Starting phenix.real_space_refine on Thu Feb 5 23:17:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mba_63771/02_2026/9mba_63771.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mba_63771/02_2026/9mba_63771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mba_63771/02_2026/9mba_63771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mba_63771/02_2026/9mba_63771.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mba_63771/02_2026/9mba_63771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mba_63771/02_2026/9mba_63771.map" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 P 6 5.49 5 S 107 5.16 5 C 13188 2.51 5 N 3476 2.21 5 O 3864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20641 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 2692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2692 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 27, 'TRANS': 312} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2622 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 26, 'TRANS': 305} Chain breaks: 5 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 5993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 769, 5993 Classifications: {'peptide': 769} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 37, 'TRANS': 731} Chain breaks: 5 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 66 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'PHE:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 2, 'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 46 Chain: "R" Number of atoms: 5984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 5984 Classifications: {'peptide': 765} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 36, 'TRANS': 728} Chain breaks: 8 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'PHE:plan': 3, 'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 34 Chain: "S" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1665 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 8, 'TRANS': 207} Chain breaks: 1 Chain: "T" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1665 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 8, 'TRANS': 207} Chain breaks: 1 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 5.17, per 1000 atoms: 0.25 Number of scatterers: 20641 At special positions: 0 Unit cell: (108, 137.25, 237, 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) S 107 16.00 P 6 15.00 O 3864 8.00 N 3476 7.00 C 13188 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS D 369 " - pdb=" SG CYS D 384 " distance=2.03 Simple disulfide: pdb=" SG CYS D 424 " - pdb=" SG CYS D 431 " distance=2.03 Simple disulfide: pdb=" SG CYS D 556 " - pdb=" SG CYS D 569 " distance=2.04 Simple disulfide: pdb=" SG CYS D 648 " - pdb=" SG CYS D 742 " distance=2.03 Simple disulfide: pdb=" SG CYS R 64 " - pdb=" SG CYS R 106 " distance=2.03 Simple disulfide: pdb=" SG CYS R 369 " - pdb=" SG CYS R 384 " distance=2.03 Simple disulfide: pdb=" SG CYS R 520 " - pdb=" SG CYS R 538 " distance=2.03 Simple disulfide: pdb=" SG CYS R 541 " - pdb=" SG CYS R 553 " distance=2.04 Simple disulfide: pdb=" SG CYS R 556 " - pdb=" SG CYS R 569 " distance=2.03 Simple disulfide: pdb=" SG CYS R 648 " - pdb=" SG CYS R 742 " distance=2.03 Simple disulfide: pdb=" SG CYS S 27 " - pdb=" SG CYS S 92 " distance=2.04 Simple disulfide: pdb=" SG CYS S 148 " - pdb=" SG CYS S 222 " distance=2.03 Simple disulfide: pdb=" SG CYS T 26 " - pdb=" SG CYS T 91 " distance=2.04 Simple disulfide: pdb=" SG CYS T 103 " - pdb=" SG CYS T 170 " distance=2.04 Simple disulfide: pdb=" SG CYS T 148 " - pdb=" SG CYS T 222 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 951.2 milliseconds 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4956 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 33 sheets defined 31.1% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'B' and resid 65 through 72 removed outlier: 3.816A pdb=" N VAL B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B 71 " --> pdb=" O ASP B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 108 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 98 through 109 Processing helix chain 'D' and resid 72 through 87 Processing helix chain 'D' and resid 108 through 116 Processing helix chain 'D' and resid 116 through 122 removed outlier: 3.809A pdb=" N VAL D 120 " --> pdb=" O SER D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 169 removed outlier: 3.507A pdb=" N ILE D 165 " --> pdb=" O MET D 161 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU D 168 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE D 169 " --> pdb=" O ILE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 185 removed outlier: 3.536A pdb=" N ASP D 185 " --> pdb=" O GLU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 213 removed outlier: 4.245A pdb=" N GLN D 202 " --> pdb=" O PRO D 198 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 244 removed outlier: 3.661A pdb=" N GLU D 241 " --> pdb=" O GLN D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 271 removed outlier: 3.776A pdb=" N GLU D 271 " --> pdb=" O LYS D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 298 removed outlier: 3.578A pdb=" N ARG D 289 " --> pdb=" O ASP D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 319 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 338 through 348 removed outlier: 3.742A pdb=" N ASP D 342 " --> pdb=" O ILE D 338 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR D 344 " --> pdb=" O GLY D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 368 Processing helix chain 'D' and resid 401 through 424 removed outlier: 3.754A pdb=" N ALA D 408 " --> pdb=" O PHE D 404 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA D 413 " --> pdb=" O VAL D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 435 Processing helix chain 'D' and resid 438 through 447 Processing helix chain 'D' and resid 581 through 608 removed outlier: 4.046A pdb=" N VAL D 586 " --> pdb=" O PRO D 582 " (cutoff:3.500A) Proline residue: D 587 - end of helix removed outlier: 3.768A pdb=" N THR D 599 " --> pdb=" O ILE D 595 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE D 600 " --> pdb=" O ILE D 596 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL D 601 " --> pdb=" O ALA D 597 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE D 602 " --> pdb=" O THR D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 618 Processing helix chain 'D' and resid 618 through 642 removed outlier: 3.928A pdb=" N THR D 636 " --> pdb=" O CYS D 632 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N PHE D 637 " --> pdb=" O TYR D 633 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU D 638 " --> pdb=" O SER D 634 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA D 642 " --> pdb=" O LEU D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 678 removed outlier: 4.159A pdb=" N ARG D 652 " --> pdb=" O CYS D 648 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY D 656 " --> pdb=" O ARG D 652 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER D 662 " --> pdb=" O GLY D 658 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N TYR D 663 " --> pdb=" O MET D 659 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE D 676 " --> pdb=" O ARG D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 715 removed outlier: 4.062A pdb=" N GLN D 706 " --> pdb=" O LEU D 702 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE D 711 " --> pdb=" O LEU D 707 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL D 712 " --> pdb=" O LEU D 708 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TRP D 713 " --> pdb=" O GLY D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 745 through 752 Processing helix chain 'D' and resid 753 through 770 removed outlier: 3.790A pdb=" N LYS D 769 " --> pdb=" O VAL D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 779 through 804 removed outlier: 3.608A pdb=" N ILE D 783 " --> pdb=" O GLU D 779 " (cutoff:3.500A) Proline residue: D 799 - end of helix Processing helix chain 'D' and resid 811 through 834 removed outlier: 3.702A pdb=" N THR D 815 " --> pdb=" O MET D 811 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 842 Processing helix chain 'R' and resid 72 through 89 removed outlier: 3.560A pdb=" N ALA R 78 " --> pdb=" O HIS R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 116 Processing helix chain 'R' and resid 116 through 121 removed outlier: 3.925A pdb=" N VAL R 120 " --> pdb=" O SER R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 169 