Starting phenix.real_space_refine on Wed Jun 18 11:50:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yih_33859/06_2025/7yih_33859.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yih_33859/06_2025/7yih_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yih_33859/06_2025/7yih_33859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yih_33859/06_2025/7yih_33859.map" model { file = "/net/cci-nas-00/data/ceres_data/7yih_33859/06_2025/7yih_33859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yih_33859/06_2025/7yih_33859.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21321 Number of models: 1 Model: "" Number of chains: 5 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: "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} Restraints were copied for chains: B, C, D Time building chain proxies: 13.43, per 1000 atoms: 0.63 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: 5.47 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 1.77 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: 6.13 Time building geometry restraints manager: 6.11 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: 3.670 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: 0.840 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 46.370 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 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 : 16.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.023 0.002 TRP C 38 HIS 0.005 0.001 HIS C 570 PHE 0.011 0.001 PHE C 293 TYR 0.014 0.002 TYR A 42 ARG 0.007 0.001 ARG D 327 Details of bonding type rmsd hydrogen bonds : bond 0.13364 ( 860) hydrogen bonds : angle 5.20462 ( 2484) covalent geometry : bond 0.00371 (21804) covalent geometry : angle 0.78313 (29584) *********************** 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 : 2.189 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: 0.2975 time to fit residues: 118.6576 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 : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 206 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 154 optimal weight: 0.9990 chunk 239 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4459 r_free = 0.4459 target = 0.220325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.197636 restraints weight = 26862.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.194051 restraints weight = 38246.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.191784 restraints weight = 39481.839| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 21804 Z= 0.247 Angle : 0.821 11.088 29584 Z= 0.441 Chirality : 0.050 0.369 3404 Planarity : 0.007 0.107 3668 Dihedral : 6.221 32.070 2864 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.99 % Allowed : 14.76 % Favored : 84.25 % Rotamer: Outliers : 1.18 % Allowed : 11.34 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.16), residues: 2616 helix: 0.24 (0.15), residues: 1184 sheet: -2.24 (0.53), residues: 112 loop : -4.03 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 38 HIS 0.006 0.001 HIS B 539 PHE 0.015 0.002 PHE B 107 TYR 0.019 0.002 TYR B 419 ARG 0.003 0.001 ARG A 631 Details of bonding type rmsd hydrogen bonds : bond 0.06670 ( 860) hydrogen bonds : angle 4.72361 ( 2484) covalent geometry : bond 0.00568 (21804) covalent geometry : angle 0.82053 (29584) *********************** 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 260 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 232 time to evaluate : 3.139 Fit side-chains REVERT: A 55 ARG cc_start: 0.4184 (mpt180) cc_final: 0.3057 (mmt-90) REVERT: A 671 ARG cc_start: 0.7021 (tpt170) cc_final: 0.6782 (tpt170) REVERT: B 55 ARG cc_start: 0.4187 (mpt180) cc_final: 0.3060 (mmt-90) REVERT: B 671 ARG cc_start: 0.7024 (tpt170) cc_final: 0.6787 (tpt170) REVERT: C 55 ARG cc_start: 0.4187 (mpt180) cc_final: 0.3061 (mmt-90) REVERT: C 671 ARG cc_start: 0.7020 (tpt170) cc_final: 0.6786 (tpt170) REVERT: D 55 ARG cc_start: 0.4185 (mpt180) cc_final: 0.3062 (mmt-90) REVERT: D 671 ARG cc_start: 0.7022 (tpt170) cc_final: 0.6789 (tpt170) outliers start: 28 outliers final: 20 residues processed: 252 average time/residue: 0.3256 time to fit residues: 127.9893 Evaluate side-chains 212 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 2.437 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 0 optimal weight: 7.9990 chunk 167 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 85 optimal weight: 0.0670 chunk 33 optimal weight: 0.5980 chunk 35 optimal weight: 0.0570 chunk 10 optimal weight: 20.0000 chunk 116 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 HIS B 12 GLN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 HIS C 12 GLN ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 HIS D 12 GLN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.226948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.204557 restraints weight = 27132.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.201107 restraints weight = 31882.