Starting phenix.real_space_refine on Thu Mar 5 20:09:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mzk_48759/03_2026/9mzk_48759.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mzk_48759/03_2026/9mzk_48759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mzk_48759/03_2026/9mzk_48759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mzk_48759/03_2026/9mzk_48759.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mzk_48759/03_2026/9mzk_48759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mzk_48759/03_2026/9mzk_48759.map" } resolution = 3.81 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= 0.003 sd= 0.030 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: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 15601 2.51 5 N 3979 2.21 5 O 4658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24374 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 5972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 5972 Classifications: {'peptide': 757} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 728} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 5892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5892 Classifications: {'peptide': 747} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 5974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 5974 Classifications: {'peptide': 757} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 728} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 5895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5895 Classifications: {'peptide': 747} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" 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: "M" 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: "N" 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: "O" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 Time building chain proxies: 5.35, per 1000 atoms: 0.22 Number of scatterers: 24374 At special positions: 0 Unit cell: (120.84, 159, 183.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 136 16.00 O 4658 8.00 N 3979 7.00 C 15601 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " NAG E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " NAG G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " NAG H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " NAG J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " NAG K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " NAG O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " NAG Q 3 " NAG-ASN " NAG A1001 " - " ASN A 423 " " NAG A1002 " - " ASN A 751 " " NAG A1003 " - " ASN A 546 " " NAG B1001 " - " ASN B 286 " " NAG B1002 " - " ASN B 412 " " NAG B1003 " - " ASN B 275 " " NAG B1004 " - " ASN B 73 " " NAG C1001 " - " ASN C 412 " " NAG C1002 " - " ASN C 423 " " NAG C1003 " - " ASN C 751 " " NAG D1001 " - " ASN D 275 " " NAG D1002 " - " ASN D 412 " " NAG E 1 " - " ASN A 430 " " NAG F 1 " - " ASN A 412 " " NAG G 1 " - " ASN A 378 " " NAG H 1 " - " ASN A 67 " " NAG I 1 " - " ASN A 275 " " NAG J 1 " - " ASN B 67 " " NAG K 1 " - " ASN B 378 " " NAG L 1 " - " ASN C 378 " " NAG M 1 " - " ASN C 430 " " NAG N 1 " - " ASN C 67 " " NAG O 1 " - " ASN C 275 " " NAG P 1 " - " ASN D 378 " " NAG Q 1 " - " ASN D 67 " Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 895.3 milliseconds 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5602 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 35 sheets defined 46.8% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.622A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 removed outlier: 4.304A pdb=" N ARG A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 185 removed outlier: 4.194A pdb=" N ILE A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.705A pdb=" N LYS A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 removed outlier: 3.777A pdb=" N ARG A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 Processing helix chain 'A' and resid 231 through 244 Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 269 through 273 removed outlier: 3.921A pdb=" N SER A 272 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY A 273 " --> pdb=" O ARG A 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 269 through 273' Processing helix chain 'A' and resid 286 through 300 removed outlier: 3.596A pdb=" N ILE A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 317 through 337 removed outlier: 3.620A pdb=" N GLN A 335 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 removed outlier: 4.004A pdb=" N LEU A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS A 364 " --> pdb=" O MET A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 426 removed outlier: 3.610A pdb=" N THR A 425 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 461 through 475 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 563 through 582 removed outlier: 3.898A pdb=" N ILE A 567 " --> pdb=" O ILE A 563 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ALA A 570 " --> pdb=" O TYR A 566 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 662 removed outlier: 3.614A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 648 " --> pdb=" O THR A 644 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 677 removed outlier: 3.655A pdb=" N CYS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 672 through 677' Processing helix chain 'A' and resid 688 through 697 removed outlier: 4.098A pdb=" N THR A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 712 removed outlier: 3.686A pdb=" N MET A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 708 " --> pdb=" O LYS A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 730 Processing helix chain 'A' and resid 739 through 749 removed outlier: 3.995A pdb=" N PHE A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 788 removed outlier: 4.395A pdb=" N LYS A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 791 No H-bonds generated for 'chain 'A' and resid 789 through 791' Processing helix chain 'A' and resid 792 through 800 removed outlier: 3.743A pdb=" N GLU A 796 " --> pdb=" O HIS A 792 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP A 799 " --> pdb=" O LYS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 834 removed outlier: 3.749A pdb=" N LEU A 827 " --> pdb=" O ILE A 823 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA A 829 " --> pdb=" O ILE A 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 88 through 101 removed outlier: 3.716A pdb=" N LEU B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.567A pdb=" N ASN B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 168 removed outlier: 4.503A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 185 through 190 removed outlier: 3.635A pdb=" N LYS B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 195 removed outlier: 4.088A pdb=" N ARG B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 210 Processing helix chain 'B' and resid 211 through 221 Processing helix chain 'B' and resid 231 through 245 Processing helix chain 'B' and resid 286 through 299 Processing helix chain 'B' and resid 317 through 335 Processing helix chain 'B' and resid 355 through 365 removed outlier: 3.541A pdb=" N SER B 361 " --> pdb=" O THR B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 458 removed outlier: 3.958A pdb=" N ASP B 457 " --> pdb=" O TYR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 475 removed outlier: 3.866A pdb=" N THR B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ILE B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 507 removed outlier: 3.737A pdb=" N LEU B 505 " --> pdb=" O MET B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 527 Processing helix chain 'B' and resid 