removed outlier: 3.977A pdb=" N LEU R 168 " --> pdb=" O ASN R 164 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 185 Processing helix chain 'R' and resid 200 through 213 removed outlier: 3.709A pdb=" N GLN R 204 " --> pdb=" O SER R 200 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU R 213 " --> pdb=" O ILE R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 243 Processing helix chain 'R' and resid 261 through 270 Processing helix chain 'R' and resid 285 through 297 removed outlier: 3.534A pdb=" N ARG R 289 " --> pdb=" O ASP R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 321 through 326 removed outlier: 3.700A pdb=" N GLU R 326 " --> pdb=" O GLU R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 347 removed outlier: 3.798A pdb=" N ASP R 342 " --> pdb=" O ILE R 338 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG R 343 " --> pdb=" O ASP R 339 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR R 344 " --> pdb=" O GLY R 340 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER R 347 " --> pdb=" O ARG R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 358 through 368 Processing helix chain 'R' and resid 399 through 401 No H-bonds generated for 'chain 'R' and resid 399 through 401' Processing helix chain 'R' and resid 402 through 424 removed outlier: 4.203A pdb=" N ILE R 406 " --> pdb=" O VAL R 402 " (cutoff:3.500A) Processing helix chain 'R' and resid 438 through 448 Processing helix chain 'R' and resid 581 through 609 removed outlier: 3.942A pdb=" N VAL R 586 " --> pdb=" O PRO R 582 " (cutoff:3.500A) Proline residue: R 587 - end of helix removed outlier: 3.769A pdb=" N PHE R 605 " --> pdb=" O VAL R 601 " (cutoff:3.500A) Processing helix chain 'R' and resid 611 through 617 Processing helix chain 'R' and resid 618 through 641 removed outlier: 3.896A pdb=" N SER R 634 " --> pdb=" O PHE R 630 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE R 635 " --> pdb=" O LEU R 631 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR R 636 " --> pdb=" O CYS R 632 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N PHE R 637 " --> pdb=" O TYR R 633 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU R 638 " --> pdb=" O SER R 634 " (cutoff:3.500A) Processing helix chain 'R' and resid 644 through 678 removed outlier: 4.237A pdb=" N GLY R 656 " --> pdb=" O ARG R 652 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU R 657 " --> pdb=" O VAL R 653 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET R 659 " --> pdb=" O LEU R 655 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER R 662 " --> pdb=" O GLY R 658 " (cutoff:3.500A) Processing helix chain 'R' and resid 691 through 717 removed outlier: 3.884A pdb=" N LEU R 696 " --> pdb=" O PRO R 692 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN R 706 " --> pdb=" O LEU R 702 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TRP R 713 " --> pdb=" O GLY R 709 " (cutoff:3.500A) Processing helix chain 'R' and resid 745 through 771 removed outlier: 3.842A pdb=" N LEU R 749 " --> pdb=" O SER R 745 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TYR R 755 " --> pdb=" O CYS R 751 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER R 756 " --> pdb=" O SER R 752 " (cutoff:3.500A) Processing helix chain 'R' and resid 779 through 804 removed outlier: 3.560A pdb=" N ILE R 783 " --> pdb=" O GLU R 779 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE R 792 " --> pdb=" O TYR R 788 " (cutoff:3.500A) Proline residue: R 799 - end of helix Processing helix chain 'R' and resid 808 through 842 removed outlier: 4.512A pdb=" N TYR R 812 " --> pdb=" O ALA R 808 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE R 813 " --> pdb=" O GLU R 809 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN R 814 " --> pdb=" O LYS R 810 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N THR R 815 " --> pdb=" O MET R 811 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR R 816 " --> pdb=" O TYR R 812 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA R 826 " --> pdb=" O MET R 822 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER R 829 " --> pdb=" O SER R 825 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET R 835 " --> pdb=" O GLY R 831 " (cutoff:3.500A) Proline residue: R 836 - end of helix Processing helix chain 'S' and resid 213 through 217 removed outlier: 3.513A pdb=" N ASP S 216 " --> pdb=" O ARG S 213 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR S 217 " --> pdb=" O ALA S 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 213 through 217' Processing helix chain 'T' and resid 82 through 86 removed outlier: 4.019A pdb=" N PHE T 86 " --> pdb=" O PRO T 83 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 112 through 117 Processing sheet with id=AA2, first strand: chain 'B' and resid 26 through 28 removed outlier: 4.056A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 9.852A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE B 80 " --> pdb=" O CYS B 59 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N PHE B 61 " --> pdb=" O ASP B 78 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ASP B 78 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N TYR B 63 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ARG B 76 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 26 through 28 removed outlier: 4.056A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 9.852A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 189 Processing sheet with id=AA5, first strand: chain 'B' and resid 207 through 209 removed outlier: 4.120A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU B 351 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 9.351A pdb=" N VAL B 319 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE B 318 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ALA B 239 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER B 320 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLN B 237 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS B 322 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL B 235 " --> pdb=" O LYS B 322 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LYS B 324 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE B 233 " --> pdb=" O LYS B 324 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS B 326 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE B 231 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B 328 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE B 231 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU B 257 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE B 233 " --> pdb=" O MET B 255 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N MET B 255 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL B 235 " --> pdb=" O VAL B 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 9 through 12 Processing sheet with id=AA7, first strand: chain 'C' and resid 26 through 28 Processing sheet with id=AA8, first strand: chain 'C' and resid 75 through 85 removed outlier: 6.643A pdb=" N CYS C 59 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL C 81 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU C 57 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASN C 83 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL C 55 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLN C 85 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL C 53 " --> pdb=" O GLN C 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 75 through 85 removed outlier: 6.643A pdb=" N CYS C 59 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL C 81 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU C 57 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASN C 83 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL C 55 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLN C 85 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL C 53 " --> pdb=" O GLN C 85 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N CYS C 140 " --> pdb=" O LEU C 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 183 through 188 Processing sheet with id=AB2, first strand: chain 'C' and resid 207 through 208 removed outlier: 3.813A pdb=" N SER C 341 " --> pdb=" O VAL C 329 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE C 349 " --> pdb=" O TYR C 321 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR C 321 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LEU C 351 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N VAL C 319 