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.199058 restraints weight = 29054.017| |-----------------------------------------------------------------------------| r_work (final): 0.4253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21804 Z= 0.155 Angle : 0.716 11.288 29584 Z= 0.382 Chirality : 0.045 0.374 3404 Planarity : 0.006 0.094 3668 Dihedral : 5.947 31.006 2864 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 1.07 % Allowed : 13.30 % Favored : 85.63 % Rotamer: Outliers : 1.18 % Allowed : 15.29 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.16), residues: 2616 helix: 0.56 (0.15), residues: 1184 sheet: -2.06 (0.52), residues: 112 loop : -3.98 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 38 HIS 0.005 0.001 HIS C 539 PHE 0.014 0.001 PHE C 107 TYR 0.015 0.001 TYR A 368 ARG 0.003 0.000 ARG A 480 Details of bonding type rmsd hydrogen bonds : bond 0.05328 ( 860) hydrogen bonds : angle 4.36636 ( 2484) covalent geometry : bond 0.00320 (21804) covalent geometry : angle 0.71615 (29584) *********************** 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 260 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 232 time to evaluate : 2.373 Fit side-chains REVERT: A 55 ARG cc_start: 0.3803 (mpt180) cc_final: 0.2887 (mmt-90) REVERT: A 59 MET cc_start: 0.3100 (tpt) cc_final: 0.2872 (tpt) REVERT: A 671 ARG cc_start: 0.6947 (tpt170) cc_final: 0.6603 (tpt170) REVERT: B 55 ARG cc_start: 0.3805 (mpt180) cc_final: 0.2894 (mmt-90) REVERT: B 59 MET cc_start: 0.3097 (tpt) cc_final: 0.2874 (tpt) REVERT: B 671 ARG cc_start: 0.6948 (tpt170) cc_final: 0.6603 (tpt170) REVERT: C 55 ARG cc_start: 0.3804 (mpt180) cc_final: 0.2894 (mmt-90) REVERT: C 59 MET cc_start: 0.3102 (tpt) cc_final: 0.2875 (tpt) REVERT: C 671 ARG cc_start: 0.6940 (tpt170) cc_final: 0.6602 (tpt170) REVERT: D 55 ARG cc_start: 0.3807 (mpt180) cc_final: 0.2892 (mmt-90) REVERT: D 59 MET cc_start: 0.3103 (tpt) cc_final: 0.2879 (tpt) REVERT: D 671 ARG cc_start: 0.6940 (tpt170) cc_final: 0.6600 (tpt170) outliers start: 28 outliers final: 16 residues processed: 256 average time/residue: 0.3252 time to fit residues: 131.9339 Evaluate side-chains 212 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ILE 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 230 ILE 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 230 ILE 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 230 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 41 optimal weight: 0.6980 chunk 186 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 chunk 211 optimal weight: 0.2980 chunk 123 optimal weight: 0.6980 chunk 138 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 208 optimal weight: 10.0000 chunk 173 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4499 r_free = 0.4499 target = 0.225134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.202152 restraints weight = 27500.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.198620 restraints weight = 36883.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.196644 restraints weight = 34553.643| |-----------------------------------------------------------------------------| r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21804 Z= 0.167 Angle : 0.708 11.524 29584 Z= 0.381 Chirality : 0.046 0.368 3404 Planarity : 0.006 0.091 3668 Dihedral : 5.886 29.943 2864 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 1.07 % Allowed : 13.15 % Favored : 85.78 % Rotamer: Outliers : 2.69 % Allowed : 15.46 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.16), residues: 2616 helix: 0.61 (0.15), residues: 1192 sheet: -1.81 (0.52), residues: 112 loop : -3.97 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 38 HIS 0.005 0.001 HIS B 539 PHE 0.011 0.001 PHE C 464 TYR 0.014 0.001 TYR A 368 ARG 0.003 0.000 ARG A 677 Details of bonding type rmsd hydrogen bonds : bond 0.05323 ( 860) hydrogen bonds : angle 4.27195 ( 2484) covalent geometry : bond 0.00362 (21804) covalent geometry : angle 0.70779 (29584) *********************** 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 276 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 212 time to evaluate : 2.592 Fit side-chains REVERT: A 55 ARG cc_start: 0.3826 (mpt180) cc_final: 0.2921 (mmt-90) REVERT: A 59 MET cc_start: 0.3107 (tpt) cc_final: 0.2812 (tpt) REVERT: A 532 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.7966 (mtm) REVERT: B 55 ARG cc_start: 0.3827 (mpt180) cc_final: 0.2926 (mmt-90) REVERT: B 59 MET cc_start: 0.3101 (tpt) cc_final: 0.2808 (tpt) REVERT: B 532 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.7968 (mtm) REVERT: C 55 ARG cc_start: 0.3828 (mpt180) cc_final: 0.2923 (mmt-90) REVERT: C 59 MET cc_start: 0.3104 (tpt) cc_final: 0.2810 (tpt) REVERT: C 532 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7972 (mtm) REVERT: D 55 ARG cc_start: 0.3830 (mpt180) cc_final: 0.2923 (mmt-90) REVERT: D 59 MET cc_start: 0.3111 (tpt) cc_final: 0.2817 (tpt) REVERT: D 532 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.7969 (mtm) outliers start: 64 outliers final: 32 residues processed: 256 average time/residue: 0.3208 time to fit residues: 132.0846 Evaluate side-chains 226 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 2.258 ------------------------------------------------------------------------------- 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 260 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 612 VAL 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 260 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 512 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 192 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 512 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 192 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 612 VAL 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 163 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 144 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 116 ASN ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.222622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.199466 restraints weight = 27149.