Starting phenix.real_space_refine on Tue Aug 26 10:53:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9czq_46425/08_2025/9czq_46425_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9czq_46425/08_2025/9czq_46425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9czq_46425/08_2025/9czq_46425_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9czq_46425/08_2025/9czq_46425_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9czq_46425/08_2025/9czq_46425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9czq_46425/08_2025/9czq_46425.map" } resolution = 2.88 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= 0.003 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: 8 Type Number sf(0) Gaussians Ca 8 9.91 5 K 4 8.98 5 P 20 5.49 5 Mg 4 5.21 5 S 244 5.16 5 C 23484 2.51 5 N 5748 2.21 5 O 6506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 152 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36018 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 893, 7116 Classifications: {'peptide': 893} Link IDs: {'PTRANS': 27, 'TRANS': 865} Chain breaks: 4 Chain: "B" Number of atoms: 7116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 893, 7116 Classifications: {'peptide': 893} Link IDs: {'PTRANS': 27, 'TRANS': 865} Chain breaks: 4 Chain: "C" Number of atoms: 7116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 893, 7116 Classifications: {'peptide': 893} Link IDs: {'PTRANS': 27, 'TRANS': 865} Chain breaks: 4 Chain: "D" Number of atoms: 7116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 893, 7116 Classifications: {'peptide': 893} Link IDs: {'PTRANS': 27, 'TRANS': 865} Chain breaks: 4 Chain: "E" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1697 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain breaks: 1 Chain: "F" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1599 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain: "G" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1599 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain: "H" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1599 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain: "A" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 257 Unusual residues: {' K': 3, ' CA': 2, ' MG': 1, 'CLR': 2, 'POV': 5} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 240 Unusual residues: {' CA': 2, ' MG': 1, 'CLR': 3, 'POV': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 199 Unusual residues: {' K': 1, ' CA': 2, ' MG': 1, 'CLR': 3, 'POV': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 240 Unusual residues: {' CA': 2, ' MG': 1, 'CLR': 3, 'POV': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 7.64, per 1000 atoms: 0.21 Number of scatterers: 36018 At special positions: 0 Unit cell: (147.675, 147.675, 166.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 8 19.99 K 4 19.00 S 244 16.00 P 20 15.00 Mg 4 11.99 O 6506 8.00 N 5748 7.00 C 23484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 178 " distance=2.03 Simple disulfide: pdb=" SG CYS E 98 " - pdb=" SG CYS E 149 " distance=1.85 Simple disulfide: pdb=" SG CYS E 102 " - pdb=" SG CYS E 106 " distance=1.55 Simple disulfide: pdb=" SG CYS E 114 " - pdb=" SG CYS E 143 " distance=2.04 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 178 " distance=2.03 Simple disulfide: pdb=" SG CYS F 98 " - pdb=" SG CYS F 149 " distance=1.85 Simple disulfide: pdb=" SG CYS F 102 " - pdb=" SG CYS F 106 " distance=1.55 Simple disulfide: pdb=" SG CYS F 114 " - pdb=" SG CYS F 143 " distance=2.04 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 178 " distance=2.03 Simple disulfide: pdb=" SG CYS G 98 " - pdb=" SG CYS G 149 " distance=1.85 Simple disulfide: pdb=" SG CYS G 102 " - pdb=" SG CYS G 106 " distance=1.55 Simple disulfide: pdb=" SG CYS G 114 " - pdb=" SG CYS G 143 " distance=2.04 Simple disulfide: pdb=" SG CYS H 84 " - pdb=" SG CYS H 178 " distance=2.03 Simple disulfide: pdb=" SG CYS H 98 " - pdb=" SG CYS H 149 " distance=1.85 Simple disulfide: pdb=" SG CYS H 102 " - pdb=" SG CYS H 106 " distance=1.55 Simple disulfide: pdb=" SG CYS H 114 " - pdb=" SG CYS H 143 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 8684 Ramachandran restraints generated. 4342 Oldfield, 0 Emsley, 4342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8334 Finding SS restraints... Secondary structure from input PDB file: 193 helices and 32 sheets defined 55.2% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 21 through 54 removed outlier: 3.906A pdb=" N PHE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR A 51 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL A 52 " --> pdb=" O TYR A 48 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N CYS A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 106 Processing helix chain 'A' and resid 109 through 134 removed outlier: 3.690A pdb=" N ILE A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 146 Processing helix chain 'A' and resid 147 through 171 Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 180 through 190 Processing helix chain 'A' and resid 190 through 200 Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 229 through 259 Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 297 through 326 removed outlier: 3.630A pdb=" N LEU A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 432 through 451 Processing helix chain 'A' and resid 463 through 470 Processing helix chain 'A' and resid 486 through 500 Processing helix chain 'A' and resid 502 through 510 removed outlier: 3.584A pdb=" N LEU A 510 " --> pdb=" O MET A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 533 removed outlier: 3.955A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 549 through 558 Processing helix chain 'A' and resid 601 through 610 removed outlier: 3.702A pdb=" N VAL A 605 " --> pdb=" O ASP A 601 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ARG A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ALA A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE A 609 " --> pdb=" O VAL A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 704 removed outlier: 3.768A pdb=" N VAL A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 734 through 742 Proline residue: A 740 - end of helix Processing helix chain 'A' and resid 747 through 751 Processing helix chain 'A' and resid 759 through 764 Processing helix chain 'A' and resid 765 through 770 removed outlier: 6.059A pdb=" N GLU A 768 " --> pdb=" O ARG A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 792 Processing helix chain 'A' and resid 793 through 797 removed outlier: 3.535A pdb=" N CYS A 797 " --> pdb=" O ILE A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 829 Processing helix chain 'A' and resid 872 through 876 removed outlier: 4.082A pdb=" N ASN A 875 " --> pdb=" O THR A 872 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 876 " --> pdb=" O GLY A 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 872 through 876' Processing helix chain 'A' and resid 884 through 891 removed outlier: 3.828A pdb=" N GLN A 889 " --> pdb=" O THR A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 905 Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 918 through 921 removed outlier: 3.633A pdb=" N ASP A 921 " --> pdb=" O SER A 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 918 through 921' Processing helix chain 'A' and resid 922 through 930 Processing helix chain 'A' and resid 931 through 943 removed outlier: 4.488A pdb=" N THR A 935 " --> pdb=" O ASP A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 957 Processing helix chain 'A' and resid 965 through 971 Processing helix chain 'A' and resid 995 through 1008 Processing helix chain 'B' and resid 21 through 54 removed outlier: 3.905A pdb=" N PHE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL B 52 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N CYS B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 106 Processing helix chain 'B' and resid 109 through 134 removed outlier: 3.690A pdb=" N ILE B 124 " --> pdb=" O PHE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 146 Processing helix chain 'B' and resid 147 through 171 Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 180 through 190 Processing helix chain 'B' and resid 190 through 200 Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 229 through 259 Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 297 through 326 removed outlier: 3.630A pdb=" N LEU B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY B 310 " --> pdb=" O PHE B 306 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU B 312 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 432 through 451 Processing helix chain 'B' and resid 463 through 470 Processing helix chain 'B' and resid 486 through 500 Processing helix chain 'B' and resid 502 through 510 removed outlier: 3.584A pdb=" N LEU B 510 " --> pdb=" O MET B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 533 removed outlier: 3.954A pdb=" N TYR B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 Processing helix chain 'B' and resid 549 through 558 Processing helix chain 'B' and resid 601 through 610 removed outlier: 3.702A pdb=" N VAL B 605 " --> pdb=" O ASP B 601 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 606 " --> pdb=" O ALA B 602 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ARG B 607 " --> pdb=" O LYS B 603 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ALA B 608 " --> pdb=" O GLU B 604 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE B 609 " --> pdb=" O VAL B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.768A pdb=" N VAL B 703 " --> pdb=" O GLU B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 734 through 742 Proline residue: B 740 - end of helix Processing helix chain 'B' and resid 747 through 751 Processing helix chain 'B' and resid 759 through 764 Processing helix chain 'B' and resid 765 through 770 removed outlier: 6.059A pdb=" N GLU B 768 " --> pdb=" O ARG B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 792 Processing helix chain 'B' and resid 793 through 797 removed outlier: 3.535A pdb=" N CYS B 797 " --> pdb=" O ILE B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 829 Processing helix chain 'B' and resid 872 through 876 removed outlier: 4.082A pdb=" N ASN B 875 " --> pdb=" O THR B 872 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 876 " --> pdb=" O GLY B 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 872 through 876' Processing helix chain 'B' and resid 884 through 891 removed outlier: 3.828A pdb=" N GLN B 889 " --> pdb=" O THR B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 905 Processing helix chain 'B' and resid 906 through 911 Processing helix chain 'B' and resid 918 through 921 removed outlier: 3.633A pdb=" N ASP B 921 " --> pdb=" O SER B 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 918 through 921' Processing helix chain 'B' and resid 922 through 930 Processing helix chain 'B' and resid 931 through 943 removed outlier: 4.489A pdb=" N THR B 935 " --> pdb=" O ASP B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 957 Processing helix chain 'B' and resid 965 through 971 Processing helix chain 'B' and resid 995 through 1008 Processing helix chain 'C' and resid 21 through 54 removed outlier: 3.906A pdb=" N PHE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR C 51 " --> pdb=" O LYS C 47 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL C 52 " --> pdb=" O TYR C 48 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N CYS C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 106 Processing helix chain 'C' and resid 109 through 134 removed outlier: 3.690A pdb=" N ILE C 124 " --> pdb=" O PHE C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 146 Processing helix chain 'C' and resid 147 through 171 Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 180 through 190 Processing helix chain 'C' and resid 190 through 200 Processing helix chain 'C' and resid 206 through 215 Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 229 through 259 Processing helix chain 'C' and resid 261 through 265 Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 297 through 326 removed outlier: 3.630A pdb=" N LEU C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY C 310 " --> pdb=" O PHE C 306 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU C 312 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 407 through 414 Processing helix chain 'C' and resid 432 through 451 Processing helix chain 'C' and resid 463 through 470 Processing helix chain 'C' and resid 486 through 500 Processing helix chain 'C' and resid 502 through 510 removed outlier: 3.584A pdb=" N LEU C 510 " --> pdb=" O MET C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 533 removed outlier: 