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS C 230 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA C 254 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N GLN C 237 " --> pdb=" O PRO C 252 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ALA C 239 " --> pdb=" O LYS C 250 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LYS C 250 " --> pdb=" O ALA C 239 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 40 through 41 removed outlier: 7.123A pdb=" N ILE D 47 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N ILE D 151 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLY D 49 " --> pdb=" O ILE D 151 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 55 through 56 Processing sheet with id=AB5, first strand: chain 'D' and resid 173 through 175 Processing sheet with id=AB6, first strand: chain 'D' and resid 246 through 253 removed outlier: 6.889A pdb=" N VAL D 218 " --> pdb=" O ILE D 247 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLN D 249 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TRP D 305 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ILE D 331 " --> pdb=" O TRP D 305 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N GLY D 307 " --> pdb=" O ILE D 331 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TYR D 471 " --> pdb=" O HIS D 490 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N HIS D 490 " --> pdb=" O TYR D 471 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE D 473 " --> pdb=" O ILE D 488 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS D 486 " --> pdb=" O GLN D 475 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 450 through 452 Processing sheet with id=AB8, first strand: chain 'D' and resid 527 through 528 Processing sheet with id=AB9, first strand: chain 'D' and resid 730 through 731 Processing sheet with id=AC1, first strand: chain 'R' and resid 40 through 41 removed outlier: 7.824A pdb=" N ILE R 47 " --> pdb=" O SER R 148 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL R 150 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY R 49 " --> pdb=" O VAL R 150 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 55 through 56 Processing sheet with id=AC3, first strand: chain 'R' and resid 173 through 175 Processing sheet with id=AC4, first strand: chain 'R' and resid 246 through 253 removed outlier: 6.667A pdb=" N VAL R 218 " --> pdb=" O ILE R 247 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN R 249 " --> pdb=" O VAL R 218 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA R 277 " --> pdb=" O TYR R 217 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL R 278 " --> pdb=" O ILE R 306 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR R 471 " --> pdb=" O HIS R 490 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N HIS R 490 " --> pdb=" O TYR R 471 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE R 473 " --> pdb=" O ILE R 488 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS R 486 " --> pdb=" O GLN R 475 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 730 through 731 Processing sheet with id=AC6, first strand: chain 'S' and resid 8 through 10 Processing sheet with id=AC7, first strand: chain 'S' and resid 14 through 15 removed outlier: 6.615A pdb=" N VAL S 37 " --> pdb=" O TYR S 53 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N TYR S 53 " --> pdb=" O VAL S 37 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP S 39 " --> pdb=" O LEU S 51 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'S' and resid 147 through 149 Processing sheet with id=AC9, first strand: chain 'S' and resid 183 through 186 removed outlier: 6.677A pdb=" N TRP S 162 " --> pdb=" O VAL S 174 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER S 176 " --> pdb=" O ILE S 160 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE S 160 " --> pdb=" O SER S 176 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N SER S 178 " --> pdb=" O SER S 158 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N SER S 158 " --> pdb=" O SER S 178 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR S 235 " --> pdb=" O ARG S 224 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'S' and resid 183 through 186 removed outlier: 6.677A pdb=" N TRP S 162 " --> pdb=" O VAL S 174 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER S 176 " --> pdb=" O ILE S 160 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE S 160 " --> pdb=" O SER S 176 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N SER S 178 " --> pdb=" O SER S 158 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N SER S 158 " --> pdb=" O SER S 178 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'T' and resid 7 through 9 Processing sheet with id=AD3, first strand: chain 'T' and resid 13 through 14 removed outlier: 6.589A pdb=" N VAL T 36 " --> pdb=" O TYR T 52 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR T 52 " --> pdb=" O VAL T 36 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP T 38 " --> pdb=" O LEU T 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 147 through 149 Processing sheet with id=AD5, first strand: chain 'T' and resid 183 through 186 removed outlier: 6.629A pdb=" N TRP T 162 " --> pdb=" O VAL T 174 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER T 176 " --> pdb=" O ILE T 160 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE T 160 " --> pdb=" O SER T 176 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N SER T 178 " --> pdb=" O SER T 158 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N SER T 158 " --> pdb=" O SER T 178 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR T 235 " --> pdb=" O ARG T 224 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ARG T 226 " --> pdb=" O LEU T 233 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LEU T 233 " --> pdb=" O ARG T 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'T' and resid 183 through 186 removed outlier: 6.629A pdb=" N TRP T 162 " --> pdb=" O VAL T 174 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER T 176 " --> pdb=" O ILE T 160 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE T 160 " --> pdb=" O SER T 176 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N SER T 178 " --> pdb=" O SER T 158 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N SER T 158 " --> pdb=" O SER T 178 " (cutoff:3.500A) 908 hydrogen bonds defined for protein. 2526 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.98 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4948 1.33 - 1.45: 4368 1.45 - 1.58: 11626 1.58 - 1.70: 7 1.70 - 1.82: 148 Bond restraints: 21097 Sorted by residual: bond pdb=" OG1 TPO R 893 " pdb=" P TPO R 893 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" OG1 TPO R 896 " pdb=" P TPO R 896 " ideal model delta sigma weight residual 1.717 1.612 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" O2P SEP R 895 " pdb=" P SEP R 895 " ideal model delta sigma weight residual 1.610 1.506 0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" O1P SEP R 895 " pdb=" P SEP R 895 " ideal model delta sigma weight residual 1.610 1.507 0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" OG1 TPO D 893 " pdb=" P TPO D 893 " ideal model delta sigma weight residual 1.717 1.615 0.102 2.00e-02 2.50e+03 2.63e+01 ... (remaining 21092 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 28240 2.52 - 5.05: 370 5.05 - 7.57: 25 7.57 - 10.09: 9 10.09 - 12.61: 2 Bond angle restraints: 28646 Sorted by residual: angle pdb=" CA PRO C 88 " pdb=" N PRO C 88 " pdb=" CD PRO C 88 " ideal model delta sigma weight residual 112.00 105.29 6.71 1.40e+00 5.10e-01 2.30e+01 angle pdb=" N PRO D 845 " pdb=" CA PRO D 845 " pdb=" C PRO D 845 " ideal model delta sigma weight residual 114.27 107.82 6.45 1.35e+00 5.49e-01 2.28e+01 angle pdb=" CA THR R 898 " pdb=" C THR R 898 " pdb=" O THR R 898 " ideal model delta sigma weight residual 122.37 117.77 4.60 1.15e+00 7.56e-01 1.60e+01 angle pdb=" N PHE R 303 " pdb=" CA PHE R 303 " pdb=" C PHE R 303 " ideal model delta sigma weight residual 111.11 115.81 -4.70 1.20e+00 6.94e-01 1.54e+01 angle pdb=" C PHE D 689 " pdb=" N ILE D 690 " pdb=" CA ILE D 690 " ideal model delta sigma weight residual 122.96 119.32 3.64 9.50e-01 1.11e+00 1.47e+01 ... (remaining 28641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 11445 17.82 - 35.64: 1016 35.64 - 53.46: 169 53.46 - 71.28: 33 71.28 - 89.10: 19 Dihedral angle restraints: 12682 sinusoidal: 4998 harmonic: 7684 Sorted by residual: dihedral pdb=" CB CYS R 541 " pdb=" SG