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 251 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7575 (m-30) cc_final: 0.7285 (m-30) REVERT: A 154 MET cc_start: 0.8919 (pmm) cc_final: 0.8375 (pmm) REVERT: A 197 LEU cc_start: 0.8908 (mt) cc_final: 0.8624 (mt) REVERT: A 224 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8477 (t0) REVERT: A 239 ASP cc_start: 0.9096 (m-30) cc_final: 0.8815 (m-30) REVERT: A 274 SER cc_start: 0.9026 (m) cc_final: 0.8597 (p) REVERT: A 335 ARG cc_start: 0.8743 (tmm160) cc_final: 0.8445 (tmm160) REVERT: A 368 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7810 (tm-30) REVERT: A 647 ASP cc_start: 0.7927 (t0) cc_final: 0.7345 (t0) REVERT: A 648 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8137 (mm-30) REVERT: B 125 MET cc_start: 0.7912 (tmm) cc_final: 0.7469 (tmm) REVERT: B 194 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7754 (t80) REVERT: B 244 MET cc_start: 0.8945 (mmm) cc_final: 0.8643 (tpp) REVERT: B 266 ILE cc_start: 0.8804 (mm) cc_final: 0.8305 (mm) REVERT: B 369 LYS cc_start: 0.8349 (tptt) cc_final: 0.7994 (tptt) REVERT: B 385 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8065 (tm-30) REVERT: B 389 TYR cc_start: 0.7739 (OUTLIER) cc_final: 0.7497 (m-80) REVERT: B 428 PHE cc_start: 0.8160 (t80) cc_final: 0.7836 (t80) REVERT: B 531 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8723 (mm) REVERT: B 598 MET cc_start: 0.8154 (tpt) cc_final: 0.7890 (tpt) outliers start: 46 outliers final: 37 residues processed: 275 average time/residue: 0.1004 time to fit residues: 40.3833 Evaluate side-chains 278 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 237 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 389 TYR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain D residue 22 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.1980 chunk 56 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 79 optimal weight: 0.6980 chunk 69 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.124023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.102561 restraints weight = 28678.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.105201 restraints weight = 15024.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.106962 restraints weight = 9535.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.108095 restraints weight = 6948.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.108863 restraints weight = 5603.845| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11636 Z= 0.167 Angle : 0.653 13.809 15696 Z= 0.332 Chirality : 0.041 0.208 1852 Planarity : 0.003 0.026 1944 Dihedral : 6.649 68.165 1621 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.09 % Allowed : 22.71 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.09 (0.22), residues: 1456 helix: 1.79 (0.18), residues: 842 sheet: 0.00 (0.41), residues: 152 loop : -1.03 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 96 TYR 0.013 0.001 TYR B 179 PHE 0.013 0.002 PHE A 257 TRP 0.019 0.002 TRP B 132 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00380 (11636) covalent geometry : angle 0.65339 (15696) hydrogen bonds : bond 0.04381 ( 681) hydrogen bonds : angle 4.16896 ( 1971) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 241 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7650 (m-30) cc_final: 0.7408 (m-30) REVERT: A 45 MET cc_start: 0.9039 (mmm) cc_final: 0.7905 (tmm) REVERT: A 154 MET cc_start: 0.8901 (pmm) cc_final: 0.8376 (pmm) REVERT: A 197 LEU cc_start: 0.8886 (mt) cc_final: 0.8602 (mt) REVERT: A 224 ASN cc_start: 0.8692 (t0) cc_final: 0.8425 (t0) REVERT: A 239 ASP cc_start: 0.9028 (m-30) cc_final: 0.8732 (m-30) REVERT: A 274 SER cc_start: 0.9068 (m) cc_final: 0.8653 (p) REVERT: A 335 ARG cc_start: 0.8706 (tmm160) cc_final: 0.8446 (tmm160) REVERT: A 368 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7469 (tm-30) REVERT: A 647 ASP cc_start: 0.7858 (t0) cc_final: 0.7457 (t0) REVERT: B 37 MET cc_start: 0.8652 (mmm) cc_final: 0.8437 (mmp) REVERT: B 125 MET cc_start: 0.7907 (tmm) cc_final: 0.7468 (tmm) REVERT: B 244 MET cc_start: 0.8848 (mmm) cc_final: 0.8380 (tpp) REVERT: B 266 ILE cc_start: 0.8882 (mm) cc_final: 0.8378 (mm) REVERT: B 369 LYS cc_start: 0.8355 (tptt) cc_final: 0.8019 (tptt) REVERT: B 385 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8033 (tm-30) REVERT: B 389 TYR cc_start: 0.7605 (OUTLIER) cc_final: 0.7373 (m-80) REVERT: B 428 PHE cc_start: 0.8286 (t80) cc_final: 0.7918 (t80) REVERT: B 531 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8798 (mm) REVERT: B 598 MET cc_start: 0.8071 (tpt) cc_final: 0.7828 (tpt) outliers start: 51 outliers final: 43 residues processed: 269 average time/residue: 0.0961 time to fit residues: 38.0982 Evaluate side-chains 281 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 236 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 389 TYR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain D residue 22 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 29 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.124761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.103544 restraints weight = 28438.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.106319 restraints weight = 14218.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.108143 restraints weight = 8742.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.109287 restraints weight = 6218.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.110073 restraints weight = 4962.775| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11636 Z= 0.134 Angle : 0.658 15.411 15696 Z= 0.331 Chirality : 0.041 0.227 1852 Planarity : 0.003 0.029 1944 Dihedral : 6.558 66.672 1621 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.45 % Allowed : 23.68 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.15 (0.23), residues: 1456 helix: 1.84 (0.18), residues: 842 sheet: 0.03 (0.42), residues: 152 loop : -1.01 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 96 TYR 0.011 0.001 TYR B 179 PHE 0.018 0.001 PHE A 715 TRP 0.019 0.001 TRP B 132 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00298 (11636) covalent geometry : angle 0.65751 (15696) hydrogen bonds : bond 0.04089 ( 681) hydrogen bonds : angle 4.08789 ( 1971) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 248 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7595 (m-30) cc_final: 0.7050 (m-30) REVERT: A 45 MET cc_start: 0.9034 (mmm) cc_final: 0.7880 (tmm) REVERT: A 197 LEU cc_start: 0.8844 (mt) cc_final: 0.8570 (mt) REVERT: A 224 ASN cc_start: 0.8769 (t0) cc_final: 0.8487 (t0) REVERT: A 239 ASP cc_start: 0.9109 (m-30) cc_final: 0.8784 (m-30) REVERT: A 274 SER cc_start: 0.9021 (m) cc_final: 0.8598 (p) REVERT: A 335 ARG cc_start: 0.8712 (tmm160) cc_final: 0.8446 (tmm160) REVERT: A 368 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7460 (tm-30) REVERT: A 647 ASP cc_start: 0.7973 (t0) cc_final: 0.7581 (t0) REVERT: C 19 MET cc_start: 0.8803 (tpp) cc_final: 0.8535 (mmm) REVERT: B 37 MET cc_start: 0.8716 (mmm) cc_final: 0.8356 (mmp) REVERT: B 125 MET cc_start: 0.7856 (tmm) cc_final: 0.7390 (tmm) REVERT: B 244 MET cc_start: 0.8893 (mmm) cc_final: 0.8437 (tpp) REVERT: B 266 ILE cc_start: 0.8789 (mm) cc_final: 0.8291 (mm) REVERT: B 350 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8142 (tm-30) REVERT: B 369 LYS cc_start: 0.8348 (tptt) cc_final: 0.8018 (tptt) REVERT: B 385 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8088 (tm-30) REVERT: B 389 TYR cc_start: 0.7728 (OUTLIER) cc_final: 0.7494 (m-80) REVERT: B 428 PHE cc_start: 0.8168 (t80) cc_final: 0.7844 (t80) REVERT: B 531 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8726 (mm) outliers start: 43 outliers final: 35 residues processed: 269 average time/residue: 0.0957 time to fit residues: 38.1772 Evaluate side-chains 278 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 389 TYR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain D residue 22 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 5 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.125246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.103752 restraints weight = 28742.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.106533 restraints weight = 14503.