551 through 555 removed outlier: 4.396A pdb=" N PHE B 555 " --> pdb=" O VAL B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 583 removed outlier: 3.623A pdb=" N MET B 565 " --> pdb=" O PRO B 561 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR B 566 " --> pdb=" O ASP B 562 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE B 567 " --> pdb=" O ILE B 563 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU B 569 " --> pdb=" O MET B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 665 Processing helix chain 'B' and resid 670 through 677 removed outlier: 3.951A pdb=" N GLN B 677 " --> pdb=" O ASP B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 696 removed outlier: 3.863A pdb=" N PHE B 694 " --> pdb=" O THR B 690 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS B 696 " --> pdb=" O THR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 712 Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.625A pdb=" N GLN B 726 " --> pdb=" O GLU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 749 removed outlier: 3.502A pdb=" N VAL B 745 " --> pdb=" O THR B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 788 removed outlier: 4.166A pdb=" N GLU B 788 " --> pdb=" O GLN B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 796 Processing helix chain 'B' and resid 821 through 839 removed outlier: 4.045A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 67 removed outlier: 3.629A pdb=" N ASN C 65 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 101 Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.617A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 121 " --> pdb=" O ALA C 117 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 125 " --> pdb=" O ILE C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 185 through 190 removed outlier: 4.042A pdb=" N LYS C 190 " --> pdb=" O GLN C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 removed outlier: 3.952A pdb=" N ARG C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 221 Processing helix chain 'C' and resid 231 through 245 removed outlier: 3.742A pdb=" N ALA C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N MET C 245 " --> pdb=" O GLN C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.456A pdb=" N TYR C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 298 Processing helix chain 'C' and resid 317 through 337 Processing helix chain 'C' and resid 356 through 365 removed outlier: 3.597A pdb=" N SER C 361 " --> pdb=" O THR C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 457 removed outlier: 4.338A pdb=" N ASP C 457 " --> pdb=" O TYR C 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 454 through 457' Processing helix chain 'C' and resid 461 through 474 Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.683A pdb=" N ARG C 503 " --> pdb=" O ASN C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.703A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 582 removed outlier: 3.739A pdb=" N MET C 565 " --> pdb=" O PRO C 561 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA C 582 " --> pdb=" O LEU C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 665 Processing helix chain 'C' and resid 671 through 677 removed outlier: 3.568A pdb=" N CYS C 676 " --> pdb=" O ASP C 672 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN C 677 " --> pdb=" O ASP C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 697 Processing helix chain 'C' and resid 699 through 712 removed outlier: 3.509A pdb=" N MET C 709 " --> pdb=" O MET C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 731 Processing helix chain 'C' and resid 739 through 749 Processing helix chain 'C' and resid 775 through 788 Processing helix chain 'C' and resid 789 through 791 No H-bonds generated for 'chain 'C' and resid 789 through 791' Processing helix chain 'C' and resid 792 through 800 removed outlier: 3.528A pdb=" N GLU C 796 " --> pdb=" O HIS C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 835 removed outlier: 3.943A pdb=" N ILE C 825 " --> pdb=" O GLY C 821 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU C 833 " --> pdb=" O ALA C 829 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER C 834 " --> pdb=" O GLY C 830 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 87 through 101 Processing helix chain 'D' and resid 111 through 126 removed outlier: 4.190A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 168 removed outlier: 3.588A pdb=" N ALA D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 185 removed outlier: 4.051A pdb=" N ILE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 190 through 195 removed outlier: 4.185A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 210 removed outlier: 3.519A pdb=" N ASP D 210 " --> pdb=" O ASP D 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 207 through 210' Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 231 through 246 removed outlier: 3.614A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.620A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 364 removed outlier: 3.857A pdb=" N MET D 360 " --> pdb=" O GLY D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 457 Processing helix chain 'D' and resid 461 through 475 Processing helix chain 'D' and resid 500 through 506 removed outlier: 3.888A pdb=" N GLU D 504 " --> pdb=" O GLY D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 550 through 554 Processing helix chain 'D' and resid 560 through 581 removed outlier: 3.975A pdb=" N TRP D 564 " --> pdb=" O SER D 560 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N MET D 565 " --> pdb=" O PRO D 561 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR D 566 " --> pdb=" O ASP D 562 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL D 577 " --> pdb=" O GLY D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 665 removed outlier: 3.699A pdb=" N SER D 650 " --> pdb=" O ILE D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 677 removed outlier: 4.271A pdb=" N LEU D 674 " --> pdb=" O SER D 670 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN D 677 " --> pdb=" O ASP D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 697 removed outlier: 3.563A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.551A pdb=" N LYS D 704 " --> pdb=" O SER D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 removed outlier: 3.511A pdb=" N ARG D 727 " --> pdb=" O GLU D 723 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 729 " --> pdb=" O ILE D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 749 Processing helix chain 'D' and resid 772 through 789 Processing helix chain 'D' and resid 789 through 797 removed outlier: 4.524A pdb=" N LYS D 795 " --> pdb=" O LEU D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 841 removed outlier: 3.785A pdb=" N ILE D 825 " --> pdb=" O GLY D 821 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 83 removed outlier: 6.034A pdb=" N LEU A 36 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ASP A 79 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE A 38 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLN A 81 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY A 40 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE A 83 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N PHE A 42 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA A 105 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ILE A 106 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N HIS A 129 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.422A pdb=" N VAL A 174 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 279 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 280 " --> pdb=" O ASP A 