Starting phenix.real_space_refine on Fri Jul 3 02:05:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7t57_25697/07_2026/7t57_25697.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t57_25697/07_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_25697/07_2026/7t57_25697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t57_25697/07_2026/7t57_25697.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7t57_25697/07_2026/7t57_25697.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7t57_25697/07_2026/7t57_25697.cif" model { file = "/net/cci-nas-00/data/ceres_data/7t57_25697/07_2026/7t57_25697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t57_25697/07_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-6108/lib/python3.11/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: 2.76, per 1000 atoms: 0.24 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: 1.01 Conformation dependent library (CDL) restraints added in 642.5 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: 0.32 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: 2.01 Time building geometry restraints manager: 1.26 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 - 16.68: 6293 16.68 - 33.35: 549 33.35 - 50.03: 132 50.03 - 66.70: 22 66.70 - 83.38: 10 Dihedral angle restraints: 7006 sinusoidal: 2784 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 7003 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: 0.03 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: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.500 Find NCS groups from input model: 0.210 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: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 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 : 13.544 83.380 4294 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/Z covalent geometry : bond 0.00313 / 0.19 (11636) covalent geometry : angle 0.73498 / 0.50 (15696) hydrogen bonds : bond 0.12793 / 8.03 ( 681) hydrogen bonds : angle 4.81229 / 3.31 ( 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 : 0.433 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 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: 0.1065 time to fit residues: 65.9098 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 : 0.517 ------------------------------------------------------------------------------- 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... 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 = 0.3855 r_free = 0.3855 target = 0.127489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.105875 restraints weight = 28835.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.108698 restraints weight = 15039.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.110586 restraints weight = 9494.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.111840 restraints weight = 6845.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.112685 restraints weight = 5432.226| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 11636 Z= 0.203 Angle : 0.665 9.379 15696 Z= 0.346 Chirality : 0.043 0.215 1852 Planarity : 0.004 0.043 1944 Dihedral : 5.023 71.713 1564 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.77 % Allowed : 12.76 % Favored : 83.47 % 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: 1.66 (0.18), residues: 850 sheet: -0.18 (0.39), residues: 150 loop : -1.23 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 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/Z covalent geometry : bond 0.00457 / 0.20 (11636) covalent geometry : angle 0.66541 / 0.35 (15696) hydrogen bonds : bond 0.04633 / 3.12 ( 681) hydrogen bonds : angle 4.30968 / 3.02 ( 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 325 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 278 time to evaluate : 0.397 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: 0.8587 (pmm) cc_final: 0.8215 (pmm) REVERT: A 224 ASN cc_start: 0.8676 (t0) cc_final: 0.8393 (t0) REVERT: A 274 SER cc_start: 0.9006 (m) cc_final: 0.8687 (p) REVERT: B 41 LYS cc_start: 0.8735 (mtpt) cc_final: 0.8424 (mtpt) REVERT: B 125 MET cc_start: 0.7127 (tmm) cc_final: 0.6782 (tmm) REVERT: B 286 THR cc_start: 0.9031 (m) cc_final: 0.8782 (m) REVERT: B 350 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: B 615 PHE cc_start: 0.8208 (t80) cc_final: 0.7999 (t80) REVERT: D 19 MET cc_start: 0.8237 (mmt) cc_final: 0.7913 (mmp) outliers start: 47 outliers final: 30 residues processed: 309 average time/residue: 0.0971 time to fit residues: 43.6412 Evaluate side-chains 272 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 241 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 402 LEU Chi-restraints excluded: chain A residue 449 ILE 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: 1.9990 chunk 96 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 68 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 60 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3883 r_free = 0.3883 target = 0.128994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.107236 restraints weight = 28643.