Starting phenix.real_space_refine on Sun Dec 29 22:23:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t57_25697/12_2024/7t57_25697.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t57_25697/12_2024/7t57_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_25697/12_2024/7t57_25697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t57_25697/12_2024/7t57_25697.map" model { file = "/net/cci-nas-00/data/ceres_data/7t57_25697/12_2024/7t57_25697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t57_25697/12_2024/7t57_25697.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.032 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 7.31, per 1000 atoms: 0.64 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: 2.70 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.27 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: 3.84 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3592 1.34 - 1.46: 1450 1.46 - 1.57: 6482 1.57 - 1.69: 8 1.69 - 1.81: 104 Bond restraints: 11636 Sorted by residual: bond pdb=" O2B ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 1.529 1.459 0.070 2.20e-02 2.07e+03 1.01e+01 bond pdb=" N ARG A 84 " pdb=" CA ARG A 84 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 6.94e+00 bond pdb=" N LEU A 80 " pdb=" CA LEU A 80 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.25e-02 6.40e+03 6.72e+00 bond pdb=" N PHE A 83 " pdb=" CA PHE A 83 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.18e-02 7.18e+03 6.25e+00 bond pdb=" O2A ATP B 801 " pdb=" PA ATP B 801 " ideal model delta sigma weight residual 1.529 1.474 0.055 2.20e-02 2.07e+03 6.20e+00 ... (remaining 11631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.84: 15664 4.84 - 9.68: 27 9.68 - 14.52: 2 14.52 - 19.37: 2 19.37 - 24.21: 1 Bond angle restraints: 15696 Sorted by residual: angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 115.66 24.21 1.00e+00 1.00e+00 5.86e+02 angle pdb=" PA ATP B 801 " pdb=" O3A ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 136.83 117.68 19.15 1.00e+00 1.00e+00 3.67e+02 angle pdb=" C5' ATP B 801 " pdb=" O5' ATP B 801 " pdb=" PA ATP B 801 " ideal model delta sigma weight residual 121.27 103.55 17.72 1.00e+00 1.00e+00 3.14e+02 angle pdb=" N VAL B 479 " pdb=" CA VAL B 479 " pdb=" C VAL B 479 " ideal model delta sigma weight residual 108.11 115.53 -7.42 1.40e+00 5.10e-01 2.81e+01 angle pdb=" N SER A 549 " pdb=" CA SER A 549 " pdb=" C SER A 549 " ideal model delta sigma weight residual 110.19 116.71 -6.52 1.24e+00 6.50e-01 2.77e+01 ... (remaining 15691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 6311 16.69 - 33.38: 566 33.38 - 50.06: 147 50.06 - 66.75: 31 66.75 - 83.44: 13 Dihedral angle restraints: 7068 sinusoidal: 2846 harmonic: 4222 Sorted by residual: dihedral pdb=" CA ILE B 110 " pdb=" C ILE B 110 " pdb=" N ILE B 111 " pdb=" CA ILE B 111 " ideal model delta harmonic sigma weight residual -180.00 -160.75 -19.25 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ILE A 110 " pdb=" C ILE A 110 " pdb=" N ILE A 111 " pdb=" CA ILE A 111 " ideal model delta harmonic sigma weight residual -180.00 -161.39 -18.61 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA ASP B 94 " pdb=" CB ASP B 94 " pdb=" CG ASP B 94 " pdb=" OD1 ASP B 94 " ideal model delta sinusoidal sigma weight residual -30.00 -89.94 59.94 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 7065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1580 0.061 - 0.122: 238 0.122 - 0.182: 27 0.182 - 0.243: 6 0.243 - 0.304: 1 Chirality restraints: 1852 Sorted by residual: chirality pdb=" CA TYR A 150 " pdb=" N TYR A 150 " pdb=" C TYR A 150 " pdb=" CB TYR A 150 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA PHE B 478 " pdb=" N PHE B 478 " pdb=" C PHE B 478 " pdb=" CB PHE B 478 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ASN A 552 " pdb=" N ASN A 552 " pdb=" C ASN A 552 " pdb=" CB ASN A 552 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1849 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 548 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C HIS A 548 " -0.049 2.00e-02 2.50e+03 pdb=" O HIS A 548 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 549 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 550 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C ILE A 550 " -0.044 2.00e-02 2.50e+03 pdb=" O ILE A 550 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS A 551 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 551 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" C LYS A 551 " -0.034 2.00e-02 2.50e+03 pdb=" O LYS A 551 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN A 552 " 0.011 2.00e-02 2.50e+03 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 32 2.44 - 3.06: 7549 3.06 - 3.67: 16710 3.67 - 4.29: 24004 4.29 - 4.90: 39867 Nonbonded interactions: 88162 Sorted by model distance: nonbonded pdb=" O2G ATP B 801 " pdb="MG MG B 802 " model vdw 1.826 2.170 nonbonded pdb=" O2B