3.955A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 546 Processing helix chain 'C' and resid 549 through 558 Processing helix chain 'C' and resid 601 through 610 removed outlier: 3.702A pdb=" N VAL C 605 " --> pdb=" O ASP C 601 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS C 606 " --> pdb=" O ALA C 602 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ARG C 607 " --> pdb=" O LYS C 603 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA C 608 " --> pdb=" O GLU C 604 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE C 609 " --> pdb=" O VAL C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 704 removed outlier: 3.769A pdb=" N VAL C 703 " --> pdb=" O GLU C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 734 through 742 Proline residue: C 740 - end of helix Processing helix chain 'C' and resid 747 through 751 Processing helix chain 'C' and resid 759 through 764 Processing helix chain 'C' and resid 765 through 770 removed outlier: 6.060A pdb=" N GLU C 768 " --> pdb=" O ARG C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 792 Processing helix chain 'C' and resid 793 through 797 removed outlier: 3.535A pdb=" N CYS C 797 " --> pdb=" O ILE C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 829 Processing helix chain 'C' and resid 872 through 876 removed outlier: 4.082A pdb=" N ASN C 875 " --> pdb=" O THR C 872 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 876 " --> pdb=" O GLY C 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 872 through 876' Processing helix chain 'C' and resid 884 through 891 removed outlier: 3.828A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 905 Processing helix chain 'C' and resid 906 through 911 Processing helix chain 'C' and resid 918 through 921 removed outlier: 3.633A pdb=" N ASP C 921 " --> pdb=" O SER C 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 918 through 921' Processing helix chain 'C' and resid 922 through 930 Processing helix chain 'C' and resid 931 through 943 removed outlier: 4.489A pdb=" N THR C 935 " --> pdb=" O ASP C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 957 Processing helix chain 'C' and resid 965 through 971 Processing helix chain 'C' and resid 995 through 1008 Processing helix chain 'D' and resid 21 through 54 removed outlier: 3.905A pdb=" N PHE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL D 52 " --> pdb=" O TYR D 48 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N CYS D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 106 Processing helix chain 'D' and resid 109 through 134 removed outlier: 3.690A pdb=" N ILE D 124 " --> pdb=" O PHE D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 146 Processing helix chain 'D' and resid 147 through 171 Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 180 through 190 Processing helix chain 'D' and resid 190 through 200 Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 229 through 259 Processing helix chain 'D' and resid 261 through 265 Processing helix chain 'D' and resid 273 through 286 Processing helix chain 'D' and resid 297 through 326 removed outlier: 3.630A pdb=" N LEU D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY D 310 " --> pdb=" O PHE D 306 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU D 312 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA D 313 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 352 through 364 Processing helix chain 'D' and resid 384 through 394 Processing helix chain 'D' and resid 407 through 414 Processing helix chain 'D' and resid 432 through 451 Processing helix chain 'D' and resid 463 through 470 Processing helix chain 'D' and resid 486 through 500 Processing helix chain 'D' and resid 502 through 510 removed outlier: 3.585A pdb=" N LEU D 510 " --> pdb=" O MET D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 533 removed outlier: 3.955A pdb=" N TYR D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 546 Processing helix chain 'D' and resid 549 through 558 Processing helix chain 'D' and resid 601 through 610 removed outlier: 3.702A pdb=" N VAL D 605 " --> pdb=" O ASP D 601 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS D 606 " --> pdb=" O ALA D 602 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ARG D 607 " --> pdb=" O LYS D 603 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA D 608 " --> pdb=" O GLU D 604 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE D 609 " --> pdb=" O VAL D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 704 removed outlier: 3.769A pdb=" N VAL D 703 " --> pdb=" O GLU D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 734 through 742 Proline residue: D 740 - end of helix Processing helix chain 'D' and resid 747 through 751 Processing helix chain 'D' and resid 759 through 764 Processing helix chain 'D' and resid 765 through 770 removed outlier: 6.059A pdb=" N GLU D 768 " --> pdb=" O ARG D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 785 through 792 Processing helix chain 'D' and resid 793 through 797 removed outlier: 3.535A pdb=" N CYS D 797 " --> pdb=" O ILE D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 829 Processing helix chain 'D' and resid 872 through 876 removed outlier: 4.082A pdb=" N ASN D 875 " --> pdb=" O THR D 872 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE D 876 " --> pdb=" O GLY D 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 872 through 876' Processing helix chain 'D' and resid 884 through 891 removed outlier: 3.827A pdb=" N GLN D 889 " --> pdb=" O THR D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 905 Processing helix chain 'D' and resid 906 through 911 Processing helix chain 'D' and resid 918 through 921 removed outlier: 3.634A pdb=" N ASP D 921 " --> pdb=" O SER D 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 918 through 921' Processing helix chain 'D' and resid 922 through 930 Processing helix chain 'D' and resid 931 through 943 removed outlier: 4.488A pdb=" N THR D 935 " --> pdb=" O ASP D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 946 through 957 Processing helix chain 'D' and resid 965 through 971 Processing helix chain 'D' and resid 995 through 1008 Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.534A pdb=" N ARG E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 78 removed outlier: 4.216A pdb=" N GLY E 43 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N SER E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) Proline residue: E 72 - end of helix Processing helix chain 'E' and resid 133 through 140 Processing helix chain 'E' and resid 152 through 169 removed outlier: 3.673A pdb=" N ASP E 169 " --> pdb=" O GLN E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 234 Proline residue: E 207 - end of helix removed outlier: 3.588A pdb=" N VAL E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 78 removed outlier: 4.217A pdb=" N GLY F 43 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N SER F 71 " --> pdb=" O PHE F 67 " (cutoff:3.500A) Proline residue: F 72 - end of helix Processing helix chain 'F' and resid 133 through 140 Processing helix chain 'F' and resid 152 through 169 removed outlier: 3.673A pdb=" N ASP F 169 " --> pdb=" O GLN F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 234 Proline residue: F 207 - end of helix removed outlier: 3.588A pdb=" N VAL F 229 " --> pdb=" O LYS F 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 78 removed outlier: 4.216A pdb=" N GLY G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N SER G 71 " --> pdb=" O PHE G 67 " (cutoff:3.500A) Proline residue: G 72 - end of helix Processing helix chain 'G' and resid 133 through 140 Processing helix chain 'G' and resid 152 through 169 removed outlier: 3.674A pdb=" N ASP G 169 " --> pdb=" O GLN G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 234 Proline residue: G 207 - end of helix removed outlier: 3.588A pdb=" N VAL G 229 " --> pdb=" O LYS G 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 78 removed outlier: 4.216A pdb=" N GLY H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N SER H 71 " --> pdb=" O PHE H 67 " (cutoff:3.500A) Proline residue: H 72 - end of helix Processing helix chain 'H' and resid 133 through 140 Processing helix chain 'H' and resid 152 through 169 removed outlier: 3.673A pdb=" N ASP H 169 " --> pdb=" O GLN H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 234 Proline residue: H 207 - end of helix removed outlier: 3.587A pdb=" N VAL H 229 " --> pdb=" O LYS H 225 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 402 removed outlier: 6.096A pdb=" N ILE A 345 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU A 378 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL A 347 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A 456 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE A 484 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR A 458 " --> pdb=" O ILE A 484 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 535 through 536 Processing sheet with id=AA4, first strand: chain 'A' and resid 535 through 536 removed outlier: 6.889A pdb=" N LEU A 594 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE A 568 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N PHE A 596 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 568 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 686 through 687 removed outlier: 4.283A pdb=" N TYR A 686 " --> pdb=" O GLY A 962 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 776 through 779 removed outlier: 6.715A pdb=" N ILE A 754 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LEU A 779 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE A 756 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 976 through 981 removed outlier: 3.703A pdb=" N LEU A 980 " --> pdb=" O ILE A1049 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A1049 " --> pdb=" O LEU A 980 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A1048 " --> pdb=" O TYR A1015 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY A1013 " --> pdb=" O PHE A1050 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU A1052 " --> pdb=" O CYS A1011 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N CYS A1011 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 139 through 141 Processing sheet with id=AA9, first strand: chain 'B' and resid 398 through 402 removed outlier: 6.096A pdb=" N ILE B 345 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU B 378 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL B 347 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE B 456 " --> pdb=" O ASP B 482 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE B 484 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR B 458 " --> pdb=" O ILE B 484 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 535 through 536 Processing sheet with id=AB2, first strand: chain 'B' and resid 535 through 536 removed outlier: 6.888A pdb=" N LEU B 594 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE B 568 " --> pdb=" O LEU B 594 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N PHE B 596 " --> pdb=" O ILE B 566 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 568 " --> pdb=" O LEU B 580 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 686 through 687 removed outlier: 4.283A pdb=" N TYR B 686 " --> pdb=" O GLY B 962 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 776 through 779 removed outlier: 6.715A pdb=" N ILE B 754 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N LEU B 779 " --> pdb=" O ILE B 754 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE B 756 " --> pdb=" O LEU B 779 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N CYS B 800 " --> pdb=" O ILE B 879 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLU B 881 " --> pdb=" O CYS B 800 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE B 802 " --> pdb=" O GLU B 881 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 976 through 981 removed outlier: 3.702A pdb=" N LEU B 980 " --> pdb=" O ILE B1049 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B1049 " --> pdb=" O LEU B 980 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B1048 " --> pdb=" O TYR B1015 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY B1013 " --> pdb=" O PHE B1050 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU B1052 " --> pdb=" O CYS B1011 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N CYS B1011 " --> pdb=" O LEU B1052 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 139 through 141 Processing sheet with id=AB7, first strand: chain 'C' and resid 398 through 402 removed outlier: 6.096A pdb=" N ILE C 345 " --> pdb=" O VAL C 376 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU C 378 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL C 347 