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.194945 restraints weight = 40208.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.191430 restraints weight = 40986.233| |-----------------------------------------------------------------------------| r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21804 Z= 0.190 Angle : 0.731 10.954 29584 Z= 0.394 Chirality : 0.047 0.360 3404 Planarity : 0.006 0.091 3668 Dihedral : 5.941 29.904 2864 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 1.07 % Allowed : 14.30 % Favored : 84.63 % Rotamer: Outliers : 2.69 % Allowed : 17.31 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.16), residues: 2616 helix: 0.63 (0.15), residues: 1184 sheet: -1.75 (0.53), residues: 112 loop : -3.99 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 38 HIS 0.005 0.001 HIS A 539 PHE 0.017 0.002 PHE C 107 TYR 0.014 0.001 TYR C 419 ARG 0.002 0.000 ARG B 671 Details of bonding type rmsd hydrogen bonds : bond 0.05704 ( 860) hydrogen bonds : angle 4.35823 ( 2484) covalent geometry : bond 0.00428 (21804) covalent geometry : angle 0.73116 (29584) *********************** 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 264 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 200 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.3956 (mpt180) cc_final: 0.2928 (mmt-90) REVERT: A 532 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7992 (mtm) REVERT: B 55 ARG cc_start: 0.3958 (mpt180) cc_final: 0.2927 (mmt-90) REVERT: B 532 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.7993 (mtm) REVERT: C 55 ARG cc_start: 0.3961 (mpt180) cc_final: 0.2929 (mmt-90) REVERT: C 532 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7991 (mtm) REVERT: D 55 ARG cc_start: 0.3959 (mpt180) cc_final: 0.2929 (mmt-90) REVERT: D 532 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7994 (mtm) outliers start: 64 outliers final: 44 residues processed: 256 average time/residue: 0.2777 time to fit residues: 117.7116 Evaluate side-chains 228 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 180 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE 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 260 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 512 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 178 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 558 CYS 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 178 HIS Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 558 CYS 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 178 HIS Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 512 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 92 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 204 optimal weight: 8.9990 chunk 251 optimal weight: 1.9990 chunk 245 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4491 r_free = 0.4491 target = 0.224100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.202211 restraints weight = 26920.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.196760 restraints weight = 37266.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.193372 restraints weight = 41878.680| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 21804 Z= 0.166 Angle : 0.707 11.874 29584 Z= 0.380 Chirality : 0.046 0.363 3404 Planarity : 0.005 0.088 3668 Dihedral : 5.873 29.472 2864 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 1.07 % Allowed : 13.46 % Favored : 85.47 % Rotamer: Outliers : 3.11 % Allowed : 17.39 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.16), residues: 2616 helix: 0.77 (0.15), residues: 1172 sheet: -1.66 (0.53), residues: 112 loop : -3.90 (0.15), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 38 HIS 0.005 0.001 HIS D 539 PHE 0.013 0.001 PHE A 28 TYR 0.015 0.001 TYR D 368 ARG 0.003 0.000 ARG A 671 Details of bonding type rmsd hydrogen bonds : bond 0.05355 ( 860) hydrogen bonds : angle 4.24563 ( 2484) covalent geometry : bond 0.00362 (21804) covalent geometry : angle 0.70691 (29584) *********************** 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 270 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 196 time to evaluate : 2.