CYS R 541 " pdb=" SG CYS R 553 " pdb=" CB CYS R 553 " ideal model delta sinusoidal sigma weight residual -86.00 -163.18 77.18 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS R 369 " pdb=" SG CYS R 369 " pdb=" SG CYS R 384 " pdb=" CB CYS R 384 " ideal model delta sinusoidal sigma weight residual -86.00 -153.96 67.96 1 1.00e+01 1.00e-02 6.00e+01 dihedral pdb=" CB CYS D 556 " pdb=" SG CYS D 556 " pdb=" SG CYS D 569 " pdb=" CB CYS D 569 " ideal model delta sinusoidal sigma weight residual -86.00 -37.18 -48.82 1 1.00e+01 1.00e-02 3.28e+01 ... (remaining 12679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2400 0.044 - 0.089: 633 0.089 - 0.133: 211 0.133 - 0.177: 17 0.177 - 0.221: 3 Chirality restraints: 3264 Sorted by residual: chirality pdb=" CA ILE D 690 " pdb=" N ILE D 690 " pdb=" C ILE D 690 " pdb=" CB ILE D 690 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ILE D 673 " pdb=" N ILE D 673 " pdb=" C ILE D 673 " pdb=" CB ILE D 673 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA ILE D 676 " pdb=" N ILE D 676 " pdb=" C ILE D 676 " pdb=" CB ILE D 676 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.63e-01 ... (remaining 3261 not shown) Planarity restraints: 3623 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS R 521 " 0.092 5.00e-02 4.00e+02 1.39e-01 3.10e+01 pdb=" N PRO R 522 " -0.241 5.00e-02 4.00e+02 pdb=" CA PRO R 522 " 0.076 5.00e-02 4.00e+02 pdb=" CD PRO R 522 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 332 " 0.081 5.00e-02 4.00e+02 1.22e-01 2.37e+01 pdb=" N PRO D 333 " -0.210 5.00e-02 4.00e+02 pdb=" CA PRO D 333 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO D 333 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 44 " -0.063 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO B 45 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO B 45 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 45 " -0.052 5.00e-02 4.00e+02 ... (remaining 3620 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1671 2.74 - 3.28: 19928 3.28 - 3.82: 31980 3.82 - 4.36: 38195 4.36 - 4.90: 68255 Nonbonded interactions: 160029 Sorted by model distance: nonbonded pdb=" O ALA D 282 " pdb=" OG SER D 310 " model vdw 2.204 3.040 nonbonded pdb=" OD1 ASP R 342 " pdb=" NE2 GLN R 398 " model vdw 2.221 3.120 nonbonded pdb=" OD2 ASP B 297 " pdb=" OH TYR T 183 " model vdw 2.229 3.040 nonbonded pdb=" OD1 ASN D 563 " pdb=" N MET D 564 " model vdw 2.238 3.120 nonbonded pdb=" OG SER B 330 " pdb=" O ALA B 339 " model vdw 2.250 3.040 ... (remaining 160024 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 'B' and (resid 6 through 89 or resid 97 through 137 or (resid 138 through \ 139 and (name N or name CA or name C or name O or name CB )) or resid 140 throu \ gh 152 or (resid 157 and (name N or name CA or name C or name O or name CB )) or \ resid 158 through 159 or (resid 160 and (name N or name CA or name C or name O \ or name CB )) or resid 161 through 190 or resid 196 through 331 or resid 339 thr \ ough 366)) selection = (chain 'C' and (resid 6 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 366)) } ncs_group { reference = (chain 'D' and (resid 38 through 298 or (resid 299 and (name N or name CA or nam \ e C or name O or name CB )) or resid 300 through 301 or (resid 302 and (name N o \ r name CA or name C or name O or name CB )) or resid 303 through 430 or resid 43 \ 5 through 506 or resid 510 through 556 or resid 561 through 649 or (resid 650 an \ d (name N or name CA or name C or name O or name CB )) or resid 651 through 710 \ or (resid 711 and (name N or name CA or name C or name O or name CB )) or resid \ 712 through 734 or (resid 735 through 736 and (name N or name CA or name C or na \ me O or name CB )) or resid 737 through 1001)) selection = (chain 'R' and (resid 38 through 56 or (resid 57 and (name N or name CA or name \ C or name O or name CB )) or resid 58 through 59 or resid 67 through 122 or resi \ d 147 through 169 or (resid 170 and (name N or name CA or name C or name O or na \ me CB )) or resid 171 through 187 or (resid 188 and (name N or name CA or name C \ or name O or name CB )) or resid 189 through 251 or (resid 252 and (name N or n \ ame CA or name C or name O or name CB )) or resid 253 through 333 or (resid 334 \ and (name N or name CA or name C or name O or name CB )) or resid 335 through 38 \ 8 or (resid 389 and (name N or name CA or name C or name O or name CB )) or resi \ d 390 through 396 or (resid 397 and (name N or name CA or name C or name O or na \ me CB )) or resid 398 through 519 or (resid 520 and (name N or name CA or name C \ or name O or name CB )) or resid 521 through 529 or (resid 530 and (name N or n \ ame CA or name C or name O or name CB )) or resid 531 through 540 or (resid 541 \ and (name N or name CA or name C or name O or name CB )) or resid 542 through 62 \ 9 or (resid 630 and (name N or name CA or name C or name O or name CB )) or resi \ d 631 through 673 or (resid 674 and (name N or name CA or name C or name O or na \ me CB )) or resid 675 through 678 or (resid 679 and (name N or name CA or name C \ or name O or name CB )) or resid 680 through 846 or (resid 847 and (name N or n \ ame CA or name C or name O or name CB )) or resid 891 through 1001)) } ncs_group { reference = chain 'S' selection = chain 'T' } 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 individual isotropic 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: 7.190 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: 0.510 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.880 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5288 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 0.108 21112 Z= 0.220 Angle : 0.686 12.615 28676 Z= 0.368 Chirality : 0.044 0.221 3264 Planarity : 0.006 0.139 3623 Dihedral : 14.003 89.098 7681 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.16), residues: 2566 helix: 0.97 (0.20), residues: 712 sheet: 0.42 (0.21), residues: 663 loop : -1.82 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 389 TYR 0.015 0.001 TYR R 217 PHE 0.020 0.001 PHE T 228 TRP 0.021 0.002 TRP D 579 HIS 0.006 0.001 HIS D 580 Details of bonding type rmsd covalent geometry : bond 0.00433 (21097) covalent geometry : angle 0.68506 (28646) SS BOND : bond 0.00474 ( 15) SS BOND : angle 1.37068 ( 30) hydrogen bonds : bond 0.15839 ( 856) hydrogen bonds : angle 6.36297 ( 2526) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.1658 time to fit residues: 84.9500 Evaluate side-chains 157 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 258 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN C 130 GLN C 219 HIS ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 GLN D 398 GLN ** R 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 274 ASN ** R 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 695 GLN R 844 HIS S 161 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.131428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.087885 restraints weight = 69845.168| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 5.21 r_work: 0.3432 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21112 Z= 0.215 Angle : 0.738 15.338 28676 Z= 0.374 Chirality : 0.046 0.194 3264 Planarity : 0.006 0.115 3623 Dihedral : 4.877 26.136 2870 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.46 % Allowed : 9.73 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.16), residues: 2566 helix: 0.77 (0.19), residues: 723 sheet: 0.63 (0.21), residues: 626 loop : -1.75 (0.16), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 164 TYR 0.028 0.002 TYR D 414 PHE 0.045 0.002 PHE D 589 TRP 0.021 0.002 TRP T 162 HIS 0.016 0.002 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00496 (21097) covalent geometry : angle 0.73731 (28646) SS BOND : bond 0.00690 ( 15) SS BOND : angle 1.20705 ( 30) hydrogen bonds : bond 0.04860 ( 856) hydrogen bonds : angle 4.82909 ( 2526) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 280 MET cc_start: 0.7269 (mtm) cc_final: 0.6874 (mtm) REVERT: D 827 SER cc_start: 0.7983 (m) cc_final: 0.7629 (p) REVERT: D 832 MET cc_start: 0.3141 (mmt) cc_final: 0.2648 (mmt) REVERT: R 195 VAL cc_start: 0.7832 (OUTLIER) cc_final: 0.7545 (p) REVERT: R 412 MET cc_start: 0.3937 (ttm) cc_final: 0.3706 (ttm) REVERT: R 496 HIS cc_start: 0.9378 (m90) cc_final: 0.9065 (t-90) REVERT: S 49 LYS cc_start: 0.6835 (mmtt) cc_final: 0.6555 (mmtt) REVERT: S 178 SER cc_start: 0.8236 (t) cc_final: 0.7691 (m) REVERT: T 207 LEU cc_start: 0.7994 (tp) cc_final: 0.7572 (tp) outliers