Starting phenix.real_space_refine on Tue Jun 10 09:48:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t57_25697/06_2025/7t57_25697.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t57_25697/06_2025/7t57_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_25697/06_2025/7t57_25697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t57_25697/06_2025/7t57_25697.map" model { file = "/net/cci-nas-00/data/ceres_data/7t57_25697/06_2025/7t57_25697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t57_25697/06_2025/7t57_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-5710/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: 7.03, per 1000 atoms: 0.61 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: 2.59 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: 1.23 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: 3.36 Time building geometry restraints manager: 3.10 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: 0.05 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: 1.880 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.350 Find NCS groups from input model: 0.360 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: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 11636 Z= 0.193 Angle : 0.735 24.206 15696 Z= 0.500 Chirality : 0.045 0.304 1852 Planarity : 0.003 0.029 1944 Dihedral : 14.109 83.440 4356 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.75 % Favored : 97.12 % Rotamer: Outliers : 0.72 % Allowed : 0.64 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.12793 ( 681) hydrogen bonds : angle 4.81229 ( 1971) covalent geometry : bond 0.00313 (11636) covalent geometry : angle 0.73498 (15696) *********************** 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 : 1.203 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: 0.2534 time to fit residues: 153.5044 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 : 1.301 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.130008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.108520 restraints weight = 28166.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.111254 restraints weight = 14910.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.113063 restraints weight = 9538.239| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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= 0.231 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 Details of bonding type rmsd hydrogen bonds : bond 0.04762 ( 681) hydrogen bonds : angle 4.36032 ( 1971) covalent geometry : bond 0.00510 (11636) covalent geometry : angle 0.68667 (15696) *********************** 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 : 1.291 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: 0.8604 (pmm) cc_final: 0.8239 (pmm) REVERT: A 224 ASN cc_start: 0.8711 (t0) cc_final: 0.8438 (t0) REVERT: A 274 SER cc_start: 0.9031 (m) cc_final: 0.8730 (p) REVERT: B 125 MET cc_start: 0.7188 (tmm) cc_final: 0.6813 (tmm) REVERT: B 286 THR cc_start: 0.9043 (m) cc_final: 0.8815 (m) REVERT: B 350 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8269 (tt0) REVERT: D 19 MET cc_start: 0.8242 (mmt) cc_final: 0.7918 (mmp) outliers start: 49 outliers final: 33 residues processed: 310 average time/residue: 0.2284 time to fit residues: 101.4012 Evaluate side-chains 274 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 240 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 350 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 37 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.126562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.104536 restraints weight = 28817.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.107408 restraints weight = 14414.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.109326 restraints weight = 8919.697| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11636 Z= 0.151 Angle : 0.599 11.518 15696 Z= 0.311 Chirality : 0.041 0.253 1852 Planarity : 0.003 0.060 1944 Dihedral : 6.967 62.360 1623 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.85 % Allowed : 16.05 % Favored : 80.10 % 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 (0.22), residues: 1456 helix: 1.70 (0.18), residues: 850 sheet: -0.10 (0.40), residues: 150 loop : -1.28 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.021 0.001 PHE B 615 TYR 0.017 0.001 TYR A 413 ARG 0.013 0.001 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.04457 ( 681) hydrogen bonds : angle 4.11887 ( 1971) covalent geometry : bond 0.00334 (11636) covalent geometry : angle 0.59897 (15696) *********************** 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 318 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 270 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7562 (m-30) cc_final: 0.7155 (m-30) REVERT: A 194 