390 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 403 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N SER A 393 " --> pdb=" O LYS A 401 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LYS A 401 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 477 through 482 removed outlier: 3.699A pdb=" N THR A 437 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 512 " --> pdb=" O ILE A 434 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA5, first strand: chain 'A' and resid 490 through 492 Processing sheet with id=AA6, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AA7, first strand: chain 'A' and resid 682 through 683 removed outlier: 5.879A pdb=" N GLY A 683 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N GLU A 738 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET A 737 " --> pdb=" O SER A 539 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 75 through 83 removed outlier: 6.515A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ASP B 79 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N PHE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLN B 81 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE B 83 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N PHE B 107 " --> pdb=" O ARG B 37 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY B 39 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 106 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.352A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR B 254 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N PHE B 279 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N PHE B 256 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N MET B 276 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 368 through 369 removed outlier: 3.942A pdb=" N TRP B 368 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR B 376 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASP B 386 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 403 through 406 removed outlier: 3.814A pdb=" N ASN B 412 " --> pdb=" O THR B 404 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 534 through 535 removed outlier: 4.013A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR B 764 " --> pdb=" O MET B 534 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 538 through 539 removed outlier: 3.740A pdb=" N MET B 737 " --> pdb=" O SER B 539 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 541 through 543 Processing sheet with id=AB6, first strand: chain 'B' and resid 682 through 683 Processing sheet with id=AB7, first strand: chain 'C' and resid 77 through 83 removed outlier: 8.677A pdb=" N PHE C 107 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY C 39 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE C 106 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.093A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR C 173 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ASP C 229 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL C 175 " --> pdb=" O ASP C 229 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE C 256 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE C 279 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY C 403 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER C 393 " --> pdb=" O LYS C 401 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LYS C 401 " --> pdb=" O SER C 393 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP C 406 " --> pdb=" O GLY C 410 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 432 through 437 removed outlier: 7.397A pdb=" N LEU C 433 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ARG C 481 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL C 435 " --> pdb=" O ARG C 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AC2, first strand: chain 'C' and resid 513 through 519 removed outlier: 6.311A pdb=" N ALA C 515 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLY C 765 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU C 517 " --> pdb=" O GLY C 763 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY C 763 " --> pdb=" O LEU C 517 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 513 through 519 removed outlier: 6.311A pdb=" N ALA C 515 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLY C 765 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU C 517 " --> pdb=" O GLY C 763 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLY C 763 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 682 through 684 removed outlier: 7.090A pdb=" N GLY C 683 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N GLU C 738 " --> pdb=" O GLY C 683 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR C 542 " --> pdb=" O THR C 753 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR C 753 " --> pdb=" O TYR C 542 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 35 through 37 removed outlier: 6.152A pdb=" N LEU D 36 " --> pdb=" O THR D 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 39 through 40 removed outlier: 7.299A pdb=" N GLY D 39 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE D 106 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 42 through 43 removed outlier: 6.187A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.401A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL D 226 " --> pdb=" O ILE D 255 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 278 through 280 removed outlier: 3.563A pdb=" N ARG D 280 " --> pdb=" O ASP D 390 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 369 through 370 Processing sheet with id=AD2, first strand: chain 'D' and resid 404 through 406 removed outlier: 3.931A pdb=" N ASP D 406 " --> pdb=" O GLY D 410 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 433 through 436 Processing sheet with id=AD4, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AD5, first strand: chain 'D' and resid 490 through 491 Processing sheet with id=AD6, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AD7, first strand: chain 'D' and resid 534 through 536 removed outlier: 3.660A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 717 through 718 removed outlier: 9.791A pdb=" N VAL D 718 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ALA D 684 " --> pdb=" O VAL D 718 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU D 681 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU D 736 " --> pdb=" O GLU D 681 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 9.889A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 10.985A pdb=" N VAL D 685 " --> pdb=" O GLU D 738 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N TYR D 733 " --> pdb=" O ARG D 543 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG D 543 " --> pdb=" O TYR D 733 " (cutoff:3.500A) 986 hydrogen bonds defined for protein. 