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.3637 (mpt180) cc_final: 0.2423 (mmt-90) REVERT: A 532 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7936 (mtm) REVERT: B 55 ARG cc_start: 0.3643 (mpt180) cc_final: 0.2431 (mmt-90) REVERT: B 532 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7938 (mtm) REVERT: C 55 ARG cc_start: 0.3648 (mpt180) cc_final: 0.2429 (mmt-90) REVERT: C 532 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.7934 (mtm) REVERT: D 55 ARG cc_start: 0.3643 (mpt180) cc_final: 0.2424 (mmt-90) REVERT: D 532 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7937 (mtm) outliers start: 74 outliers final: 58 residues processed: 258 average time/residue: 0.3053 time to fit residues: 126.4881 Evaluate side-chains 246 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 184 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 257 ILE Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 512 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 634 THR Chi-restraints excluded: chain A residue 670 LEU 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 257 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 670 LEU 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 257 ILE Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 670 LEU 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 257 ILE Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 512 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 634 THR 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 63 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 242 optimal weight: 6.9990 chunk 250 optimal weight: 0.0980 chunk 185 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 178 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 247 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4505 r_free = 0.4505 target = 0.225696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.201975 restraints weight = 27310.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.198642 restraints weight = 42380.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.195586 restraints weight = 41979.450| |-----------------------------------------------------------------------------| r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 21804 Z= 0.150 Angle : 0.700 11.734 29584 Z= 0.374 Chirality : 0.045 0.366 3404 Planarity : 0.005 0.085 3668 Dihedral : 5.819 29.838 2864 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 1.07 % Allowed : 13.30 % Favored : 85.63 % Rotamer: Outliers : 2.27 % Allowed : 19.41 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.17), residues: 2616 helix: 0.89 (0.15), residues: 1172 sheet: -1.63 (0.53), residues: 112 loop : -3.86 (0.15), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 388 HIS 0.005 0.001 HIS B 539 PHE 0.012 0.001 PHE C 652 TYR 0.014 0.001 TYR C 368 ARG 0.003 0.000 ARG D 671 Details of bonding type rmsd hydrogen bonds : bond 0.05016 ( 860) hydrogen bonds : angle 4.15898 ( 2484) covalent geometry : bond 0.00319 (21804) covalent geometry : angle 0.69958 (29584) *********************** 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 248 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 194 time to evaluate : 2.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.3641 (mpt180) cc_final: 0.2551 (mmt-90) REVERT: A 532 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7918 (mtm) REVERT: B 55 ARG cc_start: 0.3649 (mpt180) cc_final: 0.2560 (mmt-90) REVERT: B 532 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7914 (mtm) REVERT: C 55 ARG cc_start: 0.3644 (mpt180) cc_final: 0.2557 (mmt-90) REVERT: C 532 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7919 (mtm) REVERT: D 55 ARG cc_start: 0.3652 (mpt180) cc_final: 0.2557 (mmt-90) REVERT: D 532 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.7908 (mtm) outliers start: 54 outliers final: 46 residues processed: 240 average time/residue: 0.2958 time to fit residues: 114.6256 Evaluate side-chains 240 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 190 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 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 295 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 532 MET 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 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 295 ILE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 19 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 295 ILE Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain D residue 19 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 295 ILE Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 532 MET 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 38 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 173 optimal weight: 0.5980 chunk 152 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 198 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 205 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4445 r_free = 0.4445 target = 0.219121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.196633 restraints weight = 27392.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.190671 restraints weight = 41641.