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.8005 (t80) REVERT: A 224 ASN cc_start: 0.8710 (t0) cc_final: 0.8444 (t0) REVERT: A 274 SER cc_start: 0.9046 (m) cc_final: 0.8667 (p) REVERT: A 647 ASP cc_start: 0.7530 (t0) cc_final: 0.7155 (t0) REVERT: B 290 ASP cc_start: 0.8766 (m-30) cc_final: 0.8348 (m-30) REVERT: B 385 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8100 (tm-30) outliers start: 48 outliers final: 32 residues processed: 295 average time/residue: 0.2194 time to fit residues: 93.3323 Evaluate side-chains 281 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 248 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 389 TYR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 121 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 74 optimal weight: 0.0570 chunk 100 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN A 334 ASN ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** 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 = 0.3844 r_free = 0.3844 target = 0.126052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.103811 restraints weight = 28645.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.106669 restraints weight = 14513.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.108595 restraints weight = 9028.508| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11636 Z= 0.143 Angle : 0.600 13.010 15696 Z= 0.307 Chirality : 0.041 0.166 1852 Planarity : 0.003 0.050 1944 Dihedral : 6.832 63.088 1621 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.77 % Allowed : 18.94 % Favored : 77.29 % 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: 1.01 (0.22), residues: 1456 helix: 1.80 (0.18), residues: 850 sheet: 0.06 (0.40), residues: 150 loop : -1.32 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 718 HIS 0.004 0.001 HIS B 249 PHE 0.027 0.001 PHE A 715 TYR 0.014 0.001 TYR A 413 ARG 0.008 0.001 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.04294 ( 681) hydrogen bonds : angle 4.07951 ( 1971) covalent geometry : bond 0.00321 (11636) covalent geometry : angle 0.60016 (15696) *********************** 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 305 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 258 time to evaluate : 1.386 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: 0.7589 (m-30) cc_final: 0.7264 (m-30) REVERT: A 194 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7859 (t80) REVERT: A 224 ASN cc_start: 0.8749 (t0) cc_final: 0.8479 (t0) REVERT: A 239 ASP cc_start: 0.9104 (m-30) cc_final: 0.8782 (m-30) REVERT: A 274 SER cc_start: 0.9029 (m) cc_final: 0.8627 (p) REVERT: B 37 MET cc_start: 0.8609 (mmm) cc_final: 0.8301 (mmp) REVERT: B 125 MET cc_start: 0.7446 (tmm) cc_final: 0.7191 (tmm) REVERT: B 154 MET cc_start: 0.8461 (mmp) cc_final: 0.8205 (mmp) REVERT: B 194 PHE cc_start: 0.7969 (t80) cc_final: 0.7608 (t80) REVERT: B 250 VAL cc_start: 0.8774 (OUTLIER) cc_final: 0.8540 (t) REVERT: B 290 ASP cc_start: 0.8809 (m-30) cc_final: 0.8316 (m-30) REVERT: B 385 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8147 (tm-30) REVERT: B 407 ILE cc_start: 0.8994 (tt) cc_final: 0.8758 (tt) REVERT: B 428 PHE cc_start: 0.8224 (t80) cc_final: 0.7883 (t80) REVERT: B 495 TYR cc_start: 0.8677 (t80) cc_final: 0.8250 (t80) outliers start: 47 outliers final: 33 residues processed: 282 average time/residue: 0.2215 time to fit residues: 90.5781 Evaluate side-chains 271 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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 330 ILE 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 A residue 674 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 679 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 90 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 54 optimal weight: 0.0970 chunk 32 optimal weight: 2.9990 chunk 11 optimal weight: 0.0670 chunk 111 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 overall best weight: 1.4120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.124823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.103058 restraints weight = 28779.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.105826 restraints weight = 14863.