Starting phenix.real_space_refine on Sun Sep 13 05:32:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yih_33859/09_2026/7yih_33859.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yih_33859/09_2026/7yih_33859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7yih_33859/09_2026/7yih_33859.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yih_33859/09_2026/7yih_33859.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yih_33859/09_2026/7yih_33859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yih_33859/09_2026/7yih_33859.map" model { file = "/net/cci-nas-00/data/ceres_data/7yih_33859/09_2026/7yih_33859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yih_33859/09_2026/7yih_33859.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 5 8.98 5 S 128 5.16 5 C 13796 2.51 5 N 3544 2.21 5 O 3848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21321 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "B" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "C" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "D" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' K': 5} Classifications: {'undetermined': 5, 'water': 1} Link IDs: {None: 5} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.49, per 1000 atoms: 0.21 Number of scatterers: 21321 At special positions: 0 Unit cell: (158.763, 158.763, 129.897, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 5 19.00 S 128 16.00 O 3848 8.00 N 3544 7.00 C 13796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 833.6 milliseconds 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5048 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 46.4% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.858A pdb=" N THR A 153 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 211 through 238 removed outlier: 3.628A pdb=" N THR A 215 " --> pdb=" O CYS A 211 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 244 through 265 removed outlier: 3.827A pdb=" N LEU A 248 " --> pdb=" O ASN A 244 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 280 through 301 removed outlier: 6.284A pdb=" N VAL A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 328 removed outlier: 3.633A pdb=" N VAL A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 338 Processing helix chain 'A' and resid 345 through 375 removed outlier: 3.514A pdb=" N VAL A 375 " --> pdb=" O GLY A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 397 Processing helix chain 'A' and resid 414 through 431 Processing helix chain 'A' and resid 442 through 495 removed outlier: 3.823A pdb=" N LYS A 446 " --> pdb=" O THR A 442 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N MET A 474 " --> pdb=" O ILE A 470 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR A 475 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN A 477 " --> pdb=" O GLN A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 516 Processing helix chain 'A' and resid 520 through 527 removed outlier: 3.874A pdb=" N VAL A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 542 removed outlier: 3.551A pdb=" N ARG A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 563 Processing helix chain 'A' and resid 646 through 653 removed outlier: 3.665A pdb=" N LEU A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 664 removed outlier: 3.756A pdb=" N ASN A 658 " --> pdb=" O THR A 654 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 150 through 154 removed outlier: 3.858A pdb=" N THR B 153 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 211 through 238 removed outlier: 3.628A pdb=" N THR B 215 " --> pdb=" O CYS B 211 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 244 through 265 removed outlier: 3.827A pdb=" N LEU B 248 " --> pdb=" O ASN B 244 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 280 through 301 removed outlier: 6.285A pdb=" N VAL B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 328 removed outlier: 3.633A pdb=" N VAL B 325 " --> pdb=" O SER B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 338 Processing helix chain 'B' and resid 345 through 375 removed outlier: 3.514A pdb=" N VAL B 375 " --> pdb=" O GLY B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 397 Processing helix chain 'B' and resid 414 through 431 Processing helix chain 'B' and resid 442 through 495 removed outlier: 3.823A pdb=" N LYS B 446 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N MET B 474 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR B 475 " --> pdb=" O PHE B 471 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN B 477 " --> pdb=" O GLN B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 516 Processing helix chain 'B' and resid 520 through 527 removed outlier: 3.874A pdb=" N VAL B 524 " --> pdb=" O ASP B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 542 removed outlier: 3.551A pdb=" N ARG B 542 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 563 Processing helix chain 'B' and resid 646 through 653 removed outlier: 3.665A pdb=" N LEU B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 664 removed outlier: 3.756A pdb=" N ASN B 658 " --> pdb=" O THR B 654 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER B 659 " --> pdb=" O ALA B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 692 Processing helix chain 'C' and resid 83 through 88 Processing helix chain 'C' and resid 150 through 154 removed outlier: 3.858A pdb=" N THR C 153 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 183 through 187 Processing helix chain 'C' and resid 211 through 238 removed