ATP B 801 " pdb="MG MG B 802 " model vdw 1.923 2.170 nonbonded pdb=" O1B ATP A 801 " pdb="MG MG A 802 " model vdw 2.108 2.170 nonbonded pdb=" O GLY B 282 " pdb=" OG1 THR B 286 " model vdw 2.212 3.040 nonbonded pdb=" O ASP A 476 " pdb=" OD1 ASP A 476 " model vdw 2.226 3.040 ... (remaining 88157 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 27.450 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 11636 Z= 0.197 Angle : 0.735 24.206 15696 Z= 0.500 Chirality : 0.045 0.304 1852 Planarity : 0.003 0.029 1944 Dihedral : 14.109 83.440 4356 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.75 % Favored : 97.12 % Rotamer: Outliers : 0.72 % Allowed : 0.64 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.012 0.001 TRP A 132 HIS 0.006 0.001 HIS B 99 PHE 0.011 0.001 PHE B 615 TYR 0.012 0.001 TYR A 413 ARG 0.005 0.000 ARG B 122 *********************** 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 : 1.325 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: 0.7240 (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: 0.2614 time to fit residues: 158.9914 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 : 1.243 ------------------------------------------------------------------------------- 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 121 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 11636 Z= 0.329 Angle : 0.687 9.481 15696 Z= 0.361 Chirality : 0.043 0.243 1852 Planarity : 0.004 0.048 1944 Dihedral : 7.418 62.787 1626 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.93 % Allowed : 12.68 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.22), residues: 1456 helix: 1.61 (0.18), residues: 850 sheet: -0.21 (0.39), residues: 150 loop : -1.24 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 132 HIS 0.007 0.001 HIS B 249 PHE 0.013 0.002 PHE B 188 TYR 0.022 0.002 TYR A 413 ARG 0.009 0.001 ARG B 96 *********************** 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 328 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 279 time to evaluate : 1.438 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: 0.8108 (pmm) cc_final: 0.7748 (pmm) REVERT: A 644 LEU cc_start: 0.8763 (mp) cc_final: 0.8477 (mp) REVERT: B 125 MET cc_start: 0.7136 (tmm) cc_final: 0.6797 (tmm) REVERT: B 286 THR cc_start: 0.8636 (m) cc_final: 0.8306 (m) REVERT: B 335 ARG cc_start: 0.7689 (ttp80) cc_final: 0.7421 (tmm-80) REVERT: B 615 PHE cc_start: 0.7830 (t80) cc_final: 0.7555 (t80) REVERT: D 19 MET cc_start: 0.7874 (mmt) cc_final: 0.7603 (mmp) outliers start: 49 outliers final: 33 residues processed: 310 average time/residue: 0.2334 time to fit residues: 103.7750 Evaluate side-chains 272 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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 321 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 537 SER Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain C residue 17 GLU 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 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 72 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 116 optimal weight: 0.4980 chunk 129 optimal weight: 0.2980 chunk 44 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** A 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11636 Z= 0.182 Angle : 0.586 11.960 15696 Z= 0.303 Chirality : 0.041 0.213 1852 Planarity : 0.003 0.061 1944 Dihedral : 6.939 60.823 1623 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.29 % Allowed : 16.21 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.22), residues: 1456 helix: 1.76 (0.18), residues: 850 sheet: -0.10 (0.40), residues: 150 loop : -1.27 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 132 HIS 0.003 0.001 HIS A 602 PHE 0.013 0.001 PHE A 257 TYR 0.017 0.001 TYR A 413 ARG 0.006 0.001 ARG B 122 *********************** 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 310 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 269 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 ARG cc_start: 0.8170 (ttp80) cc_final: 0.7599 (ttp80) REVERT: B 495 TYR cc_start: 0.8371 (t80) cc_final: 0.7981 (t80) REVERT: B 615 PHE cc_start: 0.7696 (t80) cc_final: 0.7348 (t80) REVERT: D 19 MET cc_start: 0.7810 (mmt) cc_final: 0.7580 (mmp) outliers start: 41 outliers final: 29 residues processed: 292 average time/residue: 0.2298 time to fit residues: 96.2195 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 : 1.402 ------------------------------------------------------------------------------- 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 200 PHE Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 679 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.1980 chunk 98 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 87 optimal weight: 0.0970 chunk 131 optimal weight: 10.0000 chunk 139 optimal weight: 0.0070 chunk 68 optimal weight: 0.9990 chunk 124 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 overall best weight: 0.