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.107623 restraints weight = 9343.402| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11636 Z= 0.157 Angle : 0.596 13.598 15696 Z= 0.307 Chirality : 0.040 0.174 1852 Planarity : 0.003 0.061 1944 Dihedral : 6.755 65.736 1621 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.57 % Allowed : 19.10 % Favored : 76.32 % 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: 1.13 (0.22), residues: 1456 helix: 1.85 (0.18), residues: 840 sheet: 0.25 (0.41), residues: 146 loop : -1.13 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.016 0.001 PHE B 217 TYR 0.018 0.001 TYR B 56 ARG 0.007 0.001 ARG B 335 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 681) hydrogen bonds : angle 4.09779 ( 1971) covalent geometry : bond 0.00353 (11636) covalent geometry : angle 0.59605 (15696) *********************** 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 304 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 247 time to evaluate : 1.343 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: 0.7536 (m-30) cc_final: 0.7201 (m-30) REVERT: A 45 MET cc_start: 0.9070 (mmm) cc_final: 0.7827 (tmm) REVERT: A 194 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7973 (t80) REVERT: A 197 LEU cc_start: 0.8926 (mt) cc_final: 0.8625 (mt) REVERT: A 224 ASN cc_start: 0.8725 (t0) cc_final: 0.8453 (t0) REVERT: A 239 ASP cc_start: 0.9116 (m-30) cc_final: 0.8768 (m-30) REVERT: A 274 SER cc_start: 0.9076 (m) cc_final: 0.8672 (p) REVERT: A 593 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9052 (tp) REVERT: B 125 MET cc_start: 0.7500 (tmm) cc_final: 0.7172 (tmm) REVERT: B 244 MET cc_start: 0.9062 (mmm) cc_final: 0.8823 (tpp) REVERT: B 250 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8592 (t) REVERT: B 290 ASP cc_start: 0.8835 (m-30) cc_final: 0.8396 (m-30) REVERT: B 407 ILE cc_start: 0.8972 (tt) cc_final: 0.8767 (tt) REVERT: B 428 PHE cc_start: 0.8300 (t80) cc_final: 0.7895 (t80) REVERT: B 598 MET cc_start: 0.8184 (tpt) cc_final: 0.7915 (tpt) outliers start: 57 outliers final: 44 residues processed: 278 average time/residue: 0.2312 time to fit residues: 94.5623 Evaluate side-chains 281 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 234 time to evaluate : 1.399 ------------------------------------------------------------------------------- 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 194 PHE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 340 ASP 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 470 GLU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 679 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 13 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 125 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.126217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.104356 restraints weight = 28872.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.107156 restraints weight = 14692.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.108992 restraints weight = 9160.153| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4371 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= 0.126 Angle : 0.594 12.470 15696 Z= 0.305 Chirality : 0.040 0.171 1852 Planarity : 0.003 0.060 1944 Dihedral : 6.698 66.081 1621 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.93 % Allowed : 21.35 % 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: 1.19 (0.22), residues: 1456 helix: 1.88 (0.18), residues: 842 sheet: 0.29 (0.42), residues: 146 loop : -1.10 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 132 HIS 0.003 0.001 HIS B 249 PHE 0.047 0.001 PHE A 715 TYR 0.011 0.001 TYR B 179 ARG 0.007 0.000 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 681) hydrogen bonds : angle 3.98999 ( 1971) covalent geometry : bond 0.00277 (11636) covalent geometry : angle 0.59421 (15696) *********************** 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 308 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 259 time to evaluate : 1.198 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: 0.7554 (m-30) cc_final: 0.7201 (m-30) REVERT: A 45 MET cc_start: 0.9055 (mmm) cc_final: 0.8773 (tpt) REVERT: A 194 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7902 (t80) REVERT: A 197 LEU cc_start: 0.8847 (mt) cc_final: 0.8545 (mt) REVERT: A 224 ASN cc_start: 0.8693 (t0) cc_final: 0.8417 (t0) REVERT: A 239 ASP cc_start: 0.9106 (m-30) cc_final: 0.8761 (m-30) REVERT: A 245 GLU cc_start: 0.9311 (tm-30) cc_final: 0.8949 (tm-30) REVERT: A 274 SER cc_start: 0.9035 (m) cc_final: 0.8633 (p) REVERT: A 335 ARG cc_start: 0.8763 (tmm160) cc_final: 0.8559 (ttp80) REVERT: B 125 MET cc_start: 0.7491 (tmm) cc_final: 0.7129 (tmm) REVERT: B 250 VAL cc_start: 0.8781 (OUTLIER) cc_final: 0.8542 (t) REVERT: B 369 LYS cc_start: 0.8273 (tptt) cc_final: 0.7927 (tptt) REVERT: B 428 PHE cc_start: 0.8223 (t80) cc_final: 0.7911 (t80) REVERT: B 495 TYR cc_start: 0.8624 (t80) cc_final: 0.8224 (t80) REVERT: B 531 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8718 (mm) outliers start: 49 outliers final: 36 residues processed: 287 average time/residue: 0.2085 time to fit residues: 86.5477 Evaluate side-chains 277 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 238 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 300 LEU Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 330 ILE 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 449 ILE Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 41 LYS 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 250 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 69 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 121 optimal weight: 0.5980 chunk 10 optimal weight: 0.0270 chunk 100 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** 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 = 0.3872 r_free = 0.3872 target = 0.127786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.105664 restraints weight = 28671.