start: 33 outliers final: 19 residues processed: 202 average time/residue: 0.1622 time to fit residues: 48.7402 Evaluate side-chains 157 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 496 HIS Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain D residue 787 MET Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 201 TYR Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 611 THR Chi-restraints excluded: chain R residue 708 LEU Chi-restraints excluded: chain R residue 715 VAL Chi-restraints excluded: chain R residue 744 ILE Chi-restraints excluded: chain R residue 748 SER Chi-restraints excluded: chain R residue 844 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 135 optimal weight: 0.0870 chunk 235 optimal weight: 0.4980 chunk 145 optimal weight: 30.0000 chunk 232 optimal weight: 9.9990 chunk 215 optimal weight: 0.7980 chunk 90 optimal weight: 10.0000 chunk 214 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 45 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 ASN ** R 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 274 ASN R 283 ASN R 417 HIS R 494 GLN ** R 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 844 HIS S 161 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.132758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.089601 restraints weight = 69546.152| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 5.00 r_work: 0.3465 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21112 Z= 0.122 Angle : 0.625 14.759 28676 Z= 0.313 Chirality : 0.043 0.287 3264 Planarity : 0.005 0.102 3623 Dihedral : 4.557 23.481 2870 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.07 % Favored : 94.89 % Rotamer: Outliers : 1.24 % Allowed : 12.26 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.17), residues: 2566 helix: 1.06 (0.19), residues: 729 sheet: 0.75 (0.21), residues: 638 loop : -1.62 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 447 TYR 0.021 0.001 TYR D 414 PHE 0.022 0.001 PHE T 228 TRP 0.020 0.001 TRP R 491 HIS 0.004 0.001 HIS R 844 Details of bonding type rmsd covalent geometry : bond 0.00269 (21097) covalent geometry : angle 0.62477 (28646) SS BOND : bond 0.00332 ( 15) SS BOND : angle 0.99140 ( 30) hydrogen bonds : bond 0.03965 ( 856) hydrogen bonds : angle 4.47897 ( 2526) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 32 ASP cc_start: 0.7951 (p0) cc_final: 0.7402 (m-30) REVERT: D 280 MET cc_start: 0.7490 (mtm) cc_final: 0.7047 (mtm) REVERT: D 564 MET cc_start: 0.9206 (mmp) cc_final: 0.8614 (ptt) REVERT: D 827 SER cc_start: 0.7792 (m) cc_final: 0.7467 (p) REVERT: D 832 MET cc_start: 0.2875 (mmt) cc_final: 0.2439 (mmt) REVERT: R 412 MET cc_start: 0.3866 (ttm) cc_final: 0.3604 (ttm) REVERT: R 496 HIS cc_start: 0.9420 (m90) cc_final: 0.9192 (t70) REVERT: R 502 MET cc_start: 0.4989 (tpt) cc_final: 0.4576 (tpt) REVERT: R 835 MET cc_start: 0.8166 (mmt) cc_final: 0.7872 (tpt) REVERT: S 145 ARG cc_start: 0.8476 (tmm-80) cc_final: 0.8273 (ttp80) outliers start: 28 outliers final: 18 residues processed: 166 average time/residue: 0.1597 time to fit residues: 40.3737 Evaluate side-chains 145 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain D residue 496 HIS Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain R residue 201 TYR Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 603 VAL Chi-restraints excluded: chain R residue 708 LEU Chi-restraints excluded: chain R residue 715 VAL Chi-restraints excluded: chain R residue 748 SER Chi-restraints excluded: chain R residue 844 HIS Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 210 ASN Chi-restraints excluded: chain T residue 109 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 56 optimal weight: 7.9990 chunk 46 optimal weight: 20.0000 chunk 232 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 16 optimal weight: 0.0010 chunk 81 optimal weight: 10.0000 chunk 216 optimal weight: 4.9990 chunk 187 optimal weight: 8.9990 chunk 166 optimal weight: 30.0000 overall best weight: 4.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 ASN ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 ASN ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 679 GLN R 844 HIS S 161 HIS T 9 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.126083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.083001 restraints weight = 70079.537| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 5.64 r_work: 0.3282 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 21112 Z= 0.345 Angle : 0.820 16.486 28676 Z= 0.422 Chirality : 0.049 0.359 3264 Planarity : 0.006 0.101 3623 Dihedral : 5.233 34.292 2870 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.74 % Favored : 93.18 % Rotamer: Outliers : 2.65 % Allowed : 14.38 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.16), residues: 2566 helix: 0.46 (0.18), residues: 739 sheet: 0.32 (0.21), residues: 621 loop : -1.81 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 268 TYR 0.044 0.003 TYR D 319 PHE 0.057 0.003 PHE T 228 TRP 0.023 0.002 TRP R 713 HIS 0.020 0.002 HIS R 844 Details of bonding type rmsd covalent geometry : bond 0.00816 (21097) covalent geometry : angle 0.81832 (28646) SS BOND : bond 0.00971 ( 15) SS BOND : angle 1.67484 ( 30) hydrogen bonds : bond 0.05866 ( 856) hydrogen bonds : angle 5.01755 ( 2526) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 139 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 164 VAL cc_start: 0.8904 (OUTLIER) cc_final: 0.8516 (m) REVERT: C 32 ASP cc_start: 0.8070 (p0) cc_final: 0.7514 (m-30) REVERT: C 272 TYR cc_start: 0.6800 (m-80) cc_final: 0.6403 (m-80) REVERT: D 280 MET cc_start: 0.7699 (mtm) cc_final: 0.7342 (mtm) REVERT: D 564 MET cc_start: 0.9228 (mmp) cc_final: 0.8607 (ptt) REVERT: D 633 TYR cc_start: 0.6089 (OUTLIER) cc_final: 0.5543 (m-80) REVERT: D 832 MET cc_start: 0.3850 (mmt) cc_final: 0.2993 (mmt) REVERT: R 119 PHE cc_start: 0.8354 (m-80) cc_final: 0.7885 (m-80) REVERT: R 195 VAL cc_start: 0.7580 (OUTLIER) cc_final: 0.7240 (p) REVERT: R 252 LYS cc_start: 0.7866 (mmtm) cc_final: 0.7427 (mmmt) REVERT: R 412 MET cc_start: 0.4238 (ttm) cc_final: 0.3964 (ttm) REVERT: R 502 MET cc_start: 0.4892 (tpt) cc_final: 0.4488 (tpt) REVERT: R 592 ILE cc_start: 0.9140 (mm) cc_final: 0.8932 (mm) REVERT: T 139 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8330 (mm-40) REVERT: T 217 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8752 (t) outliers start: 60 outliers final: 41 residues processed: 186 average time/residue: 0.1571 time to fit residues: 45.2213 Evaluate side-chains 161 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 116 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 496 HIS Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 633 TYR Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain D residue 788 TYR Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 891 THR Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 201 TYR Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 419 MET Chi-restraints excluded: chain R residue 611 THR Chi-restraints excluded: chain R residue 627 THR Chi-restraints excluded: chain R residue 636 THR Chi-restraints excluded: chain R residue 647 ILE Chi-restraints excluded: chain R residue 653 VAL Chi-restraints excluded: chain R residue 708 LEU Chi-restraints excluded: chain R residue 712 VAL Chi-restraints excluded: chain R residue 715 VAL Chi-restraints excluded: chain R residue 744 ILE Chi-restraints excluded: chain R residue 787 MET Chi-restraints excluded: chain R residue 817 THR Chi-restraints excluded: chain S residue 18 SER Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 229 TRP Chi-restraints excluded: chain T residue 109 ILE Chi-restraints excluded: chain T residue 217 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 34 optimal weight: 30.0000 chunk 116 optimal weight: 6.9990 chunk 232 optimal weight: 9.9990 chunk 174 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 208 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 147 optimal weight: 7.