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11636 Z= 0.153 Angle : 0.583 13.452 15696 Z= 0.295 Chirality : 0.040 0.192 1852 Planarity : 0.003 0.050 1944 Dihedral : 6.717 57.929 1621 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.05 % Allowed : 18.62 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.22), residues: 1456 helix: 1.88 (0.18), residues: 850 sheet: 0.12 (0.40), residues: 150 loop : -1.32 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 132 HIS 0.003 0.001 HIS A 602 PHE 0.014 0.001 PHE A 257 TYR 0.015 0.001 TYR A 413 ARG 0.008 0.001 ARG B 122 *********************** 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 313 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 275 time to evaluate : 1.324 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 335 ARG cc_start: 0.8128 (ttp80) cc_final: 0.7529 (ttp80) REVERT: A 644 LEU cc_start: 0.8741 (mp) cc_final: 0.8534 (mp) REVERT: A 717 MET cc_start: 0.9167 (mmm) cc_final: 0.8967 (mmm) REVERT: B 37 MET cc_start: 0.7808 (mmm) cc_final: 0.7593 (mmp) REVERT: B 154 MET cc_start: 0.7436 (mmp) cc_final: 0.7181 (mmp) REVERT: B 385 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7447 (tm-30) REVERT: B 495 TYR cc_start: 0.8314 (t80) cc_final: 0.8009 (t80) REVERT: D 19 MET cc_start: 0.7726 (mmt) cc_final: 0.7483 (mmp) REVERT: D 21 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6980 (ttm) outliers start: 38 outliers final: 23 residues processed: 294 average time/residue: 0.2270 time to fit residues: 96.7457 Evaluate side-chains 267 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 243 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 274 SER Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 393 SER 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 D residue 21 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 0.0670 chunk 118 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 124 optimal weight: 0.4980 chunk 35 optimal weight: 0.0020 overall best weight: 0.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11636 Z= 0.157 Angle : 0.586 14.519 15696 Z= 0.298 Chirality : 0.040 0.176 1852 Planarity : 0.003 0.061 1944 Dihedral : 6.568 57.644 1620 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.25 % Allowed : 20.55 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.23), residues: 1456 helix: 1.99 (0.18), residues: 838 sheet: 0.19 (0.40), residues: 150 loop : -1.13 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 132 HIS 0.003 0.001 HIS A 602 PHE 0.017 0.001 PHE A 715 TYR 0.016 0.001 TYR B 247 ARG 0.010 0.001 ARG B 122 *********************** 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 291 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 263 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 MET cc_start: 0.8479 (mmm) cc_final: 0.7752 (tmm) REVERT: A 154 MET cc_start: 0.8114 (pmm) cc_final: 0.7804 (pmm) REVERT: A 335 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7548 (ttp80) REVERT: A 644 LEU cc_start: 0.8723 (mp) cc_final: 0.8492 (mp) REVERT: B 194 PHE cc_start: 0.7415 (t80) cc_final: 0.7119 (t80) REVERT: B 495 TYR cc_start: 0.8336 (t80) cc_final: 0.8055 (t80) REVERT: B 531 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8849 (mm) REVERT: B 615 PHE cc_start: 0.7690 (t80) cc_final: 0.7195 (t80) REVERT: D 19 MET cc_start: 0.7760 (mmt) cc_final: 0.7341 (mmp) outliers start: 28 outliers final: 21 residues processed: 278 average time/residue: 0.2287 time to fit residues: 91.9964 Evaluate side-chains 262 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 240 time to evaluate : 1.524 ------------------------------------------------------------------------------- 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 299 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 532 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 115 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11636 Z= 0.207 Angle : 0.605 14.745 15696 Z= 0.305 Chirality : 0.040 0.173 1852 Planarity : 0.003 0.040 1944 Dihedral : 6.468 58.357 1620 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.85 % Allowed : 20.63 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.22), residues: 1456 helix: 1.90 (0.18), residues: 840 sheet: 0.24 (0.41), residues: 146 loop : -1.06 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 132 HIS 0.005 0.001 HIS B 99 PHE 0.017 0.001 PHE A 383 TYR 0.020 0.001 TYR B 56 ARG 0.008 0.000 ARG B 335 *********************** 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 302 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 254 time to evaluate : 1.267 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 335 ARG cc_start: 0.8155 (ttp80) cc_final: 0.7546 (ttp80) REVERT: A 644 LEU cc_start: 0.8703 (mp) cc_final: 0.8485 (mp) REVERT: B 37 MET cc_start: 0.7865 (mmm) cc_final: 0.7458 (mmp) REVERT: B 290 ASP cc_start: 0.7843 (m-30) cc_final: 0.7574 (m-30) REVERT: B 495 TYR cc_start: 0.8481 (t80) cc_final: 