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.108552 restraints weight = 14302.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.110479 restraints weight = 8804.902| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11636 Z= 0.119 Angle : 0.609 15.757 15696 Z= 0.307 Chirality : 0.040 0.173 1852 Planarity : 0.003 0.034 1944 Dihedral : 6.566 64.126 1621 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.21 % Allowed : 22.07 % 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: 1.23 (0.22), residues: 1456 helix: 1.93 (0.18), residues: 842 sheet: 0.36 (0.42), residues: 146 loop : -1.13 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 132 HIS 0.003 0.000 HIS B 249 PHE 0.043 0.001 PHE A 715 TYR 0.010 0.001 TYR B 150 ARG 0.008 0.001 ARG B 335 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 681) hydrogen bonds : angle 3.93964 ( 1971) covalent geometry : bond 0.00257 (11636) covalent geometry : angle 0.60862 (15696) *********************** 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 292 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 252 time to evaluate : 1.454 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: 0.7532 (m-30) cc_final: 0.7157 (m-30) REVERT: A 45 MET cc_start: 0.9019 (mmm) cc_final: 0.8642 (tpt) REVERT: A 154 MET cc_start: 0.8964 (pmm) cc_final: 0.8542 (pmm) REVERT: A 194 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7753 (t80) REVERT: A 197 LEU cc_start: 0.8774 (mt) cc_final: 0.8481 (mt) REVERT: A 224 ASN cc_start: 0.8776 (OUTLIER) cc_final: 0.8507 (t0) REVERT: A 239 ASP cc_start: 0.9131 (m-30) cc_final: 0.8693 (m-30) REVERT: A 245 GLU cc_start: 0.9337 (tm-30) cc_final: 0.8963 (tm-30) REVERT: A 274 SER cc_start: 0.9004 (m) cc_final: 0.8602 (p) REVERT: A 335 ARG cc_start: 0.8783 (tmm160) cc_final: 0.8543 (ttp80) REVERT: A 368 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7347 (tm-30) REVERT: C 19 MET cc_start: 0.8838 (tpp) cc_final: 0.8459 (mmm) REVERT: B 125 MET cc_start: 0.7557 (tmm) cc_final: 0.7147 (tmm) REVERT: B 194 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7849 (t80) REVERT: B 244 MET cc_start: 0.9077 (mmm) cc_final: 0.8349 (tpp) REVERT: B 250 VAL cc_start: 0.8668 (OUTLIER) cc_final: 0.8419 (t) REVERT: B 369 LYS cc_start: 0.8269 (tptt) cc_final: 0.7966 (tptt) REVERT: B 428 PHE cc_start: 0.8114 (t80) cc_final: 0.7838 (t80) REVERT: B 495 TYR cc_start: 0.8598 (t80) cc_final: 0.8155 (t80) REVERT: B 531 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8697 (mm) REVERT: B 598 MET cc_start: 0.8303 (tpt) cc_final: 0.7959 (tpt) outliers start: 40 outliers final: 27 residues processed: 269 average time/residue: 0.2637 time to fit residues: 102.2861 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 : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 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 442 LEU Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 571 ILE 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 210 SER 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 531 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 575 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.125242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.103625 restraints weight = 28968.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.106332 restraints weight = 15140.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.108158 restraints weight = 9604.820| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4654 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= 0.149 Angle : 0.618 14.395 15696 Z= 0.316 Chirality : 0.041 0.197 1852 Planarity : 0.003 0.027 1944 Dihedral : 6.482 65.074 1620 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.53 % Allowed : 21.91 % Favored : 74.56 % 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: 1.93 (0.18), residues: 840 sheet: 0.38 (0.42), residues: 146 loop : -1.17 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.044 0.002 PHE A 715 TYR 0.024 0.001 TYR B 56 ARG 0.004 0.000 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.04125 ( 681) hydrogen bonds : angle 4.02887 ( 1971) covalent geometry : bond 0.00340 (11636) covalent geometry : angle 0.61775 (15696) *********************** 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 296 