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.110135 restraints weight = 14525.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.112038 restraints weight = 8985.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.113283 restraints weight = 6424.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.114019 restraints weight = 5105.905| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11636 Z= 0.125 Angle : 0.582 11.569 15696 Z= 0.300 Chirality : 0.041 0.203 1852 Planarity : 0.003 0.058 1944 Dihedral : 4.649 69.956 1559 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.21 % Allowed : 16.37 % Favored : 80.42 % 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: 1.78 (0.18), residues: 850 sheet: 0.00 (0.40), residues: 150 loop : -1.28 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 122 TYR 0.017 0.001 TYR A 413 PHE 0.014 0.001 PHE A 715 TRP 0.013 0.001 TRP B 132 HIS 0.003 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (11636) covalent geometry : angle 0.58235 / 0.30 (15696) hydrogen bonds : bond 0.04171 / 2.79 ( 681) hydrogen bonds : angle 4.02050 / 2.81 ( 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 314 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 274 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: A 20 ASP cc_start: 0.7481 (m-30) cc_final: 0.7150 (m-30) REVERT: A 154 MET cc_start: 0.8582 (pmm) cc_final: 0.8369 (pmm) REVERT: A 194 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7816 (t80) REVERT: A 224 ASN cc_start: 0.8675 (t0) cc_final: 0.8416 (t0) REVERT: A 274 SER cc_start: 0.8945 (m) cc_final: 0.8614 (p) REVERT: A 335 ARG cc_start: 0.8608 (ttp80) cc_final: 0.7577 (ttp80) REVERT: B 41 LYS cc_start: 0.8782 (mtpt) cc_final: 0.8468 (mtpt) REVERT: B 290 ASP cc_start: 0.8635 (m-30) cc_final: 0.8389 (m-30) REVERT: B 385 GLU cc_start: 0.8421 (tm-30) cc_final: 0.7977 (tm-30) REVERT: B 495 TYR cc_start: 0.8568 (t80) cc_final: 0.8099 (t80) REVERT: B 615 PHE cc_start: 0.7982 (t80) cc_final: 0.7732 (t80) REVERT: D 19 MET cc_start: 0.8109 (mmt) cc_final: 0.7830 (mmp) outliers start: 40 outliers final: 24 residues processed: 292 average time/residue: 0.0909 time to fit residues: 38.5318 Evaluate side-chains 266 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 241 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 326 PHE 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 537 SER Chi-restraints excluded: chain B residue 11 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 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: 0.9980 chunk 58 optimal weight: 8.9990 chunk 127 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 ASN ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** B 99 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 = 0.3869 r_free = 0.3869 target = 0.127534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.105407 restraints weight = 28725.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.108305 restraints weight = 14488.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.110222 restraints weight = 8970.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.111512 restraints weight = 6398.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.112284 restraints weight = 5046.872| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11636 Z= 0.144 Angle : 0.591 12.659 15696 Z= 0.302 Chirality : 0.041 0.175 1852 Planarity : 0.003 0.044 1944 Dihedral : 4.602 71.881 1558 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.61 % Allowed : 18.30 % Favored : 78.09 % 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: 1.16 (0.22), residues: 1456 helix: 1.92 (0.18), residues: 838 sheet: 0.11 (0.40), residues: 150 loop : -1.16 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 335 TYR 0.015 0.001 TYR B 247 PHE 0.013 0.001 PHE A 257 TRP 0.011 0.002 TRP A 718 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (11636) covalent geometry : angle 0.59110 / 0.30 (15696) hydrogen bonds : bond 0.04178 / 2.81 ( 681) hydrogen bonds : angle 4.04399 / 2.83 ( 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 297 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 252 time to evaluate : 0.460 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: 0.7522 (m-30) cc_final: 0.7258 (m-30) REVERT: A 154 MET cc_start: 0.8610 (pmm) cc_final: 0.8365 (pmm) REVERT: A 194 