Starting phenix.real_space_refine on Sun Aug 24 11:38:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ayf_43990/08_2025/9ayf_43990.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ayf_43990/08_2025/9ayf_43990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ayf_43990/08_2025/9ayf_43990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ayf_43990/08_2025/9ayf_43990.map" model { file = "/net/cci-nas-00/data/ceres_data/9ayf_43990/08_2025/9ayf_43990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ayf_43990/08_2025/9ayf_43990.cif" } resolution = 3.6 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= 0.002 sd= 0.040 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: 7 Type Number sf(0) Gaussians Ca 8 9.91 5 P 2 5.49 5 S 118 5.16 5 Cl 2 4.86 5 C 12592 2.51 5 N 3218 2.21 5 O 3690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 19630 Number of models: 1 Model: "" Number of chains: 14 Chain: "Q" Number of atoms: 6202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6202 Classifications: {'peptide': 780} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 748} Chain breaks: 3 Chain: "R" Number of atoms: 6499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6499 Classifications: {'peptide': 816} Link IDs: {'CIS': 1, 'PTRANS': 32, 'TRANS': 782} Chain breaks: 2 Chain: "H" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1733 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 212} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 447 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'NAG': 3, 'TCR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Unusual residues: {' CA': 4, '9IG': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "R" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'NAG': 3, 'TCR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 99 Unusual residues: {' CA': 4, '9IG': 1, 'AV0': 1, 'PO4': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 5.26, per 1000 atoms: 0.27 Number of scatterers: 19630 At special positions: 0 Unit cell: (118.16, 132.508, 248.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 8 19.99 Cl 2 17.00 S 118 16.00 P 2 15.00 O 3690 8.00 N 3218 7.00 C 12592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS Q 60 " - pdb=" SG CYS Q 101 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 236 " - pdb=" SG CYS Q 561 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 358 " - pdb=" SG CYS Q 395 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 437 " - pdb=" SG CYS Q 449 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 542 " - pdb=" SG CYS Q 562 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 546 " - pdb=" SG CYS Q 565 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 677 " - pdb=" SG CYS Q 765 " distance=2.03 Simple disulfide: pdb=" SG CYS R 60 " - pdb=" SG CYS R 101 " distance=2.03 Simple disulfide: pdb=" SG CYS R 236 " - pdb=" SG CYS R 561 " distance=2.03 Simple disulfide: pdb=" SG CYS R 358 " - pdb=" SG CYS R 395 " distance=2.03 Simple disulfide: pdb=" SG CYS R 437 " - pdb=" SG CYS R 449 " distance=2.03 Simple disulfide: pdb=" SG CYS R 542 " - pdb=" SG CYS R 562 " distance=2.03 Simple disulfide: pdb=" SG CYS R 546 " - pdb=" SG CYS R 565 " distance=2.03 Simple disulfide: pdb=" SG CYS R 568 " - pdb=" SG CYS R 582 " distance=2.03 Simple disulfide: pdb=" SG CYS R 585 " - pdb=" SG CYS R 598 " distance=2.03 Simple disulfide: pdb=" SG CYS R 677 " - pdb=" SG CYS R 765 " distance=2.03 Simple disulfide: pdb=" SG CYS H 42 " - pdb=" SG CYS H 116 " distance=2.03 Simple disulfide: pdb=" SG CYS H 179 " - pdb=" SG CYS H 249 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN Q 488 " " NAG D 1 " - " ASN Q 541 " " NAG E 1 " - " ASN R 488 " " NAG F 1 " - " ASN R 541 " " NAG Q1001 " - " ASN Q 261 " " NAG Q1002 " - " ASN Q 287 " " NAG Q1003 " - " ASN Q 468 " " NAG R1001 " - " ASN R 261 " " NAG R1002 " - " ASN R 287 " " NAG R1003 " - " ASN R 468 " Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 922.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 26 sheets defined 41.1% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'Q' and resid 64 through 84 removed outlier: 3.664A pdb=" N PHE Q 68 " --> pdb=" O ASN Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 115 removed outlier: 3.547A pdb=" N ALA Q 107 " --> pdb=" O THR Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 124 Processing helix chain 'Q' and resid 146 through 159 Processing helix chain 'Q' and resid 171 through 176 removed outlier: 3.738A pdb=" N ASN Q 176 " --> pdb=" O LEU Q 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 190 through 204 Processing helix chain 'Q' and resid 218 through 233 removed outlier: 3.858A pdb=" N GLY Q 222 " --> pdb=" O TYR Q 218 " (cutoff:3.500A) Processing helix chain 'Q' and resid 248 through 261 Processing helix chain 'Q' and resid 272 through 287 Proline residue: Q 278 - end of helix Processing helix chain 'Q' and resid 307 through 309 No H-bonds generated for 'chain 'Q' and resid 307 through 309' Processing helix chain 'Q' and resid 310 through 315 Processing helix chain 'Q' and resid 329 through 336 Processing helix chain 'Q' and resid 347 through 357 Processing helix chain 'Q' and resid 416 through 436 Processing helix chain 'Q' and resid 444 through 448 Processing helix chain 'Q' and resid 456 through 466 removed outlier: 3.500A pdb=" N VAL Q 460 " --> pdb=" O GLU Q 456 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS Q 466 " --> pdb=" O LYS Q 462 " (cutoff:3.500A) Processing helix chain 'Q' and resid 525 through 528 Processing helix chain 'Q' and resid 529 through 533 Processing helix chain 'Q' and resid 610 through 637 Processing helix chain 'Q' and resid 640 through 646 Processing helix chain 'Q' and resid 647 through 664 Processing helix chain 'Q' and resid 665 through 669 removed outlier: 3.717A pdb=" N PHE Q 668 " --> pdb=" O SER Q 665 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE Q 669 " --> pdb=" O LEU Q 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 665 through 669' Processing helix chain 'Q' and resid 673 through 698 removed outlier: 5.128A pdb=" N GLN Q 681 " --> pdb=" O CYS Q 677 " (cutoff:3.500A) Proline residue: Q 682 - end of helix Processing helix chain 'Q' and resid 723 through 746 removed outlier: 3.769A pdb=" N LEU Q 730 " --> pdb=" O LEU Q 726 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N CYS Q 731 " --> pdb=" O LEU Q 727 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR Q 732 " --> pdb=" O VAL Q 728 " (cutoff:3.500A) Processing helix chain 'Q' and resid 769 through 794 removed outlier: 3.618A pdb=" N LEU Q 773 " --> pdb=" O SER Q 769 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER Q 794 " --> pdb=" O PHE Q 790 " (cutoff:3.500A) Processing helix chain 'Q' and resid 798 through 828 removed outlier: 3.730A pdb=" N GLU Q 803 " --> pdb=" O GLU Q 799 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA Q 804 " --> pdb=" O ASN Q 800 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS Q 805 " --> pdb=" O PHE Q 801 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE Q 806 " --> pdb=" O ASN Q 802 " (cutoff:3.500A) Proline residue: Q 823 - end of helix Processing helix chain 'Q' and resid 832 through 854 removed outlier: 3.664A pdb=" N GLU Q 837 " --> pdb=" O VAL Q 833 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU Q 842 " --> pdb=" O VAL Q 838 " (cutoff:3.500A) Processing helix chain 'Q' and resid 854 through 861 Processing helix chain 'R' and resid 64 through 83 removed outlier: 3.508A pdb=" N PHE R 68 " --> pdb=" O ASN R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 115 removed outlier: 3.651A pdb=" N ALA R 107 " --> pdb=" O THR R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 124 Processing helix chain 'R' and resid 146 through 159 removed outlier: 3.746A pdb=" N LEU R 156 " --> pdb=" O ALA R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 176 removed outlier: 3.561A pdb=" N ASN R 176 " --> pdb=" O LEU R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 204 Processing helix chain 'R' and resid 218 through 233 removed outlier: 4.048A pdb=" N GLY R 222 " --> pdb=" O TYR R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 262 removed outlier: 3.557A pdb=" N ILE R 252 " --> pdb=" O ASP R 248 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER R 262 " --> pdb=" O VAL R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 287 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 307 through 309 No H-bonds generated for 'chain 'R' and resid 307 through 309' Processing helix chain 'R' and resid 310 through 315 Processing helix chain 'R' and resid 329 through 336 removed outlier: 3.535A pdb=" N PHE R 333 " --> pdb=" O GLY R 329 " (cutoff:3.500A) Processing helix chain 'R' and resid 347 through 357 Processing helix chain 'R' and resid 415 through 436 removed outlier: 3.600A pdb=" N ASN R 419 " --> pdb=" O ARG R 415 " (cutoff:3.500A) Processing helix chain 'R' and resid 444 through 448 Processing helix chain 'R' and resid 456 through 