outlier: 3.628A pdb=" N THR C 215 " --> pdb=" O CYS C 211 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 244 through 265 removed outlier: 3.827A pdb=" N LEU C 248 " --> pdb=" O ASN C 244 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 280 through 301 removed outlier: 6.285A pdb=" N VAL C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE C 295 " --> pdb=" O THR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 328 removed outlier: 3.633A pdb=" N VAL C 325 " --> pdb=" O SER C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 338 Processing helix chain 'C' and resid 345 through 375 removed outlier: 3.514A pdb=" N VAL C 375 " --> pdb=" O GLY C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 397 Processing helix chain 'C' and resid 414 through 431 Processing helix chain 'C' and resid 442 through 495 removed outlier: 3.823A pdb=" N LYS C 446 " --> pdb=" O THR C 442 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET C 447 " --> pdb=" O ASP C 443 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N MET C 474 " --> pdb=" O ILE C 470 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR C 475 " --> pdb=" O PHE C 471 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN C 477 " --> pdb=" O GLN C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 516 Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.874A pdb=" N VAL C 524 " --> pdb=" O ASP C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 542 removed outlier: 3.551A pdb=" N ARG C 542 " --> pdb=" O VAL C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 563 Processing helix chain 'C' and resid 646 through 653 removed outlier: 3.665A pdb=" N LEU C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 664 removed outlier: 3.756A pdb=" N ASN C 658 " --> pdb=" O THR C 654 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER C 659 " --> pdb=" O ALA C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 692 Processing helix chain 'D' and resid 83 through 88 Processing helix chain 'D' and resid 150 through 154 removed outlier: 3.858A pdb=" N THR D 153 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 162 Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'D' and resid 211 through 238 removed outlier: 3.628A pdb=" N THR D 215 " --> pdb=" O CYS D 211 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 244 through 265 removed outlier: 3.827A pdb=" N LEU D 248 " --> pdb=" O ASN D 244 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 280 through 301 removed outlier: 6.285A pdb=" N VAL D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE D 295 " --> pdb=" O THR D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 328 removed outlier: 3.633A pdb=" N VAL D 325 " --> pdb=" O SER D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 338 Processing helix chain 'D' and resid 345 through 375 removed outlier: 3.514A pdb=" N VAL D 375 " --> pdb=" O GLY D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 397 Processing helix chain 'D' and resid 414 through 431 Processing helix chain 'D' and resid 442 through 495 removed outlier: 3.823A pdb=" N LYS D 446 " --> pdb=" O THR D 442 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET D 447 " --> pdb=" O ASP D 443 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N MET D 474 " --> pdb=" O ILE D 470 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR D 475 " --> pdb=" O PHE D 471 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN D 477 " --> pdb=" O GLN D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 516 Processing helix chain 'D' and resid 520 through 527 removed outlier: 3.874A pdb=" N VAL D 524 " --> pdb=" O ASP D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 542 removed outlier: 3.551A pdb=" N ARG D 542 " --> pdb=" O VAL D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 563 Processing helix chain 'D' and resid 646 through 653 removed outlier: 3.665A pdb=" N LEU D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 664 removed outlier: 3.756A pdb=" N ASN D 658 " --> pdb=" O THR D 654 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER D 659 " --> pdb=" O ALA D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 692 Processing sheet with id=AA1, first strand: chain 'A' and resid 270 through 271 removed outlier: 4.075A pdb=" N PHE A 270 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 567 through 571 removed outlier: 3.661A pdb=" N SER A 592 " --> pdb=" O ASP A 637 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N HIS A 639 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL A 590 " --> pdb=" O HIS A 639 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 602 through 607 removed outlier: 3.636A pdb=" N GLU A 602 " --> pdb=" O GLN A 599 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL A 597 " --> pdb=" O VAL A 604 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE A 606 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU A 595 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 596 " --> pdb=" O ARG A 631 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 270 through 271 removed outlier: 4.075A pdb=" N PHE B 270 " --> pdb=" O ILE B 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 567 through 571 removed outlier: 3.663A pdb=" N SER B 592 " --> pdb=" O ASP B 637 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N HIS B 639 " --> pdb=" O VAL B 590 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL B 590 " --> pdb=" O HIS B 639 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 602 through 607 removed outlier: 