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7763 (t80) REVERT: A 197 LEU cc_start: 0.8867 (mt) cc_final: 0.8662 (mt) REVERT: A 224 ASN cc_start: 0.8771 (t0) cc_final: 0.8502 (t0) REVERT: A 239 ASP cc_start: 0.9130 (m-30) cc_final: 0.8789 (m-30) REVERT: A 274 SER cc_start: 0.9006 (m) cc_final: 0.8603 (p) REVERT: A 335 ARG cc_start: 0.8537 (ttp80) cc_final: 0.7478 (ttp80) REVERT: A 647 ASP cc_start: 0.7976 (t0) cc_final: 0.7049 (t0) REVERT: A 648 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7907 (mm-30) REVERT: B 37 MET cc_start: 0.8707 (mmm) cc_final: 0.8391 (mmp) REVERT: B 41 LYS cc_start: 0.8793 (mtpt) cc_final: 0.8504 (mtpt) REVERT: B 125 MET cc_start: 0.7489 (tmm) cc_final: 0.7172 (tmm) REVERT: B 194 PHE cc_start: 0.7910 (t80) cc_final: 0.7591 (t80) REVERT: B 250 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.8428 (t) REVERT: B 290 ASP cc_start: 0.8746 (m-30) cc_final: 0.8227 (m-30) REVERT: B 385 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8049 (tm-30) REVERT: B 428 PHE cc_start: 0.8157 (t80) cc_final: 0.7740 (t80) REVERT: D 21 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7780 (ttm) outliers start: 45 outliers final: 29 residues processed: 275 average time/residue: 0.0946 time to fit residues: 38.3276 Evaluate side-chains 269 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 237 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 194 PHE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 326 PHE 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 449 ILE Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 ASP 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 250 VAL 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 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 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: 0.8980 chunk 126 optimal weight: 0.1980 chunk 131 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 HIS B 64 GLN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.128127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.106496 restraints weight = 28646.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.109258 restraints weight = 14876.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.111079 restraints weight = 9367.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.112253 restraints weight = 6761.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.112936 restraints weight = 5431.437| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11636 Z= 0.124 Angle : 0.584 14.307 15696 Z= 0.298 Chirality : 0.040 0.176 1852 Planarity : 0.003 0.053 1944 Dihedral : 4.571 74.221 1558 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.61 % Allowed : 19.90 % Favored : 76.48 % 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: 1.25 (0.22), residues: 1456 helix: 1.98 (0.18), residues: 840 sheet: 0.24 (0.41), residues: 146 loop : -1.13 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 122 TYR 0.012 0.001 TYR A 413 PHE 0.014 0.001 PHE A 715 TRP 0.008 0.001 TRP B 132 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (11636) covalent geometry : angle 0.58421 / 0.30 (15696) hydrogen bonds : bond 0.03970 / 2.66 ( 681) hydrogen bonds : angle 3.95020 / 2.76 ( 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 298 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 253 time to evaluate : 0.465 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 45 MET cc_start: 0.9049 (mmm) cc_final: 0.7813 (tmm) REVERT: A 154 MET cc_start: 0.8521 (pmm) cc_final: 0.8155 (pmm) REVERT: A 194 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7594 (t80) REVERT: A 197 LEU cc_start: 0.8721 (mt) cc_final: 0.8493 (mt) REVERT: A 224 ASN cc_start: 0.8603 (t0) cc_final: 0.8346 (t0) REVERT: A 239 ASP cc_start: 0.9062 (m-30) cc_final: 0.8720 (m-30) REVERT: A 274 SER cc_start: 0.9015 (m) cc_final: 0.8593 (p) REVERT: A 335 ARG cc_start: 0.8521 (ttp80) cc_final: 0.7547 (ttp80) REVERT: A 387 MET cc_start: 0.9004 (mmp) cc_final: 0.8733 (tpp) REVERT: A 647 ASP cc_start: 0.7955 (t0) cc_final: 0.7298 (t0) REVERT: B 125 MET cc_start: 0.7525 (tmm) cc_final: 0.7252 (tmm) REVERT: B 194 PHE cc_start: 0.7857 (t80) cc_final: 0.7566 (t80) REVERT: B 250 VAL cc_start: 0.8764 (OUTLIER) cc_final: 0.8539 (t) REVERT: B 290 ASP cc_start: 0.8636 (m-30) cc_final: 0.8231 (m-30) REVERT: B 385 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8052 (tm-30) REVERT: B 428 PHE cc_start: 0.8141 (t80) cc_final: 0.7853 (t80) REVERT: B 495 TYR cc_start: 0.8612 (t80) cc_final: 0.8177 (t80) REVERT: D 21 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7782 (ttm) outliers start: 45 outliers final: 28 residues processed: 276 average time/residue: 0.0889 time to fit residues: 36.5970 