466 removed outlier: 3.516A pdb=" N HIS R 466 " --> pdb=" O LYS R 462 " (cutoff:3.500A) Processing helix chain 'R' and resid 525 through 528 Processing helix chain 'R' and resid 610 through 637 Processing helix chain 'R' and resid 640 through 646 removed outlier: 3.584A pdb=" N THR R 646 " --> pdb=" O ILE R 642 " (cutoff:3.500A) Processing helix chain 'R' and resid 647 through 665 removed outlier: 3.773A pdb=" N SER R 665 " --> pdb=" O CYS R 661 " (cutoff:3.500A) Processing helix chain 'R' and resid 666 through 669 Processing helix chain 'R' and resid 673 through 708 removed outlier: 4.764A pdb=" N GLN R 681 " --> pdb=" O CYS R 677 " (cutoff:3.500A) Proline residue: R 682 - end of helix removed outlier: 3.747A pdb=" N GLY R 685 " --> pdb=" O GLN R 681 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA R 708 " --> pdb=" O LEU R 704 " (cutoff:3.500A) Processing helix chain 'R' and resid 722 through 746 removed outlier: 3.660A pdb=" N LEU R 726 " --> pdb=" O ASN R 722 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N MET R 734 " --> pdb=" O LEU R 730 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLN R 735 " --> pdb=" O CYS R 731 " (cutoff:3.500A) Processing helix chain 'R' and resid 769 through 794 removed outlier: 3.832A pdb=" N LEU R 773 " --> pdb=" O SER R 769 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER R 794 " --> pdb=" O PHE R 790 " (cutoff:3.500A) Processing helix chain 'R' and resid 798 through 802 Processing helix chain 'R' and resid 803 through 827 Proline residue: R 823 - end of helix Processing helix chain 'R' and resid 830 through 862 removed outlier: 4.273A pdb=" N SER R 834 " --> pdb=" O GLY R 830 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE R 854 " --> pdb=" O ALA R 850 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ASN R 855 " --> pdb=" O CYS R 851 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LYS R 856 " --> pdb=" O ILE R 852 " (cutoff:3.500A) Processing helix chain 'R' and resid 863 through 867 removed outlier: 4.098A pdb=" N ARG R 866 " --> pdb=" O LYS R 863 " (cutoff:3.500A) Processing helix chain 'R' and resid 868 through 877 removed outlier: 3.803A pdb=" N VAL R 872 " --> pdb=" O THR R 868 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 52 removed outlier: 3.530A pdb=" N PHE H 52 " --> pdb=" O PHE H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 96 No H-bonds generated for 'chain 'H' and resid 94 through 96' Processing helix chain 'H' and resid 107 through 111 removed outlier: 3.541A pdb=" N THR H 111 " --> pdb=" O SER H 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.712A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 92 through 101 removed outlier: 4.286A pdb=" N ILE A 97 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N HIS A 98 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS A 99 " --> pdb=" O TRP A 96 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 101 " --> pdb=" O HIS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 130 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.829A pdb=" N ILE A 160 " --> pdb=" O PRO A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.716A pdb=" N ALA A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 226 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.738A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Q' and resid 26 through 28 removed outlier: 6.411A pdb=" N ILE Q 32 " --> pdb=" O GLY Q 94 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ARG Q 96 " --> pdb=" O ILE Q 32 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU Q 34 " --> pdb=" O ARG Q 96 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N PHE Q 98 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY Q 36 " --> pdb=" O PHE Q 98 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE Q 33 " --> pdb=" O THR Q 138 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA Q 140 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N VAL Q 165 " --> pdb=" O ILE Q 139 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL Q 141 " --> pdb=" O VAL Q 165 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 236 through 243 removed outlier: 8.063A pdb=" N VAL Q 209 " --> pdb=" O ASP Q 238 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N SER Q 240 " --> pdb=" O VAL Q 209 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N THR Q 211 " --> pdb=" O SER Q 240 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU Q 242 " --> pdb=" O THR Q 211 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA Q 213 " --> pdb=" O LEU Q 242 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TRP Q 208 " --> pdb=" O VAL Q 266 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N VAL Q 268 " --> pdb=" O TRP Q 208 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLY Q 210 " --> pdb=" O VAL Q 268 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N PHE Q 270 " --> pdb=" O GLY Q 210 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE Q 212 " --> pdb=" O PHE Q 270 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N TRP Q 293 " --> pdb=" O ILE Q 318 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N PHE Q 320 " --> pdb=" O TRP Q 293 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ALA Q 295 " --> pdb=" O PHE Q 320 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY Q 509 " --> pdb=" O ILE Q 491 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ASN Q 493 " --> pdb=" O GLU Q 507 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLU Q 507 " --> pdb=" O ASN Q 493 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N HIS Q 495 " --> pdb=" O PHE Q 505 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N PHE Q 505 " --> pdb=" O HIS Q 495 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Q' and resid 468 through 470 Processing sheet with id=AA4, first strand: chain 'Q' and resid 550 through 552 Processing sheet with id=AA5, first strand: chain 'Q' and resid 572 through 573 Processing sheet with id=AA6, first strand: chain 'Q' and resid 589 through 591 Processing sheet with id=AA7, first strand: chain 'Q' and resid 602 through 604 removed outlier: 6.228A pdb=" N GLU Q 602 " --> pdb=" O ILE Q 761 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE Q 763 " --> pdb=" O GLU Q 602 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU Q 604 " --> pdb=" O ILE Q 763 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N CYS Q 765 " --> pdb=" O GLU Q 604 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N ILE Q 760 " --> pdb=" O GLU Q 755 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N GLU Q 755 " --> pdb=" O ILE Q 760 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 26 through 28 removed outlier: 6.147A pdb=" N ILE R 32 " --> pdb=" O GLY R 94 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ARG R 96 " --> pdb=" O ILE R 32 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU R 34 " --> pdb=" O ARG R 96 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N PHE R 98 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY R 36 " --> pdb=" O PHE R 98 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE R 33 " --> pdb=" O THR R 138 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA R 140 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N VAL R 165 " --> pdb=" O ILE R 139 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL R 141 " --> pdb=" O VAL R 165 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLN R 164 " --> pdb=" O LEU R 184 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 236 through 243 removed outlier: 8.205A pdb=" N VAL R 209 " --> pdb=" O ASP R 238 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N SER R 240 " --> pdb=" O VAL R 209 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR R 211 " --> pdb=" O SER R 240 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU R 242 " --> pdb=" O THR R 211 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA R 213 " --> pdb=" O LEU R 242 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N TRP R 208 " --> pdb=" O VAL R 266 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N VAL R 268 " --> pdb=" O TRP R 208 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY R 210 " --> pdb=" O VAL R 268 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N PHE R 270 " --> pdb=" O GLY R 210 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE R 212 " --> pdb=" O PHE R 270 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TRP R 293 " --> pdb=" O ILE R 318 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N PHE R 320 " --> pdb=" O TRP R 293 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ALA R 295 " --> pdb=" O PHE R 320 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR R 489 " --> pdb=" O TYR R 510 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR R 510 " --> pdb=" O TYR R 489 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE R 491 " --> pdb=" O VAL R 508 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 469 through 470 removed outlier: 3.782A pdb=" N PHE R 469 " --> pdb=" O VAL R 477 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 550 through 554 Processing sheet with id=AB3, first strand: chain 'R' and resid 572 through 573 Processing sheet with id=AB4, first strand: chain 'R' and resid 589 through 591 Processing sheet with id=AB5, first strand: chain 'R' and resid 602 through 604 removed outlier: 6.037A pdb=" N GLU R 602 " --> pdb=" O ILE R 761 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE R 763 " --> pdb=" O GLU R 602 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU R 604 " --> pdb=" O ILE R 763 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N CYS R 765 " --> pdb=" O GLU R 604 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 23 through 27 Processing sheet with id=AB7, first strand: chain 'H' and resid 30 through 32 removed outlier: 6.367A pdb=" N GLY H 30 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N MET H 54 " --> pdb=" O TYR H 70 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR H 70 " --> pdb=" O MET H 54 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TRP H 56 " --> pdb=" O VAL H 68 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 166 through 168 removed outlier: 5.778A pdb=" N VAL H 167 " --> pdb=" O GLU H 266 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE H 209 " --> pdb=" O TRP H 196 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU H 198 " --> pdb=" O LEU H 207 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LEU H 207 " --> pdb=" O LEU H 198 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 175 through 180 Processing sheet with id=AC1, first strand: chain 'A' and resid 70 through 75 removed outlier: 3.707A pdb=" N ALA A 105 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A 139 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N HIS A 197 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A 141 " --> pdb=" O HIS A 197 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.035A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.975A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.772A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.952A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.650A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 242 " --> pdb=" O CYS B 233 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.328A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 315 through 320 869 hydrogen bonds defined for protein. 2478 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: 4.55 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6208 1.34 - 1.46: 5080 1.46 - 1.58: 8636 1.58 - 1.70: 2 1.70 - 1.82: 154 Bond restraints: 20080 Sorted by residual: bond pdb=" CB PRO R 308 " pdb=" CG PRO R 308 " ideal model delta sigma weight residual 1.492 1.683 -0.191 5.00e-02 4.00e+02 1.46e+01 bond pdb=" C05 9IG Q1010 " pdb=" O09 9IG Q1010 " ideal model delta sigma weight residual 1.348 1.410 -0.062 2.00e-02 2.50e+03 9.48e+00 bond pdb=" O3 PO4 R1005 " pdb=" P PO4 R1005 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.43e+00 bond pdb=" C05 9IG R1011 " pdb=" O09 9IG R1011 " ideal model delta sigma weight residual 1.348 1.409 -0.061 2.00e-02 2.50e+03 9.28e+00 bond pdb=" O4 PO4 Q1005 " pdb=" P PO4 Q1005 " ideal model delta sigma weight residual 1.568 1.508 0.060 2.00e-02 2.50e+03 9.14e+00 ... (remaining 20075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 27048 3.27 - 6.55: 143 6.55 - 9.82: 14 9.82 - 13.09: 2 13.09 - 16.36: 2 Bond angle restraints: 27209 Sorted by residual: angle pdb=" CA PRO R 308 " pdb=" N PRO R 308 " pdb=" CD PRO R 308 " ideal model delta sigma weight residual 112.00 95.64 16.36 1.40e+00 5.10e-01 1.37e+02 angle pdb=" CA PRO R 89 " pdb=" N PRO R 89 " pdb=" CD PRO R 89 " ideal model delta sigma weight residual 112.00 96.02 15.98 1.40e+00 5.10e-01 1.30e+02 angle pdb=" N PRO R 308 " pdb=" CD PRO R 308 " pdb=" CG PRO R 308 " ideal model delta sigma weight residual 103.20 94.52 8.68 1.50e+00 4.44e-01 3.35e+01 angle pdb=" N PRO R 89 " pdb=" CD PRO R 89 " pdb=" CG PRO R 89 " ideal model delta sigma weight residual 103.20 95.00 8.20 1.50e+00 4.44e-01 2.99e+01 angle pdb=" N PRO R 308 " pdb=" CA PRO R 308 " pdb=" CB PRO R 308 " ideal model delta sigma weight residual 103.25 98.68 4.57 1.05e+00 9.07e-01 1.89e+01 ... (remaining 27204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.89: 11187 21.89 - 43.77: 808 43.77 - 65.66: 114 65.66 - 87.54: 25 87.54 - 109.43: 6 Dihedral angle restraints: 12140 sinusoidal: 5057 harmonic: 7083 Sorted by residual: dihedral pdb=" CB CYS H 42 " pdb=" SG CYS H 42 " pdb=" SG CYS H 116 " pdb=" CB CYS H 116 " ideal model delta sinusoidal sigma weight residual 93.00 135.58 -42.58 1 1.00e+01 1.00e-02 2.53e+01 dihedral pdb=" CB CYS Q 546 " pdb=" SG CYS Q 546 " pdb=" SG CYS Q 565 " pdb=" CB CYS Q 565 " ideal model delta sinusoidal sigma weight residual -86.00 -126.25 40.25 1 1.00e+01 1.00e-02 2.27e+01 dihedral pdb=" CA GLN R 260 " pdb=" C GLN R 260 " pdb=" N ASN R 261 " pdb=" CA ASN R 261 " ideal model delta harmonic sigma weight residual -180.00 -157.54 -22.46 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 12137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2910 0.094 - 0.189: 146 0.189 - 0.283: 8 0.283 - 0.377: 4 0.377 - 0.471: 1 Chirality restraints: 3069 Sorted by residual: chirality pdb=" C1 NAG R1001 " pdb=" ND2 ASN R 261 " pdb=" C2 NAG R1001 " pdb=" O5 NAG R1001 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" CCV AV0 R1010 " pdb=" CCR AV0 R1010 " pdb=" CCT AV0 R1010 " pdb=" OAU AV0 R1010 " both_signs ideal model delta sigma weight residual False -2.30 -2.66 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CCW AV0 R1010 " pdb=" CCS AV0 R1010 " pdb=" CCU AV0 R1010 " pdb=" OAV AV0 R1010 " both_signs ideal model delta sigma weight residual False -2.29 -2.61 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 3066 not shown) Planarity restraints: 3438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 88 " -0.106 5.00e-02 4.00e+02 1.47e-01 3.44e+01 pdb=" N PRO R 89 " 0.253 5.00e-02 4.00e+02 pdb=" CA PRO R 89 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO R 89 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET R 307 " 0.103 5.00e-02 4.00e+02 1.43e-01 3.25e+01 pdb=" N PRO R 308 " -0.246 5.00e-02 4.00e+02 pdb=" CA PRO R 308 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO R 308 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS R 863 " 0.056 5.00e-02 4.00e+02 8.46e-02 1.15e+01 pdb=" N PRO R 864 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO R 864 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO R 864 " 0.046 5.00e-02 4.00e+02 ... (remaining 3435 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1194 2.73 - 3.27: 18960 3.27 - 3.82: 31475 3.82 - 4.36: 38623 4.36 - 4.90: 66552 Nonbonded interactions: 156804 Sorted by model distance: nonbonded pdb=" O ARG R 795 " pdb=" OAS AV0 R1010 " model vdw 2.191 3.040 nonbonded pdb=" O PHE Q 351 " pdb=" OG1 THR Q 355 " model vdw 2.228 3.040 nonbonded pdb=" NE2 GLN R 117 " pdb=" O ILE R 135 " model vdw 2.229 3.120 nonbonded pdb=" O SER R 171 " pdb=" NH2 ARG R 185 " model vdw 2.302 3.120 nonbonded pdb=" ND2 ASN B 340 " pdb=" OD1 ASN G 59 " model vdw 2.323 3.120 ... (remaining 156799 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 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'Q' and (resid 22 through 1002 or resid 1006 through 1008 or resid 1010)) \ selection = (chain 'R' and (resid 22 through 698 or resid 722 through 865 or resid 1002 thro \ ugh 1003 or resid 1007 through 1009 or resid 1011)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.730 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.191 20112 Z= 0.184 Angle : 0.679 16.364 27287 Z= 0.372 Chirality : 0.045 0.471 3069 Planarity : 0.006 0.147 3428 Dihedral : 14.714 109.431 7510 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 15.11 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.09 % 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: 0.19 (0.17), residues: 2413 helix: 1.44 (0.17), residues: 909 sheet: -0.23 (0.23), residues: 505 loop : -0.86 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 678 TYR 0.014 0.001 TYR Q 435 PHE 0.013 0.001 PHE Q 854 TRP 0.018 0.001 TRP A 96 HIS 0.006 0.001 HIS Q 312 Details of bonding type rmsd covalent geometry : bond 0.00398 (20080) covalent geometry : angle 0.67381 (27209) SS BOND : bond 0.00237 ( 18) SS BOND : angle 0.73008 ( 36) hydrogen bonds : bond 0.13475 ( 869) hydrogen bonds : angle 5.55059 ( 2478) link_BETA1-4 : bond 0.00347 ( 4) link_BETA1-4 : angle 1.34187 ( 12) link_NAG-ASN : bond 0.00335 ( 10) link_NAG-ASN : angle 2.37410 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 117 GLN cc_start: 0.6293 (tp-100) cc_final: 0.5861 (tm-30) REVERT: Q 728 VAL cc_start: 0.7627 (p) cc_final: 0.7267 (p) REVERT: R 248 ASP cc_start: 0.7464 (p0) cc_final: 0.7234 (p0) REVERT: R 284 VAL cc_start: 0.8341 (p) cc_final: 0.8082 (p) REVERT: R 285 ARG cc_start: 0.6947 (ttt180) cc_final: 0.6730 (ttt180) REVERT: R 481 GLU cc_start: 0.6783 (pm20) cc_final: 0.6530 (pm20) REVERT: R 486 VAL cc_start: 0.8109 (m) cc_final: 0.7898 (p) REVERT: A 20 ASP cc_start: 0.7815 (m-30) cc_final: 0.7422 (m-30) REVERT: A 53 MET cc_start: 0.5196 (tpp) cc_final: 0.4936 (tpt) REVERT: A 222 ASN cc_start: 0.8104 (m-40) cc_final: 0.7684 (m-40) REVERT: B 86 THR cc_start: 0.8551 (p) cc_final: 0.8338 (m) REVERT: B 130 GLU cc_start: 0.7834 (mp0) cc_final: 0.7572 (mp0) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.1660 time to fit residues: 90.2338 Evaluate side-chains 342 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 117 GLN ** Q 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 647 ASN R 253 GLN ** R 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 495 HIS R 583 ASN H 59 GLN H 214 ASN A 73 HIS A 131 ASN B 155 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.106231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.087787 restraints weight = 33029.