2832 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: 4.89 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7616 1.34 - 1.46: 6024 1.46 - 1.58: 11022 1.58 - 1.70: 0 1.70 - 1.82: 232 Bond restraints: 24894 Sorted by residual: bond pdb=" N MET D 664 " pdb=" CA MET D 664 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.16e+00 bond pdb=" N MET A 664 " pdb=" CA MET A 664 " ideal model delta sigma weight residual 1.459 1.485 -0.027 1.25e-02 6.40e+03 4.56e+00 bond pdb=" N MET B 664 " pdb=" CA MET B 664 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.55e+00 bond pdb=" N MET C 664 " pdb=" CA MET C 664 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.23e-02 6.61e+03 4.13e+00 bond pdb=" CB ASP B 177 " pdb=" CG ASP B 177 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.31e+00 ... (remaining 24889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 33338 2.38 - 4.76: 306 4.76 - 7.14: 53 7.14 - 9.51: 12 9.51 - 11.89: 7 Bond angle restraints: 33716 Sorted by residual: angle pdb=" CB MET D 770 " pdb=" CG MET D 770 " pdb=" SD MET D 770 " ideal model delta sigma weight residual 112.70 124.59 -11.89 3.00e+00 1.11e-01 1.57e+01 angle pdb=" CA ILE C 41 " pdb=" CB ILE C 41 " pdb=" CG1 ILE C 41 " ideal model delta sigma weight residual 110.40 117.08 -6.68 1.70e+00 3.46e-01 1.54e+01 angle pdb=" CB MET C 794 " pdb=" CG MET C 794 " pdb=" SD MET C 794 " ideal model delta sigma weight residual 112.70 124.38 -11.68 3.00e+00 1.11e-01 1.51e+01 angle pdb=" CB MET C 248 " pdb=" CG MET C 248 " pdb=" SD MET C 248 " ideal model delta sigma weight residual 112.70 123.46 -10.76 3.00e+00 1.11e-01 1.29e+01 angle pdb=" CB MET A 298 " pdb=" CG MET A 298 " pdb=" SD MET A 298 " ideal model delta sigma weight residual 112.70 123.38 -10.68 3.00e+00 1.11e-01 1.27e+01 ... (remaining 33711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 13198 17.88 - 35.76: 1727 35.76 - 53.65: 422 53.65 - 71.53: 66 71.53 - 89.41: 25 Dihedral angle restraints: 15438 sinusoidal: 6726 harmonic: 8712 Sorted by residual: dihedral pdb=" CB CYS C 750 " pdb=" SG CYS C 750 " pdb=" SG CYS C 804 " pdb=" CB CYS C 804 " ideal model delta sinusoidal sigma weight residual -86.00 -144.72 58.72 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CB CYS D 750 " pdb=" SG CYS D 750 " pdb=" SG CYS D 804 " pdb=" CB CYS D 804 " ideal model delta sinusoidal sigma weight residual 93.00 144.36 -51.36 1 1.00e+01 1.00e-02 3.61e+01 dihedral pdb=" CB CYS D 96 " pdb=" SG CYS D 96 " pdb=" SG CYS D 347 " pdb=" CB CYS D 347 " ideal model delta sinusoidal sigma weight residual 93.00 141.56 -48.56 1 1.00e+01 1.00e-02 3.25e+01 ... (remaining 15435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3716 0.087 - 0.174: 212 0.174 - 0.261: 4 0.261 - 0.348: 1 0.348 - 0.435: 1 Chirality restraints: 3934 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 67 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.72e+00 chirality pdb=" C1 NAG C1003 " pdb=" ND2 ASN C 751 " pdb=" C2 NAG C1003 " pdb=" O5 NAG C1003 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN B 378 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 3931 not shown) Planarity restraints: 4223 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 41 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C ILE C 41 " -0.034 2.00e-02 2.50e+03 pdb=" O ILE C 41 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE C 42 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 555 " -0.012 2.00e-02 2.50e+03 1.44e-02 3.62e+00 pdb=" CG PHE B 555 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE B 555 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 555 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 555 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 555 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 555 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 304 " 0.031 5.00e-02 4.00e+02 4.62e-02 3.42e+00 pdb=" N PRO A 305 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 305 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 305 " 0.026 5.00e-02 4.00e+02 ... (remaining 4220 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 11578 2.96 - 3.45: 26325 3.45 - 3.93: 40135 3.93 - 4.42: 45236 4.42 - 4.90: 70910 Nonbonded interactions: 194184 Sorted by model distance: nonbonded pdb=" C4 NAG I 2 " pdb=" O5 BMA I 3 " model vdw 2.477 2.776 nonbonded pdb=" C4 NAG Q 1 " pdb=" O5 NAG Q 2 " model vdw 2.520 2.776 nonbonded pdb=" C4 NAG J 2 " pdb=" O5 NAG J 3 " model vdw 2.543 2.776 nonbonded pdb=" O2 BMA I 3 " pdb=" O3 BMA I 3 " model vdw 2.568 2.432 nonbonded pdb=" O LEU D 259 " pdb=" OD1 ASP D 260 " model vdw 2.583 3.040 ... (remaining 194179 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 417 or resid 432 through 582 or resid 631 throu \ gh 836 or resid 1002 through 1003)) selection = (chain 'B' and (resid 33 through 582 or resid 631 through 836 or resid 1003 thro \ ugh 1004)) selection = (chain 'C' and (resid 33 through 417 or resid 432 through 836 or resid 1002 thro \ ugh 1003)) selection = (chain 'D' and (resid 33 through 836 or resid 1001 through 1002)) } ncs_group { reference = (chain 'E' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) } ncs_group { reference = chain 'F' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' } 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.520 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 : 0.002 0.035 24948 Z= 0.105 Angle : 0.614 11.893 33870 Z= 0.287 Chirality : 0.041 0.435 3934 Planarity : 0.003 0.046 4198 Dihedral : 16.472 89.410 9812 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.12 % Allowed : 28.64 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.16), residues: 2988 helix: 0.38 (0.15), residues: 1241 sheet: -1.57 (0.29), residues: 355 loop : -1.40 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 775 TYR 0.013 0.001 TYR B 566 PHE 0.033 0.001 PHE B 555 TRP 0.028 0.001 TRP C 368 HIS 0.004 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00225 (24894) covalent geometry : angle 0.59655 (33716) SS BOND : bond 0.00079 ( 8) SS BOND : angle 0.45974 ( 16) hydrogen bonds : bond 0.23898 ( 984) hydrogen bonds : angle 7.81121 ( 2832) link_BETA1-4 : bond 0.00495 ( 21) link_BETA1-4 : angle 2.01264 ( 63) link_NAG-ASN : bond 0.00484 ( 25) link_NAG-ASN : angle 2.57124 ( 75) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 266 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8426 (tmm) REVERT: A 316 MET cc_start: 0.9302 (mmm) cc_final: 0.8797 (tpt) REVERT: A 340 MET cc_start: 0.7218 (mmm) cc_final: 0.6282 (mmm) REVERT: A 444 VAL cc_start: 0.8496 (t) cc_final: 0.8220 (t) REVERT: A 645 LEU cc_start: 0.8705 (mt) cc_final: 0.8396 (mt) REVERT: A 717 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8608 (mm) REVERT: B 50 MET cc_start: 0.7828 (ppp) cc_final: 0.7007 (ppp) REVERT: B 111 HIS cc_start: 0.6169 (p-80) cc_final: 0.5299 (p-80) REVERT: B 210 ASP cc_start: 0.7626 (m-30) cc_final: 0.6880 (t0) REVERT: B 217 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8395 (tm-30) REVERT: B 234 MET cc_start: 0.8559 (tpp) cc_final: 0.8299 (tpp) REVERT: B 298 MET cc_start: 0.9117 (ptp) cc_final: 0.8823 (ptp) REVERT: B 335 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8690 (tt0) REVERT: B 340 MET cc_start: 0.8280 (tmm) cc_final: 0.7616 (tmm) REVERT: B 433 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7903 (pp) REVERT: C 116 ASN cc_start: 0.9228 (t0) cc_final: 0.8963 (t0) REVERT: C 247 MET cc_start: 0.7962 (pmm) cc_final: 0.7630 (pmm) REVERT: C 520 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8938 (p) REVERT: C 691 MET cc_start: 0.8680 (ppp) cc_final: 0.8195 (ppp) REVERT: C 705 MET cc_start: 0.8859 (mmm) cc_final: 0.8453 (tpp) REVERT: D 153 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8028 (t80) REVERT: D 316 MET cc_start: 0.9107 (mmm) cc_final: 0.8556 (tpt) REVERT: D 501 MET cc_start: 0.7987 (tpp) cc_final: 0.7750 (tpt) REVERT: D 541 LEU cc_start: 0.9068 (tp) cc_final: 0.8726 (tt) REVERT: D 549 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.8202 (p0) REVERT: D 647 ILE cc_start: 0.9276 (mm) cc_final: 0.8986 (mm) outliers start: 81 outliers final: 63 residues processed: 327 average time/residue: 0.1289 time to fit residues: 72.9634 Evaluate side-chains 326 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 256 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 764 TYR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 463 CYS Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 396 GLU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 549 ASN Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 794 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 197 optimal weight: 0.1980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS ** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 HIS ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.105070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.073693 restraints weight = 66195.