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 252 time to evaluate : 1.384 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: 0.7477 (m-30) cc_final: 0.7032 (m-30) REVERT: A 194 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7786 (t80) REVERT: A 197 LEU cc_start: 0.8743 (mt) cc_final: 0.8458 (mt) REVERT: A 224 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.8396 (t0) REVERT: A 239 ASP cc_start: 0.9031 (m-30) cc_final: 0.8633 (m-30) REVERT: A 245 GLU cc_start: 0.9288 (tm-30) cc_final: 0.8963 (tm-30) REVERT: A 274 SER cc_start: 0.9049 (m) cc_final: 0.8664 (p) REVERT: A 335 ARG cc_start: 0.8705 (tmm160) cc_final: 0.8438 (tmm160) REVERT: C 19 MET cc_start: 0.8859 (tpp) cc_final: 0.8512 (mmm) REVERT: B 125 MET cc_start: 0.7632 (tmm) cc_final: 0.7219 (tmm) REVERT: B 194 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.7830 (t80) REVERT: B 244 MET cc_start: 0.8958 (mmm) cc_final: 0.8244 (tpp) REVERT: B 250 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8611 (t) REVERT: B 350 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8606 (tm-30) REVERT: B 369 LYS cc_start: 0.8332 (tptt) cc_final: 0.7996 (tptt) REVERT: B 428 PHE cc_start: 0.8211 (t80) cc_final: 0.7929 (t80) REVERT: B 531 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8810 (mm) REVERT: B 598 MET cc_start: 0.8155 (tpt) cc_final: 0.7896 (tpt) outliers start: 44 outliers final: 34 residues processed: 275 average time/residue: 0.2282 time to fit residues: 92.7357 Evaluate side-chains 278 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 239 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 340 ASP 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 457 ASN Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 210 SER 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 390 ILE 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 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 124 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 66 optimal weight: 0.0770 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 43 optimal weight: 0.0000 chunk 137 optimal weight: 5.9990 chunk 129 optimal weight: 0.4980 chunk 123 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.131005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.109769 restraints weight = 28443.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.112696 restraints weight = 14592.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.114635 restraints weight = 9078.646| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11636 Z= 0.121 Angle : 0.646 14.604 15696 Z= 0.324 Chirality : 0.041 0.213 1852 Planarity : 0.003 0.027 1944 Dihedral : 6.399 63.169 1620 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.89 % Allowed : 22.71 % Favored : 74.40 % 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: 1.93 (0.18), residues: 840 sheet: 0.38 (0.42), residues: 146 loop : -1.18 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 132 HIS 0.003 0.000 HIS A 602 PHE 0.045 0.001 PHE A 715 TYR 0.019 0.001 TYR B 56 ARG 0.007 0.001 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 681) hydrogen bonds : angle 3.89248 ( 1971) covalent geometry : bond 0.00260 (11636) covalent geometry : angle 0.64551 (15696) *********************** 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 287 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 251 time to evaluate : 1.694 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: 0.7470 (m-30) cc_final: 0.7004 (m-30) REVERT: A 154 MET cc_start: 0.8887 (pmm) cc_final: 0.8269 (pmm) REVERT: A 194 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7606 (t80) REVERT: A 197 LEU cc_start: 0.8664 (mt) cc_final: 0.8409 (mt) REVERT: A 224 ASN cc_start: 0.8649 (OUTLIER) cc_final: 0.8384 (t0) REVERT: A 239 ASP cc_start: 0.9032 (m-30) cc_final: 0.8604 (m-30) REVERT: A 245 GLU cc_start: 0.9264 (tm-30) cc_final: 0.8932 (tm-30) REVERT: A 274 SER cc_start: 0.9049 (m) cc_final: 0.8639 (p) REVERT: C 19 MET cc_start: 0.8848 (tpp) cc_final: 0.8468 (mmm) REVERT: B 125 MET cc_start: 0.7564 (tmm) cc_final: 0.7170 (tmm) REVERT: B 194 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7819 (t80) REVERT: B 244 MET cc_start: 0.8810 (mmm) cc_final: 0.8590 (tpp) REVERT: B 250 VAL cc_start: 0.8761 (OUTLIER) cc_final: 0.8520 (t) REVERT: B 350 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8323 (tm-30) REVERT: B 369 LYS cc_start: 0.8252 (tptt) cc_final: 0.7958 (tptt) REVERT: B 428 PHE cc_start: 0.8042 (t80) cc_final: 0.7815 (t80) REVERT: B 495 TYR cc_start: 0.8618 (t80) cc_final: 0.8189 (t80) REVERT: B 531 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8770 (mm) outliers start: 36 outliers final: 28 residues processed: 269 average time/residue: 0.3091 time to fit residues: 124.8737 Evaluate side-chains 279 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 246 time to evaluate : 2.757 ------------------------------------------------------------------------------- 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 224 ASN Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 330 ILE 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 457 ASN Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain B residue 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 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 393 SER 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 52 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.125950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.104522 restraints weight = 28884.