Evaluate side-chains 264 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 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 389 TYR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 442 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 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 178 LEU 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 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 679 HIS Chi-restraints excluded: chain D residue 21 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 84 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 0.0970 chunk 79 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 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 = 0.3836 r_free = 0.3836 target = 0.125930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.104362 restraints weight = 28889.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.107068 restraints weight = 15089.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.108881 restraints weight = 9541.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.109949 restraints weight = 6885.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.110734 restraints weight = 5586.547| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11636 Z= 0.174 Angle : 0.627 14.639 15696 Z= 0.319 Chirality : 0.041 0.175 1852 Planarity : 0.003 0.046 1944 Dihedral : 4.702 79.241 1558 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.09 % Allowed : 20.71 % Favored : 75.20 % 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: 0.31 (0.41), residues: 146 loop : -1.15 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 122 TYR 0.013 0.001 TYR B 179 PHE 0.014 0.001 PHE A 257 TRP 0.021 0.002 TRP B 132 HIS 0.005 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (11636) covalent geometry : angle 0.62738 / 0.32 (15696) hydrogen bonds : bond 0.04278 / 2.88 ( 681) hydrogen bonds : angle 4.13687 / 2.88 ( 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 293 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 242 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 45 MET cc_start: 0.9036 (mmm) cc_final: 0.8771 (tpt) REVERT: A 197 LEU cc_start: 0.8795 (mt) cc_final: 0.8543 (mt) REVERT: A 224 ASN cc_start: 0.8687 (t0) cc_final: 0.8412 (t0) REVERT: A 239 ASP cc_start: 0.9098 (m-30) cc_final: 0.8720 (m-30) REVERT: A 274 SER cc_start: 0.9063 (m) cc_final: 0.8654 (p) REVERT: A 647 ASP cc_start: 0.8007 (t0) cc_final: 0.7393 (t0) REVERT: A 648 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7880 (mm-30) REVERT: B 37 MET cc_start: 0.8603 (mmm) cc_final: 0.8305 (mmp) REVERT: B 41 LYS cc_start: 0.8619 (mtpt) cc_final: 0.8350 (mtpt) REVERT: B 125 MET cc_start: 0.7654 (tmm) cc_final: 0.7256 (tmm) REVERT: B 250 VAL cc_start: 0.8835 (OUTLIER) cc_final: 0.8587 (t) REVERT: B 369 LYS cc_start: 0.8376 (tptt) cc_final: 0.8027 (tptt) REVERT: B 428 PHE cc_start: 0.8244 (t80) cc_final: 0.7875 (t80) REVERT: B 531 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8747 (mm) REVERT: B 598 MET cc_start: 0.8166 (tpt) cc_final: 0.7916 (tpt) REVERT: D 21 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7885 (ttm) outliers start: 51 outliers final: 40 residues processed: 270 average time/residue: 0.0902 time to fit residues: 35.6845 Evaluate side-chains 271 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 228 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 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 327 ASN 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 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 457 ASN Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain B residue 20 ASP 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 236 MET Chi-restraints excluded: chain B residue 250 VAL 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 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 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 21 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 61 optimal weight: 0.0570 chunk 0 optimal weight: 7.9990 chunk 41 optimal weight: 0.0870 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** 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 = 0.3860 r_free = 0.3860 target = 0.126976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.105033 restraints weight = 28554.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.107873 restraints weight = 14575.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.109729 restraints weight = 9069.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.110960 restraints weight = 6512.