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.076349 restraints weight = 36066.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.076832 restraints weight = 21540.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.077987 restraints weight = 20414.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.078065 restraints weight = 17834.147| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 24948 Z= 0.215 Angle : 0.637 13.624 33870 Z= 0.310 Chirality : 0.043 0.360 3934 Planarity : 0.004 0.046 4198 Dihedral : 7.085 59.525 4320 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 6.71 % Allowed : 24.87 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.16), residues: 2988 helix: 0.93 (0.14), residues: 1301 sheet: -1.79 (0.29), residues: 343 loop : -1.45 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 775 TYR 0.023 0.001 TYR A 566 PHE 0.017 0.001 PHE A 533 TRP 0.020 0.001 TRP C 368 HIS 0.008 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00481 (24894) covalent geometry : angle 0.61794 (33716) SS BOND : bond 0.00052 ( 8) SS BOND : angle 0.87396 ( 16) hydrogen bonds : bond 0.05023 ( 984) hydrogen bonds : angle 5.20066 ( 2832) link_BETA1-4 : bond 0.00384 ( 21) link_BETA1-4 : angle 2.07975 ( 63) link_NAG-ASN : bond 0.00606 ( 25) link_NAG-ASN : angle 2.81793 ( 75) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 255 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8038 (ttp80) REVERT: A 122 CYS cc_start: 0.9159 (m) cc_final: 0.8950 (m) REVERT: A 180 THR cc_start: 0.9250 (OUTLIER) cc_final: 0.9039 (m) REVERT: A 316 MET cc_start: 0.9256 (mmm) cc_final: 0.8853 (tpt) REVERT: A 444 VAL cc_start: 0.8610 (t) cc_final: 0.8358 (t) REVERT: A 507 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8145 (t70) REVERT: A 645 LEU cc_start: 0.8724 (mt) cc_final: 0.8437 (mt) REVERT: A 712 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8553 (ttm110) REVERT: A 717 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8866 (mm) REVERT: A 752 LEU cc_start: 0.8704 (tp) cc_final: 0.8433 (tp) REVERT: A 754 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8308 (tt0) REVERT: B 50 MET cc_start: 0.8064 (ppp) cc_final: 0.7052 (ppp) REVERT: B 217 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8086 (tm-30) REVERT: B 234 MET cc_start: 0.8295 (tpp) cc_final: 0.7980 (tpp) REVERT: B 269 TYR cc_start: 0.9162 (OUTLIER) cc_final: 0.8883 (m-10) REVERT: B 340 MET cc_start: 0.8226 (tmm) cc_final: 0.7570 (tmm) REVERT: B 433 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8006 (pp) REVERT: B 635 ILE cc_start: 0.8943 (mm) cc_final: 0.8733 (mt) REVERT: B 696 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8016 (mppt) REVERT: C 116 ASN cc_start: 0.9320 (t0) cc_final: 0.8983 (t0) REVERT: C 536 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8974 (pp) REVERT: C 565 MET cc_start: 0.8432 (mmp) cc_final: 0.8189 (mmm) REVERT: C 691 MET cc_start: 0.8728 (ppp) cc_final: 0.8393 (ppp) REVERT: D 153 PHE cc_start: 0.9319 (OUTLIER) cc_final: 0.8164 (t80) REVERT: D 316 MET cc_start: 0.9131 (mmm) cc_final: 0.8597 (tpt) REVERT: D 359 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8411 (t80) REVERT: D 501 MET cc_start: 0.8043 (tpp) cc_final: 0.7684 (tpp) REVERT: D 505 LEU cc_start: 0.6650 (OUTLIER) cc_final: 0.6422 (mm) REVERT: D 541 LEU cc_start: 0.9257 (tp) cc_final: 0.9008 (tt) REVERT: D 794 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6809 (pmm) outliers start: 174 outliers final: 105 residues processed: 405 average time/residue: 0.1294 time to fit residues: 89.9959 Evaluate side-chains 367 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 248 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 754 GLN Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 764 TYR Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 696 LYS Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 557 ASN Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 802 CYS Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 549 ASN Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 744 PHE Chi-restraints excluded: chain D residue 794 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 82 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 251 optimal weight: 9.9990 chunk 10 optimal weight: 0.3980 chunk 260 optimal weight: 3.9990 chunk 194 optimal weight: 0.0980 chunk 255 optimal weight: 6.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS D 111 HIS ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.105595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.074120 restraints weight = 66247.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.076898 restraints weight = 35588.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.077571 restraints weight = 21122.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.078057 restraints weight = 19384.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.078208 restraints weight = 17835.681| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24948 Z= 0.168 Angle : 0.606 14.052 33870 Z= 0.289 Chirality : 0.043 0.439 3934 Planarity : 0.003 0.047 4198 Dihedral : 6.679 59.263 4277 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 6.67 % Allowed : 25.67 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.16), residues: 2988 helix: 1.10 (0.15), residues: 1301 sheet: -1.73 (0.28), residues: 353 loop : -1.49 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 775 TYR 0.022 0.001 TYR A 566 PHE 0.018 0.001 PHE A 735 TRP 0.023 0.001 TRP C 368 HIS 0.006 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00383 (24894) covalent geometry : angle 0.58600 (33716) SS BOND : bond 0.00161 ( 8) SS BOND : angle 0.69491 ( 16) hydrogen bonds : bond 0.04037 ( 984) hydrogen bonds : angle 4.80761 ( 2832) link_BETA1-4 : bond 0.00419 ( 21) link_BETA1-4 : angle 2.05918 ( 63) link_NAG-ASN : bond 0.00541 ( 25) link_NAG-ASN : angle 2.83692 ( 75) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 264 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8080 (ttp80) REVERT: A 90 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8461 (tp30) REVERT: A 180 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8979 (m) REVERT: A 484 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7797 (mt-10) REVERT: A 507 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8135 (t70) REVERT: A 645 LEU cc_start: 0.8729 (mt) cc_final: 0.8438 (mt) REVERT: A 712 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8570 (ttm110) REVERT: A 752 LEU cc_start: 0.8673 (tp) cc_final: 0.8329 (tp) REVERT: A 754 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8213 (tt0) REVERT: B 50 MET cc_start: 0.7899 (ppp) cc_final: 0.7179 (ppp) REVERT: B 152 ASP cc_start: 0.8116 (t70) cc_final: 0.7794 (t70) REVERT: B 217 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8050 (tm-30) REVERT: B 234 MET cc_start: 0.8278 (tpp) cc_final: 0.7911 (tpp) REVERT: B 269 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.8867 (m-10) REVERT: B 335 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8763 (tt0) REVERT: B 340 MET cc_start: 0.8252 (tmm) cc_final: 0.7719 (tmm) REVERT: B 433 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7998 (pp) REVERT: B 635 ILE cc_start: 0.8905 (mm) cc_final: 0.8678 (mt) REVERT: B 735 PHE cc_start: 0.7619 (t80) cc_final: 0.6954 (t80) REVERT: B 737 MET cc_start: 0.7948 (tpp) cc_final: 0.7575 (tpp) REVERT: C 54 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6471 (tm-30) REVERT: C 116 ASN cc_start: 0.9297 (t0) cc_final: 0.8988 (t0) REVERT: C 319 ASP cc_start: 0.8427 (p0) cc_final: 0.8215 (p0) REVERT: C 520 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8965 (p) REVERT: C 536 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8981 (pp) REVERT: C 564 TRP cc_start: 0.8040 (m-10) cc_final: 0.7586 (m-10) REVERT: C 565 MET cc_start: 0.8495 (mmp) cc_final: 0.8247 (mmm) REVERT: C 691 MET cc_start: 0.8746 (ppp) cc_final: 0.8385 (ppp) REVERT: D 50 MET cc_start: 0.8271 (tmm) cc_final: 0.7898 (tmm) REVERT: D 71 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8897 (pp) REVERT: D 136 HIS cc_start: 0.8518 (OUTLIER) cc_final: 0.8297 (t70) REVERT: D 153 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.8060 (t80) REVERT: D 360 MET cc_start: 0.8910 (mmm) cc_final: 0.7328 (mmm) REVERT: D 579 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6379 (p90) REVERT: D 647 ILE cc_start: 0.9454 (mm) cc_final: 0.9100 (mm) REVERT: D 794 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.6998 (pmm) outliers start: 173 outliers final: 116 residues processed: 410 average time/residue: 0.1299 time to fit residues: 90.0319 Evaluate side-chains 384 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 250 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 754 GLN Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 764 TYR Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 566 TYR Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 557 ASN Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 802 CYS Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 549 ASN Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 579 PHE Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 744 PHE Chi-restraints excluded: chain D residue 794 MET Chi-restraints excluded: chain D residue 815 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 165 optimal weight: 0.7980 chunk 268 optimal weight: 20.0000 chunk 262 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 144 optimal weight: 0.0870 chunk 135 optimal weight: 3.9990 chunk 279 optimal weight: 0.9980 chunk 175 optimal weight: 9.9990 overall best weight: 2.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 HIS ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.105673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.072588 restraints weight = 67529.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.076287 restraints weight = 37206.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.076949 restraints weight = 22796.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.077394 restraints weight = 18224.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.077592 restraints weight = 17759.452| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24948 Z= 0.163 Angle : 0.601 14.421 33870 Z= 0.286 Chirality : 0.042 0.430 3934 Planarity : 0.003 0.047 4198 Dihedral : 6.654 59.136 4271 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 6.90 % Allowed : 25.98 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.16), residues: 2988 helix: 1.21 (0.15), residues: 1301 sheet: -1.75 (0.28), residues: 356 loop : -1.51 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 158 TYR 0.020 0.001 TYR A 566 PHE 0.016 0.001 PHE A 735 TRP 0.023 0.001 TRP C 368 HIS 0.006 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00372 (24894) covalent geometry : angle 0.58036 (33716) SS BOND : bond 0.00057 ( 8) SS BOND : angle 1.17386 ( 16) hydrogen bonds : bond 0.03618 ( 984) hydrogen bonds : angle 4.64379 ( 2832) link_BETA1-4 : bond 0.00416 ( 21) link_BETA1-4 : angle 2.07261 ( 63) link_NAG-ASN : bond 0.00532 ( 25) link_NAG-ASN : angle 2.81398 ( 75) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 262 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8461 (tp30) REVERT: A 155 SER cc_start: 0.9273 (OUTLIER) cc_final: 0.8875 (t) REVERT: A 444 VAL cc_start: 0.8649 (t) cc_final: 0.8402 (t) REVERT: A 469 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8399 (tp30) REVERT: A 484 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7824 (mt-10) REVERT: A 507 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8132 (t70) REVERT: A 645 LEU cc_start: 0.8749 (mt) cc_final: 0.8425 (mt) REVERT: A 712 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8575 (ttm110) REVERT: A 717 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8897 (mm) REVERT: A 754 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8205 (tt0) REVERT: B 50 MET cc_start: 0.7836 (ppp) cc_final: 0.7260 (ppp) REVERT: B 217 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8058 (tm-30) REVERT: B 234 MET cc_start: 0.8262 (tpp) cc_final: 0.7878 (tpp) REVERT: B 269 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.8830 (m-10) REVERT: B 335 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8764 (tt0) REVERT: B 340 MET cc_start: 0.8277 (tmm) cc_final: 0.7786 (tmm) REVERT: B 433 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8003 (pp) REVERT: B 635 ILE cc_start: 0.8928 (mm) cc_final: 0.8702 (mt) REVERT: B 735 PHE cc_start: 0.7591 (t80) cc_final: 0.7239 (t80) REVERT: C 54 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6466 (tm-30) REVERT: C 116 ASN cc_start: 0.9319 (t0) cc_final: 0.9013 (t0) REVERT: C 520 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8957 (p) REVERT: C 564 TRP cc_start: 0.8001 (m-10) cc_final: 0.7637 (m-10) REVERT: C 565 MET cc_start: 0.8591 (mmp) cc_final: 0.8327 (mmm) REVERT: C 691 MET cc_start: 0.8774 (ppp) cc_final: 0.8385 (ppp) REVERT: D 50 MET cc_start: 0.8080 (tmm) cc_final: 0.7675 (tmm) REVERT: D 71 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8875 (pp) REVERT: D 136 HIS cc_start: 0.8545 (OUTLIER) cc_final: 0.8339 (t70) REVERT: D 153 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8327 (t80) REVERT: D 316 MET cc_start: 0.9100 (mmm) cc_final: 0.8588 (tpt) REVERT: D 501 MET cc_start: 0.7953 (tpp) cc_final: 0.7588 (tpp) REVERT: D 505 LEU cc_start: 0.6372 (OUTLIER) cc_final: 0.6156 (mm) REVERT: D 579 PHE cc_start: 0.6914 (OUTLIER) cc_final: 0.6379 (p90) REVERT: D 647 ILE cc_start: 0.9477 (mm) cc_final: 0.9115 (mm) REVERT: D 794 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.7087 (pmm) outliers start: 179 outliers final: 126 residues processed: 415 average time/residue: 0.1298 time to fit residues: 91.7944 Evaluate side-chains 393 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 248 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 754 GLN Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 764 TYR Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 557 ASN Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 802 CYS Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 549 ASN Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 579 PHE Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 744 PHE Chi-restraints excluded: chain D residue 794 MET Chi-restraints excluded: chain D residue 800 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 173 optimal weight: 0.7980 chunk 259 optimal weight: 0.8980 chunk 234 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 257 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 229 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 109 optimal weight: 0.0870 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 HIS ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.107019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.076316 restraints weight = 65630.