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE C 456 " --> pdb=" O ASP C 482 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE C 484 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N THR C 458 " --> pdb=" O ILE C 484 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 535 through 536 Processing sheet with id=AB9, first strand: chain 'C' and resid 535 through 536 removed outlier: 6.889A pdb=" N LEU C 594 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE C 568 " --> pdb=" O LEU C 594 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N PHE C 596 " --> pdb=" O ILE C 566 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE C 568 " --> pdb=" O LEU C 580 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 686 through 687 removed outlier: 4.283A pdb=" N TYR C 686 " --> pdb=" O GLY C 962 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 776 through 779 removed outlier: 6.715A pdb=" N ILE C 754 " --> pdb=" O SER C 777 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N LEU C 779 " --> pdb=" O ILE C 754 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE C 756 " --> pdb=" O LEU C 779 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N CYS C 800 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLU C 881 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE C 802 " --> pdb=" O GLU C 881 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 976 through 981 removed outlier: 3.703A pdb=" N LEU C 980 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C1049 " --> pdb=" O LEU C 980 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU C1048 " --> pdb=" O TYR C1015 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY C1013 " --> pdb=" O PHE C1050 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU C1052 " --> pdb=" O CYS C1011 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N CYS C1011 " --> pdb=" O LEU C1052 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 139 through 141 Processing sheet with id=AC5, first strand: chain 'D' and resid 398 through 402 removed outlier: 6.097A pdb=" N ILE D 345 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU D 378 " --> pdb=" O ILE D 345 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL D 347 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE D 456 " --> pdb=" O ASP D 482 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE D 484 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR D 458 " --> pdb=" O ILE D 484 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 535 through 536 Processing sheet with id=AC7, first strand: chain 'D' and resid 535 through 536 removed outlier: 6.889A pdb=" N LEU D 594 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE D 568 " --> pdb=" O LEU D 594 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N PHE D 596 " --> pdb=" O ILE D 566 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE D 568 " --> pdb=" O LEU D 580 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 686 through 687 removed outlier: 4.283A pdb=" N TYR D 686 " --> pdb=" O GLY D 962 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 776 through 779 removed outlier: 6.715A pdb=" N ILE D 754 " --> pdb=" O SER D 777 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LEU D 779 " --> pdb=" O ILE D 754 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE D 756 " --> pdb=" O LEU D 779 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N CYS D 800 " --> pdb=" O ILE D 879 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLU D 881 " --> pdb=" O CYS D 800 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE D 802 " --> pdb=" O GLU D 881 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 976 through 981 removed outlier: 3.703A pdb=" N LEU D 980 " --> pdb=" O ILE D1049 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D1049 " --> pdb=" O LEU D 980 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU D1048 " --> pdb=" O TYR D1015 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY D1013 " --> pdb=" O PHE D1050 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU D1052 " --> pdb=" O CYS D1011 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N CYS D1011 " --> pdb=" O LEU D1052 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 80 through 83 removed outlier: 5.041A pdb=" N ASN E 181 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASP E 188 " --> pdb=" O ASN E 181 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA E 128 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N VAL E 117 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 10.641A pdb=" N GLY E 108 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N GLU E 97 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 10.269A pdb=" N SER E 110 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N VAL E 95 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N TYR E 112 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N GLY E 93 " --> pdb=" O TYR E 112 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N CYS E 114 " --> pdb=" O GLN E 91 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLN E 91 " --> pdb=" O CYS E 114 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLN E 116 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL E 89 " --> pdb=" O GLN E 116 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR E 118 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR E 85 " --> pdb=" O ASN E 120 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 80 through 83 removed outlier: 5.041A pdb=" N ASN F 181 " --> pdb=" O ASP F 188 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASP F 188 " --> pdb=" O ASN F 181 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA F 128 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N VAL F 117 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 10.641A pdb=" N GLY F 108 " --> pdb=" O GLU F 97 " (cutoff:3.500A) removed outlier: 9.345A pdb=" N GLU F 97 " --> pdb=" O GLY F 108 " (cutoff:3.500A) removed outlier: 10.269A pdb=" N SER F 110 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N VAL F 95 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N TYR F 112 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N GLY F 93 " --> pdb=" O TYR F 112 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N CYS F 114 " --> pdb=" O GLN F 91 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLN F 91 " --> pdb=" O CYS F 114 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLN F 116 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL F 89 " --> pdb=" O GLN F 116 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR F 118 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR F 85 " --> pdb=" O ASN F 120 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 80 through 83 removed outlier: 5.040A pdb=" N ASN G 181 " --> pdb=" O ASP G 188 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASP G 188 " --> pdb=" O ASN G 181 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA G 128 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N VAL G 117 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 10.641A pdb=" N GLY G 108 " --> pdb=" O GLU G 97 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N GLU G 97 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N SER G 110 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N VAL G 95 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N TYR G 112 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N GLY G 93 " --> pdb=" O TYR G 112 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N CYS G 114 " --> pdb=" O GLN G 91 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLN G 91 " --> pdb=" O CYS G 114 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLN G 116 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL G 89 " --> pdb=" O GLN G 116 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR G 118 " --> pdb=" O LEU G 87 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR G 85 " --> pdb=" O ASN G 120 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 80 through 83 removed outlier: 5.041A pdb=" N ASN H 181 " --> pdb=" O ASP H 188 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASP H 188 " --> pdb=" O ASN H 181 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA H 128 " --> pdb=" O VAL H 119 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL H 117 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 10.641A pdb=" N GLY H 108 " --> pdb=" O GLU H 97 " (cutoff:3.500A) removed outlier: 9.347A pdb=" N GLU H 97 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 10.269A pdb=" N SER H 110 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N VAL H 95 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N TYR H 112 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N GLY H 93 " --> pdb=" O TYR H 112 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N CYS H 114 " --> pdb=" O GLN H 91 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLN H 91 " --> pdb=" O CYS H 114 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLN H 116 " --> pdb=" O VAL H 89 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL H 89 " --> pdb=" O GLN H 116 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR H 118 " --> pdb=" O LEU H 87 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR H 85 " --> pdb=" O ASN H 120 " (cutoff:3.500A) 1765 hydrogen bonds defined for protein. 4947 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: 7.30 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 5712 1.29 - 1.42: 9663 1.42 - 1.56: 21052 1.56 - 1.69: 55 1.69 - 1.82: 340 Bond restraints: 36822 Sorted by residual: bond pdb=" C HIS H 131 " pdb=" O HIS H 131 " ideal model delta sigma weight residual 1.235 1.161 0.074 1.13e-02 7.83e+03 4.27e+01 bond pdb=" C HIS E 131 " pdb=" O HIS E 131 " ideal model delta sigma weight residual 1.235 1.161 0.073 1.13e-02 7.83e+03 4.22e+01 bond pdb=" C31 POV B1110 " pdb=" O31 POV B1110 " ideal model delta sigma weight residual 1.327 1.457 -0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" C31 POV A1113 " pdb=" O31 POV A1113 " ideal model delta sigma weight residual 1.327 1.457 -0.130 2.00e-02 2.50e+03 4.20e+01 bond pdb=" C HIS G 131 " pdb=" O HIS G 131 " ideal model delta sigma weight residual 1.235 1.162 0.073 1.13e-02 7.83e+03 4.19e+01 ... (remaining 36817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.13: 49540 5.13 - 10.25: 380 10.25 - 15.38: 12 15.38 - 20.50: 0 20.50 - 25.63: 12 Bond angle restraints: 49944 Sorted by residual: angle pdb=" C12 POV C1105 " pdb=" N POV C1105 " pdb=" C15 POV C1105 " ideal model delta sigma weight residual 112.10 86.47 25.63 3.00e+00 1.11e-01 7.30e+01 angle pdb=" C12 POV A1104 " pdb=" N POV A1104 " pdb=" C15 POV A1104 " ideal model delta sigma weight residual 112.10 86.51 25.59 3.00e+00 1.11e-01 7.28e+01 angle pdb=" C12 POV D1104 " pdb=" N POV D1104 " pdb=" C15 POV D1104 " ideal model delta sigma weight residual 112.10 86.53 25.57 3.00e+00 1.11e-01 7.26e+01 angle pdb=" C12 POV B1104 " pdb=" N POV B1104 " pdb=" C15 POV B1104 " ideal model delta sigma weight residual 112.10 86.56 25.54 3.00e+00 1.11e-01 7.25e+01 angle pdb=" N THR F 36 " pdb=" CA THR F 36 " pdb=" C THR F 36 " ideal model delta sigma weight residual 113.50 103.88 9.62 1.23e+00 6.61e-01 6.12e+01 ... (remaining 49939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.21: 20972 24.21 - 48.43: 1170 48.43 - 72.64: 211 72.64 - 96.86: 68 96.86 - 121.07: 7 Dihedral angle restraints: 22428 sinusoidal: 9578 harmonic: 12850 Sorted by residual: dihedral pdb=" CB CYS E 98 " pdb=" SG CYS E 98 " pdb=" SG CYS E 149 " pdb=" CB CYS E 149 " ideal model delta sinusoidal sigma weight residual -86.00 -173.79 87.79 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS H 98 " pdb=" SG CYS H 98 " pdb=" SG CYS H 149 " pdb=" CB CYS H 149 " ideal model delta sinusoidal sigma weight residual -86.00 -173.77 87.77 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS G 98 " pdb=" SG CYS G 98 " pdb=" SG CYS G 149 " pdb=" CB CYS G 149 " ideal model delta sinusoidal sigma weight residual -86.00 -173.76 87.76 1 1.00e+01 1.00e-02 9.22e+01 ... (remaining 22425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 4863 0.116 - 0.232: 688 0.232 - 0.348: 127 0.348 - 0.464: 4 0.464 - 0.580: 8 Chirality restraints: 5690 Sorted by residual: chirality pdb=" CA TYR B 332 " pdb=" N TYR B 332 " pdb=" C TYR B 332 " pdb=" CB TYR B 332 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.40e+00 chirality pdb=" CA TYR A 332 " pdb=" N TYR A 332 " pdb=" C TYR A 332 " pdb=" CB TYR A 332 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.35e+00 chirality pdb=" CA TYR D 332 " pdb=" N TYR D 332 " pdb=" C TYR D 332 " pdb=" CB TYR D 332 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.32e+00 ... (remaining 5687 not shown) Planarity restraints: 