0.8175 (t80) REVERT: B 531 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8897 (mm) REVERT: B 598 MET cc_start: 0.7584 (tpt) cc_final: 0.7342 (tpt) REVERT: B 615 PHE cc_start: 0.7699 (t80) cc_final: 0.7412 (t80) outliers start: 48 outliers final: 34 residues processed: 281 average time/residue: 0.2297 time to fit residues: 93.2748 Evaluate side-chains 277 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 1.365 ------------------------------------------------------------------------------- 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 274 SER Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 301 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 330 ILE Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 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 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 388 LEU Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 613 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 138 optimal weight: 0.0040 chunk 86 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11636 Z= 0.182 Angle : 0.621 14.266 15696 Z= 0.309 Chirality : 0.040 0.177 1852 Planarity : 0.003 0.031 1944 Dihedral : 6.429 58.394 1620 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.05 % Allowed : 22.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.22), residues: 1456 helix: 1.90 (0.18), residues: 840 sheet: 0.33 (0.41), residues: 146 loop : -1.05 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 132 HIS 0.009 0.001 HIS B 99 PHE 0.017 0.001 PHE A 383 TYR 0.023 0.001 TYR B 56 ARG 0.003 0.000 ARG A 96 *********************** 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: 38 poor density : 250 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8367 (tm-30) REVERT: A 644 LEU cc_start: 0.8680 (mp) cc_final: 0.8456 (mp) REVERT: B 37 MET cc_start: 0.7810 (mmm) cc_final: 0.7476 (mmp) REVERT: B 194 PHE cc_start: 0.7561 (OUTLIER) cc_final: 0.7330 (t80) REVERT: B 286 THR cc_start: 0.8680 (m) cc_final: 0.8332 (m) REVERT: B 290 ASP cc_start: 0.7957 (m-30) cc_final: 0.7660 (m-30) REVERT: B 495 TYR cc_start: 0.8492 (t80) cc_final: 0.8112 (t80) REVERT: B 531 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8872 (mm) REVERT: B 598 MET cc_start: 0.7525 (tpt) cc_final: 0.7248 (tpt) REVERT: B 615 PHE cc_start: 0.7636 (t80) cc_final: 0.7370 (t80) outliers start: 38 outliers final: 27 residues processed: 269 average time/residue: 0.2258 time to fit residues: 87.8301 Evaluate side-chains 268 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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 274 SER Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 343 LYS 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 502 LEU 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 188 PHE Chi-restraints excluded: chain B residue 194 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 388 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 532 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 0.0170 chunk 27 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11636 Z= 0.180 Angle : 0.641 14.365 15696 Z= 0.319 Chirality : 0.040 0.188 1852 Planarity : 0.003 0.040 1944 Dihedral : 6.395 58.131 1620 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.57 % Allowed : 22.79 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.22), residues: 1456 helix: 1.89 (0.18), residues: 840 sheet: 0.37 (0.41), residues: 146 loop : -1.02 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 132 HIS 0.008 0.001 HIS B 99 PHE 0.014 0.001 PHE A 257 TYR 0.017 0.001 TYR B 56 ARG 0.006 0.000 ARG B 122 *********************** 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 278 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 246 time to evaluate : 1.286 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 644 LEU cc_start: 0.8665 (mp) cc_final: 0.8436 (mp) REVERT: B 286 THR cc_start: 0.8706 (m) cc_final: 0.8275 (m) REVERT: B 290 ASP cc_start: 0.7966 (m-30) cc_final: 0.7647 (m-30) REVERT: B 495 TYR cc_start: 0.8488 (t80) cc_final: 0.8125 (t80) REVERT: B 531 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8872 (mm) REVERT: B 615 PHE cc_start: 0.7590 (t80) cc_final: 0.7335 (t80) outliers start: 32 outliers final: 25 residues processed: 260 average time/residue: 0.2295 time to fit residues: 86.7282 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 : 1.329 ------------------------------------------------------------------------------- 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 151 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 340 ASP 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 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 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 531 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 575 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.2980 chunk 121 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 128 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 HIS A 704 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11636 Z= 0.178 Angle : 0.644 15.038 15696 Z= 0.321 Chirality : 0.040 0.184 1852 Planarity : 0.003 0.026 1944 Dihedral : 6.334 57.514 1620 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.33 % Allowed : 22.