3.636A pdb=" N GLU B 602 " --> pdb=" O GLN B 599 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL B 597 " --> pdb=" O VAL B 604 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE B 606 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU B 595 " --> pdb=" O ILE B 606 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 596 " --> pdb=" O ARG B 631 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 270 through 271 removed outlier: 4.075A pdb=" N PHE C 270 " --> pdb=" O ILE C 278 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 567 through 571 removed outlier: 3.663A pdb=" N SER C 592 " --> pdb=" O ASP C 637 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N HIS C 639 " --> pdb=" O VAL C 590 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL C 590 " --> pdb=" O HIS C 639 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 602 through 607 removed outlier: 3.636A pdb=" N GLU C 602 " --> pdb=" O GLN C 599 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL C 597 " --> pdb=" O VAL C 604 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE C 606 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU C 595 " --> pdb=" O ILE C 606 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 596 " --> pdb=" O ARG C 631 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 270 through 271 removed outlier: 4.075A pdb=" N PHE D 270 " --> pdb=" O ILE D 278 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 567 through 571 removed outlier: 3.661A pdb=" N SER D 592 " --> pdb=" O ASP D 637 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N HIS D 639 " --> pdb=" O VAL D 590 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL D 590 " --> pdb=" O HIS D 639 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 602 through 607 removed outlier: 3.636A pdb=" N GLU D 602 " --> pdb=" O GLN D 599 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL D 597 " --> pdb=" O VAL D 604 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE D 606 " --> pdb=" O LEU D 595 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU D 595 " --> pdb=" O ILE D 606 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU D 596 " --> pdb=" O ARG D 631 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2484 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: 3.61 Time building geometry restraints manager: 2.19 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: 6656 1.34 - 1.46: 4337 1.46 - 1.58: 10619 1.58 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 21804 Sorted by residual: bond pdb=" N TRP B 38 " pdb=" CA TRP B 38 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.41e-02 5.03e+03 3.70e+00 bond pdb=" N TRP C 38 " pdb=" CA TRP C 38 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.41e-02 5.03e+03 3.70e+00 bond pdb=" N TRP D 38 " pdb=" CA TRP D 38 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.41e-02 5.03e+03 3.70e+00 bond pdb=" N TRP A 38 " pdb=" CA TRP A 38 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.41e-02 5.03e+03 3.70e+00 bond pdb=" N VAL C 36 " pdb=" CA VAL C 36 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.25e-02 6.40e+03 3.12e+00 ... (remaining 21799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 28980 2.36 - 4.72: 536 4.72 - 7.08: 40 7.08 - 9.45: 16 9.45 - 11.81: 12 Bond angle restraints: 29584 Sorted by residual: angle pdb=" N PRO A 39 " pdb=" CA PRO A 39 " pdb=" C PRO A 39 " ideal model delta sigma weight residual 112.47 124.04 -11.57 2.06e+00 2.36e-01 3.15e+01 angle pdb=" N PRO D 39 " pdb=" CA PRO D 39 " pdb=" C PRO D 39 " ideal model delta sigma weight residual 112.47 124.04 -11.57 2.06e+00 2.36e-01 3.15e+01 angle pdb=" N PRO B 39 " pdb=" CA PRO B 39 " pdb=" C PRO B 39 " ideal model delta sigma weight residual 112.47 124.04 -11.57 2.06e+00 2.36e-01 3.15e+01 angle pdb=" N PRO C 39 " pdb=" CA PRO C 39 " pdb=" C PRO C 39 " ideal model delta sigma weight residual 112.47 124.04 -11.57 2.06e+00 2.36e-01 3.15e+01 angle pdb=" CA PRO A 549 " pdb=" N PRO A 549 " pdb=" CD PRO A 549 " ideal model delta sigma weight residual 112.00 104.71 7.29 1.40e+00 5.10e-01 2.71e+01 ... (remaining 29579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11627 17.95 - 35.91: 1105 35.91 - 53.86: 160 53.86 - 71.81: 24 71.81 - 89.77: 16 Dihedral angle restraints: 12932 sinusoidal: 5144 harmonic: 7788 Sorted by residual: dihedral pdb=" CA PRO C 39 " pdb=" C PRO C 39 " pdb=" N VAL C 40 " pdb=" CA VAL C 40 " ideal model delta harmonic sigma weight residual 180.00 146.66 33.34 0 5.00e+00 4.00e-02 4.45e+01 dihedral pdb=" CA PRO B 39 " pdb=" C PRO B 39 " pdb=" N VAL B 40 " pdb=" CA VAL B 40 " ideal model delta harmonic sigma weight residual 180.00 146.66 33.34 0 5.00e+00 4.00e-02 4.45e+01 dihedral pdb=" CA PRO A 39 " pdb=" C PRO A 39 " pdb=" N VAL A 40 " pdb=" CA VAL A 40 " ideal model delta harmonic sigma weight residual 180.00 146.66 33.34 0 5.00e+00 4.00e-02 4.45e+01 ... (remaining 12929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3116 0.077 - 0.154: 276 0.154 - 0.231: 8 0.231 - 0.308: 0 0.308 - 0.384: 4 Chirality restraints: 3404 Sorted by residual: chirality pdb=" CA PRO A 39 " pdb=" N PRO A 39 " pdb=" C PRO A 39 " pdb=" CB PRO A 39 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA PRO B 39 " pdb=" N PRO B 39 " pdb=" C PRO B 39 " pdb=" CB PRO B 39 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA PRO D 39 " pdb=" N PRO D 39 " pdb=" C PRO D 39 " pdb=" CB PRO D 39 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.38 2.00e-01 2.50e+01 3.69e+00 ... (remaining 3401 