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.111718 restraints weight = 5182.926| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11636 Z= 0.128 Angle : 0.621 14.075 15696 Z= 0.317 Chirality : 0.041 0.180 1852 Planarity : 0.003 0.046 1944 Dihedral : 4.717 79.587 1558 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.45 % Allowed : 21.75 % Favored : 74.80 % 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: 1.18 (0.22), residues: 1456 helix: 1.89 (0.18), residues: 842 sheet: 0.39 (0.42), residues: 146 loop : -1.17 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 122 TYR 0.011 0.001 TYR B 179 PHE 0.031 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/Z covalent geometry : bond 0.00282 / 0.13 (11636) covalent geometry : angle 0.62095 / 0.32 (15696) hydrogen bonds : bond 0.04054 / 2.74 ( 681) hydrogen bonds : angle 4.01667 / 2.80 ( 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 288 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 245 time to evaluate : 0.399 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 45 MET cc_start: 0.9007 (mmm) cc_final: 0.8649 (tpt) REVERT: A 154 MET cc_start: 0.8795 (pmm) cc_final: 0.8390 (pmm) REVERT: A 224 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8432 (t0) REVERT: A 239 ASP cc_start: 0.9123 (m-30) cc_final: 0.8695 (m-30) REVERT: A 274 SER cc_start: 0.9018 (m) cc_final: 0.8609 (p) REVERT: A 368 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7307 (tm-30) REVERT: A 647 ASP cc_start: 0.8063 (t0) cc_final: 0.7530 (t0) REVERT: A 648 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7887 (mm-30) REVERT: B 125 MET cc_start: 0.7651 (tmm) cc_final: 0.7266 (tmm) REVERT: B 194 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7749 (t80) REVERT: B 244 MET cc_start: 0.9038 (mmm) cc_final: 0.8313 (tpp) REVERT: B 250 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8443 (t) REVERT: B 369 LYS cc_start: 0.8362 (tptt) cc_final: 0.8006 (tptt) REVERT: B 428 PHE cc_start: 0.8172 (t80) cc_final: 0.7836 (t80) REVERT: B 495 TYR cc_start: 0.8648 (t80) cc_final: 0.8273 (t80) REVERT: B 531 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8700 (mm) REVERT: B 598 MET cc_start: 0.8192 (tpt) cc_final: 0.7912 (tpt) outliers start: 43 outliers final: 30 residues processed: 265 average time/residue: 0.0924 time to fit residues: 35.8585 Evaluate side-chains 272 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 299 ILE Chi-restraints excluded: chain A residue 300 LEU 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 449 ILE Chi-restraints excluded: chain A residue 537 SER 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 236 MET Chi-restraints excluded: chain B residue 250 VAL 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 GLN ** 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 = 0.3854 r_free = 0.3854 target = 0.127403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.105708 restraints weight = 28505.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.108506 restraints weight = 14750.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.110365 restraints weight = 9254.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.111534 restraints weight = 6657.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.112297 restraints weight = 5333.590| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11636 Z= 0.144 Angle : 0.643 13.819 15696 Z= 0.324 Chirality : 0.041 0.195 1852 Planarity : 0.003 0.033 1944 Dihedral : 4.758 80.985 1558 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.61 % Allowed : 22.15 % Favored : 74.24 % 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: 1.18 (0.22), residues: 1456 helix: 1.90 (0.18), residues: 842 sheet: 0.40 (0.42), residues: 146 loop : -1.20 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 458 TYR 0.011 0.001 TYR B 179 PHE 0.027 0.001 PHE A 715 TRP 0.015 0.001 TRP B 132 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (11636) covalent geometry : angle 0.64341 / 0.32 (15696) hydrogen bonds : bond 0.04088 / 2.76 ( 681) hydrogen bonds : angle 4.01399 / 2.81 ( 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 291 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 246 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8319 (t70) cc_final: 0.8080 (t70) REVERT: A 154 MET cc_start: 0.8799 (pmm) cc_final: 0.8517 (pmm) REVERT: A 224 ASN cc_start: 0.8754 (t0) cc_final: 0.8471 (t0) REVERT: A 239 ASP cc_start: 0.9127 (m-30) cc_final: 0.8693 (m-30) REVERT: A 274 SER cc_start: 0.8988 (m) cc_final: 0.8613 (p) REVERT: A 335 ARG cc_start: 0.8762 (tmm160) cc_final: 0.8298 (tmm160) REVERT: A 387 MET cc_start: 0.8960 (mmp) cc_final: 0.8694 (tpp) REVERT: A 647 ASP cc_start: 0.8090 (t0) cc_final: 0.7565 (t0) REVERT: A 648 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7980 (mm-30) REVERT: B 37 MET cc_start: 