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.087431 restraints weight = 29998.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.087650 restraints weight = 29313.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.088120 restraints weight = 27151.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.088360 restraints weight = 24180.540| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 20112 Z= 0.206 Angle : 0.612 10.950 27287 Z= 0.321 Chirality : 0.044 0.220 3069 Planarity : 0.005 0.072 3428 Dihedral : 7.109 99.257 3069 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.33 % Allowed : 14.11 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.09 % 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: 0.18 (0.17), residues: 2413 helix: 1.48 (0.17), residues: 908 sheet: -0.23 (0.23), residues: 504 loop : -0.92 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 96 TYR 0.020 0.002 TYR H 210 PHE 0.029 0.002 PHE R 637 TRP 0.022 0.002 TRP R 719 HIS 0.010 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00495 (20080) covalent geometry : angle 0.60695 (27209) SS BOND : bond 0.00580 ( 18) SS BOND : angle 0.89130 ( 36) hydrogen bonds : bond 0.06000 ( 869) hydrogen bonds : angle 4.69695 ( 2478) link_BETA1-4 : bond 0.00185 ( 4) link_BETA1-4 : angle 1.59424 ( 12) link_NAG-ASN : bond 0.00228 ( 10) link_NAG-ASN : angle 2.09213 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 346 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 25 ARG cc_start: 0.7929 (ptp-170) cc_final: 0.7635 (ptp90) REVERT: Q 624 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8169 (mp) REVERT: Q 728 VAL cc_start: 0.7684 (p) cc_final: 0.7394 (p) REVERT: R 185 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7549 (ptp-170) REVERT: R 481 GLU cc_start: 0.6782 (pm20) cc_final: 0.6578 (pm20) REVERT: R 637 PHE cc_start: 0.7786 (m-80) cc_final: 0.7518 (m-80) REVERT: A 112 LEU cc_start: 0.5878 (mt) cc_final: 0.5619 (tp) REVERT: A 120 GLU cc_start: 0.5715 (OUTLIER) cc_final: 0.5388 (pm20) REVERT: A 131 ASN cc_start: 0.7682 (m110) cc_final: 0.7295 (m110) REVERT: B 130 GLU cc_start: 0.7956 (mp0) cc_final: 0.7725 (mp0) REVERT: B 234 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7250 (t80) REVERT: B 303 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7473 (t0) outliers start: 70 outliers final: 47 residues processed: 389 average time/residue: 0.1616 time to fit residues: 94.5567 Evaluate side-chains 393 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 341 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 232 GLU Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain Q residue 443 LEU Chi-restraints excluded: chain Q residue 486 VAL Chi-restraints excluded: chain Q residue 560 THR Chi-restraints excluded: chain Q residue 578 ASP Chi-restraints excluded: chain Q residue 624 ILE Chi-restraints excluded: chain Q residue 634 PHE Chi-restraints excluded: chain Q residue 650 LEU Chi-restraints excluded: chain Q residue 698 LYS Chi-restraints excluded: chain Q residue 723 LEU Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 738 ILE Chi-restraints excluded: chain Q residue 743 LEU Chi-restraints excluded: chain Q residue 834 SER Chi-restraints excluded: chain Q residue 836 VAL Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 185 ARG Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 646 THR Chi-restraints excluded: chain R residue 705 VAL Chi-restraints excluded: chain R residue 761 ILE Chi-restraints excluded: chain R residue 812 LEU Chi-restraints excluded: chain R residue 833 VAL Chi-restraints excluded: chain R residue 861 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 26 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 157 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 130 optimal weight: 0.4980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 647 ASN R 312 HIS ** R 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 495 HIS R 753 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.105958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.087554 restraints weight = 33182.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.087320 restraints weight = 29574.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.087448 restraints weight = 28728.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.087648 restraints weight = 28106.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.088016 restraints weight = 25380.038| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20112 Z= 0.199 Angle : 0.587 8.296 27287 Z= 0.310 Chirality : 0.044 0.191 3069 Planarity : 0.004 0.056 3428 Dihedral : 6.815 97.934 3069 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.71 % Allowed : 15.25 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.09 % 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: 0.17 (0.17), residues: 2413 helix: 1.50 (0.17), residues: 908 sheet: -0.22 (0.23), residues: 508 loop : -0.98 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 185 TYR 0.018 0.002 TYR H 210 PHE 0.023 0.002 PHE R 814 TRP 0.021 0.002 TRP R 719 HIS 0.005 0.001 HIS H 55 Details of bonding type rmsd covalent geometry : bond 0.00478 (20080) covalent geometry : angle 0.58073 (27209) SS BOND : bond 0.00443 ( 18) SS BOND : angle 1.19265 ( 36) hydrogen bonds : bond 0.05814 ( 869) hydrogen bonds : angle 4.62729 ( 2478) link_BETA1-4 : bond 0.00371 ( 4) link_BETA1-4 : angle 1.62839 ( 12) link_NAG-ASN : bond 0.00187 ( 10) link_NAG-ASN : angle 2.06456 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 346 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 624 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8163 (mp) REVERT: Q 728 VAL cc_start: 0.7688 (p) cc_final: 0.7394 (p) REVERT: Q 849 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8129 (tp) REVERT: R 637 PHE cc_start: 0.7772 (m-80) cc_final: 0.7526 (m-80) REVERT: A 118 MET cc_start: 0.6159 (tmm) cc_final: 0.5872 (tmm) REVERT: A 120 GLU cc_start: 0.5709 (OUTLIER) cc_final: 0.5399 (pm20) REVERT: B 234 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7412 (t80) REVERT: B 303 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7501 (t0) REVERT: B 340 ASN cc_start: 0.7541 (t0) cc_final: 0.7340 (t0) outliers start: 78 outliers final: 59 residues processed: 393 average time/residue: 0.1664 time to fit residues: 97.9316 Evaluate side-chains 403 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 339 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 24 GLN Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 232 GLU Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 443 LEU Chi-restraints excluded: chain Q residue 486 VAL Chi-restraints excluded: chain Q residue 560 THR Chi-restraints excluded: chain Q residue 578 ASP Chi-restraints excluded: chain Q residue 624 ILE Chi-restraints excluded: chain Q residue 634 PHE Chi-restraints excluded: chain Q residue 650 LEU Chi-restraints excluded: chain Q residue 676 THR Chi-restraints excluded: chain Q residue 698 LYS Chi-restraints excluded: chain Q residue 723 LEU Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 738 ILE Chi-restraints excluded: chain Q residue 834 SER Chi-restraints excluded: chain Q residue 836 VAL Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 412 THR Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 599 ILE Chi-restraints excluded: chain R residue 646 THR Chi-restraints excluded: chain R residue 690 LEU Chi-restraints excluded: chain R residue 705 VAL Chi-restraints excluded: chain R residue 715 HIS Chi-restraints excluded: chain R residue 761 ILE Chi-restraints excluded: chain R residue 812 LEU Chi-restraints excluded: chain R residue 833 VAL Chi-restraints excluded: chain R residue 861 LEU Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 212 MET Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 227 optimal weight: 0.8980 chunk 209 optimal weight: 0.0970 chunk 205 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 chunk 230 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 191 optimal weight: 2.9990 chunk 140 optimal weight: 0.2980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 312 HIS Q 400 ASN R 495 HIS H 133 GLN A 131 ASN B 155 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.107568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.089452 restraints weight = 33208.