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.22), residues: 1456 helix: 1.90 (0.18), residues: 840 sheet: 0.44 (0.41), residues: 146 loop : -1.04 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 132 HIS 0.008 0.001 HIS B 99 PHE 0.023 0.001 PHE A 715 TYR 0.020 0.001 TYR B 319 ARG 0.006 0.000 ARG B 122 *********************** 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 277 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 248 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 644 LEU cc_start: 0.8691 (mp) cc_final: 0.8463 (mp) REVERT: B 125 MET cc_start: 0.7421 (tmm) cc_final: 0.6917 (tmm) REVERT: B 286 THR cc_start: 0.8680 (m) cc_final: 0.8238 (m) REVERT: B 290 ASP cc_start: 0.7966 (m-30) cc_final: 0.7636 (m-30) REVERT: B 495 TYR cc_start: 0.8419 (t80) cc_final: 0.8069 (t80) REVERT: B 531 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8862 (mm) outliers start: 29 outliers final: 25 residues processed: 263 average time/residue: 0.2296 time to fit residues: 87.4154 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 : 1.377 ------------------------------------------------------------------------------- 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 151 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 343 LYS 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 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 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 393 SER Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 432 LEU 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 136 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 chunk 88 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11636 Z= 0.190 Angle : 0.694 15.798 15696 Z= 0.342 Chirality : 0.041 0.211 1852 Planarity : 0.003 0.059 1944 Dihedral : 6.330 57.296 1620 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.01 % Allowed : 23.68 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.22), residues: 1456 helix: 1.86 (0.18), residues: 840 sheet: 0.43 (0.41), residues: 146 loop : -1.05 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 132 HIS 0.008 0.001 HIS B 99 PHE 0.030 0.001 PHE A 715 TYR 0.016 0.001 TYR B 56 ARG 0.013 0.001 ARG A 96 ********************** 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 264 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 239 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 MET cc_start: 0.8197 (mmp) cc_final: 0.7938 (mpp) REVERT: A 434 TYR cc_start: 0.8072 (m-80) cc_final: 0.7596 (m-80) REVERT: A 644 LEU cc_start: 0.8723 (mp) cc_final: 0.8466 (mp) REVERT: B 125 MET cc_start: 0.7450 (tmm) cc_final: 0.6897 (tmm) REVERT: B 286 THR cc_start: 0.8679 (m) cc_final: 0.8186 (m) REVERT: B 331 GLN cc_start: 0.7508 (tm-30) cc_final: 0.7305 (tm-30) REVERT: B 495 TYR cc_start: 0.8428 (t80) cc_final: 0.8079 (t80) REVERT: B 531 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8883 (mm) outliers start: 25 outliers final: 21 residues processed: 249 average time/residue: 0.2346 time to fit residues: 84.2507 Evaluate side-chains 253 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 231 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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 274 SER Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 343 LYS 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 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 274 SER Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 432 LEU 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 121 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 117 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.132959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.111607 restraints weight = 27821.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.114583 restraints weight = 14105.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.116507 restraints weight = 8696.271| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11636 Z= 0.182 Angle : 0.685 15.788 15696 Z= 0.337 Chirality : 0.041 0.200 1852 Planarity : 0.003 0.037 1944 Dihedral : 6.279 56.967 1620 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.17 % Allowed : 23.76 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.22), residues: 1456 helix: 1.83 (0.19), residues: 840 sheet: 0.44 (0.41), residues: 146 loop : -1.02 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 132 HIS 0.008 0.001 HIS B 99 PHE 0.025 0.001 PHE A 715 TYR 0.022 0.001 TYR B 319 ARG 0.008 0.001 ARG B 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2646.07 seconds wall clock time: 49 minutes 24.52 seconds (2964.52 seconds total)