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.188019 restraints weight = 45244.154| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 21804 Z= 0.232 Angle : 0.771 10.786 29584 Z= 0.417 Chirality : 0.048 0.360 3404 Planarity : 0.006 0.087 3668 Dihedral : 6.033 29.231 2864 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 1.07 % Allowed : 14.22 % Favored : 84.71 % Rotamer: Outliers : 3.28 % Allowed : 19.58 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.16), residues: 2616 helix: 0.65 (0.15), residues: 1184 sheet: -1.77 (0.54), residues: 112 loop : -3.92 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 217 HIS 0.005 0.001 HIS A 539 PHE 0.014 0.002 PHE A 464 TYR 0.018 0.002 TYR B 419 ARG 0.003 0.000 ARG B 671 Details of bonding type rmsd hydrogen bonds : bond 0.06209 ( 860) hydrogen bonds : angle 4.44112 ( 2484) covalent geometry : bond 0.00544 (21804) covalent geometry : angle 0.77138 (29584) *********************** 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 268 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 190 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.4107 (mpt180) cc_final: 0.2667 (mmt-90) REVERT: A 532 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8084 (mtm) REVERT: B 55 ARG cc_start: 0.4117 (mpt180) cc_final: 0.2681 (mmt-90) REVERT: B 532 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8085 (mtm) REVERT: C 55 ARG cc_start: 0.4118 (mpt180) cc_final: 0.2681 (mmt-90) REVERT: C 532 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8084 (mtm) REVERT: D 55 ARG cc_start: 0.4117 (mpt180) cc_final: 0.2675 (mmt-90) REVERT: D 532 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8092 (mtm) outliers start: 78 outliers final: 62 residues processed: 260 average time/residue: 0.2957 time to fit residues: 125.3827 Evaluate side-chains 246 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 180 time to evaluate : 2.424 ------------------------------------------------------------------------------- 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 257 ILE Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 512 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 634 THR 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 257 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 634 THR 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 257 ILE Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 634 THR 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 257 ILE Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 512 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 634 THR 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 33 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 39 optimal weight: 0.0970 chunk 71 optimal weight: 0.9990 chunk 154 optimal weight: 0.1980 chunk 199 optimal weight: 8.9990 chunk 261 optimal weight: 0.8980 chunk 147 optimal weight: 6.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4495 r_free = 0.4495 target = 0.224927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.203034 restraints weight = 27890.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.197190 restraints weight = 40126.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.194195 restraints weight = 46181.369| |-----------------------------------------------------------------------------| r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.2221 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= 0.149 Angle : 0.703 11.371 29584 Z= 0.378 Chirality : 0.045 0.363 3404 Planarity : 0.005 0.084 3668 Dihedral : 5.785 29.317 2864 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 1.07 % Allowed : 13.26 % Favored : 85.67 % Rotamer: Outliers : 2.39 % Allowed : 20.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.17), residues: 2616 helix: 0.98 (0.15), residues: 1160 sheet: -1.60 (0.54), residues: 112 loop : -3.80 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 38 HIS 0.005 0.001 HIS C 539 PHE 0.014 0.001 PHE C 652 TYR 0.015 0.001 TYR C 368 ARG 0.003 0.000 ARG C 671 Details of bonding type rmsd hydrogen bonds : bond 0.05072 ( 860) hydrogen bonds : angle 4.16831 ( 2484) covalent geometry : bond 0.00314 (21804) covalent geometry : angle 0.70291 (29584) *********************** 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 265 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 208 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.3851 (mpt180) cc_final: 0.2399 (mmt-90) REVERT: A 532 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7923 (mtm) REVERT: B 55 ARG cc_start: 0.3860 (mpt180) cc_final: 0.2413 (mmt-90) REVERT: B 532 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7929 (mtm) REVERT: C 55 ARG cc_start: 0.3855 (mpt180) cc_final: 0.2411 (mmt-90) REVERT: C 532 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7929 (mtm) REVERT: D 55 ARG cc_start: 0.3857 (mpt180) cc_final: 0.2404 (mmt-90) REVERT: D 532 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7928 (mtm) outliers start: 57 outliers final: 48 residues processed: 253 average time/residue: 0.3081 time to fit residues: 127.2581 Evaluate side-chains 252 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 200 time to evaluate : 2.307 ------------------------------------------------------------------------------- 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 295 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 532 MET 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 295 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 634 THR 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 295 ILE Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 634 THR 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 295 ILE Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 532 MET 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 39 optimal weight: 0.5980 chunk 121 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 190 optimal weight: 0.0060 chunk 216 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 224 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 overall best weight: 1.