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 548 " 0.108 5.00e-02 4.00e+02 1.59e-01 4.06e+01 pdb=" N PRO C 549 " -0.275 5.00e-02 4.00e+02 pdb=" CA PRO C 549 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO C 549 " 0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 548 " -0.108 5.00e-02 4.00e+02 1.59e-01 4.06e+01 pdb=" N PRO D 549 " 0.275 5.00e-02 4.00e+02 pdb=" CA PRO D 549 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO D 549 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 548 " -0.108 5.00e-02 4.00e+02 1.59e-01 4.06e+01 pdb=" N PRO A 549 " 0.275 5.00e-02 4.00e+02 pdb=" CA PRO A 549 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO A 549 " -0.078 5.00e-02 4.00e+02 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.68: 480 2.68 - 3.30: 24200 3.30 - 3.91: 40714 3.91 - 4.53: 52640 4.53 - 5.14: 83488 Nonbonded interactions: 201522 Sorted by model distance: nonbonded pdb=" O ARG A 677 " pdb=" N TRP D 38 " model vdw 2.066 3.120 nonbonded pdb=" N TRP A 38 " pdb=" O ARG B 677 " model vdw 2.066 3.120 nonbonded pdb=" N TRP C 38 " pdb=" O ARG D 677 " model vdw 2.066 3.120 nonbonded pdb=" N TRP B 38 " pdb=" O ARG C 677 " model vdw 2.066 3.120 nonbonded pdb=" N VAL B 36 " pdb=" O LYS C 678 " model vdw 2.233 3.120 ... (remaining 201517 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 692) selection = chain 'B' selection = 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: 6.170 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.000 Find NCS groups from input model: 0.480 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 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 : 0.004 0.079 21804 Z= 0.181 Angle : 0.783 11.808 29584 Z= 0.436 Chirality : 0.047 0.384 3404 Planarity : 0.008 0.159 3668 Dihedral : 14.228 89.766 7884 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 1.07 % Allowed : 13.91 % Favored : 85.02 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.16), residues: 2616 helix: 0.17 (0.15), residues: 1184 sheet: 0.42 (0.91), residues: 48 loop : -3.85 (0.14), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 327 TYR 0.014 0.002 TYR A 42 PHE 0.011 0.001 PHE C 293 TRP 0.023 0.002 TRP C 38 HIS 0.005 0.001 HIS C 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 (21804) covalent geometry : angle 0.78313 / 0.44 (29584) hydrogen bonds : bond 0.13364 / 8.88 ( 860) hydrogen bonds : angle 5.20462 / 3.60 ( 2484) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.688 Fit side-chains REVERT: A 394 LEU cc_start: 0.8471 (tp) cc_final: 0.8191 (tp) REVERT: B 394 LEU cc_start: 0.8462 (tp) cc_final: 0.8181 (tp) REVERT: C 394 LEU cc_start: 0.8479 (tp) cc_final: 0.8230 (tp) REVERT: D 394 LEU cc_start: 0.8484 (tp) cc_final: 0.8197 (tp) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.1325 time to fit residues: 53.5401 Evaluate side-chains 200 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 HIS A 570 HIS B 118 HIS B 570 HIS C 118 HIS C 570 HIS D 118 HIS D 570 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.215795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.193180 restraints weight = 26926.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.188751 restraints weight = 41919.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.186372 restraints weight = 40255.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.184990 restraints weight = 42130.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.183719 restraints weight = 37776.143| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 21804 Z= 0.347 Angle : 0.919 11.249 29584 Z= 0.494 Chirality : 0.054 0.374 3404 Planarity : 0.007 0.107 3668 Dihedral : 6.476 32.483 2864 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 1.07 % Allowed : 15.14 % Favored : 83.79 % Rotamer: Outliers : 1.34 % Allowed : 12.61 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.16), residues: 2616 helix: -0.07 (0.15), residues: 1192 sheet: -2.38 (0.52), residues: 112 loop : -4.16 (0.14), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 327 TYR 0.021 0.002 TYR C 419 PHE 0.020 0.002 PHE C 107 TRP 0.018 0.002 TRP C 38 HIS 0.006 0.002 HIS B 539 Details of bonding type rmsd/Z covalent geometry : bond 0.00828 / 0.35 (21804) covalent geometry : angle 0.91892 / 0.49 (29584) hydrogen bonds : bond 0.07564 / 5.00 ( 860) hydrogen bonds : angle 5.02233 / 3.45 ( 2484) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 224 time to evaluate : 0.854 Fit side-chains REVERT: A 55 ARG cc_start: 0.4484 (mpt180) cc_final: 0.3221 (mpt180) REVERT: A 59 MET cc_start: 0.2148 (tpt) cc_final: 0.1893 (tpt) REVERT: A 671 ARG cc_start: 0.7112 (tpt170) cc_final: 0.6891 (tpt170) REVERT: B 55 ARG cc_start: 0.4491 (mpt180) cc_final: 0.3227 (mpt180) REVERT: B 59 MET cc_start: 0.2142 (tpt) cc_final: 0.1893 (tpt) REVERT: B 671 ARG cc_start: 0.7108 (tpt170) cc_final: 0.6888 (tpt170) REVERT: C 55 ARG cc_start: 0.4490 (mpt180) cc_final: 0.3230 (mpt180) REVERT: C 59 MET cc_start: 0.2150 (tpt) cc_final: 0.1899 (tpt) REVERT: C 671 ARG cc_start: 0.7104 (tpt170) cc_final: 0.6884 (tpt170) REVERT: D 55 ARG cc_start: 0.4487 (mpt180) cc_final: 0.3227 (mpt180) REVERT: D 59 MET cc_start: 0.2142 (tpt) cc_final: 0.1890 (tpt) REVERT: D 671 ARG cc_start: 0.7107 (tpt170) cc_final: 0.6886 (tpt170) outliers start: 32 outliers final: 24 residues processed: 252 average time/residue: 0.1608 time to fit residues: 62.9842 Evaluate side-chains 208 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 162 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 124 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 58.5441 > 50:) chunk 30 optimal weight: 3.9990 chunk 146 optimal weight: 0.0870 chunk 190 optimal weight: 0.0050 chunk 237 optimal weight: 0.5980 chunk 58 optimal weight: 0.0980 chunk 154 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 170 optimal weight: 0.5980 overall best weight: 0.2772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 HIS ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 HIS ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.226614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.203206 restraints weight = 27291.