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.089112 restraints weight = 30294.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.089515 restraints weight = 28275.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.089853 restraints weight = 27416.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.090033 restraints weight = 24019.852| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20112 Z= 0.121 Angle : 0.508 7.882 27287 Z= 0.270 Chirality : 0.041 0.175 3069 Planarity : 0.004 0.054 3428 Dihedral : 6.437 97.110 3069 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.90 % Allowed : 16.91 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.09 % 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: 0.41 (0.17), residues: 2413 helix: 1.75 (0.17), residues: 908 sheet: -0.12 (0.23), residues: 508 loop : -0.89 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 465 TYR 0.014 0.001 TYR H 210 PHE 0.016 0.001 PHE Q 854 TRP 0.021 0.001 TRP R 719 HIS 0.008 0.001 HIS R 338 Details of bonding type rmsd covalent geometry : bond 0.00273 (20080) covalent geometry : angle 0.50327 (27209) SS BOND : bond 0.00353 ( 18) SS BOND : angle 1.02916 ( 36) hydrogen bonds : bond 0.04747 ( 869) hydrogen bonds : angle 4.43724 ( 2478) link_BETA1-4 : bond 0.00378 ( 4) link_BETA1-4 : angle 1.35562 ( 12) link_NAG-ASN : bond 0.00327 ( 10) link_NAG-ASN : angle 1.75859 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 345 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 595 HIS cc_start: 0.7102 (m170) cc_final: 0.6854 (m170) REVERT: Q 624 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8096 (mp) REVERT: Q 728 VAL cc_start: 0.7676 (p) cc_final: 0.7378 (p) REVERT: Q 849 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8175 (tp) REVERT: R 637 PHE cc_start: 0.7702 (m-80) cc_final: 0.7453 (m-80) REVERT: A 120 GLU cc_start: 0.5701 (OUTLIER) cc_final: 0.5399 (pm20) REVERT: A 136 ASP cc_start: 0.7483 (t0) cc_final: 0.7092 (t0) REVERT: B 234 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7302 (t80) REVERT: B 303 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7526 (t0) REVERT: B 340 ASN cc_start: 0.7482 (t0) cc_final: 0.7219 (t0) outliers start: 61 outliers final: 46 residues processed: 384 average time/residue: 0.1689 time to fit residues: 96.7553 Evaluate side-chains 389 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 338 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 24 GLN Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 232 GLU Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 443 LEU Chi-restraints excluded: chain Q residue 578 ASP Chi-restraints excluded: chain Q residue 624 ILE Chi-restraints excluded: chain Q residue 634 PHE Chi-restraints excluded: chain Q residue 650 LEU Chi-restraints excluded: chain Q residue 698 LYS Chi-restraints excluded: chain Q residue 723 LEU Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 743 LEU Chi-restraints excluded: chain Q residue 834 SER Chi-restraints excluded: chain Q residue 836 VAL Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 412 THR Chi-restraints excluded: chain R residue 455 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 503 ILE Chi-restraints excluded: chain R residue 554 ILE Chi-restraints excluded: chain R residue 583 ASN Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 618 LEU Chi-restraints excluded: chain R residue 619 PHE Chi-restraints excluded: chain R residue 689 VAL Chi-restraints excluded: chain R residue 715 HIS Chi-restraints excluded: chain R residue 761 ILE Chi-restraints excluded: chain R residue 812 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain H residue 212 MET Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 9 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 201 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 86 optimal weight: 0.0050 chunk 156 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 253 GLN ** R 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 495 HIS B 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.105287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.086825 restraints weight = 33152.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.086351 restraints weight = 31465.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.086517 restraints weight = 31531.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.086875 restraints weight = 28599.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.087152 restraints weight = 26005.387| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20112 Z= 0.219 Angle : 0.599 8.181 27287 Z= 0.315 Chirality : 0.044 0.183 3069 Planarity : 0.004 0.056 3428 Dihedral : 6.477 96.110 3069 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.47 % Allowed : 16.34 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.09 % 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: 0.20 (0.17), residues: 2413 helix: 1.61 (0.17), residues: 902 sheet: -0.20 (0.23), residues: 508 loop : -1.03 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 185 TYR 0.017 0.002 TYR H 210 PHE 0.028 0.002 PHE R 814 TRP 0.024 0.002 TRP R 719 HIS 0.007 0.001 HIS H 55 Details of bonding type rmsd covalent geometry : bond 0.00532 (20080) covalent geometry : angle 0.59344 (27209) SS BOND : bond 0.00484 ( 18) SS BOND : angle 1.15504 ( 36) hydrogen bonds : bond 0.05969 ( 869) hydrogen bonds : angle 4.59522 ( 2478) link_BETA1-4 : bond 0.00352 ( 4) link_BETA1-4 : angle 1.68557 ( 12) link_NAG-ASN : bond 0.00209 ( 10) link_NAG-ASN : angle 2.17228 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 354 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 624 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8141 (mp) REVERT: Q 728 VAL cc_start: 0.7739 (p) cc_final: 0.7423 (p) REVERT: Q 849 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8152 (tp) REVERT: R 185 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7505 (ptp-170) REVERT: R 730 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.6978 (mp) REVERT: R 795 ARG cc_start: 0.6870 (ptt-90) cc_final: 0.6499 (ptt-90) REVERT: R 870 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6935 (mt-10) REVERT: A 120 GLU cc_start: 0.5715 (OUTLIER) cc_final: 0.5421 (pm20) REVERT: A 131 ASN cc_start: 0.7755 (OUTLIER) cc_final: 0.7522 (m-40) REVERT: A 136 ASP cc_start: 0.7515 (t0) cc_final: 0.7142 (t0) REVERT: B 234 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7454 (t80) REVERT: B 303 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7546 (t0) REVERT: B 340 ASN cc_start: 0.7586 (t0) cc_final: 0.7264 (t0) outliers start: 94 outliers final: 73 residues processed: 415 average time/residue: 0.1636 time to fit residues: 101.8981 Evaluate side-chains 421 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 339 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 24 GLN Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 232 GLU Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain Q residue 395 CYS Chi-restraints excluded: chain Q residue 401 ILE Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 443 LEU Chi-restraints excluded: chain Q residue 486 VAL Chi-restraints excluded: chain Q residue 560 THR Chi-restraints excluded: chain Q residue 578 ASP Chi-restraints excluded: chain Q residue 624 ILE Chi-restraints excluded: chain Q residue 629 PHE Chi-restraints excluded: chain Q residue 634 PHE Chi-restraints excluded: chain Q residue 650 LEU Chi-restraints excluded: chain Q residue 676 THR Chi-restraints excluded: chain Q residue 698 LYS Chi-restraints excluded: chain Q residue 723 LEU Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 738 ILE Chi-restraints excluded: chain Q residue 755 GLU Chi-restraints excluded: chain Q residue 834 SER Chi-restraints excluded: chain Q residue 836 VAL Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 185 ARG Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 412 THR Chi-restraints excluded: chain R residue 455 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 503 ILE Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 583 ASN Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 599 ILE Chi-restraints excluded: chain R residue 618 LEU Chi-restraints excluded: chain R residue 619 PHE Chi-restraints excluded: chain R residue 646 THR Chi-restraints excluded: chain R residue 690 LEU Chi-restraints excluded: chain R residue 705 VAL Chi-restraints excluded: chain R residue 715 HIS Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 761 ILE Chi-restraints excluded: chain R residue 788 PHE Chi-restraints excluded: chain R residue 812 LEU Chi-restraints excluded: chain R residue 833 VAL Chi-restraints excluded: chain R residue 861 LEU Chi-restraints excluded: chain R residue 870 GLU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 212 MET Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 166 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 30 optimal weight: 0.0870 chunk 162 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 143 optimal weight: 0.0570 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 253 GLN ** R 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 495 HIS H 133 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.106808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.088234 restraints weight = 33266.