6143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 767 " 0.107 2.00e-02 2.50e+03 5.89e-02 8.66e+01 pdb=" CG TRP D 767 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP D 767 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP D 767 " -0.073 2.00e-02 2.50e+03 pdb=" NE1 TRP D 767 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TRP D 767 " -0.026 2.00e-02 2.50e+03 pdb=" CE3 TRP D 767 " -0.083 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 767 " 0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 767 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 767 " 0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 767 " -0.107 2.00e-02 2.50e+03 5.87e-02 8.62e+01 pdb=" CG TRP A 767 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 767 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 767 " 0.073 2.00e-02 2.50e+03 pdb=" NE1 TRP A 767 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TRP A 767 " 0.026 2.00e-02 2.50e+03 pdb=" CE3 TRP A 767 " 0.083 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 767 " -0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 767 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 767 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 767 " -0.107 2.00e-02 2.50e+03 5.87e-02 8.62e+01 pdb=" CG TRP B 767 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP B 767 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP B 767 " 0.073 2.00e-02 2.50e+03 pdb=" NE1 TRP B 767 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TRP B 767 " 0.026 2.00e-02 2.50e+03 pdb=" CE3 TRP B 767 " 0.083 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 767 " -0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 767 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 767 " -0.082 2.00e-02 2.50e+03 ... (remaining 6140 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.65: 351 2.65 - 3.27: 36661 3.27 - 3.90: 70930 3.90 - 4.52: 92319 4.52 - 5.14: 149911 Nonbonded interactions: 350172 Sorted by model distance: nonbonded pdb=" OE2 GLU A 399 " pdb="MG MG A1101 " model vdw 2.031 2.170 nonbonded pdb=" OE2 GLU B 399 " pdb="MG MG B1101 " model vdw 2.034 2.170 nonbonded pdb=" OE2 GLU C 399 " pdb="MG MG C1102 " model vdw 2.035 2.170 nonbonded pdb=" OE2 GLU D 399 " pdb="MG MG D1101 " model vdw 2.035 2.170 nonbonded pdb=" O SER B 533 " pdb="CA CA B1102 " model vdw 2.143 2.510 ... (remaining 350167 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 1056 or resid 1103 or resid 1106 or (resid 1110 \ and (name C1 or name C11 or name C12 or name C2 or name C21 or name C22 or name \ C23 or name C24 or name C25 or name C26 or name C27 or name C3 or name C31 or n \ ame C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name O11 or name O12 or name O13 or name O14 or name O21 or name \ O22 or name O31 or name O32 or name P or name C310 or name C311 or name C312 or \ name C313)))) selection = (chain 'B' and (resid 19 through 1056 or resid 1103 or resid 1106 or (resid 1110 \ and (name C1 or name C11 or name C12 or name C2 or name C21 or name C22 or name \ C23 or name C24 or name C25 or name C26 or name C27 or name C3 or name C31 or n \ ame C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name O11 or name O12 or name O13 or name O14 or name O21 or name \ O22 or name O31 or name O32 or name P or name C310 or name C311 or name C312 or \ name C313)))) selection = (chain 'C' and (resid 19 through 1056 or resid 1103 or resid 1106 or (resid 1110 \ and (name C1 or name C11 or name C12 or name C2 or name C21 or name C22 or name \ C23 or name C24 or name C25 or name C26 or name C27 or name C3 or name C31 or n \ ame C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name O11 or name O12 or name O13 or name O14 or name O21 or name \ O22 or name O31 or name O32 or name P or name C310 or name C311 or name C312 or \ name C313)))) selection = (chain 'D' and (resid 19 through 1056 or resid 1103 or resid 1106 or (resid 1110 \ and (name C1 or name C11 or name C12 or name C2 or name C21 or name C22 or name \ C23 or name C24 or name C25 or name C26 or name C27 or name C3 or name C31 or n \ ame C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name O11 or name O12 or name O13 or name O14 or name O21 or name \ O22 or name O31 or name O32 or name P or name C310 or name C311 or name C312 or \ name C313)))) } ncs_group { reference = (chain 'E' and resid 34 through 301) selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 3.480 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: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 28.750 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 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 : 0.013 0.483 36838 Z= 0.699 Angle : 1.649 37.978 49976 Z= 1.024 Chirality : 0.085 0.580 5690 Planarity : 0.010 0.084 6143 Dihedral : 15.825 121.070 14046 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 0.46 % Allowed : 10.95 % Favored : 88.59 % Cbeta Deviations : 0.19 % 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 aren not related in a simple way. whole: -0.12 (0.12), residues: 4342 helix: 0.26 (0.11), residues: 2208 sheet: 0.15 (0.26), residues: 392 loop : -0.40 (0.15), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 972 TYR 0.089 0.011 TYR C 996 PHE 0.055 0.008 PHE D 692 TRP 0.107 0.018 TRP D 767 HIS 0.013 0.003 HIS H 131 Details of bonding type rmsd covalent geometry : bond 0.01146 (36822) covalent geometry : angle 1.59149 (49944) SS BOND : bond 0.25770 ( 16) SS BOND : angle 17.19916 ( 32) hydrogen bonds : bond 0.15879 ( 1757) hydrogen bonds : angle 6.14436 ( 4947) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8684 Ramachandran restraints generated. 4342 Oldfield, 0 Emsley, 4342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8684 Ramachandran restraints generated. 4342 Oldfield, 0 Emsley, 4342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 501 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 PHE cc_start: 0.8838 (m-10) cc_final: 0.8631 (m-10) REVERT: A 370 ASP cc_start: 0.7354 (p0) cc_final: 0.7056 (p0) REVERT: A 520 GLU cc_start: 0.7430 (pt0) cc_final: 0.6585 (tp30) REVERT: A 545 PHE cc_start: 0.6823 (m-80) cc_final: 0.6358 (m-80) REVERT: A 609 PHE cc_start: 0.7555 (t80) cc_final: 0.7226 (t80) REVERT: A 999 LEU cc_start: 0.8300 (tp) cc_final: 0.8032 (tt) REVERT: B 20 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6820 (ptm160) REVERT: B 50 TRP cc_start: 0.7091 (t-100) cc_final: 0.6640 (t-100) REVERT: B 94 MET cc_start: 0.8507 (mmt) cc_final: 0.7906 (mpp) REVERT: B 913 THR cc_start: 0.9004 (m) cc_final: 0.8707 (p) REVERT: B 952 LEU cc_start: 0.8709 (mm) cc_final: 0.8491 (mp) REVERT: B 971 ASN cc_start: 0.5777 (m-40) cc_final: 0.5545 (m110) REVERT: C 460 MET cc_start: 0.8325 (mmm) cc_final: 0.8060 (tpp) REVERT: C 519 ILE cc_start: 0.6521 (OUTLIER) cc_final: 0.5926 (pp) REVERT: C 610 PHE cc_start: 0.6915 (t80) cc_final: 0.6427 (t80) REVERT: C 987 PHE cc_start: 0.7519 (m-80) cc_final: 0.7274 (m-80) REVERT: C 1039 TYR cc_start: 0.8089 (t80) cc_final: 0.7797 (t80) REVERT: D 194 PHE cc_start: 0.8798 (m-10) cc_final: 0.8568 (m-10) REVERT: D 321 GLU cc_start: 0.8448 (tt0) cc_final: 0.7924 (tp30) REVERT: D 610 PHE cc_start: 0.6811 (t80) cc_final: 0.6000 (t80) REVERT: D 739 MET cc_start: 0.7878 (mtp) cc_final: 0.7453 (ttm) REVERT: E 196 ASP cc_start: 0.8155 (m-30) cc_final: 0.7886 (t0) REVERT: F 193 ARG cc_start: 0.6716 (mmt90) cc_final: 0.6409 (ptm-80) REVERT: G 161 MET cc_start: 0.8424 (mmm) cc_final: 0.8185 (tmm) REVERT: G 230 LYS cc_start: 0.8027 (mttp) cc_final: 0.7554 (pptt) REVERT: H 76 ASP cc_start: 0.8475 (t0) cc_final: 0.8216 (t0) REVERT: H 125 ASN cc_start: 0.6252 (m110) cc_final: 0.5650 (t0) REVERT: H 134 GLU cc_start: 0.8001 (tt0) cc_final: 0.7677 (mm-30) REVERT: H 230 LYS cc_start: 0.7720 (mttp) cc_final: 0.7424 (pptt) outliers start: 18 outliers final: 3 residues processed: 511 average time/residue: 0.7004 time to fit residues: 422.6353 Evaluate side-chains 258 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 253 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain E residue 2 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 465 ASN A 468 HIS ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN B 468 HIS B 534 ASN B 816 GLN B 884 ASN ** B1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 ASN C 200 ASN C 772 ASN D 157 ASN D 182 ASN D 534 ASN E 78 GLN E 125 ASN E 156 ASN F 78 GLN F 121 ASN G 78 GLN G 125 ASN H 78 GLN H 120 ASN H 131 HIS H 136 GLN H 195 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.105450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.076639 restraints weight = 83270.125| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.46 r_work: 0.3143 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 36838 Z= 0.133 Angle : 0.591 10.054 49976 Z= 0.309 Chirality : 0.042 0.285 5690 Planarity : 0.004 0.049 6143 Dihedral : 11.122 97.992 5984 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.60 % Allowed : 14.40 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.13), residues: 4342 helix: 1.32 (0.11), residues: 2200 sheet: 0.03 (0.23), residues: 518 loop : 0.09 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 960 TYR 0.016 0.001 TYR E 166 PHE 0.023 0.001 PHE C 550 TRP 0.021 0.001 TRP B 477 HIS 0.007 0.001 HIS H 195 Details of bonding type rmsd covalent geometry : bond 0.00287 (36822) covalent geometry : angle 0.58705 (49944) SS BOND : bond 0.00346 ( 16) SS BOND : angle 2.79114 ( 32) hydrogen bonds : bond 0.04872 ( 1757) hydrogen bonds : angle 4.50913 ( 4947) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8684 Ramachandran restraints generated. 4342 Oldfield, 0 Emsley, 4342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8684 Ramachandran restraints generated. 4342 Oldfield, 0 Emsley, 4342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 309 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.8000 (mmt) REVERT: A 182 ASN cc_start: 0.7960 (OUTLIER) cc_final: 0.7567 (m110) REVERT: A 370 ASP cc_start: 0.7292 (p0) cc_final: 0.7035 (p0) REVERT: A 520 GLU cc_start: 0.7422 (pt0) cc_final: 0.6623 (tp30) REVERT: A 545 PHE cc_start: 0.6452 (m-80) cc_final: 0.6095 (m-80) REVERT: A 565 MET cc_start: 0.8708 (mtm) cc_final: 0.8490 (mtp) REVERT: A 580 LEU cc_start: 0.6276 (mm) cc_final: 0.6026 (mm) REVERT: A 604 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: A 609 PHE cc_start: 0.7508 (t80) cc_final: 0.7182 (t80) REVERT: B 50 TRP cc_start: 0.6936 (t-100) cc_final: 0.6449 (t-100) REVERT: B 94 MET cc_start: 0.8403 (mmt) cc_final: 0.7771 (mpp) REVERT: B 104 MET cc_start: 0.9130 (tpp) cc_final: 0.8843 (tpp) REVERT: B 264 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8159 (mp0) REVERT: B 519 ILE cc_start: 0.4393 (OUTLIER) cc_final: 0.3198 (tp) REVERT: B 761 GLU cc_start: 0.8737 (mp0) cc_final: 0.8406 (tm-30) REVERT: B 913 THR cc_start: 0.9139 (m) cc_final: 0.8750 (p) REVERT: B 976 ARG cc_start: 0.6438 (OUTLIER) cc_final: 0.6053 (pmt-80) REVERT: B 1039 TYR cc_start: 0.7999 (t80) cc_final: 0.7797 (t80) REVERT: C 578 ARG cc_start: 0.4729 (mmt-90) cc_final: 0.4358 (pmt-80) REVERT: C 604 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: C 610 PHE cc_start: 0.6878 (t80) cc_final: 0.6465 (t80) REVERT: C 1000 PHE cc_start: 0.8265 (t80) cc_final: 0.7836 (t80) REVERT: D 519 ILE cc_start: 0.6730 (OUTLIER) cc_final: 0.5936 (tp) REVERT: D 751 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6673 (mp) REVERT: D 799 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8541 (mmm) REVERT: D 1053 MET cc_start: 0.6686 (mtp) cc_final: 0.6319 (mtp) REVERT: E 196 ASP cc_start: 0.8289 (m-30) cc_final: 0.7561 (t0) REVERT: F 127 ARG cc_start: 0.6166 (ttm170) cc_final: 0.5790 (tpt-90) REVERT: F 140 ASN cc_start: 0.8171 (t0) cc_final: 0.7933 (t0) REVERT: F 183 HIS cc_start: 0.8217 (OUTLIER) cc_final: 0.7822 (m90) REVERT: F 195 HIS cc_start: 0.6817 (t-90) cc_final: 0.6511 (t-170) REVERT: G 44 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8301 (mm-30) REVERT: G 152 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6882 (pm20) REVERT: G 161 MET cc_start: 0.8982 (mmm) cc_final: 0.8472 (tmm) REVERT: G 188 ASP cc_start: 0.7642 (m-30) cc_final: 0.7349 (m-30) REVERT: G 230 LYS cc_start: 0.7670 (mttp) cc_final: 0.7126 (tmtt) REVERT: H 45 ASP cc_start: 0.8537 (m-30) cc_final: 0.8279 (m-30) REVERT: H 125 ASN cc_start: 0.6315 (m110) cc_final: 0.5838 (t0) REVERT: H 134 GLU cc_start: 0.8130 (tt0) cc_final: 0.7678 (tp30) REVERT: H 142 LYS cc_start: 0.8315 (mmtt) cc_final: 0.7982 (tptt) REVERT: H 158 GLU cc_start: 0.8533 (pt0) cc_final: 0.8271 (pp20) REVERT: H 230 LYS cc_start: 0.7591 (mttp) cc_final: 0.7192 (pptt) outliers start: 101 outliers final: 14 residues processed: 380 average time/residue: 0.7228 time to fit residues: 332.3574 Evaluate side-chains 