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.198138 restraints weight = 38709.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.194164 restraints weight = 38264.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.193139 restraints weight = 41801.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.192298 restraints weight = 38007.876| |-----------------------------------------------------------------------------| r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 21804 Z= 0.155 Angle : 0.716 11.287 29584 Z= 0.383 Chirality : 0.045 0.377 3404 Planarity : 0.006 0.096 3668 Dihedral : 5.998 31.214 2864 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 1.07 % Allowed : 13.46 % Favored : 85.47 % Rotamer: Outliers : 1.18 % Allowed : 15.08 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.16), residues: 2616 helix: 0.45 (0.15), residues: 1184 sheet: -2.12 (0.52), residues: 112 loop : -4.04 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 480 TYR 0.015 0.001 TYR C 368 PHE 0.013 0.001 PHE C 107 TRP 0.013 0.002 TRP A 106 HIS 0.004 0.001 HIS D 539 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 (21804) covalent geometry : angle 0.71578 / 0.38 (29584) hydrogen bonds : bond 0.05414 / 3.65 ( 860) hydrogen bonds : angle 4.42067 / 3.04 ( 2484) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.681 Fit side-chains REVERT: A 55 ARG cc_start: 0.3986 (mpt180) cc_final: 0.2946 (mmt-90) REVERT: A 671 ARG cc_start: 0.7028 (tpt170) cc_final: 0.6684 (tpt170) REVERT: B 55 ARG cc_start: 0.3985 (mpt180) cc_final: 0.2941 (mmt-90) REVERT: B 671 ARG cc_start: 0.7020 (tpt170) cc_final: 0.6685 (tpt170) REVERT: C 55 ARG cc_start: 0.3988 (mpt180) cc_final: 0.2947 (mmt-90) REVERT: C 671 ARG cc_start: 0.7031 (tpt170) cc_final: 0.6695 (tpt170) REVERT: D 55 ARG cc_start: 0.3990 (mpt180) cc_final: 0.2945 (mmt-90) REVERT: D 671 ARG cc_start: 0.7018 (tpt170) cc_final: 0.6684 (tpt170) outliers start: 28 outliers final: 12 residues processed: 252 average time/residue: 0.1523 time to fit residues: 60.4273 Evaluate side-chains 212 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 200 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 670 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 214 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 251 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 206 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 HIS ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 HIS ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 ASN D 570 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.219054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.197109 restraints weight = 27036.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.192322 restraints weight = 40801.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.190462 restraints weight = 36582.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.189284 restraints weight = 38598.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.187484 restraints weight = 37536.230| |-----------------------------------------------------------------------------| r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 21804 Z= 0.239 Angle : 0.783 10.826 29584 Z= 0.423 Chirality : 0.049 0.364 3404 Planarity : 0.006 0.096 3668 Dihedral : 6.178 30.543 2864 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 1.07 % Allowed : 14.60 % Favored : 84.33 % Rotamer: Outliers : 2.56 % Allowed : 16.47 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.16), residues: 2616 helix: 0.32 (0.15), residues: 1192 sheet: -2.14 (0.50), residues: 112 loop : -4.13 (0.14), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 677 TYR 0.017 0.002 TYR A 419 PHE 0.017 0.002 PHE C 107 TRP 0.014 0.002 TRP C 38 HIS 0.006 0.001 HIS C 539 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.24 (21804) covalent geometry : angle 0.78322 / 0.42 (29584) hydrogen bonds : bond 0.06363 / 4.24 ( 860) hydrogen bonds : angle 4.56407 / 3.14 ( 2484) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 203 time to evaluate : 0.811 Fit side-chains REVERT: A 55 ARG cc_start: 0.4226 (mpt180) cc_final: 0.3210 (mmt-90) REVERT: A 59 MET cc_start: 0.3756 (tpt) cc_final: 0.3344 (tpt) REVERT: A 671 ARG cc_start: 0.7152 (tpt170) cc_final: 0.6881 (tpt170) REVERT: B 55 ARG cc_start: 0.4233 (mpt180) cc_final: 0.3218 (mmt-90) REVERT: B 59 MET cc_start: 0.3742 (tpt) cc_final: 0.3333 (tpt) REVERT: B 671 ARG cc_start: 0.7147 (tpt170) cc_final: 0.6878 (tpt170) REVERT: C 55 ARG cc_start: 0.4226 (mpt180) cc_final: 0.3213 (mmt-90) REVERT: C 59 MET cc_start: 0.3744 (tpt) cc_final: 0.3334 (tpt) REVERT: C 671 ARG cc_start: 0.7135 (tpt170) cc_final: 0.6875 (tpt170) REVERT: D 55 ARG cc_start: 0.4232 (mpt180) cc_final: 0.3217 (mmt-90) REVERT: D 59 MET cc_start: 0.3745 (tpt) cc_final: 0.3338 (tpt) REVERT: D 671 ARG cc_start: 0.7138 (tpt170) cc_final: 0.6876 (tpt170) outliers start: 61 outliers final: 40 residues