0.8651 (mmm) cc_final: 0.8376 (mmp) REVERT: B 125 MET cc_start: 0.7780 (tmm) cc_final: 0.7335 (tmm) REVERT: B 244 MET cc_start: 0.9022 (mmm) cc_final: 0.8180 (tpp) REVERT: B 250 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8463 (t) REVERT: B 369 LYS cc_start: 0.8338 (tptt) cc_final: 0.7982 (tptt) REVERT: B 428 PHE cc_start: 0.8180 (t80) cc_final: 0.7862 (t80) REVERT: B 495 TYR cc_start: 0.8604 (t80) cc_final: 0.8205 (t80) REVERT: B 531 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8725 (mm) REVERT: B 598 MET cc_start: 0.8059 (tpt) cc_final: 0.7712 (tpt) outliers start: 45 outliers final: 33 residues processed: 267 average time/residue: 0.0790 time to fit residues: 31.1338 Evaluate side-chains 270 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 235 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 345 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 442 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 45 MET 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 236 MET Chi-restraints excluded: chain B residue 250 VAL 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 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 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 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: 1.9990 chunk 31 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 14 optimal weight: 0.0370 chunk 140 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 84 optimal weight: 0.0010 overall best weight: 0.5264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3867 r_free = 0.3867 target = 0.127672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.106058 restraints weight = 28673.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.108899 restraints weight = 14656.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.110794 restraints weight = 9156.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.112023 restraints weight = 6554.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.112820 restraints weight = 5218.420| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4634 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= 0.124 Angle : 0.663 15.347 15696 Z= 0.330 Chirality : 0.041 0.211 1852 Planarity : 0.003 0.046 1944 Dihedral : 4.757 80.863 1558 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.73 % Allowed : 22.79 % Favored : 74.48 % 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: 1.20 (0.22), residues: 1456 helix: 1.93 (0.18), residues: 842 sheet: 0.37 (0.42), residues: 146 loop : -1.19 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 96 TYR 0.020 0.001 TYR B 319 PHE 0.026 0.001 PHE A 715 TRP 0.016 0.001 TRP B 132 HIS 0.005 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (11636) covalent geometry : angle 0.66257 / 0.33 (15696) hydrogen bonds : bond 0.03870 / 2.63 ( 681) hydrogen bonds : angle 3.92975 / 2.75 ( 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 286 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 252 time to evaluate : 0.289 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 154 MET cc_start: 0.8741 (pmm) cc_final: 0.8471 (pmm) REVERT: A 224 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8454 (t0) REVERT: A 239 ASP cc_start: 0.9118 (m-30) cc_final: 0.8672 (m-30) REVERT: A 245 GLU cc_start: 0.9300 (tm-30) cc_final: 0.9001 (tm-30) REVERT: A 274 SER cc_start: 0.8980 (m) cc_final: 0.8585 (p) REVERT: A 368 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7967 (tp30) REVERT: A 647 ASP cc_start: 0.8086 (t0) cc_final: 0.7669 (t0) REVERT: B 125 MET cc_start: 0.7693 (tmm) cc_final: 0.7333 (tmm) REVERT: B 244 MET cc_start: 0.8844 (mmm) cc_final: 0.8375 (tpp) REVERT: B 250 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8400 (t) REVERT: B 369 LYS cc_start: 0.8312 (tptt) cc_final: 0.7961 (tptt) REVERT: B 428 PHE cc_start: 0.8088 (t80) cc_final: 0.7784 (t80) REVERT: B 495 TYR cc_start: 0.8551 (t80) cc_final: 0.8206 (t80) REVERT: B 531 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8706 (mm) outliers start: 34 outliers final: 26 residues processed: 267 average time/residue: 0.0897 time to fit residues: 35.2590 Evaluate side-chains 275 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 246 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 324 THR Chi-restraints excluded: chain A residue 345 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 442 LEU Chi-restraints excluded: chain A residue 537 SER 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 236 MET Chi-restraints excluded: chain B residue 250 VAL 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 531 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 575 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 5 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 HIS ** 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 = 0.3858 r_free = 0.3858 target = 0.127265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.105552 restraints weight = 28909.