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.088286 restraints weight = 30901.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.088795 restraints weight = 28495.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.089050 restraints weight = 25514.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.089198 restraints weight = 24143.830| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20112 Z= 0.139 Angle : 0.519 7.858 27287 Z= 0.276 Chirality : 0.042 0.174 3069 Planarity : 0.004 0.053 3428 Dihedral : 6.228 95.450 3069 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.66 % Allowed : 17.15 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.09 % 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: 0.37 (0.17), residues: 2413 helix: 1.75 (0.17), residues: 906 sheet: -0.14 (0.23), residues: 512 loop : -0.93 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 465 TYR 0.014 0.001 TYR H 210 PHE 0.018 0.001 PHE R 814 TRP 0.028 0.002 TRP R 719 HIS 0.003 0.001 HIS H 55 Details of bonding type rmsd covalent geometry : bond 0.00325 (20080) covalent geometry : angle 0.51424 (27209) SS BOND : bond 0.00338 ( 18) SS BOND : angle 0.91923 ( 36) hydrogen bonds : bond 0.04882 ( 869) hydrogen bonds : angle 4.44341 ( 2478) link_BETA1-4 : bond 0.00286 ( 4) link_BETA1-4 : angle 1.40827 ( 12) link_NAG-ASN : bond 0.00216 ( 10) link_NAG-ASN : angle 1.87306 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 337 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 624 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8047 (mp) REVERT: Q 728 VAL cc_start: 0.7725 (p) cc_final: 0.7409 (p) REVERT: Q 849 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8251 (tp) REVERT: R 185 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7503 (ptp-170) REVERT: R 730 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.6963 (mp) REVERT: R 795 ARG cc_start: 0.6814 (ptt-90) cc_final: 0.6517 (ptt-90) REVERT: A 120 GLU cc_start: 0.5668 (OUTLIER) cc_final: 0.5373 (pm20) REVERT: A 131 ASN cc_start: 0.7763 (OUTLIER) cc_final: 0.7499 (m-40) REVERT: A 136 ASP cc_start: 0.7509 (t0) cc_final: 0.7086 (t0) REVERT: B 234 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7313 (t80) REVERT: B 303 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7498 (t0) REVERT: B 340 ASN cc_start: 0.7533 (t0) cc_final: 0.7188 (t0) outliers start: 77 outliers final: 58 residues processed: 389 average time/residue: 0.1638 time to fit residues: 95.7778 Evaluate side-chains 399 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 333 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 232 GLU Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 443 LEU Chi-restraints excluded: chain Q residue 486 VAL Chi-restraints excluded: chain Q residue 560 THR Chi-restraints excluded: chain Q residue 578 ASP Chi-restraints excluded: chain Q residue 624 ILE Chi-restraints excluded: chain Q residue 634 PHE Chi-restraints excluded: chain Q residue 650 LEU Chi-restraints excluded: chain Q residue 676 THR Chi-restraints excluded: chain Q residue 698 LYS Chi-restraints excluded: chain Q residue 723 LEU Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 738 ILE Chi-restraints excluded: chain Q residue 743 LEU Chi-restraints excluded: chain Q residue 834 SER Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 185 ARG Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 404 VAL Chi-restraints excluded: chain R residue 412 THR Chi-restraints excluded: chain R residue 455 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 503 ILE Chi-restraints excluded: chain R residue 583 ASN Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 618 LEU Chi-restraints excluded: chain R residue 619 PHE Chi-restraints excluded: chain R residue 689 VAL Chi-restraints excluded: chain R residue 715 HIS Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 761 ILE Chi-restraints excluded: chain R residue 812 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain H residue 212 MET Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 130 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 189 optimal weight: 0.6980 chunk 180 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 253 GLN ** R 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 495 HIS A 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.106309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.087848 restraints weight = 33265.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.087711 restraints weight = 30277.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.088144 restraints weight = 29182.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.088359 restraints weight = 26230.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.088626 restraints weight = 24813.459| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20112 Z= 0.158 Angle : 0.540 7.739 27287 Z= 0.286 Chirality : 0.042 0.172 3069 Planarity : 0.004 0.053 3428 Dihedral : 6.189 94.618 3069 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.90 % Allowed : 17.24 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.09 % 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: 0.39 (0.17), residues: 2413 helix: 1.79 (0.17), residues: 903 sheet: -0.11 (0.23), residues: 511 loop : -0.95 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.016 0.001 TYR H 210 PHE 0.022 0.002 PHE R 814 TRP 0.020 0.002 TRP R 719 HIS 0.005 0.001 HIS H 55 Details of bonding type rmsd covalent geometry : bond 0.00376 (20080) covalent geometry : angle 0.53517 (27209) SS BOND : bond 0.00379 ( 18) SS BOND : angle 0.95621 ( 36) hydrogen bonds : bond 0.05149 ( 869) hydrogen bonds : angle 4.43767 ( 2478) link_BETA1-4 : bond 0.00288 ( 4) link_BETA1-4 : angle 1.48000 ( 12) link_NAG-ASN : bond 0.00188 ( 10) link_NAG-ASN : angle 1.95632 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 341 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 307 MET cc_start: 0.7364 (mtt) cc_final: 0.7117 (mtt) REVERT: Q 624 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.8055 (mp) REVERT: Q 654 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8140 (tt) REVERT: Q 728 VAL cc_start: 0.7683 (p) cc_final: 0.7386 (p) REVERT: Q 849 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8267 (tp) REVERT: R 185 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7517 (ptp-170) REVERT: R 730 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.6980 (mp) REVERT: R 870 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6963 (mt-10) REVERT: A 120 GLU cc_start: 0.5677 (OUTLIER) cc_final: 0.5376 (pm20) REVERT: A 131 ASN cc_start: 0.7764 (OUTLIER) cc_final: 0.7442 (m-40) REVERT: A 136 ASP cc_start: 0.7512 (t0) cc_final: 0.7087 (t0) REVERT: B 87 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8568 (m) REVERT: B 234 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7310 (t80) REVERT: B 303 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7482 (t0) REVERT: B 340 ASN cc_start: 0.7529 (t0) cc_final: 0.7174 (t0) outliers start: 82 outliers final: 65 residues processed: 396 average time/residue: 0.1679 time to fit residues: 99.3765 Evaluate side-chains 413 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 337 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 24 GLN Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 232 GLU Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain Q residue 395 CYS Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 443 LEU Chi-restraints excluded: chain Q residue 486 VAL Chi-restraints excluded: chain Q residue 560 THR Chi-restraints excluded: chain Q residue 578 ASP Chi-restraints excluded: chain Q residue 624 ILE Chi-restraints excluded: chain Q residue 634 PHE Chi-restraints excluded: chain Q residue 650 LEU Chi-restraints excluded: chain Q residue 654 LEU Chi-restraints excluded: chain Q residue 676 THR Chi-restraints excluded: chain Q residue 698 LYS Chi-restraints excluded: chain Q residue 723 LEU Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 738 ILE Chi-restraints excluded: chain Q residue 743 LEU Chi-restraints excluded: chain Q residue 755 GLU Chi-restraints excluded: chain Q residue 834 SER Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 185 ARG Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 412 THR Chi-restraints excluded: chain R residue 455 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 503 ILE Chi-restraints excluded: chain R residue 583 ASN Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 618 LEU Chi-restraints excluded: chain R residue 619 PHE Chi-restraints excluded: chain R residue 646 THR Chi-restraints excluded: chain R residue 689 VAL Chi-restraints excluded: chain R residue 690 LEU Chi-restraints excluded: chain R residue 715 HIS Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 761 ILE Chi-restraints excluded: chain R residue 812 LEU Chi-restraints excluded: chain R residue 861 LEU Chi-restraints excluded: chain R residue 870 GLU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain H residue 212 MET Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 96 optimal weight: 0.0980 chunk 99 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 234 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 226 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 253 GLN ** R 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 754 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.106252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.087727 restraints weight = 33111.