269 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 243 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 905 LEU Chi-restraints excluded: chain B residue 976 ARG Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain C residue 1016 ARG Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 799 MET Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 183 HIS Chi-restraints excluded: chain G residue 152 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 285 optimal weight: 0.9990 chunk 350 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 302 optimal weight: 5.9990 chunk 366 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 392 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 157 optimal weight: 0.0670 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 HIS A 534 ASN B 157 ASN B 468 HIS B 971 ASN ** B1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN C 465 ASN C 887 ASN D 449 ASN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN H 162 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.103645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.074606 restraints weight = 82661.881| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.44 r_work: 0.3100 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 36838 Z= 0.134 Angle : 0.534 9.269 49976 Z= 0.278 Chirality : 0.041 0.236 5690 Planarity : 0.004 0.040 6143 Dihedral : 10.151 80.587 5974 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.12 % Allowed : 15.79 % Favored : 81.10 % 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 aren not related in a simple way. whole: 1.17 (0.13), residues: 4342 helix: 1.56 (0.11), residues: 2197 sheet: 0.03 (0.23), residues: 512 loop : 0.06 (0.16), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 151 TYR 0.013 0.001 TYR H 166 PHE 0.026 0.001 PHE B 610 TRP 0.047 0.001 TRP E 4 HIS 0.006 0.001 HIS F 192 Details of bonding type rmsd covalent geometry : bond 0.00303 (36822) covalent geometry : angle 0.53311 (49944) SS BOND : bond 0.00215 ( 16) SS BOND : angle 1.27840 ( 32) hydrogen bonds : bond 0.04636 ( 1757) hydrogen bonds : angle 4.39242 ( 4947) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8684 Ramachandran restraints generated. 4342 Oldfield, 0 Emsley, 4342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8684 Ramachandran restraints generated. 4342 Oldfield, 0 Emsley, 4342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 269 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.8010 (mmt) REVERT: A 370 ASP cc_start: 0.7250 (p0) cc_final: 0.7005 (p0) REVERT: A 520 GLU cc_start: 0.7358 (pt0) cc_final: 0.6626 (tp30) REVERT: A 565 MET cc_start: 0.8587 (mtm) cc_final: 0.8381 (mtp) REVERT: A 579 ILE cc_start: 0.4831 (OUTLIER) cc_final: 0.4609 (pp) REVERT: A 580 LEU cc_start: 0.6145 (mm) cc_final: 0.5842 (mm) REVERT: A 581 ILE cc_start: 0.6630 (OUTLIER) cc_final: 0.6426 (pp) REVERT: A 604 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6633 (mm-30) REVERT: A 609 PHE cc_start: 0.7633 (t80) cc_final: 0.7187 (t80) REVERT: B 50 TRP cc_start: 0.6953 (t-100) cc_final: 0.6474 (t-100) REVERT: B 94 MET cc_start: 0.8408 (mmt) cc_final: 0.7942 (mpp) REVERT: B 182 ASN cc_start: 0.8126 (OUTLIER) cc_final: 0.7862 (m110) REVERT: B 264 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: B 519 ILE cc_start: 0.4534 (OUTLIER) cc_final: 0.3283 (tp) REVERT: B 555 GLU cc_start: 0.8652 (tp30) cc_final: 0.7960 (tp30) REVERT: B 558 PHE cc_start: 0.7205 (t80) cc_final: 0.6580 (t80) REVERT: B 761 GLU cc_start: 0.8713 (mp0) cc_final: 0.8429 (tm-30) REVERT: B 913 THR cc_start: 0.9193 (m) cc_final: 0.8877 (p) REVERT: B 1039 TYR cc_start: 0.8003 (t80) cc_final: 0.7721 (t80) REVERT: C 330 LYS cc_start: 0.8071 (pptt) cc_final: 0.7533 (pptt) REVERT: C 519 ILE cc_start: 0.6742 (OUTLIER) cc_final: 0.6023 (pp) REVERT: C 578 ARG cc_start: 0.4994 (mmt-90) cc_final: 0.4530 (pmt-80) REVERT: C 604 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: C 610 PHE cc_start: 0.6806 (t80) cc_final: 0.6387 (t80) REVERT: C 798 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8172 (m-30) REVERT: C 1000 PHE cc_start: 0.8128 (t80) cc_final: 0.7888 (t80) REVERT: D 519 ILE cc_start: 0.6650 (OUTLIER) cc_final: 0.5765 (tp) REVERT: D 587 LEU cc_start: 0.6477 (OUTLIER) cc_final: 0.6113 (mm) REVERT: D 604 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: D 799 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8584 (mmm) REVERT: D 995 CYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7235 (t) REVERT: D 1002 LYS cc_start: 0.8386 (tmmt) cc_final: 0.8125 (tmtt) REVERT: D 1009 MET cc_start: 0.4494 (mmp) cc_final: 0.4257 (mmp) REVERT: D 1053 MET cc_start: 0.6458 (mtp) cc_final: 0.5973 (tpp) REVERT: E 142 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8525 (tppp) REVERT: F 45 ASP cc_start: 0.8189 (m-30) cc_final: 0.7966 (m-30) REVERT: F 127 ARG cc_start: 0.6142 (ttm170) cc_final: 0.5580 (tpt170) REVERT: F 150 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7617 (mmmt) REVERT: F 183 HIS cc_start: 0.8206 (OUTLIER) cc_final: 0.7815 (m90) REVERT: G 158 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8710 (mt-10) REVERT: G 161 MET cc_start: 0.8999 (mmm) cc_final: 0.8499 (tmm) REVERT: G 188 ASP cc_start: 0.7959 (m-30) cc_final: 0.7541 (m-30) REVERT: G 230 LYS cc_start: 0.7657 (mttp) cc_final: 0.7126 (tmtt) REVERT: H 45 ASP cc_start: 0.8658 (m-30) cc_final: 0.8342 (m-30) REVERT: H 76 ASP cc_start: 0.8329 (t70) cc_final: 0.8090 (t0) REVERT: H 125 ASN cc_start: 0.6276 (m110) cc_final: 0.5942 (t0) REVERT: H 134 GLU cc_start: 0.8215 (tt0) cc_final: 0.7759 (tp30) REVERT: H 142 LYS cc_start: 0.8367 (mmtt) cc_final: 0.8152 (tptt) REVERT: H 230 LYS cc_start: 0.7478 (mttp) cc_final: 0.7169 (tmtt) outliers start: 121 outliers final: 31 residues processed: 363 average time/residue: 0.6714 time to fit residues: 299.0905 Evaluate side-chains 279 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 230 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 831 GLN Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 964 SER Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain C residue 798 ASP Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 1016 ARG Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 604 GLU Chi-restraints excluded: chain D residue 609 PHE Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 799 MET Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 995 CYS Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 183 HIS Chi-restraints excluded: chain H residue 98 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 25 optimal weight: 1.9990 chunk 384 optimal weight: 20.0000 chunk 426 optimal weight: 20.0000 chunk 219 optimal weight: 7.9990 chunk 308 optimal weight: 6.9990 chunk 397 optimal weight: 0.6980 chunk 272 optimal weight: 0.0470 chunk 303 optimal weight: 0.8980 chunk 391 optimal weight: 5.9990 chunk 320 optimal weight: 2.9990 chunk 359 optimal weight: 2.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 HIS A 887 ASN B 971 ASN B1008 ASN D 884 ASN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN H 125 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.104116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.075107 restraints weight = 82528.767| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.45 r_work: 0.3114 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 36838 Z= 0.110 Angle : 0.499 9.680 49976 Z= 0.258 Chirality : 0.040 0.200 5690 Planarity : 0.003 0.046 6143 Dihedral : 9.667 78.864 5974 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.04 % Allowed : 16.51 % Favored : 80.45 % 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 aren not related in a simple way. whole: 1.29 (0.13), residues: 4342 helix: 1.71 (0.11), residues: 2204 sheet: 0.00 (0.23), residues: 510 loop : 0.07 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 151 TYR 0.016 0.001 TYR F 166 PHE 0.013 0.001 PHE D 148 TRP 0.050 0.001 TRP E 4 HIS 0.004 0.001 HIS F 192 Details of bonding type rmsd covalent geometry : bond 0.00241 (36822) covalent geometry : angle 0.49901 (49944) SS BOND : bond 0.00218 ( 16) SS BOND : angle 0.99888 ( 32) hydrogen bonds : bond 0.04122 ( 1757) hydrogen bonds : angle 4.26197 ( 4947) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8684 Ramachandran restraints generated. 4342 Oldfield, 0 Emsley, 4342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8684 Ramachandran restraints generated. 4342 Oldfield, 0 Emsley, 4342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 254 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7938 (mmt) REVERT: A 370 ASP cc_start: 0.7268 (p0) cc_final: 0.7019 (p0) REVERT: A 520 GLU cc_start: 0.7381 (pt0) cc_final: 0.6693 (tp30) REVERT: A 565 MET cc_start: 0.8533 (mtm) cc_final: 0.8319 (mtp) REVERT: A 579 ILE cc_start: 0.4624 (OUTLIER) cc_final: 0.4404 (pp) REVERT: A 580 LEU cc_start: 0.6162 (OUTLIER) cc_final: 0.5865 (mm) REVERT: A 604 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6695 (mm-30) REVERT: A 609 PHE cc_start: 0.7726 (t80) cc_final: 0.7291 (t80) REVERT: B 50 TRP cc_start: 0.6930 (t-100) cc_final: 0.6454 (t-100) REVERT: B 94 MET cc_start: 0.8434 (mmt) cc_final: 0.8035 (mpp) REVERT: B 154 MET cc_start: 0.8909 (tpt) cc_final: 0.8628 (tpt) REVERT: B 182 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7871 (m110) REVERT: B 264 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8229 (mp0) REVERT: B 519 ILE cc_start: 0.4556 (OUTLIER) cc_final: 0.3355 (tp) REVERT: B 558 PHE cc_start: 0.7042 (t80) cc_final: 0.6598 (t80) REVERT: B 761 GLU cc_start: 0.8730 (mp0) cc_final: 0.8442 (tm-30) REVERT: B 913 THR cc_start: 0.9150 (m) cc_final: 0.8812 (p) REVERT: B 1039 TYR cc_start: 0.8023 (t80) cc_final: 0.7749 (t80) REVERT: C 330 LYS cc_start: 0.8104 (pptt) cc_final: 0.7604 (pptt) REVERT: C 477 TRP cc_start: 0.7801 (OUTLIER) cc_final: 0.7491 (p90) REVERT: C 519 ILE cc_start: 0.6695 (OUTLIER) cc_final: 0.6026 (pp) REVERT: C 578 ARG cc_start: 0.5043 (mmt-90) cc_final: 0.4620 (pmt-80) REVERT: C 604 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: C 610 PHE cc_start: 0.6771 (t80) cc_final: 0.6327 (t80) REVERT: C 798 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8255 (m-30) REVERT: C 1008 ASN cc_start: 0.7647 (m-40) cc_final: 0.7001 (p0) REVERT: D 519 ILE cc_start: 0.6672 (OUTLIER) cc_final: 0.5802 (tp) REVERT: D 751 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7047 (mp) REVERT: D 799 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8544 (mmm) REVERT: D 995 CYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7335 (t) REVERT: D 1002 LYS cc_start: 0.8442 (tmmt) cc_final: 0.8080 (ttpt) REVERT: D 1007 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.6641 (t80) REVERT: D 1009 MET cc_start: 0.4611 (mmp) cc_final: 0.4258 (mmp) REVERT: D 1053 MET cc_start: 0.6644 (mtp) cc_final: 0.6185 (tpp) REVERT: E 13 TYR cc_start: 0.6768 (OUTLIER) cc_final: 0.6398 (m-80) REVERT: F 45 ASP cc_start: 0.8339 (m-30) cc_final: 0.8129 (m-30) REVERT: F 102 CYS cc_start: 0.4450 (OUTLIER) cc_final: 0.4182 (p) REVERT: F 150 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7601 (mmmt) REVERT: F 183 HIS cc_start: 0.8230 (OUTLIER) cc_final: 0.7849 (m90) REVERT: G 134 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7662 (tt0) REVERT: G 158 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8710 (mt-10) REVERT: G 161 MET cc_start: 0.9000 (mmm) cc_final: 0.8536 (tmm) REVERT: G 187 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7062 (t70) REVERT: G 230 LYS cc_start: 0.7582 (mttp) cc_final: 0.7092 (tmtt) REVERT: H 45 ASP cc_start: 0.8662 (m-30) cc_final: 0.8315 (m-30) REVERT: H 76 ASP cc_start: 0.8416 (t70) cc_final: 0.8182 (t0) REVERT: H 125 ASN cc_start: 0.6325 (m-40) cc_final: 0.5972 (t0) REVERT: H 127 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.6664 (tmm-80) REVERT: H 134 GLU cc_start: 0.8281 (tt0) cc_final: 0.7846 (tp30) REVERT: H 150 LYS cc_start: 0.7219 (mmtm) cc_final: 0.6684 (mmtm) REVERT: H 155 LYS cc_start: 0.8766 (mtmm) cc_final: 0.8305 (mtmm) REVERT: H 230 LYS cc_start: 0.7345 (mttp) cc_final: 0.7045 (tmtt) outliers start: 118 outliers final: 39 residues processed: 351 average time/residue: 0.6341 time to fit residues: 273.2277 Evaluate side-chains 280 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 218 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 831 GLN Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 964 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 477 TRP Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 798 ASP Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1016 ARG Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 609 PHE Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 799 MET Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 995 CYS Chi-restraints excluded: chain D residue 1007 TYR Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 13 TYR Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 150 LYS Chi-restraints excluded: chain F residue 183 HIS Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 102 CYS Chi-restraints excluded: chain H residue 127 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 407 optimal weight: 0.0970 chunk 431 optimal weight: 8.9990 chunk 205 optimal weight: 10.0000 chunk 254 optimal weight: 10.0000 chunk 313 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 overall best weight: 2.