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 HIS ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 GLN ** R 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 565 ASN R 679 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.126269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.082787 restraints weight = 69144.745| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 5.64 r_work: 0.3304 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 21112 Z= 0.235 Angle : 0.717 16.123 28676 Z= 0.361 Chirality : 0.045 0.314 3264 Planarity : 0.005 0.090 3623 Dihedral : 5.070 55.200 2870 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.27 % Favored : 93.65 % Rotamer: Outliers : 2.61 % Allowed : 16.73 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.16), residues: 2566 helix: 0.64 (0.19), residues: 740 sheet: 0.30 (0.21), residues: 632 loop : -1.80 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 268 TYR 0.020 0.002 TYR D 319 PHE 0.047 0.002 PHE T 228 TRP 0.022 0.002 TRP R 713 HIS 0.005 0.001 HIS C 353 Details of bonding type rmsd covalent geometry : bond 0.00555 (21097) covalent geometry : angle 0.71125 (28646) SS BOND : bond 0.00374 ( 15) SS BOND : angle 2.82480 ( 30) hydrogen bonds : bond 0.04893 ( 856) hydrogen bonds : angle 4.75584 ( 2526) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 128 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 32 ASP cc_start: 0.8098 (p0) cc_final: 0.7511 (m-30) REVERT: D 280 MET cc_start: 0.7822 (mtm) cc_final: 0.7512 (mtm) REVERT: D 299 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7427 (tp40) REVERT: D 560 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7412 (pp30) REVERT: D 564 MET cc_start: 0.9225 (mmp) cc_final: 0.8601 (ptt) REVERT: D 832 MET cc_start: 0.4004 (mmt) cc_final: 0.3126 (mmt) REVERT: R 119 PHE cc_start: 0.8307 (m-80) cc_final: 0.7958 (m-80) REVERT: R 195 VAL cc_start: 0.7589 (OUTLIER) cc_final: 0.7261 (p) REVERT: R 412 MET cc_start: 0.4218 (ttm) cc_final: 0.3935 (ttm) REVERT: R 502 MET cc_start: 0.5019 (tpt) cc_final: 0.4613 (tpt) REVERT: R 649 SER cc_start: 0.9211 (t) cc_final: 0.8995 (m) REVERT: R 811 MET cc_start: 0.7549 (ttt) cc_final: 0.7190 (tmm) REVERT: T 139 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8360 (mm-40) REVERT: T 213 ARG cc_start: 0.7787 (mmt-90) cc_final: 0.7532 (mmp80) outliers start: 59 outliers final: 41 residues processed: 171 average time/residue: 0.1583 time to fit residues: 42.0410 Evaluate side-chains 160 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 116 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 496 HIS Chi-restraints excluded: chain D residue 560 GLN Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 661 PHE Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain D residue 788 TYR Chi-restraints excluded: chain D residue 791 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 201 TYR Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 419 MET Chi-restraints excluded: chain R residue 488 ILE Chi-restraints excluded: chain R residue 496 HIS Chi-restraints excluded: chain R residue 521 LYS Chi-restraints excluded: chain R residue 586 VAL Chi-restraints excluded: chain R residue 611 THR Chi-restraints excluded: chain R residue 627 THR Chi-restraints excluded: chain R residue 653 VAL Chi-restraints excluded: chain R residue 708 LEU Chi-restraints excluded: chain R residue 715 VAL Chi-restraints excluded: chain R residue 757 ILE Chi-restraints excluded: chain R residue 787 MET Chi-restraints excluded: chain S residue 18 SER Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 229 TRP Chi-restraints excluded: chain T residue 81 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 23 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 217 optimal weight: 0.5980 chunk 107 optimal weight: 0.0470 chunk 87 optimal weight: 0.0970 chunk 28 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 HIS ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 HIS ** R 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.128334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.085401 restraints weight = 69030.694| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 5.73 r_work: 0.3369 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21112 Z= 0.119 Angle : 0.628 15.672 28676 Z= 0.313 Chirality : 0.042 0.205 3264 Planarity : 0.005 0.082 3623 Dihedral : 4.659 51.533 2870 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.04 % Favored : 93.92 % Rotamer: Outliers : 2.39 % Allowed : 17.21 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.16), residues: 2566 helix: 1.02 (0.19), residues: 735 sheet: 0.52 (0.21), residues: 625 loop : -1.66 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 268 TYR 0.025 0.001 TYR D 319 PHE 0.027 0.001 PHE T 228 TRP 0.015 0.001 TRP S 162 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00266 (21097) covalent geometry : angle 0.62497 (28646) SS BOND : bond 0.00278 ( 15) SS BOND : angle 2.03006 ( 30) hydrogen bonds : bond 0.03890 ( 856) hydrogen bonds : angle 4.38354 ( 2526) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 131 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 32 ASP cc_start: 0.8001 (p0) cc_final: 0.7322 (m-30) REVERT: D 280 MET cc_start: 0.7997 (mtm) cc_final: 0.7664 (mtm) REVERT: D 299 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7595 (tp40) REVERT: D 507 ARG cc_start: 0.8162 (mmm160) cc_final: 0.7737 (mpt90) REVERT: D 564 MET cc_start: 0.9212 (mmp) cc_final: 0.8640 (ptt) REVERT: D 633 TYR cc_start: 0.6305 (OUTLIER) cc_final: 0.5565 (m-80) REVERT: R 119 PHE cc_start: 0.8286 (m-80) cc_final: 0.7953 (m-80) REVERT: R 195 VAL cc_start: 0.7546 (OUTLIER) cc_final: 0.7225 (p) REVERT: R 412 MET cc_start: 0.4076 (ttm) cc_final: 0.3793 (ttm) REVERT: R 502 MET cc_start: 0.4947 (tpt) cc_final: 0.4571 (tpt) REVERT: R 564 MET cc_start: 0.8636 (mpp) cc_final: 0.8222 (ptp) REVERT: R 811 MET cc_start: 0.7322 (ttt) cc_final: 0.6880 (tmm) REVERT: S 46 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8553 (pttp) REVERT: T 139 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8399 (mm-40) REVERT: T 207 LEU cc_start: 0.8027 (tp) cc_final: 0.7819 (tp) outliers start: 54 outliers final: 33 residues processed: 171 average time/residue: 0.1477 time to fit residues: 39.8553 Evaluate side-chains 157 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 120 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 496 HIS Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 633 TYR Chi-restraints excluded: chain D residue 661 PHE Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 791 CYS Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 201 TYR Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 419 MET Chi-restraints excluded: chain R residue 496 HIS Chi-restraints excluded: chain R residue 521 LYS Chi-restraints excluded: chain R residue 529 VAL Chi-restraints excluded: chain R residue 653 VAL Chi-restraints excluded: chain R residue 708 LEU Chi-restraints excluded: chain R residue 715 VAL Chi-restraints excluded: chain R residue 787 MET Chi-restraints excluded: chain R residue 827 SER Chi-restraints excluded: chain S residue 18 SER Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 210 ASN Chi-restraints excluded: chain S residue 229 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 253 optimal weight: 0.6980 chunk 170 optimal weight: 20.0000 chunk 240 optimal weight: 7.9990 chunk 172 optimal weight: 30.0000 chunk 220 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 43 optimal weight: 0.0170 chunk 2 optimal weight: 3.9990 overall best weight: 1.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 HIS ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.127304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.084193 restraints weight = 69517.761| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 5.07 r_work: 0.3367 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21112 Z= 0.162 Angle : 0.648 16.666 28676 Z= 0.322 Chirality : 0.043 0.214 3264 Planarity : 0.005 0.074 3623 Dihedral : 4.689 53.050 2870 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.12 % Favored : 93.84 % Rotamer: Outliers : 2.43 % Allowed : 17.88 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.16), residues: 2566 helix: 1.05 (0.19), residues: 736 sheet: 0.49 (0.21), residues: 623 loop : -1.66 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 615 TYR 0.022 0.001 TYR D 319 PHE 0.037 0.001 PHE T 228 TRP 0.019 0.001 TRP R 713 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00387 (21097) covalent geometry : angle 0.64548 (28646) SS BOND : bond 0.00320 ( 15) SS BOND : angle 1.99221 ( 30) hydrogen bonds : bond 0.04146 ( 856) hydrogen bonds : angle 4.38403 ( 2526) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 121 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 164 VAL cc_start: 0.8841 (t) cc_final: 0.8350 (m) REVERT: C 32 ASP cc_start: 0.7866 (p0) cc_final: 0.7132 (m-30) REVERT: C 79 