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.087268 restraints weight = 32622.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.087574 restraints weight = 31002.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.087831 restraints weight = 28578.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.087968 restraints weight = 26860.541| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20112 Z= 0.164 Angle : 0.543 7.726 27287 Z= 0.287 Chirality : 0.042 0.171 3069 Planarity : 0.004 0.054 3428 Dihedral : 6.175 94.417 3069 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.23 % Allowed : 17.01 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.09 % 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: 0.39 (0.17), residues: 2413 helix: 1.79 (0.17), residues: 903 sheet: -0.11 (0.23), residues: 512 loop : -0.95 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.016 0.001 TYR H 210 PHE 0.022 0.002 PHE R 814 TRP 0.027 0.002 TRP R 719 HIS 0.005 0.001 HIS H 55 Details of bonding type rmsd covalent geometry : bond 0.00393 (20080) covalent geometry : angle 0.53802 (27209) SS BOND : bond 0.00394 ( 18) SS BOND : angle 0.95106 ( 36) hydrogen bonds : bond 0.05172 ( 869) hydrogen bonds : angle 4.43664 ( 2478) link_BETA1-4 : bond 0.00331 ( 4) link_BETA1-4 : angle 1.49699 ( 12) link_NAG-ASN : bond 0.00190 ( 10) link_NAG-ASN : angle 1.98095 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 341 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 307 MET cc_start: 0.7380 (mtt) cc_final: 0.7122 (mtt) REVERT: Q 624 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8061 (mp) REVERT: Q 654 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8145 (tt) REVERT: Q 728 VAL cc_start: 0.7681 (OUTLIER) cc_final: 0.7377 (p) REVERT: Q 849 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8279 (tp) REVERT: R 185 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7516 (ptp-170) REVERT: R 592 ASN cc_start: 0.7737 (OUTLIER) cc_final: 0.6997 (m110) REVERT: R 730 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.6988 (mp) REVERT: R 870 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6962 (mt-10) REVERT: A 120 GLU cc_start: 0.5680 (OUTLIER) cc_final: 0.5384 (pm20) REVERT: A 136 ASP cc_start: 0.7506 (t0) cc_final: 0.7089 (t0) REVERT: B 87 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8563 (m) REVERT: B 234 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7338 (t80) REVERT: B 303 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7483 (t0) outliers start: 89 outliers final: 72 residues processed: 401 average time/residue: 0.1687 time to fit residues: 100.9999 Evaluate side-chains 424 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 340 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 24 GLN Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 232 GLU Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain Q residue 395 CYS Chi-restraints excluded: chain Q residue 401 ILE Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 443 LEU Chi-restraints excluded: chain Q residue 486 VAL Chi-restraints excluded: chain Q residue 540 SER Chi-restraints excluded: chain Q residue 560 THR Chi-restraints excluded: chain Q residue 578 ASP Chi-restraints excluded: chain Q residue 624 ILE Chi-restraints excluded: chain Q residue 634 PHE Chi-restraints excluded: chain Q residue 650 LEU Chi-restraints excluded: chain Q residue 654 LEU Chi-restraints excluded: chain Q residue 676 THR Chi-restraints excluded: chain Q residue 698 LYS Chi-restraints excluded: chain Q residue 723 LEU Chi-restraints excluded: chain Q residue 728 VAL Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 738 ILE Chi-restraints excluded: chain Q residue 743 LEU Chi-restraints excluded: chain Q residue 834 SER Chi-restraints excluded: chain Q residue 836 VAL Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 185 ARG Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 262 SER Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 404 VAL Chi-restraints excluded: chain R residue 412 THR Chi-restraints excluded: chain R residue 455 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 503 ILE Chi-restraints excluded: chain R residue 583 ASN Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 599 ILE Chi-restraints excluded: chain R residue 618 LEU Chi-restraints excluded: chain R residue 619 PHE Chi-restraints excluded: chain R residue 646 THR Chi-restraints excluded: chain R residue 689 VAL Chi-restraints excluded: chain R residue 690 LEU Chi-restraints excluded: chain R residue 715 HIS Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 761 ILE Chi-restraints excluded: chain R residue 812 LEU Chi-restraints excluded: chain R residue 833 VAL Chi-restraints excluded: chain R residue 861 LEU Chi-restraints excluded: chain R residue 870 GLU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain H residue 212 MET Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 15 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 63 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 196 optimal weight: 0.0970 chunk 50 optimal weight: 0.5980 chunk 173 optimal weight: 0.0980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.108350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.088243 restraints weight = 32971.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.089873 restraints weight = 23910.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.091057 restraints weight = 19484.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.091690 restraints weight = 16955.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.092222 restraints weight = 15588.583| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20112 Z= 0.117 Angle : 0.499 7.319 27287 Z= 0.265 Chirality : 0.041 0.186 3069 Planarity : 0.004 0.052 3428 Dihedral : 6.017 93.670 3069 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.61 % Allowed : 17.72 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.09 % 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: 0.54 (0.17), residues: 2413 helix: 1.91 (0.17), residues: 907 sheet: -0.03 (0.23), residues: 511 loop : -0.87 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.014 0.001 TYR H 210 PHE 0.016 0.001 PHE A 76 TRP 0.029 0.001 TRP R 719 HIS 0.003 0.001 HIS H 55 Details of bonding type rmsd covalent geometry : bond 0.00266 (20080) covalent geometry : angle 0.49461 (27209) SS BOND : bond 0.00302 ( 18) SS BOND : angle 0.81912 ( 36) hydrogen bonds : bond 0.04425 ( 869) hydrogen bonds : angle 4.31604 ( 2478) link_BETA1-4 : bond 0.00325 ( 4) link_BETA1-4 : angle 1.31672 ( 12) link_NAG-ASN : bond 0.00221 ( 10) link_NAG-ASN : angle 1.76421 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 333 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 25 ARG cc_start: 0.8040 (ptp-170) cc_final: 0.7766 (ptp90) REVERT: Q 307 MET cc_start: 0.7425 (mtt) cc_final: 0.7176 (mtt) REVERT: Q 624 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7929 (mp) REVERT: Q 728 VAL cc_start: 0.7735 (OUTLIER) cc_final: 0.7430 (p) REVERT: Q 834 SER cc_start: 0.8098 (OUTLIER) cc_final: 0.7360 (p) REVERT: Q 849 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8221 (tp) REVERT: R 246 TYR cc_start: 0.7293 (m-10) cc_final: 0.7052 (m-80) REVERT: R 592 ASN cc_start: 0.7766 (OUTLIER) cc_final: 0.6967 (m110) REVERT: R 659 LEU cc_start: 0.8192 (mt) cc_final: 0.7970 (mt) REVERT: R 730 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.6917 (mp) REVERT: A 120 GLU cc_start: 0.5655 (OUTLIER) cc_final: 0.5345 (pm20) REVERT: A 131 ASN cc_start: 0.7759 (OUTLIER) cc_final: 0.7455 (m-40) REVERT: A 136 ASP cc_start: 0.7553 (t0) cc_final: 0.7118 (t0) REVERT: B 87 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8516 (m) REVERT: B 155 ASN cc_start: 0.7594 (m110) cc_final: 0.7366 (t0) REVERT: B 234 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7274 (t80) REVERT: B 262 MET cc_start: 0.7880 (tpp) cc_final: 0.7391 (tpp) REVERT: B 303 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7460 (t0) REVERT: B 340 ASN cc_start: 0.7547 (t0) cc_final: 0.7282 (t0) outliers start: 76 outliers final: 60 residues processed: 388 average time/residue: 0.1625 time to fit residues: 95.2886 Evaluate side-chains 400 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 329 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 232 GLU Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain Q residue 395 CYS Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 443 LEU Chi-restraints excluded: chain Q residue 486 VAL Chi-restraints excluded: chain Q residue 560 THR Chi-restraints excluded: chain Q residue 624 ILE Chi-restraints excluded: chain Q residue 634 PHE Chi-restraints excluded: chain Q residue 650 LEU Chi-restraints excluded: chain Q residue 676 THR Chi-restraints excluded: chain Q residue 698 LYS Chi-restraints excluded: chain Q residue 723 LEU Chi-restraints excluded: chain Q residue 728 VAL Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 743 LEU Chi-restraints excluded: chain Q residue 834 SER Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 262 SER Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 404 VAL Chi-restraints excluded: chain R residue 412 THR Chi-restraints excluded: chain R residue 455 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 503 ILE Chi-restraints excluded: chain R residue 554 ILE Chi-restraints excluded: chain R residue 583 ASN Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 618 LEU Chi-restraints excluded: chain R residue 619 PHE Chi-restraints excluded: chain R residue 646 THR Chi-restraints excluded: chain R residue 689 VAL Chi-restraints excluded: chain R residue 715 HIS Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 761 ILE Chi-restraints excluded: chain R residue 812 LEU Chi-restraints excluded: chain R residue 833 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 217 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 216 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 81 optimal weight: 0.2980 chunk 80 optimal weight: 0.5980 chunk 237 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 27 GLN ** R 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 495 HIS A 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.107309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.087108 restraints weight = 33241.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.088754 restraints weight = 24164.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.089846 restraints weight = 19628.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.090271 restraints weight = 17185.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.090954 restraints weight = 16050.003| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20112 Z= 0.155 Angle : 0.543 12.196 27287 Z= 0.286 Chirality : 0.042 0.164 3069 Planarity : 0.004 0.053 3428 Dihedral : 6.063 93.801 3069 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.75 % Allowed : 17.96 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.09 % 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: 0.48 (0.17), residues: 2413 helix: 1.86 (0.17), residues: 906 sheet: -0.04 (0.23), residues: 511 loop : -0.91 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.015 0.001 TYR H 210 PHE 0.022 0.002 PHE R 814 TRP 0.027 0.002 TRP R 719 HIS 0.005 0.001 HIS H 55 Details of bonding type rmsd covalent geometry : bond 0.00368 (20080) covalent geometry : angle 0.53809 (27209) SS BOND : bond 0.00370 ( 18) SS BOND : angle 0.88535 ( 36) hydrogen bonds : bond 0.04915 ( 869) hydrogen bonds : angle 4.39024 ( 2478) link_BETA1-4 : bond 0.00323 ( 4) link_BETA1-4 : angle 1.43429 ( 12) link_NAG-ASN : bond 0.00179 ( 10) link_NAG-ASN : angle 1.90355 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 330 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 25 ARG cc_start: 0.8065 (ptp-170) cc_final: 0.7773 (ptp90) REVERT: Q 307 MET cc_start: 0.7433 (mtt) cc_final: 0.7174 (mtt) REVERT: Q 624 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.7959 (mp) REVERT: Q 728 VAL cc_start: 0.7760 (OUTLIER) cc_final: 0.7445 (p) REVERT: Q 849 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8196 (tp) REVERT: R 592 ASN cc_start: 0.7811 (OUTLIER) cc_final: 0.7020 (m110) REVERT: R 730 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6927 (mp) REVERT: R 870 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6888 (mt-10) REVERT: A 120 GLU cc_start: 0.5704 (OUTLIER) cc_final: 0.5381 (pm20) REVERT: A 131 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7313 (m110) REVERT: A 136 ASP cc_start: 0.7562 (t0) cc_final: 0.7129 (t0) REVERT: B 86 THR cc_start: 0.8630 (p) cc_final: 0.8399 (m) REVERT: B 87 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8568 (m) REVERT: B 155 ASN cc_start: 0.7627 (m110) cc_final: 0.7384 (t0) REVERT: B 234 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7246 (t80) REVERT: B 340 ASN cc_start: 0.7571 (t0) cc_final: 0.7286 (t0) outliers start: 79 outliers final: 64 residues processed: 385 average time/residue: 0.1621 time to fit residues: 94.2188 Evaluate side-chains 403 residues out of total 2105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 329 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 232 GLU Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain Q residue 395 CYS Chi-restraints excluded: chain Q residue 401 ILE Chi-restraints excluded: chain Q residue 443 LEU Chi-restraints excluded: chain Q residue 486 VAL Chi-restraints excluded: chain Q residue 560 THR Chi-restraints excluded: chain Q residue 624 ILE Chi-restraints excluded: chain Q residue 634 PHE Chi-restraints excluded: chain Q residue 650 LEU Chi-restraints excluded: chain Q residue 676 THR Chi-restraints excluded: chain Q residue 698 LYS Chi-restraints excluded: chain Q residue 723 LEU Chi-restraints excluded: chain Q residue 728 VAL Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 743 LEU Chi-restraints excluded: chain Q residue 834 SER Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 262 SER Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 404 VAL Chi-restraints excluded: chain R residue 412 THR Chi-restraints excluded: chain R residue 455 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 503 ILE Chi-restraints excluded: chain R residue 554 ILE Chi-restraints excluded: chain R residue 583 ASN Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 599 ILE Chi-restraints excluded: chain R residue 618 LEU Chi-restraints excluded: chain R residue 619 PHE Chi-restraints excluded: chain R residue 646 THR Chi-restraints excluded: chain R residue 689 VAL Chi-restraints excluded: chain R residue 715 HIS Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 761 ILE Chi-restraints excluded: chain R residue 812 LEU Chi-restraints excluded: chain R residue 833 VAL Chi-restraints excluded: chain R residue 870 GLU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 100 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 66 optimal weight: 0.0570 chunk 237 optimal weight: 0.8980 chunk 180 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 111 optimal weight: 0.0870 chunk 212 optimal weight: 0.9980 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 27 GLN ** R 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.107308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.089067 restraints weight = 33302.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.088631 restraints weight = 31031.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.088945 restraints weight = 28737.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.089183 restraints weight = 26387.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.089551 restraints weight = 25061.889| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.198 20112 Z= 0.171 Angle : 0.713 59.200 27287 Z= 0.409 Chirality : 0.042 0.187 3069 Planarity : 0.004 0.076 3428 Dihedral : 6.075 93.796 3069 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.80 % Allowed : 17.81 % Favored : 78.38 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.09 % 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: 0.48 (0.17), residues: 2413 helix: 1.87 (0.17), residues: 905 sheet: -0.04 (0.23), residues: 511 loop : -0.92 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.053 0.001 ARG B 197 TYR 0.015 0.001 TYR H 210 PHE 0.022 0.001 PHE R 814 TRP 0.024 0.001 TRP R 719 HIS 0.005 0.001 HIS H 55 Details of bonding type rmsd covalent geometry : bond 0.00393 (20080) covalent geometry : angle 0.70956 (27209) SS BOND : bond 0.00364 ( 18) SS BOND : angle 0.87527 ( 36) hydrogen bonds : bond 0.04898 ( 869) hydrogen bonds : angle 4.39205 ( 2478) link_BETA1-4 : bond 0.00253 ( 4) link_BETA1-4 : angle 1.46337 ( 12) link_NAG-ASN : bond 0.00177 ( 10) link_NAG-ASN : angle 1.90189 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3741.12 seconds wall clock time: 65 minutes 35.89 seconds (3935.89 seconds total)