processed: 260 average time/residue: 0.1434 time to fit residues: 60.2872 Evaluate side-chains 228 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 634 THR Chi-restraints excluded: chain D residue 670 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 105 optimal weight: 0.4980 chunk 212 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 0.2980 chunk 159 optimal weight: 3.9990 chunk 246 optimal weight: 0.0870 chunk 66 optimal weight: 7.9990 chunk 259 optimal weight: 0.0470 chunk 107 optimal weight: 0.6980 chunk 258 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A 116 ASN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 GLN B 116 ASN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 GLN C 116 ASN ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 GLN D 116 ASN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.227641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.203954 restraints weight = 27177.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.200488 restraints weight = 41709.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.197537 restraints weight = 43633.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.195756 restraints weight = 42786.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.194118 restraints weight = 40999.498| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21804 Z= 0.150 Angle : 0.694 11.410 29584 Z= 0.373 Chirality : 0.044 0.366 3404 Planarity : 0.006 0.091 3668 Dihedral : 5.881 29.595 2864 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 1.07 % Allowed : 13.15 % Favored : 85.78 % Rotamer: Outliers : 1.34 % Allowed : 19.29 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.16), residues: 2616 helix: 0.64 (0.15), residues: 1184 sheet: -1.70 (0.53), residues: 112 loop : -4.00 (0.14), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 480 TYR 0.015 0.001 TYR C 368 PHE 0.013 0.001 PHE C 107 TRP 0.011 0.001 TRP D 38 HIS 0.005 0.001 HIS C 539 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (21804) covalent geometry : angle 0.69372 / 0.37 (29584) hydrogen bonds : bond 0.04996 / 3.38 ( 860) hydrogen bonds : angle 4.23853 / 2.92 ( 2484) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.3796 (mpt180) cc_final: 0.2845 (mmt-90) REVERT: A 59 MET cc_start: 0.3554 (tpt) cc_final: 0.3185 (tpt) REVERT: B 55 ARG cc_start: 0.3801 (mpt180) cc_final: 0.2847 (mmt-90) REVERT: B 59 MET cc_start: 0.3539 (tpt) cc_final: 0.3179 (tpt) REVERT: C 55 ARG cc_start: 0.3793 (mpt180) cc_final: 0.2839 (mmt-90) REVERT: C 59 MET cc_start: 0.3547 (tpt) cc_final: 0.3181 (tpt) REVERT: D 55 ARG cc_start: 0.3804 (mpt180) cc_final: 0.2847 (mmt-90) REVERT: D 59 MET cc_start: 0.3539 (tpt) cc_final: 0.3174 (tpt) outliers start: 32 outliers final: 20 residues processed: 233 average time/residue: 0.1426 time to fit residues: 53.7102 Evaluate side-chains 216 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 670 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 100 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 241 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 254 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 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 = 0.4473 r_free = 0.4473 target = 0.221819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.199340 restraints weight = 27109.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.194337 restraints weight = 41618.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.190659 restraints weight = 39584.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.188559 restraints weight = 40872.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.187614 restraints weight = 37413.374| |-----------------------------------------------------------------------------| r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 21804 Z= 0.200 Angle : 0.728 10.823 29584 Z= 0.393 Chirality : 0.047 0.362 3404 Planarity : 0.006 0.090 3668 Dihedral : 5.984 30.323 2864 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 1.07 % Allowed : 14.37 % Favored : 84.56 % Rotamer: Outliers : 2.35 % Allowed : 19.50 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.16), residues: 2616 helix: 0.62 (0.15), residues: 1184 sheet: -1.67 (0.53), residues: 112 loop : -4.00 (0.14), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 560 TYR 0.014 0.002 TYR A 419 PHE 0.012 0.001 PHE B 464 TRP 0.011 0.001 TRP C 38 HIS 0.005 0.001 HIS B 539 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (21804) covalent geometry : angle 0.72753 / 0.39 (29584) hydrogen bonds : bond 0.05745 / 3.84 ( 860) hydrogen bonds : angle 4.38010 / 3.02 ( 2484) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 204 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.3972 (mpt180) cc_final: 0.2945 (mmt-90) REVERT: B 55 ARG cc_start: 0.3980 (mpt180) cc_final: 0.2952 (mmt-90) REVERT: C 55 ARG cc_start: 0.3978 (mpt180) cc_final: 0.2949 (mmt-90) REVERT: D 55 ARG cc_start: 0.3980 (mpt180) cc_final: 0.2947 (mmt-90) outliers start: 56 outliers final: 44 residues processed: 252 average time/residue: 0.1392 time to fit residues: 57.3181 Evaluate side-chains 232 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 670 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 6 optimal weight: 8.9990 chunk 41 optimal weight: 0.5980 chunk 191 optimal weight: 0.8980 chunk 235 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 210 optimal weight: 0.9980 chunk 237 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 HIS ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.224752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.201068 restraints weight = 27247.