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7303 (mp) REVERT: D 255 ARG cc_start: 0.5402 (mmp80) cc_final: 0.5100 (mmp80) REVERT: D 280 MET cc_start: 0.8058 (mtm) cc_final: 0.7749 (mtm) REVERT: D 299 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7663 (tp40) REVERT: D 564 MET cc_start: 0.9212 (mmp) cc_final: 0.8658 (ptt) REVERT: D 633 TYR cc_start: 0.6390 (OUTLIER) cc_final: 0.5509 (m-80) REVERT: R 119 PHE cc_start: 0.8254 (m-80) cc_final: 0.7951 (m-80) REVERT: R 195 VAL cc_start: 0.7558 (OUTLIER) cc_final: 0.7208 (p) REVERT: R 267 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8806 (ptpt) REVERT: R 412 MET cc_start: 0.4015 (ttm) cc_final: 0.3733 (ttm) REVERT: R 502 MET cc_start: 0.4977 (tpt) cc_final: 0.4601 (tpt) REVERT: R 811 MET cc_start: 0.7485 (ttt) cc_final: 0.7053 (tmm) REVERT: S 46 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8484 (pttp) REVERT: S 215 GLU cc_start: 0.5598 (pm20) cc_final: 0.5325 (pm20) REVERT: T 139 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8442 (mm-40) outliers start: 55 outliers final: 43 residues processed: 161 average time/residue: 0.1501 time to fit residues: 37.4941 Evaluate side-chains 168 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 119 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 496 HIS Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 633 TYR Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 791 CYS Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 201 TYR Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 267 LYS Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 403 GLN Chi-restraints excluded: chain R residue 419 MET Chi-restraints excluded: chain R residue 488 ILE Chi-restraints excluded: chain R residue 496 HIS Chi-restraints excluded: chain R residue 521 LYS Chi-restraints excluded: chain R residue 529 VAL Chi-restraints excluded: chain R residue 627 THR Chi-restraints excluded: chain R residue 653 VAL Chi-restraints excluded: chain R residue 708 LEU Chi-restraints excluded: chain R residue 715 VAL Chi-restraints excluded: chain R residue 760 MET Chi-restraints excluded: chain R residue 787 MET Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 827 SER Chi-restraints excluded: chain R residue 838 VAL Chi-restraints excluded: chain S residue 18 SER Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 229 TRP Chi-restraints excluded: chain T residue 105 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 32 optimal weight: 0.9980 chunk 236 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 257 optimal weight: 0.8980 chunk 138 optimal weight: 0.5980 chunk 238 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 106 optimal weight: 30.0000 chunk 52 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 HIS ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 679 GLN ** T 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.128106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.084765 restraints weight = 69398.824| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 5.32 r_work: 0.3369 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21112 Z= 0.119 Angle : 0.626 16.623 28676 Z= 0.309 Chirality : 0.042 0.173 3264 Planarity : 0.005 0.072 3623 Dihedral : 4.506 48.607 2870 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.73 % Favored : 94.23 % Rotamer: Outliers : 2.52 % Allowed : 18.10 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.17), residues: 2566 helix: 1.21 (0.19), residues: 730 sheet: 0.58 (0.21), residues: 627 loop : -1.59 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 737 TYR 0.022 0.001 TYR D 319 PHE 0.026 0.001 PHE D 689 TRP 0.018 0.001 TRP R 713 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00279 (21097) covalent geometry : angle 0.62352 (28646) SS BOND : bond 0.00303 ( 15) SS BOND : angle 1.88011 ( 30) hydrogen bonds : bond 0.03769 ( 856) hydrogen bonds : angle 4.25757 ( 2526) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 133 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 164 VAL cc_start: 0.8804 (t) cc_final: 0.8286 (m) REVERT: C 32 ASP cc_start: 0.7842 (p0) cc_final: 0.7087 (m-30) REVERT: C 79 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7263 (mp) REVERT: D 255 ARG cc_start: 0.5364 (mmp80) cc_final: 0.5056 (mmp80) REVERT: D 280 MET cc_start: 0.8079 (mtm) cc_final: 0.7787 (mtm) REVERT: D 299 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7737 (tp40) REVERT: D 564 MET cc_start: 0.9220 (mmp) cc_final: 0.8650 (ptt) REVERT: R 119 PHE cc_start: 0.8228 (m-80) cc_final: 0.7934 (m-80) REVERT: R 195 VAL cc_start: 0.7469 (OUTLIER) cc_final: 0.7129 (p) REVERT: R 252 LYS cc_start: 0.7834 (mmtm) cc_final: 0.7111 (mmtp) REVERT: R 267 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8795 (ptpt) REVERT: R 412 MET cc_start: 0.4023 (ttm) cc_final: 0.3761 (ttm) REVERT: R 502 MET cc_start: 0.5017 (tpt) cc_final: 0.4646 (tpt) REVERT: R 564 MET cc_start: 0.8739 (mpp) cc_final: 0.8293 (ptp) REVERT: R 811 MET cc_start: 0.7384 (ttt) cc_final: 0.6922 (tmm) REVERT: S 46 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8514 (pttp) REVERT: T 139 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8330 (mm-40) REVERT: T 207 LEU cc_start: 0.7968 (tp) cc_final: 0.7744 (tp) REVERT: T 221 TYR cc_start: 0.8559 (m-10) cc_final: 0.8186 (m-10) outliers start: 57 outliers final: 45 residues processed: 173 average time/residue: 0.1640 time to fit residues: 44.0767 Evaluate side-chains 173 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 123 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 496 HIS Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 791 CYS Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 201 TYR Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 267 LYS Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 419 MET Chi-restraints excluded: chain R residue 488 ILE Chi-restraints excluded: chain R residue 496 HIS Chi-restraints excluded: chain R residue 521 LYS Chi-restraints excluded: chain R residue 529 VAL Chi-restraints excluded: chain R residue 627 THR Chi-restraints excluded: chain R residue 636 THR Chi-restraints excluded: chain R residue 653 VAL Chi-restraints excluded: chain R residue 708 LEU Chi-restraints excluded: chain R residue 715 VAL Chi-restraints excluded: chain R residue 731 LEU Chi-restraints excluded: chain R residue 760 MET Chi-restraints excluded: chain R residue 787 MET Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 827 SER Chi-restraints excluded: chain R residue 838 VAL Chi-restraints excluded: chain S residue 18 SER Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 210 ASN Chi-restraints excluded: chain S residue 229 TRP Chi-restraints excluded: chain T residue 109 ILE Chi-restraints excluded: chain T residue 195 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 250 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 chunk 120 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 HIS ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 ASN D 570 GLN ** R 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.124962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.077075 restraints weight = 69633.581| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.90 r_work: 0.3302 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 21112 Z= 0.262 Angle : 0.742 17.485 28676 Z= 0.372 Chirality : 0.046 0.322 3264 Planarity : 0.005 0.066 3623 Dihedral : 4.954 42.803 2870 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.21 % Favored : 92.75 % Rotamer: Outliers : 2.92 % Allowed : 18.10 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.16), residues: 2566 helix: 0.79 (0.19), residues: 742 sheet: 0.28 (0.20), residues: 631 loop : -1.67 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 615 TYR 0.021 0.002 TYR R 544 PHE 0.055 0.002 PHE T 228 TRP 0.031 0.002 TRP R 713 HIS 0.004 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00626 (21097) covalent geometry : angle 0.73973 (28646) SS BOND : bond 0.00353 ( 15) SS BOND : angle 1.99087 ( 30) hydrogen bonds : bond 0.05138 ( 856) hydrogen bonds : angle 4.65982 ( 2526) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 124 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 79 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7300 (mp) REVERT: C 272 TYR cc_start: 0.6782 (m-80) cc_final: 0.6294 (m-80) REVERT: D 299 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7585 (tp40) REVERT: D 507 ARG cc_start: 0.8222 (mmm160) cc_final: 0.7835 (mpt180) REVERT: D 564 MET cc_start: 