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 ASN A 468 HIS A 884 ASN B 449 ASN B 971 ASN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN H 136 GLN H 162 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.102558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.073435 restraints weight = 82435.026| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.44 r_work: 0.3074 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 36838 Z= 0.151 Angle : 0.531 9.519 49976 Z= 0.274 Chirality : 0.041 0.189 5690 Planarity : 0.004 0.052 6143 Dihedral : 9.513 77.987 5974 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.27 % Allowed : 16.82 % Favored : 79.91 % 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 aren not related in a simple way. whole: 1.21 (0.13), residues: 4342 helix: 1.65 (0.11), residues: 2204 sheet: -0.06 (0.23), residues: 508 loop : 0.03 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 151 TYR 0.027 0.002 TYR E 166 PHE 0.029 0.002 PHE B 550 TRP 0.068 0.002 TRP E 4 HIS 0.006 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00347 (36822) covalent geometry : angle 0.53036 (49944) SS BOND : bond 0.00181 ( 16) SS BOND : angle 1.00492 ( 32) hydrogen bonds : bond 0.04634 ( 1757) hydrogen bonds : angle 4.32871 ( 4947) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8684 Ramachandran restraints generated. 4342 Oldfield, 0 Emsley, 4342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8684 Ramachandran restraints generated. 4342 Oldfield, 0 Emsley, 4342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 243 time to evaluate : 1.462 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7994 (mmt) REVERT: A 370 ASP cc_start: 0.7326 (p0) cc_final: 0.7069 (p0) REVERT: A 565 MET cc_start: 0.8559 (mtm) cc_final: 0.8329 (mtp) REVERT: A 579 ILE cc_start: 0.4687 (OUTLIER) cc_final: 0.4480 (pp) REVERT: A 580 LEU cc_start: 0.6157 (OUTLIER) cc_final: 0.5885 (mm) REVERT: A 604 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6720 (mm-30) REVERT: A 609 PHE cc_start: 0.7684 (t80) cc_final: 0.7228 (t80) REVERT: A 942 THR cc_start: 0.7707 (OUTLIER) cc_final: 0.7170 (p) REVERT: B 21 MET cc_start: 0.9060 (mmm) cc_final: 0.8687 (mmp) REVERT: B 50 TRP cc_start: 0.6848 (t-100) cc_final: 0.6393 (t-100) REVERT: B 154 MET cc_start: 0.8912 (tpt) cc_final: 0.8563 (tpt) REVERT: B 264 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8269 (mp0) REVERT: B 519 ILE cc_start: 0.4771 (OUTLIER) cc_final: 0.3578 (tp) REVERT: B 536 MET cc_start: 0.8610 (ttp) cc_final: 0.8400 (ttm) REVERT: B 558 PHE cc_start: 0.7024 (t80) cc_final: 0.6665 (t80) REVERT: B 761 GLU cc_start: 0.8734 (mp0) cc_final: 0.8501 (tm-30) REVERT: B 913 THR cc_start: 0.9232 (m) cc_final: 0.8917 (p) REVERT: B 1039 TYR cc_start: 0.8052 (t80) cc_final: 0.7825 (t80) REVERT: C 330 LYS cc_start: 0.8084 (pptt) cc_final: 0.7606 (pptt) REVERT: C 477 TRP cc_start: 0.7800 (OUTLIER) cc_final: 0.7361 (p90) REVERT: C 519 ILE cc_start: 0.6727 (OUTLIER) cc_final: 0.5981 (pp) REVERT: C 604 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6922 (mp0) REVERT: C 610 PHE cc_start: 0.6710 (t80) cc_final: 0.6266 (t80) REVERT: C 798 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8427 (m-30) REVERT: C 960 ARG cc_start: 0.7729 (mmt-90) cc_final: 0.7283 (mmm160) REVERT: D 519 ILE cc_start: 0.7027 (OUTLIER) cc_final: 0.6112 (tp) REVERT: D 587 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6241 (mm) REVERT: D 751 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7255 (mp) REVERT: D 942 THR cc_start: 0.7808 (OUTLIER) cc_final: 0.7402 (p) REVERT: D 995 CYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7459 (t) REVERT: D 1002 LYS cc_start: 0.8501 (tmmt) cc_final: 0.8148 (ttpt) REVERT: D 1007 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.6955 (t80) REVERT: D 1009 MET cc_start: 0.4721 (mmp) cc_final: 0.4421 (mmp) REVERT: D 1053 MET cc_start: 0.6953 (mtp) cc_final: 0.6457 (tpp) REVERT: E 13 TYR cc_start: 0.6816 (OUTLIER) cc_final: 0.6421 (m-80) REVERT: E 167 TRP cc_start: 0.8693 (OUTLIER) cc_final: 0.7978 (m-90) REVERT: F 168 LYS cc_start: 0.8429 (pmtt) cc_final: 0.8179 (pmtt) REVERT: F 183 HIS cc_start: 0.8218 (OUTLIER) cc_final: 0.7810 (m90) REVERT: G 134 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: G 158 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8705 (mt-10) REVERT: G 161 MET cc_start: 0.9000 (mmm) cc_final: 0.8542 (tmm) REVERT: G 187 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7046 (t70) REVERT: G 230 LYS cc_start: 0.7622 (mttp) cc_final: 0.7106 (tmtt) REVERT: H 45 ASP cc_start: 0.8701 (m-30) cc_final: 0.8441 (m-30) REVERT: H 76 ASP cc_start: 0.8453 (t70) cc_final: 0.8211 (t0) REVERT: H 97 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8119 (tp30) REVERT: H 125 ASN cc_start: 0.6369 (m-40) cc_final: 0.6013 (t0) REVERT: H 127 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.6687 (tmm-80) REVERT: H 134 GLU cc_start: 0.8312 (tt0) cc_final: 0.7885 (tp30) REVERT: H 150 LYS cc_start: 0.7313 (mmtm) cc_final: 0.7024 (mmtm) REVERT: H 230 LYS cc_start: 0.7321 (mttp) cc_final: 0.7025 (tmtt) outliers start: 127 outliers final: 52 residues processed: 345 average time/residue: 0.6497 time to fit residues: 276.2604 Evaluate side-chains 296 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 221 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 831 GLN Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 942 THR Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 964 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 477 TRP Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 798 ASP Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1016 ARG Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 609 PHE Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 755 VAL Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 942 THR Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 995 CYS Chi-restraints excluded: chain D residue 1007 TYR Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 13 TYR Chi-restraints excluded: chain E residue 167 TRP Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 183 HIS Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 102 CYS Chi-restraints excluded: chain H residue 127 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 380 optimal weight: 4.9990 chunk 332 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 252 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 275 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 206 optimal weight: 0.0970 chunk 396 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 HIS B 971 ASN D 451 HIS E 121 ASN E 125 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.103482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.074553 restraints weight = 82441.847| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.43 r_work: 0.3097 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 36838 Z= 0.116 Angle : 0.501 9.677 49976 Z= 0.257 Chirality : 0.040 0.171 5690 Planarity : 0.003 0.051 6143 Dihedral : 9.144 76.914 5974 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.35 % Allowed : 17.28 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.13), residues: 4342 helix: 1.74 (0.11), residues: 2204 sheet: -0.16 (0.23), residues: 510 loop : 0.01 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 151 TYR 0.021 0.001 TYR F 166 PHE 0.010 0.001 PHE C1012 TRP 0.033 0.001 TRP B 477 HIS 0.003 0.001 HIS C 468 Details of bonding type rmsd covalent geometry : bond 0.00259 (36822) covalent geometry : angle 0.49911 (49944) SS BOND : bond 0.00177 ( 16) SS BOND : angle 1.56059 ( 32) hydrogen bonds : bond 0.04117 ( 1757) hydrogen bonds : angle 4.22178 ( 4947) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8684 Ramachandran restraints generated. 4342 Oldfield, 0 Emsley, 4342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8684 Ramachandran restraints generated. 4342 Oldfield, 0 Emsley, 4342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 243 time to evaluate : 1.608 Fit side-chains revert: symmetry clash REVERT: A 370 ASP cc_start: 0.7343 (p0) cc_final: 0.7084 (p0) REVERT: A 565 MET cc_start: 0.8399 (mtm) cc_final: 0.8167 (mtp) REVERT: A 580 LEU cc_start: 0.6058 (OUTLIER) cc_final: 0.5777 (mm) REVERT: A 604 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6817 (mm-30) REVERT: A 609 PHE cc_start: 0.7730 (t80) cc_final: 0.7229 (t80) REVERT: A 942 THR cc_start: 0.7637 (OUTLIER) cc_final: 0.7102 (p) REVERT: B 21 MET cc_start: 0.9038 (mmm) cc_final: 0.8702 (mmp) REVERT: B 94 MET cc_start: 0.8384 (mpt) cc_final: 0.7851 (mpp) REVERT: B 154 MET cc_start: 0.8856 (tpt) cc_final: 0.8544 (tpt) REVERT: B 264 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8259 (mp0) REVERT: B 519 ILE cc_start: 0.4813 (OUTLIER) cc_final: 0.3716 (tp) REVERT: B 558 PHE cc_start: 0.6993 (t80) cc_final: 0.6452 (t80) REVERT: B 761 GLU cc_start: 0.8716 (mp0) cc_final: 0.8494 (tm-30) REVERT: B 913 THR cc_start: 0.9201 (m) cc_final: 0.8879 (p) REVERT: C 330 LYS cc_start: 0.8081 (pptt) cc_final: 0.7573 (pptt) REVERT: C 477 TRP cc_start: 0.7790 (OUTLIER) cc_final: 0.7356 (p90) REVERT: C 519 ILE cc_start: 0.6688 (OUTLIER) cc_final: 0.5958 (pp) REVERT: C 536 MET cc_start: 0.8554 (ttp) cc_final: 0.8342 (ttm) REVERT: C 604 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7071 (mt-10) REVERT: C 610 PHE cc_start: 0.6712 (t80) cc_final: 0.6246 (t80) REVERT: C 798 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8452 (m-30) REVERT: C 960 ARG cc_start: 0.7623 (mmt-90) cc_final: 0.7299 (mmm160) REVERT: D 519 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6176 (tp) REVERT: D 587 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6300 (mm) REVERT: D 751 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7190 (mp) REVERT: D 799 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8630 (mmm) REVERT: D 942 THR cc_start: 0.7824 (OUTLIER) cc_final: 0.7435 (p) REVERT: D 995 CYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7503 (t) REVERT: D 1002 LYS cc_start: 0.8500 (tmmt) cc_final: 0.8268 (tptp) REVERT: D 1007 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.7088 (t80) REVERT: D 1009 MET cc_start: 0.4789 (mmp) cc_final: 0.4525 (mmp) REVERT: D 1053 MET cc_start: 0.6998 (mtp) cc_final: 0.6572 (tpp) REVERT: E 13 TYR cc_start: 0.6824 (OUTLIER) cc_final: 0.6369 (m-80) REVERT: E 187 ASP cc_start: 0.7782 (p0) cc_final: 0.6722 (t0) REVERT: F 183 HIS cc_start: 0.8244 (OUTLIER) cc_final: 0.7841 (m90) REVERT: G 134 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: G 158 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8704 (mt-10) REVERT: G 161 MET cc_start: 0.9004 (mmm) cc_final: 0.8539 (tmm) REVERT: G 187 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.6974 (t70) REVERT: G 230 LYS cc_start: 0.7618 (mttp) cc_final: 0.7107 (tmtt) REVERT: H 45 ASP cc_start: 0.8709 (m-30) cc_final: 0.8434 (m-30) REVERT: H 127 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.6722 (tmm-80) REVERT: H 134 GLU cc_start: 0.8324 (tt0) cc_final: 0.7893 (tp30) REVERT: H 150 LYS cc_start: 0.7372 (mmtm) cc_final: 0.6844 (mmtm) REVERT: H 155 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8660 (mtmm) REVERT: H 230 LYS cc_start: 0.7307 (mttp) cc_final: 0.7001 (tmtt) outliers start: 130 outliers final: 52 residues processed: 348 average time/residue: 0.6201 time to fit residues: 268.0230 Evaluate side-chains 290 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 216 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 831 GLN Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 942 THR Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1015 TYR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 964 SER Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 477 TRP Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 604 GLU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 798 ASP Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1016 ARG Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 609 PHE Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 799 MET Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 942 THR Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 995 CYS Chi-restraints excluded: chain D residue 1007 TYR Chi-restraints excluded: chain D residue 1010 LEU Chi-restraints excluded: chain D residue 1015 TYR Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 13 TYR Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 183 HIS Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 102 CYS Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain H residue 155 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 248 optimal weight: 7.9990 chunk 316 optimal weight: 8.9990 chunk 436 optimal weight: 5.9990 chunk 166 optimal weight: 9.9990 chunk 335 optimal weight: 30.0000 chunk 131 optimal weight: 10.0000 chunk 239 optimal weight: 2.9990 chunk 41 optimal weight: 0.0270 chunk 252 optimal weight: 6.9990 chunk 277 optimal weight: 2.9990 chunk 330 optimal weight: 6.