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4479 r_free = 0.4479 target = 0.222972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.200670 restraints weight = 27864.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.196319 restraints weight = 42665.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.193449 restraints weight = 39377.141| |-----------------------------------------------------------------------------| r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2306 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= 0.171 Angle : 0.721 11.007 29584 Z= 0.388 Chirality : 0.046 0.364 3404 Planarity : 0.005 0.082 3668 Dihedral : 5.809 29.238 2864 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 1.07 % Allowed : 12.69 % Favored : 86.24 % Rotamer: Outliers : 2.73 % Allowed : 20.63 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.17), residues: 2616 helix: 0.98 (0.15), residues: 1164 sheet: -1.62 (0.54), residues: 112 loop : -3.77 (0.15), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 38 HIS 0.005 0.001 HIS D 539 PHE 0.012 0.001 PHE B 28 TYR 0.014 0.001 TYR D 368 ARG 0.003 0.000 ARG C 671 Details of bonding type rmsd hydrogen bonds : bond 0.05394 ( 860) hydrogen bonds : angle 4.21738 ( 2484) covalent geometry : bond 0.00382 (21804) covalent geometry : angle 0.72144 (29584) ********************** 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 265 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 200 time to evaluate : 2.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.3921 (mpt180) cc_final: 0.2513 (mmt-90) REVERT: A 532 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7967 (mtm) REVERT: B 55 ARG cc_start: 0.3928 (mpt180) cc_final: 0.2526 (mmt-90) REVERT: B 532 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7966 (mtm) REVERT: C 55 ARG cc_start: 0.3928 (mpt180) cc_final: 0.2527 (mmt-90) REVERT: C 532 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7970 (mtm) REVERT: D 55 ARG cc_start: 0.3926 (mpt180) cc_final: 0.2520 (mmt-90) REVERT: D 532 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7968 (mtm) outliers start: 65 outliers final: 54 residues processed: 253 average time/residue: 0.2824 time to fit residues: 116.7392 Evaluate side-chains 258 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 200 time to evaluate : 2.065 ------------------------------------------------------------------------------- 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 295 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 634 THR 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 295 ILE Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 634 THR 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 295 ILE Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 512 THR Chi-restraints excluded: chain C residue 532 MET Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 634 THR 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 295 ILE Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 512 THR Chi-restraints excluded: chain D residue 532 MET Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 634 THR 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 238 optimal weight: 0.5980 chunk 195 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 252 optimal weight: 0.7980 chunk 57 optimal weight: 0.0770 chunk 112 optimal weight: 0.0770 chunk 44 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4501 r_free = 0.4501 target = 0.225537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.203597 restraints weight = 28152.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.198147 restraints weight = 39300.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.195784 restraints weight = 45221.620| |-----------------------------------------------------------------------------| r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 21804 Z= 0.146 Angle : 0.707 10.967 29584 Z= 0.379 Chirality : 0.045 0.365 3404 Planarity : 0.005 0.079 3668 Dihedral : 5.732 29.376 2864 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 1.07 % Allowed : 12.50 % Favored : 86.43 % Rotamer: Outliers : 2.86 % Allowed : 20.34 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.17), residues: 2616 helix: 1.09 (0.15), residues: 1160 sheet: -1.59 (0.54), residues: 112 loop : -3.75 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 38 HIS 0.005 0.001 HIS D 539 PHE 0.016 0.001 PHE B 652 TYR 0.014 0.001 TYR B 368 ARG 0.003 0.000 ARG A 671 Details of bonding type rmsd hydrogen bonds : bond 0.04959 ( 860) hydrogen bonds : angle 4.12618 ( 2484) covalent geometry : bond 0.00313 (21804) covalent geometry : angle 0.70697 (29584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5852.64 seconds wall clock time: 103 minutes 31.40 seconds (6211.40 seconds total)