0.9208 (mmp) cc_final: 0.8607 (ptt) REVERT: D 570 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7478 (mp10) REVERT: D 633 TYR cc_start: 0.6726 (OUTLIER) cc_final: 0.5620 (m-80) REVERT: D 832 MET cc_start: 0.5058 (OUTLIER) cc_final: 0.4287 (tpp) REVERT: R 195 VAL cc_start: 0.7445 (OUTLIER) cc_final: 0.7112 (p) REVERT: R 267 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8793 (ptpt) REVERT: R 412 MET cc_start: 0.4168 (ttm) cc_final: 0.3884 (ttm) REVERT: R 419 MET cc_start: 0.5682 (OUTLIER) cc_final: 0.5196 (mtp) REVERT: R 502 MET cc_start: 0.5043 (tpt) cc_final: 0.4706 (tpt) REVERT: R 811 MET cc_start: 0.7735 (ttt) cc_final: 0.7343 (tmm) REVERT: S 46 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8488 (pttp) REVERT: T 139 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8364 (mm-40) outliers start: 66 outliers final: 50 residues processed: 170 average time/residue: 0.1582 time to fit residues: 42.1386 Evaluate side-chains 180 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 121 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 496 HIS Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 633 TYR Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 791 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 832 MET Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 201 TYR Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 267 LYS Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 419 MET Chi-restraints excluded: chain R residue 488 ILE Chi-restraints excluded: chain R residue 496 HIS Chi-restraints excluded: chain R residue 521 LYS Chi-restraints excluded: chain R residue 529 VAL Chi-restraints excluded: chain R residue 611 THR Chi-restraints excluded: chain R residue 627 THR Chi-restraints excluded: chain R residue 636 THR Chi-restraints excluded: chain R residue 653 VAL Chi-restraints excluded: chain R residue 708 LEU Chi-restraints excluded: chain R residue 715 VAL Chi-restraints excluded: chain R residue 731 LEU Chi-restraints excluded: chain R residue 760 MET Chi-restraints excluded: chain R residue 787 MET Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 827 SER Chi-restraints excluded: chain R residue 838 VAL Chi-restraints excluded: chain S residue 18 SER Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 229 TRP Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain T residue 109 ILE Chi-restraints excluded: chain T residue 195 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 27 optimal weight: 0.5980 chunk 220 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 159 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 103 optimal weight: 20.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 HIS ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 679 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.125186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.083225 restraints weight = 69759.138| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 6.71 r_work: 0.3250 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.193 21112 Z= 0.229 Angle : 0.860 59.186 28676 Z= 0.458 Chirality : 0.045 0.306 3264 Planarity : 0.005 0.065 3623 Dihedral : 4.950 42.450 2870 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.29 % Favored : 92.67 % Rotamer: Outliers : 2.79 % Allowed : 18.50 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.16), residues: 2566 helix: 0.77 (0.19), residues: 742 sheet: 0.24 (0.20), residues: 631 loop : -1.68 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 615 TYR 0.020 0.002 TYR R 544 PHE 0.051 0.002 PHE T 228 TRP 0.031 0.002 TRP R 713 HIS 0.004 0.001 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00542 (21097) covalent geometry : angle 0.85809 (28646) SS BOND : bond 0.00348 ( 15) SS BOND : angle 1.99138 ( 30) hydrogen bonds : bond 0.05024 ( 856) hydrogen bonds : angle 4.64886 ( 2526) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 121 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 79 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7308 (mp) REVERT: D 299 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7611 (tp40) REVERT: D 507 ARG cc_start: 0.8186 (mmm160) cc_final: 0.7803 (mpt180) REVERT: D 564 MET cc_start: 0.9219 (mmp) cc_final: 0.8608 (ptt) REVERT: D 633 TYR cc_start: 0.6782 (OUTLIER) cc_final: 0.5661 (m-80) REVERT: D 832 MET cc_start: 0.5129 (OUTLIER) cc_final: 0.4347 (tpp) REVERT: R 195 VAL cc_start: 0.7476 (OUTLIER) cc_final: 0.7141 (p) REVERT: R 267 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8796 (ptpt) REVERT: R 412 MET cc_start: 0.4315 (ttm) cc_final: 0.4013 (ttm) REVERT: R 419 MET cc_start: 0.5675 (OUTLIER) cc_final: 0.5170 (mtp) REVERT: R 502 MET cc_start: 0.4952 (tpt) cc_final: 0.4615 (tpt) REVERT: R 811 MET cc_start: 0.7766 (ttt) cc_final: 0.7370 (tmm) REVERT: S 46 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8493 (pttp) REVERT: T 139 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8372 (mm-40) outliers start: 63 outliers final: 52 residues processed: 164 average time/residue: 0.1592 time to fit residues: 40.6648 Evaluate side-chains 179 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 119 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 353 HIS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 496 HIS Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain D residue 601 VAL Chi-restraints excluded: chain D residue 633 TYR Chi-restraints excluded: chain D residue 661 PHE Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 791 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 832 MET Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 201 TYR Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 267 LYS Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 419 MET Chi-restraints excluded: chain R residue 488 ILE Chi-restraints excluded: chain R residue 496 HIS Chi-restraints excluded: chain R residue 521 LYS Chi-restraints excluded: chain R residue 529 VAL Chi-restraints excluded: chain R residue 611 THR Chi-restraints excluded: chain R residue 627 THR Chi-restraints excluded: chain R residue 636 THR Chi-restraints excluded: chain R residue 653 VAL Chi-restraints excluded: chain R residue 708 LEU Chi-restraints excluded: chain R residue 715 VAL Chi-restraints excluded: chain R residue 731 LEU Chi-restraints excluded: chain R residue 760 MET Chi-restraints excluded: chain R residue 787 MET Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 827 SER Chi-restraints excluded: chain R residue 838 VAL Chi-restraints excluded: chain S residue 18 SER Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 229 TRP Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain T residue 109 ILE Chi-restraints excluded: chain T residue 195 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 246 optimal weight: 7.9990 chunk 247 optimal weight: 0.9990 chunk 165 optimal weight: 10.0000 chunk 223 optimal weight: 0.0270 chunk 196 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 48 optimal weight: 30.0000 chunk 130 optimal weight: 0.0030 chunk 194 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.6052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 HIS ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 679 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.125183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.077387 restraints weight = 69670.371| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.92 r_work: 0.3308 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.5476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.193 21112 Z= 0.229 Angle : 0.860 59.186 28676 Z= 0.458 Chirality : 0.045 0.306 3264 Planarity : 0.005 0.065 3623 Dihedral : 4.950 42.450 2870 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.29 % Favored : 92.67 % Rotamer: Outliers : 2.74 % Allowed : 18.58 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.16), residues: 2566 helix: 0.77 (0.19), residues: 742 sheet: 0.24 (0.20), residues: 631 loop : -1.68 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 615 TYR 0.020 0.002 TYR R 544 PHE 0.051 0.002 PHE T 228 TRP 0.031 0.002 TRP R 713 HIS 0.004 0.001 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00542 (21097) covalent geometry : angle 0.85809 (28646) SS BOND : bond 0.00348 ( 15) SS BOND : angle 1.99138 ( 30) hydrogen bonds : bond 0.05024 ( 856) hydrogen bonds : angle 4.64886 ( 2526) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8574.86 seconds wall clock time: 146 minutes 39.15 seconds (8799.15 seconds total)