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 HIS B 971 ASN C 468 HIS C 534 ASN D 747 HIS ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.101369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.072350 restraints weight = 83032.306| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.42 r_work: 0.3048 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 36838 Z= 0.202 Angle : 0.582 10.580 49976 Z= 0.298 Chirality : 0.043 0.176 5690 Planarity : 0.004 0.055 6143 Dihedral : 9.534 78.440 5974 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.53 % Allowed : 17.59 % Favored : 78.88 % 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 aren not related in a simple way. whole: 1.04 (0.13), residues: 4342 helix: 1.59 (0.11), residues: 2180 sheet: -0.28 (0.22), residues: 510 loop : -0.11 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 151 TYR 0.019 0.002 TYR A 928 PHE 0.034 0.002 PHE B 550 TRP 0.034 0.002 TRP B 477 HIS 0.007 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00476 (36822) covalent geometry : angle 0.57989 (49944) SS BOND : bond 0.00196 ( 16) SS BOND : angle 1.95240 ( 32) hydrogen bonds : bond 0.05001 ( 1757) hydrogen bonds : angle 4.42025 ( 4947) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8684 Ramachandran restraints generated. 4342 Oldfield, 0 Emsley, 4342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8684 Ramachandran restraints generated. 4342 Oldfield, 0 Emsley, 4342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 228 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 ASP cc_start: 0.7382 (p0) cc_final: 0.7164 (p0) REVERT: A 556 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8139 (mp) REVERT: A 565 MET cc_start: 0.8554 (mtm) cc_final: 0.8270 (mtp) REVERT: A 579 ILE cc_start: 0.4776 (OUTLIER) cc_final: 0.4565 (pp) REVERT: A 580 LEU cc_start: 0.6018 (OUTLIER) cc_final: 0.5769 (mm) REVERT: A 604 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6738 (mm-30) REVERT: A 609 PHE cc_start: 0.7697 (t80) cc_final: 0.7187 (t80) REVERT: A 942 THR cc_start: 0.7772 (OUTLIER) cc_final: 0.7316 (t) REVERT: B 21 MET cc_start: 0.9036 (mmm) cc_final: 0.8688 (mmp) REVERT: B 94 MET cc_start: 0.8434 (mpt) cc_final: 0.8015 (mpp) REVERT: B 154 MET cc_start: 0.8943 (tpt) cc_final: 0.8594 (tpt) REVERT: B 264 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8284 (mp0) REVERT: B 519 ILE cc_start: 0.5212 (OUTLIER) cc_final: 0.3997 (tp) REVERT: B 558 PHE cc_start: 0.7021 (t80) cc_final: 0.6425 (t80) REVERT: B 761 GLU cc_start: 0.8754 (mp0) cc_final: 0.8553 (tm-30) REVERT: B 1010 LEU cc_start: 0.6356 (OUTLIER) cc_final: 0.6118 (pt) REVERT: C 330 LYS cc_start: 0.8111 (pptt) cc_final: 0.7582 (pptt) REVERT: C 477 TRP cc_start: 0.7867 (OUTLIER) cc_final: 0.7295 (p90) REVERT: C 519 ILE cc_start: 0.6696 (OUTLIER) cc_final: 0.5927 (pp) REVERT: C 610 PHE cc_start: 0.6543 (t80) cc_final: 0.6182 (t80) REVERT: D 558 PHE cc_start: 0.7100 (t80) cc_final: 0.6649 (t80) REVERT: D 587 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6342 (mm) REVERT: D 751 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7187 (mp) REVERT: D 799 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8690 (mmm) REVERT: D 942 THR cc_start: 0.7808 (OUTLIER) cc_final: 0.7451 (p) REVERT: D 995 CYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7566 (t) REVERT: D 1007 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.7268 (t80) REVERT: D 1053 MET cc_start: 0.7137 (mtp) cc_final: 0.6718 (mtp) REVERT: E 13 TYR cc_start: 0.6900 (OUTLIER) cc_final: 0.6418 (m-80) REVERT: F 183 HIS cc_start: 0.8226 (OUTLIER) cc_final: 0.7833 (m90) REVERT: G 134 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7853 (tt0) REVERT: G 151 ARG cc_start: 0.6675 (mmm160) cc_final: 0.6184 (tpt-90) REVERT: G 158 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8674 (mt-10) REVERT: G 161 MET cc_start: 0.8992 (mmm) cc_final: 0.8580 (tmm) REVERT: G 187 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.6928 (t70) REVERT: G 230 LYS cc_start: 0.7659 (mttp) cc_final: 0.7099 (tmtt) REVERT: H 45 ASP cc_start: 0.8754 (m-30) cc_final: 0.8519 (m-30) REVERT: H 127 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6682 (tmm-80) REVERT: H 134 GLU cc_start: 0.8386 (tt0) cc_final: 0.7952 (tp30) REVERT: H 150 LYS cc_start: 0.7442 (mmtm) cc_final: 0.6891 (mmtm) REVERT: H 155 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8616 (mtmm) REVERT: H 230 LYS cc_start: 0.7414 (mttp) cc_final: 0.7091 (tmtt) outliers start: 137 outliers final: 69 residues processed: 335 average time/residue: 0.5359 time to fit residues: 224.4527 Evaluate side-chains 308 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 217 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 942 THR Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1015 TYR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 818 LYS Chi-restraints excluded: chain B residue 964 SER Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 477 TRP Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 905 LEU Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1016 ARG Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 609 PHE Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 799 MET Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 942 THR Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 995 CYS Chi-restraints excluded: chain D residue 1007 TYR Chi-restraints excluded: chain D residue 1010 LEU Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 13 TYR Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain F residue 183 HIS Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 102 CYS Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain H residue 155 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 35 optimal weight: 0.9990 chunk 322 optimal weight: 0.0470 chunk 80 optimal weight: 0.0010 chunk 115 optimal weight: 0.8980 chunk 356 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 338 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.9888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 468 HIS B 971 ASN C 468 HIS C1036 ASN D 465 ASN D 468 HIS E 121 ASN F 125 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.103613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.074884 restraints weight = 82192.775| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.41 r_work: 0.3106 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 36838 Z= 0.104 Angle : 0.509 11.890 49976 Z= 0.258 Chirality : 0.040 0.170 5690 Planarity : 0.003 0.054 6143 Dihedral : 8.993 77.796 5974 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.52 % Allowed : 18.70 % Favored : 78.78 % 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 aren not related in a simple way. whole: 1.24 (0.13), residues: 4342 helix: 1.82 (0.11), residues: 2176 sheet: -0.49 (0.22), residues: 534 loop : 0.03 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 151 TYR 0.012 0.001 TYR E 166 PHE 0.012 0.001 PHE A1000 TRP 0.041 0.001 TRP E 4 HIS 0.005 0.001 HIS C 468 Details of bonding type rmsd covalent geometry : bond 0.00222 (36822) covalent geometry : angle 0.50781 (49944) SS BOND : bond 0.00102 ( 16) SS BOND : angle 1.27005 ( 32) hydrogen bonds : bond 0.03943 ( 1757) hydrogen bonds : angle 4.20921 ( 4947) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8684 Ramachandran restraints generated. 4342 Oldfield, 0 Emsley, 4342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8684 Ramachandran restraints generated. 4342 Oldfield, 0 Emsley, 4342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 239 time to evaluate : 1.393 Fit side-chains revert: symmetry clash REVERT: A 370 ASP cc_start: 0.7329 (p0) cc_final: 0.7094 (p0) REVERT: A 556 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8173 (mp) REVERT: A 565 MET cc_start: 0.8471 (mtm) cc_final: 0.8193 (mtp) REVERT: A 580 LEU cc_start: 0.5961 (OUTLIER) cc_final: 0.5748 (mm) REVERT: A 604 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6836 (mm-30) REVERT: A 609 PHE cc_start: 0.7768 (t80) cc_final: 0.7227 (t80) REVERT: A 942 THR cc_start: 0.7634 (OUTLIER) cc_final: 0.7104 (p) REVERT: B 21 MET cc_start: 0.9044 (mmm) cc_final: 0.8635 (mmp) REVERT: B 94 MET cc_start: 0.8388 (mpt) cc_final: 0.7960 (mpp) REVERT: B 154 MET cc_start: 0.8866 (tpt) cc_final: 0.8549 (tpt) REVERT: B 264 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8248 (mp0) REVERT: B 519 ILE cc_start: 0.4986 (OUTLIER) cc_final: 0.3945 (tp) REVERT: B 558 PHE cc_start: 0.7007 (t80) cc_final: 0.6471 (t80) REVERT: B 761 GLU cc_start: 0.8736 (mp0) cc_final: 0.8486 (tm-30) REVERT: B 913 THR cc_start: 0.9186 (m) cc_final: 0.8866 (p) REVERT: C 330 LYS cc_start: 0.8090 (pptt) cc_final: 0.7592 (pptt) REVERT: C 477 TRP cc_start: 0.7805 (OUTLIER) cc_final: 0.7307 (p90) REVERT: C 519 ILE cc_start: 0.6704 (OUTLIER) cc_final: 0.5997 (pp) REVERT: C 536 MET cc_start: 0.8486 (ttp) cc_final: 0.8278 (ttm) REVERT: C 610 PHE cc_start: 0.6441 (t80) cc_final: 0.6061 (t80) REVERT: C 1053 MET cc_start: 0.6934 (mmm) cc_final: 0.6262 (mpp) REVERT: D 558 PHE cc_start: 0.7042 (t80) cc_final: 0.6604 (t80) REVERT: D 587 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6273 (mm) REVERT: D 799 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8630 (mmm) REVERT: D 942 THR cc_start: 0.7773 (OUTLIER) cc_final: 0.7401 (p) REVERT: D 995 CYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7475 (t) REVERT: D 1007 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.7190 (t80) REVERT: D 1053 MET cc_start: 0.7029 (mtp) cc_final: 0.6635 (mtp) REVERT: E 13 TYR cc_start: 0.6971 (OUTLIER) cc_final: 0.6440 (m-80) REVERT: E 187 ASP cc_start: 0.7739 (p0) cc_final: 0.6722 (t0) REVERT: G 134 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7893 (tt0) REVERT: G 146 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8131 (mp) REVERT: G 158 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8672 (mt-10) REVERT: G 161 MET cc_start: 0.9016 (mmm) cc_final: 0.8567 (tmm) REVERT: G 187 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.6992 (t70) REVERT: G 230 LYS cc_start: 0.7588 (mttp) cc_final: 0.7094 (tmtt) REVERT: H 45 ASP cc_start: 0.8689 (m-30) cc_final: 0.8407 (m-30) REVERT: H 134 GLU cc_start: 0.8346 (tt0) cc_final: 0.7923 (tp30) REVERT: H 150 LYS cc_start: 0.7474 (mmtm) cc_final: 0.7083 (mppt) REVERT: H 155 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8801 (ptmt) REVERT: H 230 LYS cc_start: 0.7458 (mttp) cc_final: 0.7137 (tmtt) outliers start: 98 outliers final: 40 residues processed: 317 average time/residue: 0.6141 time to fit residues: 241.7306 Evaluate side-chains 277 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 219 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 799 MET Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 942 THR Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1015 TYR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 964 SER Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 477 TRP Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 1016 ARG Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 799 MET Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 942 THR Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 995 CYS Chi-restraints excluded: chain D residue 1007 TYR Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 13 TYR Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 102 CYS Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 155 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 307 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 282 optimal weight: 1.9990 chunk 406 optimal weight: 0.0980 chunk 88 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 256 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 285 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 468 HIS B 971 ASN C 468 HIS D 468 HIS D 585 ASN H 195 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.102093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.073201 restraints weight = 82544.550| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.42 r_work: 0.3069 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 36838 Z= 0.155 Angle : 0.560 12.124 49976 Z= 0.284 Chirality : 0.041 0.212 5690 Planarity : 0.004 0.072 6143 Dihedral : 9.134 78.693 5974 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.81 % Allowed : 18.59 % Favored : 78.60 % 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 aren not related in a simple way. whole: 1.15 (0.13), residues: 4342 helix: 1.74 (0.11), residues: 2176 sheet: -0.36 (0.22), residues: 518 loop : -0.08 (0.16), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG G 151 TYR 0.026 0.001 TYR G 166 PHE 0.041 0.001 PHE B 550 TRP 0.041 0.002 TRP D 477 HIS 0.006 0.001 HIS C 468 Details of bonding type rmsd covalent geometry : bond 0.00362 (36822) covalent geometry : angle 0.55756 (49944) SS BOND : bond 0.00178 ( 16) SS BOND : angle 2.18768 ( 32) hydrogen bonds : bond 0.04532 ( 1757) hydrogen bonds : angle 4.31335 ( 4947) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8684 Ramachandran restraints generated. 