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.197693 restraints weight = 42413.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.193351 restraints weight = 41040.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.190884 restraints weight = 42792.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.190300 restraints weight = 41032.199| |-----------------------------------------------------------------------------| r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21804 Z= 0.156 Angle : 0.706 11.788 29584 Z= 0.379 Chirality : 0.045 0.369 3404 Planarity : 0.005 0.087 3668 Dihedral : 5.859 29.869 2864 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 1.07 % Allowed : 13.15 % Favored : 85.78 % Rotamer: Outliers : 2.48 % Allowed : 20.80 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.16), residues: 2616 helix: 0.78 (0.15), residues: 1184 sheet: -1.64 (0.53), residues: 112 loop : -3.97 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 677 TYR 0.014 0.001 TYR A 368 PHE 0.012 0.001 PHE D 652 TRP 0.008 0.001 TRP A 388 HIS 0.005 0.001 HIS C 539 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (21804) covalent geometry : angle 0.70627 / 0.38 (29584) hydrogen bonds : bond 0.05161 / 3.48 ( 860) hydrogen bonds : angle 4.23364 / 2.92 ( 2484) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 204 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.3660 (mpt180) cc_final: 0.2494 (mmt-90) REVERT: B 55 ARG cc_start: 0.3667 (mpt180) cc_final: 0.2497 (mmt-90) REVERT: C 55 ARG cc_start: 0.3674 (mpt180) cc_final: 0.2495 (mmt-90) REVERT: D 55 ARG cc_start: 0.3673 (mpt180) cc_final: 0.2499 (mmt-90) outliers start: 59 outliers final: 51 residues processed: 248 average time/residue: 0.1413 time to fit residues: 56.9299 Evaluate side-chains 247 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 196 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 670 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 96 optimal weight: 0.8980 chunk 162 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 148 optimal weight: 40.0000 chunk 250 optimal weight: 0.0000 chunk 253 optimal weight: 0.9980 chunk 255 optimal weight: 0.7980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 HIS ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 HIS ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.223665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.201672 restraints weight = 27867.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.196081 restraints weight = 39041.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.193259 restraints weight = 42771.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.191901 restraints weight = 42708.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.190389 restraints weight = 45186.733| |-----------------------------------------------------------------------------| r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 21804 Z= 0.151 Angle : 0.702 11.392 29584 Z= 0.373 Chirality : 0.045 0.365 3404 Planarity : 0.005 0.084 3668 Dihedral : 5.741 29.483 2864 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 1.07 % Allowed : 13.04 % Favored : 85.89 % Rotamer: Outliers : 2.44 % Allowed : 20.55 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.16), residues: 2616 helix: 0.99 (0.15), residues: 1164 sheet: -1.54 (0.54), residues: 112 loop : -3.86 (0.15), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 671 TYR 0.014 0.001 TYR C 368 PHE 0.009 0.001 PHE A 28 TRP 0.009 0.001 TRP D 38 HIS 0.005 0.001 HIS C 539 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (21804) covalent geometry : angle 0.70233 / 0.37 (29584) hydrogen bonds : bond 0.04943 / 3.33 ( 860) hydrogen bonds : angle 4.16787 / 2.87 ( 2484) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 204 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.3657 (mpt180) cc_final: 0.2455 (mmt-90) REVERT: B 55 ARG cc_start: 0.3667 (mpt180) cc_final: 0.2467 (mmt-90) REVERT: C 55 ARG cc_start: 0.3669 (mpt180) cc_final: 0.2468 (mmt-90) REVERT: D 55 ARG cc_start: 0.3673 (mpt180) cc_final: 0.2466 (mmt-90) outliers start: 58 outliers final: 46 residues processed: 250 average time/residue: 0.1389 time to fit residues: 56.7448 Evaluate side-chains 238 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 192 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 670 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 215 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 132 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 239 optimal weight: 0.9990 chunk 192 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** 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 = 0.4483 r_free = 0.4483 target = 0.223249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.200541 restraints weight = 27937.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.198894 restraints weight = 43154.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.197163 restraints weight = 29721.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.194686 restraints weight = 31433.