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.108363 restraints weight = 14923.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.110235 restraints weight = 9364.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.111499 restraints weight = 6734.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.112214 restraints weight = 5335.415| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11636 Z= 0.132 Angle : 0.691 15.994 15696 Z= 0.340 Chirality : 0.041 0.219 1852 Planarity : 0.003 0.043 1944 Dihedral : 4.779 81.596 1558 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.41 % Allowed : 23.11 % Favored : 74.48 % 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: 1.26 (0.23), residues: 1456 helix: 1.96 (0.18), residues: 842 sheet: 0.42 (0.42), residues: 146 loop : -1.15 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 96 TYR 0.014 0.001 TYR B 179 PHE 0.022 0.001 PHE A 715 TRP 0.012 0.001 TRP B 132 HIS 0.003 0.001 HIS A 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (11636) covalent geometry : angle 0.69078 / 0.34 (15696) hydrogen bonds : bond 0.03864 / 2.61 ( 681) hydrogen bonds : angle 3.94476 / 2.76 ( 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 273 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 243 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8748 (pmm) cc_final: 0.8448 (pmm) REVERT: A 224 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8460 (t0) REVERT: A 239 ASP cc_start: 0.9128 (m-30) cc_final: 0.8653 (m-30) REVERT: A 274 SER cc_start: 0.9002 (m) cc_final: 0.8604 (p) REVERT: A 368 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7988 (tp30) REVERT: A 387 MET cc_start: 0.8499 (tpp) cc_final: 0.7853 (mpp) REVERT: A 647 ASP cc_start: 0.8116 (t0) cc_final: 0.7703 (t0) REVERT: B 125 MET cc_start: 0.7673 (tmm) cc_final: 0.7231 (tmm) REVERT: B 244 MET cc_start: 0.8842 (mmm) cc_final: 0.8451 (tpp) REVERT: B 250 VAL cc_start: 0.8676 (OUTLIER) cc_final: 0.8429 (t) REVERT: B 369 LYS cc_start: 0.8320 (tptt) cc_final: 0.7969 (tptt) REVERT: B 428 PHE cc_start: 0.8111 (t80) cc_final: 0.7797 (t80) REVERT: B 495 TYR cc_start: 0.8552 (t80) cc_final: 0.8212 (t80) REVERT: B 531 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8718 (mm) outliers start: 30 outliers final: 23 residues processed: 256 average time/residue: 0.0954 time to fit residues: 36.0237 Evaluate side-chains 266 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 240 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 224 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 345 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 442 LEU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 97 LEU 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 236 MET Chi-restraints excluded: chain B residue 250 VAL 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 531 LEU Chi-restraints excluded: chain B residue 532 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 103 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 76 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3957 r_free = 0.3957 target = 0.131139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.109522 restraints weight = 28202.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.112482 restraints weight = 14251.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.114437 restraints weight = 8811.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.115708 restraints weight = 6259.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.116481 restraints weight = 4939.755| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11636 Z= 0.136 Angle : 0.690 15.857 15696 Z= 0.341 Chirality : 0.041 0.224 1852 Planarity : 0.003 0.044 1944 Dihedral : 4.802 83.084 1558 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.25 % Allowed : 23.03 % Favored : 74.72 % 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: 1.23 (0.23), residues: 1456 helix: 1.93 (0.18), residues: 842 sheet: 0.17 (0.42), residues: 150 loop : -1.06 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 96 TYR 0.022 0.001 TYR B 319 PHE 0.023 0.001 PHE A 715 TRP 0.020 0.002 TRP B 132 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (11636) covalent geometry : angle 0.69016 / 0.34 (15696) hydrogen bonds : bond 0.03850 / 2.60 ( 681) hydrogen bonds : angle 3.95944 / 2.77 ( 1971) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1856.56 seconds wall clock time: 32 minutes 56.00 seconds (1976.00 seconds total)