4342 Oldfield, 0 Emsley, 4342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8684 Ramachandran restraints generated. 4342 Oldfield, 0 Emsley, 4342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 226 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 ASP cc_start: 0.7314 (p0) cc_final: 0.7085 (p0) REVERT: A 556 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8180 (mp) REVERT: A 565 MET cc_start: 0.8522 (mtm) cc_final: 0.8219 (mtp) REVERT: A 580 LEU cc_start: 0.5894 (OUTLIER) cc_final: 0.5688 (mm) REVERT: A 604 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6830 (mm-30) REVERT: A 609 PHE cc_start: 0.7740 (t80) cc_final: 0.7187 (t80) REVERT: A 942 THR cc_start: 0.7726 (OUTLIER) cc_final: 0.7194 (p) REVERT: B 94 MET cc_start: 0.8421 (mpt) cc_final: 0.7992 (mpp) REVERT: B 154 MET cc_start: 0.8915 (tpt) cc_final: 0.8593 (tpt) REVERT: B 264 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8265 (mp0) REVERT: B 519 ILE cc_start: 0.5239 (OUTLIER) cc_final: 0.3916 (tp) REVERT: B 558 PHE cc_start: 0.6973 (t80) cc_final: 0.6401 (t80) REVERT: B 761 GLU cc_start: 0.8744 (mp0) cc_final: 0.8542 (tm-30) REVERT: B 1010 LEU cc_start: 0.5992 (OUTLIER) cc_final: 0.5771 (pt) REVERT: C 330 LYS cc_start: 0.8065 (pptt) cc_final: 0.7578 (pptt) REVERT: C 477 TRP cc_start: 0.7834 (OUTLIER) cc_final: 0.7270 (p90) REVERT: C 519 ILE cc_start: 0.6727 (OUTLIER) cc_final: 0.5994 (pp) REVERT: C 536 MET cc_start: 0.8563 (ttp) cc_final: 0.8340 (ttm) REVERT: C 610 PHE cc_start: 0.6433 (t80) cc_final: 0.6034 (t80) REVERT: D 558 PHE cc_start: 0.7015 (t80) cc_final: 0.6559 (t80) REVERT: D 587 LEU cc_start: 0.6734 (OUTLIER) cc_final: 0.6316 (mm) REVERT: D 799 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8654 (mmm) REVERT: D 942 THR cc_start: 0.7822 (OUTLIER) cc_final: 0.7437 (p) REVERT: D 995 CYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7525 (t) REVERT: D 1007 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7415 (t80) REVERT: D 1009 MET cc_start: 0.4691 (mmp) cc_final: 0.2886 (mtt) REVERT: D 1053 MET cc_start: 0.7059 (mtp) cc_final: 0.6699 (mtp) REVERT: E 4 TRP cc_start: 0.5283 (OUTLIER) cc_final: 0.4696 (t60) REVERT: G 134 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: G 151 ARG cc_start: 0.6597 (mmm160) cc_final: 0.6086 (tpt-90) REVERT: G 158 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8679 (mt-10) REVERT: G 161 MET cc_start: 0.9027 (mmm) cc_final: 0.8619 (tmm) REVERT: G 187 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.6962 (t70) REVERT: G 230 LYS cc_start: 0.7596 (mttp) cc_final: 0.7074 (tmtt) REVERT: H 45 ASP cc_start: 0.8738 (m-30) cc_final: 0.8476 (m-30) REVERT: H 134 GLU cc_start: 0.8411 (tt0) cc_final: 0.7977 (tp30) REVERT: H 155 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8815 (ptmt) REVERT: H 230 LYS cc_start: 0.7473 (mttp) cc_final: 0.7127 (tmtt) outliers start: 109 outliers final: 60 residues processed: 311 average time/residue: 0.5251 time to fit residues: 205.4513 Evaluate side-chains 297 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 219 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 942 THR Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1015 TYR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 818 LYS Chi-restraints excluded: chain B residue 964 SER Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 477 TRP Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 1016 ARG Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 585 ASN Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 609 PHE Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 799 MET Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 942 THR Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 995 CYS Chi-restraints excluded: chain D residue 1007 TYR Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain E residue 4 TRP Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 102 CYS Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 195 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 156 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 376 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 320 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 350 optimal weight: 20.0000 chunk 169 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 468 HIS B 971 ASN C 468 HIS D 468 HIS D 585 ASN H 195 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.101581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.072642 restraints weight = 82503.991| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.42 r_work: 0.3057 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 36838 Z= 0.177 Angle : 0.580 14.475 49976 Z= 0.294 Chirality : 0.042 0.206 5690 Planarity : 0.004 0.058 6143 Dihedral : 9.306 79.782 5974 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.47 % Allowed : 19.03 % Favored : 78.50 % 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 aren not related in a simple way. whole: 1.03 (0.13), residues: 4342 helix: 1.60 (0.11), residues: 2200 sheet: -0.36 (0.22), residues: 510 loop : -0.13 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG G 151 TYR 0.022 0.002 TYR G 166 PHE 0.021 0.002 PHE D 148 TRP 0.044 0.002 TRP D 477 HIS 0.008 0.001 HIS C 468 Details of bonding type rmsd covalent geometry : bond 0.00415 (36822) covalent geometry : angle 0.57821 (49944) SS BOND : bond 0.00243 ( 16) SS BOND : angle 1.94344 ( 32) hydrogen bonds : bond 0.04748 ( 1757) hydrogen bonds : angle 4.36342 ( 4947) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8684 Ramachandran restraints generated. 4342 Oldfield, 0 Emsley, 4342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8684 Ramachandran restraints generated. 4342 Oldfield, 0 Emsley, 4342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 224 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 ASP cc_start: 0.7311 (p0) cc_final: 0.7086 (p0) REVERT: A 556 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8193 (mp) REVERT: A 565 MET cc_start: 0.8570 (mtm) cc_final: 0.8280 (mtp) REVERT: A 604 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6827 (mm-30) REVERT: A 942 THR cc_start: 0.7717 (OUTLIER) cc_final: 0.7189 (p) REVERT: B 21 MET cc_start: 0.9065 (mmm) cc_final: 0.8653 (mmp) REVERT: B 94 MET cc_start: 0.8451 (mpt) cc_final: 0.8031 (mpp) REVERT: B 154 MET cc_start: 0.8935 (tpt) cc_final: 0.8599 (tpt) REVERT: B 264 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8288 (mp0) REVERT: B 519 ILE cc_start: 0.5280 (OUTLIER) cc_final: 0.3908 (tp) REVERT: B 558 PHE cc_start: 0.6981 (t80) cc_final: 0.6346 (t80) REVERT: B 761 GLU cc_start: 0.8756 (mp0) cc_final: 0.8550 (tm-30) REVERT: C 330 LYS cc_start: 0.8078 (pptt) cc_final: 0.7587 (pptt) REVERT: C 477 TRP cc_start: 0.7858 (OUTLIER) cc_final: 0.7301 (p90) REVERT: C 519 ILE cc_start: 0.6738 (OUTLIER) cc_final: 0.6007 (pp) REVERT: C 610 PHE cc_start: 0.6423 (t80) cc_final: 0.6025 (t80) REVERT: C 1053 MET cc_start: 0.6856 (mmm) cc_final: 0.6052 (mpp) REVERT: D 558 PHE cc_start: 0.6992 (t80) cc_final: 0.6511 (t80) REVERT: D 587 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6362 (mm) REVERT: D 799 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8673 (mmm) REVERT: D 942 THR cc_start: 0.7854 (OUTLIER) cc_final: 0.7483 (p) REVERT: D 995 CYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7547 (t) REVERT: D 1007 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7518 (t80) REVERT: D 1009 MET cc_start: 0.4647 (mmp) cc_final: 0.2886 (mtt) REVERT: D 1053 MET cc_start: 0.7067 (mtp) cc_final: 0.6679 (mtp) REVERT: G 76 ASP cc_start: 0.8243 (t70) cc_final: 0.8019 (t0) REVERT: G 134 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7933 (tt0) REVERT: G 150 LYS cc_start: 0.7866 (ttmt) cc_final: 0.7414 (ttpt) REVERT: G 151 ARG cc_start: 0.6609 (mmm160) cc_final: 0.6056 (tpt-90) REVERT: G 158 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8652 (mt-10) REVERT: G 161 MET cc_start: 0.9053 (mmm) cc_final: 0.8620 (tmm) REVERT: G 187 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.6948 (t70) REVERT: G 230 LYS cc_start: 0.7609 (mttp) cc_final: 0.7069 (tmtt) REVERT: H 45 ASP cc_start: 0.8751 (m-30) cc_final: 0.8433 (m-30) REVERT: H 134 GLU cc_start: 0.8415 (tt0) cc_final: 0.7965 (tp30) REVERT: H 150 LYS cc_start: 0.7514 (mmtm) cc_final: 0.7158 (mppt) REVERT: H 155 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8674 (ptpp) REVERT: H 196 ASP cc_start: 0.6825 (t0) cc_final: 0.6612 (t0) REVERT: H 230 LYS cc_start: 0.7551 (mttp) cc_final: 0.7155 (tmtt) outliers start: 96 outliers final: 64 residues processed: 299 average time/residue: 0.6196 time to fit residues: 230.4459 Evaluate side-chains 298 residues out of total 3883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 219 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 728 SER Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 942 THR Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1015 TYR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 818 LYS Chi-restraints excluded: chain B residue 964 SER Chi-restraints excluded: chain B residue 1015 TYR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 477 TRP Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 755 VAL Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 905 LEU Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 995 CYS Chi-restraints excluded: chain C residue 1016 ARG Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 609 PHE Chi-restraints excluded: chain D residue 728 SER Chi-restraints excluded: chain D residue 799 MET Chi-restraints excluded: chain D residue 830 MET Chi-restraints excluded: chain D residue 874 VAL Chi-restraints excluded: chain D residue 942 THR Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 995 CYS Chi-restraints excluded: chain D residue 1007 TYR Chi-restraints excluded: chain E residue 2 PHE Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 102 CYS Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 102 CYS Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 195 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 133 optimal weight: 0.9990 chunk 344 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 202 optimal weight: 0.7980 chunk 345 optimal weight: 9.9990 chunk 293 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 159 optimal weight: 0.6980 chunk 424 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 468 HIS B 971 ASN C 468 HIS D 468 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.102853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.074133 restraints weight = 82207.749| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.41 r_work: 0.3086 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36838 Z= 0.118 Angle : 0.541 14.030 49976 Z= 0.273 Chirality : 0.040 0.200 5690 Planarity : 0.004 0.058 6143 Dihedral : 9.051 79.526 5974 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.27 % Allowed : 19.31 % Favored : 78.42 % 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 aren not related in a simple way. whole: 1.16 (0.13), residues: 4342 helix: 1.72 (0.11), residues: 2198 sheet: -0.35 (0.22), residues: 518 loop : -0.07 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG G 151 TYR 0.022 0.001 TYR G 166 PHE 0.041 0.001 PHE B 550 TRP 0.089 0.001 TRP E 4 HIS 0.016 0.001 HIS H 195 Details of bonding type rmsd covalent geometry : bond 0.00264 (36822) covalent geometry : angle 0.53926 (49944) SS BOND : bond 0.00206 ( 16) SS BOND : angle 1.58636 ( 32) hydrogen bonds : bond 0.04182 ( 1757) hydrogen bonds : angle 4.25837 ( 4947) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14196.30 seconds wall clock time: 242 minutes 21.45 seconds (14541.45 seconds total)