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.193979 restraints weight = 35389.879| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 21804 Z= 0.169 Angle : 0.724 11.105 29584 Z= 0.386 Chirality : 0.046 0.365 3404 Planarity : 0.005 0.082 3668 Dihedral : 5.775 28.973 2864 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 1.07 % Allowed : 14.03 % Favored : 84.90 % Rotamer: Outliers : 2.18 % Allowed : 21.68 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.17), residues: 2616 helix: 0.99 (0.15), residues: 1164 sheet: -1.54 (0.54), residues: 112 loop : -3.84 (0.15), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 671 TYR 0.014 0.001 TYR D 368 PHE 0.014 0.001 PHE B 652 TRP 0.010 0.001 TRP D 38 HIS 0.005 0.001 HIS C 539 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (21804) covalent geometry : angle 0.72378 / 0.39 (29584) hydrogen bonds : bond 0.05234 / 3.51 ( 860) hydrogen bonds : angle 4.20050 / 2.88 ( 2484) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 204 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.3841 (mpt180) cc_final: 0.2422 (mmt-90) REVERT: B 55 ARG cc_start: 0.3850 (mpt180) cc_final: 0.2435 (mmt-90) REVERT: C 55 ARG cc_start: 0.3851 (mpt180) cc_final: 0.2434 (mmt-90) REVERT: D 55 ARG cc_start: 0.3850 (mpt180) cc_final: 0.2426 (mmt-90) outliers start: 52 outliers final: 52 residues processed: 244 average time/residue: 0.1413 time to fit residues: 56.2922 Evaluate side-chains 256 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 204 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 670 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 31 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 170 optimal weight: 0.0470 chunk 88 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 256 optimal weight: 0.9980 chunk 202 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.1280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** 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 = 0.4476 r_free = 0.4476 target = 0.222457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.199436 restraints weight = 27350.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.195015 restraints weight = 42974.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.191956 restraints weight = 42104.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.190403 restraints weight = 41590.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.189186 restraints weight = 36395.957| |-----------------------------------------------------------------------------| r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 21804 Z= 0.175 Angle : 0.732 11.077 29584 Z= 0.391 Chirality : 0.046 0.359 3404 Planarity : 0.005 0.081 3668 Dihedral : 5.845 29.278 2864 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 1.07 % Allowed : 14.22 % Favored : 84.71 % Rotamer: Outliers : 2.52 % Allowed : 21.51 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.17), residues: 2616 helix: 0.97 (0.15), residues: 1164 sheet: -1.57 (0.54), residues: 112 loop : -3.86 (0.15), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 671 TYR 0.015 0.001 TYR D 368 PHE 0.011 0.001 PHE D 464 TRP 0.015 0.001 TRP D 38 HIS 0.005 0.001 HIS C 539 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (21804) covalent geometry : angle 0.73151 / 0.39 (29584) hydrogen bonds : bond 0.05508 / 3.69 ( 860) hydrogen bonds : angle 4.25162 / 2.92 ( 2484) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 200 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.3695 (mpt180) cc_final: 0.2338 (mmt-90) REVERT: B 55 ARG cc_start: 0.3706 (mpt180) cc_final: 0.2351 (mmt-90) REVERT: C 55 ARG cc_start: 0.3710 (mpt180) cc_final: 0.2355 (mmt-90) REVERT: D 55 ARG cc_start: 0.3700 (mpt180) cc_final: 0.2343 (mmt-90) outliers start: 60 outliers final: 60 residues processed: 248 average time/residue: 0.1350 time to fit residues: 55.3399 Evaluate side-chains 260 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 200 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 670 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 123 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 206 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 164 optimal weight: 0.9980 chunk 218 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** 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 = 0.4478 r_free = 0.4478 target = 0.222700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.200172 restraints weight = 27342.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.195674 restraints weight = 40931.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.192584 restraints weight = 40439.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.191119 restraints weight = 37608.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.189340 restraints weight = 39402.615| |-----------------------------------------------------------------------------| r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 21804 Z= 0.171 Angle : 0.724 10.946 29584 Z= 0.386 Chirality : 0.046 0.358 3404 Planarity : 0.005 0.080 3668 Dihedral : 5.810 29.495 2864 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 1.07 % Allowed : 14.22 % Favored : 84.71 % Rotamer: Outliers : 3.07 % Allowed : 21.13 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.17), residues: 2616 helix: 0.96 (0.15), residues: 1164 sheet: -1.58 (0.54), residues: 112 loop : -3.82 (0.15), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 671 TYR 0.014 0.001 TYR C 368 PHE 0.015 0.001 PHE B 652 TRP 0.015 0.001 TRP C 38 HIS 0.005 0.001 HIS A 539 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (21804) covalent geometry : angle 0.72381 / 0.39 (29584) hydrogen bonds : bond 0.05422 / 3.64 ( 860) hydrogen bonds : angle 4.24923 / 2.91 ( 2484) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3187.77 seconds wall clock time: 56 minutes 54.45 seconds (3414.45 seconds total)