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.108383 restraints weight = 9006.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.109650 restraints weight = 6420.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.110459 restraints weight = 5051.612| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11636 Z= 0.138 Angle : 0.677 16.082 15696 Z= 0.337 Chirality : 0.041 0.228 1852 Planarity : 0.003 0.048 1944 Dihedral : 6.500 65.764 1621 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.21 % Allowed : 24.40 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.17 (0.23), residues: 1456 helix: 1.86 (0.18), residues: 842 sheet: 0.19 (0.42), residues: 150 loop : -1.04 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 96 TYR 0.021 0.001 TYR B 319 PHE 0.013 0.001 PHE B 83 TRP 0.012 0.001 TRP B 132 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00314 (11636) covalent geometry : angle 0.67707 (15696) hydrogen bonds : bond 0.04061 ( 681) hydrogen bonds : angle 4.05985 ( 1971) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 250 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7495 (m-30) cc_final: 0.6996 (m-30) REVERT: A 45 MET cc_start: 0.9025 (mmm) cc_final: 0.7873 (tmm) REVERT: A 197 LEU cc_start: 0.8816 (mt) cc_final: 0.8559 (mt) REVERT: A 224 ASN cc_start: 0.8725 (t0) cc_final: 0.8450 (t0) REVERT: A 239 ASP cc_start: 0.9103 (m-30) cc_final: 0.8777 (m-30) REVERT: A 274 SER cc_start: 0.9005 (m) cc_final: 0.8585 (p) REVERT: A 335 ARG cc_start: 0.8707 (tmm160) cc_final: 0.8463 (tmm160) REVERT: A 368 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7417 (tm-30) REVERT: A 647 ASP cc_start: 0.7877 (t0) cc_final: 0.7424 (t0) REVERT: B 125 MET cc_start: 0.7829 (tmm) cc_final: 0.7367 (tmm) REVERT: B 244 MET cc_start: 0.8857 (mmm) cc_final: 0.8437 (tpp) REVERT: B 350 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8691 (tm-30) REVERT: B 369 LYS cc_start: 0.8344 (tptt) cc_final: 0.7966 (tptt) REVERT: B 385 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8098 (tm-30) REVERT: B 389 TYR cc_start: 0.7731 (OUTLIER) cc_final: 0.7517 (m-80) REVERT: B 428 PHE cc_start: 0.8165 (t80) cc_final: 0.7858 (t80) REVERT: B 531 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8715 (mm) outliers start: 40 outliers final: 37 residues processed: 272 average time/residue: 0.0994 time to fit residues: 39.7862 Evaluate side-chains 279 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 240 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 389 TYR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 679 HIS Chi-restraints excluded: chain D residue 22 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 103 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.124615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.103350 restraints weight = 28770.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.105984 restraints weight = 14919.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.107753 restraints weight = 9419.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.108911 restraints weight = 6796.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.109593 restraints weight = 5431.835| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11636 Z= 0.163 Angle : 0.697 15.581 15696 Z= 0.345 Chirality : 0.041 0.231 1852 Planarity : 0.003 0.049 1944 Dihedral : 6.505 66.583 1621 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.37 % Allowed : 24.40 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.11 (0.22), residues: 1456 helix: 1.80 (0.18), residues: 842 sheet: 0.16 (0.42), residues: 150 loop : -1.06 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 458 TYR 0.014 0.001 TYR B 179 PHE 0.012 0.001 PHE A 257 TRP 0.014 0.002 TRP B 132 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00376 (11636) covalent geometry : angle 0.69653 (15696) hydrogen bonds : bond 0.04183 ( 681) hydrogen bonds : angle 4.13499 ( 1971) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1957.65 seconds wall clock time: 34 minutes 41.68 seconds (2081.68 seconds total)