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.107310 restraints weight = 14784.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.109182 restraints weight = 9211.212| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11636 Z= 0.143 Angle : 0.663 15.379 15696 Z= 0.333 Chirality : 0.041 0.217 1852 Planarity : 0.003 0.027 1944 Dihedral : 6.383 63.458 1620 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.97 % Allowed : 22.95 % 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: 1.90 (0.18), residues: 842 sheet: 0.37 (0.42), residues: 146 loop : -1.17 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.041 0.001 PHE A 715 TYR 0.026 0.001 TYR B 247 ARG 0.005 0.001 ARG A 458 Details of bonding type rmsd hydrogen bonds : bond 0.03938 ( 681) hydrogen bonds : angle 3.99085 ( 1971) covalent geometry : bond 0.00323 (11636) covalent geometry : angle 0.66335 (15696) ********************** 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 278 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 1.418 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: 0.7580 (m-30) cc_final: 0.7024 (m-30) REVERT: A 194 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.7697 (t80) REVERT: A 197 LEU cc_start: 0.8751 (mt) cc_final: 0.8459 (mt) REVERT: A 224 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8467 (t0) REVERT: A 239 ASP cc_start: 0.9085 (m-30) cc_final: 0.8628 (m-30) REVERT: A 245 GLU cc_start: 0.9339 (tm-30) cc_final: 0.8984 (tm-30) REVERT: A 274 SER cc_start: 0.9040 (m) cc_final: 0.8643 (p) REVERT: B 125 MET cc_start: 0.7595 (tmm) cc_final: 0.7226 (tmm) REVERT: B 250 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8496 (t) REVERT: B 350 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8436 (tm-30) REVERT: B 369 LYS cc_start: 0.8335 (tptt) cc_final: 0.7996 (tptt) REVERT: B 428 PHE cc_start: 0.8177 (t80) cc_final: 0.7854 (t80) REVERT: B 531 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8736 (mm) outliers start: 37 outliers final: 26 residues processed: 262 average time/residue: 0.3553 time to fit residues: 135.9897 Evaluate side-chains 270 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 1.833 ------------------------------------------------------------------------------- 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 224 ASN Chi-restraints excluded: chain A residue 300 LEU 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 457 ASN Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain C residue 17 GLU 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 210 SER 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 393 SER 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 679 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 57 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 0.0470 chunk 99 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.130957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.109405 restraints weight = 28096.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.112379 restraints weight = 14077.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.114275 restraints weight = 8659.034| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4831 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= 0.123 Angle : 0.665 15.844 15696 Z= 0.331 Chirality : 0.041 0.213 1852 Planarity : 0.003 0.034 1944 Dihedral : 6.332 62.387 1620 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.65 % Allowed : 23.19 % Favored : 74.16 % 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: 1.17 (0.22), residues: 1456 helix: 1.90 (0.18), residues: 842 sheet: 0.13 (0.41), residues: 150 loop : -1.12 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 132 HIS 0.003 0.001 HIS A 602 PHE 0.041 0.001 PHE A 715 TYR 0.019 0.001 TYR B 56 ARG 0.009 0.001 ARG B 122 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 681) hydrogen bonds : angle 3.92949 ( 1971) covalent geometry : bond 0.00271 (11636) covalent geometry : angle 0.66469 (15696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4822.08 seconds wall clock time: 89 minutes 0.34 seconds (5340.34 seconds total)