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.078241 restraints weight = 36632.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.078546 restraints weight = 22955.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.079291 restraints weight = 22481.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.079357 restraints weight = 19399.495| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24948 Z= 0.112 Angle : 0.591 14.842 33870 Z= 0.276 Chirality : 0.042 0.443 3934 Planarity : 0.003 0.048 4198 Dihedral : 6.563 59.207 4270 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 5.40 % Allowed : 27.91 % Favored : 66.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.16), residues: 2988 helix: 1.22 (0.15), residues: 1306 sheet: -1.64 (0.28), residues: 356 loop : -1.50 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 800 TYR 0.019 0.001 TYR A 566 PHE 0.015 0.001 PHE A 735 TRP 0.025 0.001 TRP B 706 HIS 0.004 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00256 (24894) covalent geometry : angle 0.57078 (33716) SS BOND : bond 0.00218 ( 8) SS BOND : angle 1.29867 ( 16) hydrogen bonds : bond 0.03338 ( 984) hydrogen bonds : angle 4.49533 ( 2832) link_BETA1-4 : bond 0.00460 ( 21) link_BETA1-4 : angle 2.04007 ( 63) link_NAG-ASN : bond 0.00471 ( 25) link_NAG-ASN : angle 2.69741 ( 75) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 271 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8376 (tp30) REVERT: A 215 LEU cc_start: 0.9651 (OUTLIER) cc_final: 0.9424 (mm) REVERT: A 316 MET cc_start: 0.9163 (mmm) cc_final: 0.8687 (tpt) REVERT: A 444 VAL cc_start: 0.8671 (t) cc_final: 0.8423 (t) REVERT: A 469 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8328 (tp30) REVERT: A 507 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8085 (t70) REVERT: A 645 LEU cc_start: 0.8815 (mt) cc_final: 0.8445 (mt) REVERT: A 712 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8589 (ttm110) REVERT: A 717 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8811 (mm) REVERT: B 50 MET cc_start: 0.7786 (ppp) cc_final: 0.7248 (ppp) REVERT: B 217 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8014 (tm-30) REVERT: B 234 MET cc_start: 0.8192 (tpp) cc_final: 0.7868 (tpp) REVERT: B 269 TYR cc_start: 0.9075 (OUTLIER) cc_final: 0.8701 (m-10) REVERT: B 335 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8771 (tt0) REVERT: B 340 MET cc_start: 0.8274 (tmm) cc_final: 0.7850 (tmm) REVERT: B 433 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7988 (pp) REVERT: B 487 LYS cc_start: 0.6563 (OUTLIER) cc_final: 0.6244 (pttt) REVERT: B 649 SER cc_start: 0.9356 (p) cc_final: 0.8948 (t) REVERT: B 735 PHE cc_start: 0.7462 (t80) cc_final: 0.7215 (t80) REVERT: C 54 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6364 (tm-30) REVERT: C 116 ASN cc_start: 0.9230 (t0) cc_final: 0.8924 (t0) REVERT: C 132 THR cc_start: 0.8361 (t) cc_final: 0.8054 (t) REVERT: C 247 MET cc_start: 0.8005 (pmm) cc_final: 0.7570 (pmm) REVERT: C 323 MET cc_start: 0.9288 (tpp) cc_final: 0.9018 (tpp) REVERT: C 520 THR cc_start: 0.9198 (OUTLIER) cc_final: 0.8956 (p) REVERT: C 564 TRP cc_start: 0.7957 (m-10) cc_final: 0.7706 (m-10) REVERT: C 565 MET cc_start: 0.8573 (mmp) cc_final: 0.8357 (mmm) REVERT: C 691 MET cc_start: 0.8789 (ppp) cc_final: 0.8402 (ppp) REVERT: C 705 MET cc_start: 0.8848 (mmm) cc_final: 0.8485 (mmt) REVERT: C 747 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.7740 (tp-100) REVERT: D 50 MET cc_start: 0.8049 (tmm) cc_final: 0.7634 (tmm) REVERT: D 71 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8925 (pp) REVERT: D 153 PHE cc_start: 0.9190 (OUTLIER) cc_final: 0.8351 (t80) REVERT: D 316 MET cc_start: 0.9111 (mmm) cc_final: 0.8564 (tpt) REVERT: D 579 PHE cc_start: 0.6891 (OUTLIER) cc_final: 0.6318 (p90) REVERT: D 647 ILE cc_start: 0.9432 (mm) cc_final: 0.9093 (mm) REVERT: D 794 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.7184 (pmm) outliers start: 140 outliers final: 96 residues processed: 385 average time/residue: 0.1272 time to fit residues: 84.2198 Evaluate side-chains 369 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 256 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 764 TYR Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 269 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 557 ASN Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 747 GLN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 802 CYS Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 549 ASN Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 579 PHE Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 744 PHE Chi-restraints excluded: chain D residue 794 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 194 optimal weight: 7.9990 chunk 259 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 119 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 chunk 216 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 HIS ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.103141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.070443 restraints weight = 66704.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.072820 restraints weight = 35287.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.074353 restraints weight = 24232.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.075358 restraints weight = 19270.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.075971 restraints weight = 16679.932| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 24948 Z= 0.285 Angle : 0.705 15.028 33870 Z= 0.340 Chirality : 0.045 0.389 3934 Planarity : 0.004 0.048 4198 Dihedral : 6.918 58.964 4265 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 6.78 % Allowed : 26.95 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.16), residues: 2988 helix: 1.18 (0.15), residues: 1305 sheet: -2.04 (0.27), residues: 357 loop : -1.61 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 712 TYR 0.021 0.002 TYR A 566 PHE 0.018 0.002 PHE A 735 TRP 0.028 0.002 TRP B 706 HIS 0.012 0.002 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00639 (24894) covalent geometry : angle 0.68474 (33716) SS BOND : bond 0.00190 ( 8) SS BOND : angle 1.58379 ( 16) hydrogen bonds : bond 0.03725 ( 984) hydrogen bonds : angle 4.73406 ( 2832) link_BETA1-4 : bond 0.00421 ( 21) link_BETA1-4 : angle 2.23922 ( 63) link_NAG-ASN : bond 0.00745 ( 25) link_NAG-ASN : angle 3.00506 ( 75) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 252 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8485 (tp30) REVERT: A 155 SER cc_start: 0.9357 (OUTLIER) cc_final: 0.8971 (t) REVERT: A 180 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.9031 (m) REVERT: A 444 VAL cc_start: 0.8624 (t) cc_final: 0.8377 (t) REVERT: A 469 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8355 (tp30) REVERT: A 484 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7749 (mt-10) REVERT: A 507 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8084 (t70) REVERT: A 645 LEU cc_start: 0.8849 (mt) cc_final: 0.8498 (mt) REVERT: A 712 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8546 (ttm110) REVERT: A 737 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7794 (ppp) REVERT: A 754 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: B 50 MET cc_start: 0.8093 (ppp) cc_final: 0.7748 (ppp) REVERT: B 84 ASN cc_start: 0.7750 (m-40) cc_final: 0.7485 (m-40) REVERT: B 217 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8035 (tm-30) REVERT: B 234 MET cc_start: 0.8479 (tpp) cc_final: 0.8201 (mmm) REVERT: B 335 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8783 (tt0) REVERT: B 340 MET cc_start: 0.8201 (tmm) cc_final: 0.7874 (tmm) REVERT: B 433 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7991 (pp) REVERT: B 487 LYS cc_start: 0.6839 (OUTLIER) cc_final: 0.6455 (pttt) REVERT: B 635 ILE cc_start: 0.8879 (mm) cc_final: 0.8664 (mm) REVERT: B 735 PHE cc_start: 0.7559 (t80) cc_final: 0.7103 (t80) REVERT: C 116 ASN cc_start: 0.9311 (t0) cc_final: 0.9028 (t0) REVERT: C 319 ASP cc_start: 0.8537 (p0) cc_final: 0.7763 (p0) REVERT: C 495 ASN cc_start: 0.9049 (p0) cc_final: 0.8606 (p0) REVERT: C 520 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8930 (p) REVERT: C 564 TRP cc_start: 0.8018 (m-10) cc_final: 0.7591 (m-10) REVERT: C 565 MET cc_start: 0.8501 (mmp) cc_final: 0.8263 (mmm) REVERT: C 691 MET cc_start: 0.8737 (ppp) cc_final: 0.8279 (ppp) REVERT: C 709 MET cc_start: 0.9015 (mmm) cc_final: 0.8744 (mmm) REVERT: C 747 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8006 (tp-100) REVERT: D 50 MET cc_start: 0.8013 (tmm) cc_final: 0.7602 (tmm) REVERT: D 153 PHE cc_start: 0.9335 (OUTLIER) cc_final: 0.7926 (t80) REVERT: D 264 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.8925 (tp) REVERT: D 269 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.8739 (m-10) REVERT: D 501 MET cc_start: 0.7567 (tpp) cc_final: 0.7290 (tpp) REVERT: D 505 LEU cc_start: 0.6436 (OUTLIER) cc_final: 0.6103 (mm) REVERT: D 579 PHE cc_start: 0.6904 (OUTLIER) cc_final: 0.6377 (p90) REVERT: D 794 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7204 (pmm) outliers start: 176 outliers final: 133 residues processed: 396 average time/residue: 0.1352 time to fit residues: 91.8260 Evaluate side-chains 395 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 242 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 754 GLN Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 764 TYR Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 641 TRP Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 745 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 802 CYS Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 557 ASN Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 747 GLN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 802 CYS Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 269 TYR Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 549 ASN Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 579 PHE Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 744 PHE Chi-restraints excluded: chain D residue 794 MET Chi-restraints excluded: chain D residue 800 ARG Chi-restraints excluded: chain D residue 815 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 286 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 167 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 264 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS D 111 HIS ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.106223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.074652 restraints weight = 66977.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.076653 restraints weight = 36756.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.076815 restraints weight = 23753.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.077323 restraints weight = 23106.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.077495 restraints weight = 20296.752| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24948 Z= 0.132 Angle : 0.625 15.205 33870 Z= 0.292 Chirality : 0.043 0.438 3934 Planarity : 0.003 0.049 4198 Dihedral : 6.676 59.387 4260 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.82 % Allowed : 27.95 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.16), residues: 2988 helix: 1.29 (0.15), residues: 1301 sheet: -1.88 (0.28), residues: 346 loop : -1.53 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 800 TYR 0.020 0.001 TYR A 566 PHE 0.018 0.001 PHE A 735 TRP 0.026 0.001 TRP C 368 HIS 0.005 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00305 (24894) covalent geometry : angle 0.60487 (33716) SS BOND : bond 0.00163 ( 8) SS BOND : angle 1.29247 ( 16) hydrogen bonds : bond 0.03261 ( 984) hydrogen bonds : angle 4.46808 ( 2832) link_BETA1-4 : bond 0.00447 ( 21) link_BETA1-4 : angle 2.07948 ( 63) link_NAG-ASN : bond 0.00501 ( 25) link_NAG-ASN : angle 2.81048 ( 75) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 258 time to evaluate : 0.957 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: A 90 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8456 (tp30) REVERT: A 155 SER cc_start: 0.9289 (OUTLIER) cc_final: 0.8888 (t) REVERT: A 444 VAL cc_start: 0.8732 (t) cc_final: 0.8509 (t) REVERT: A 469 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8369 (tp30) REVERT: A 484 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7826 (mt-10) REVERT: A 507 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8122 (t70) REVERT: A 645 LEU cc_start: 0.8864 (mt) cc_final: 0.8498 (mt) REVERT: A 712 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8599 (ttm110) REVERT: A 754 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: B 84 ASN cc_start: 0.7810 (m-40) cc_final: 0.7496 (m110) REVERT: B 217 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8003 (tm-30) REVERT: B 234 MET cc_start: 0.8267 (tpp) cc_final: 0.7862 (tpp) REVERT: B 335 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8748 (tt0) REVERT: B 340 MET cc_start: 0.8290 (tmm) cc_final: 0.8011 (tmm) REVERT: B 487 LYS cc_start: 0.6857 (OUTLIER) cc_final: 0.6466 (pttt) REVERT: B 635 ILE cc_start: 0.8906 (mm) cc_final: 0.8689 (mm) REVERT: B 649 SER cc_start: 0.9373 (p) cc_final: 0.9009 (t) REVERT: B 735 PHE cc_start: 0.7335 (t80) cc_final: 0.7006 (t80) REVERT: C 42 PHE cc_start: 0.7856 (m-10) cc_final: 0.7633 (m-10) REVERT: C 50 MET cc_start: 0.7994 (tmm) cc_final: 0.7326 (tmm) REVERT: C 54 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6257 (tm-30) REVERT: C 111 HIS cc_start: 0.5233 (OUTLIER) cc_final: 0.4477 (p90) REVERT: C 116 ASN cc_start: 0.9285 (t0) cc_final: 0.9008 (t0) REVERT: C 520 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.8978 (p) REVERT: C 564 TRP cc_start: 0.7982 (m-10) cc_final: 0.7727 (m-10) REVERT: C 565 MET cc_start: 0.8628 (mmp) cc_final: 0.8406 (mmm) REVERT: C 691 MET cc_start: 0.8789 (ppp) cc_final: 0.8362 (ppp) REVERT: C 705 MET cc_start: 0.8825 (mmm) cc_final: 0.8416 (mmt) REVERT: C 709 MET cc_start: 0.8970 (mmm) cc_final: 0.8678 (mmm) REVERT: C 747 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.7848 (tp-100) REVERT: D 50 MET cc_start: 0.7864 (tmm) cc_final: 0.7475 (tmm) REVERT: D 153 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8372 (t80) REVERT: D 264 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8871 (tp) REVERT: D 316 MET cc_start: 0.9088 (mmm) cc_final: 0.8570 (tpt) REVERT: D 501 MET cc_start: 0.7543 (tpp) cc_final: 0.7261 (tpp) REVERT: D 505 LEU cc_start: 0.6306 (OUTLIER) cc_final: 0.6042 (mm) REVERT: D 579 PHE cc_start: 0.6966 (OUTLIER) cc_final: 0.6377 (p90) REVERT: D 794 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7327 (pmm) outliers start: 151 outliers final: 111 residues processed: 383 average time/residue: 0.1290 time to fit residues: 84.8106 Evaluate side-chains 378 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 249 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 754 GLN Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 764 TYR Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 557 ASN Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 747 GLN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 802 CYS Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 549 ASN Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 579 PHE Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 744 PHE Chi-restraints excluded: chain D residue 794 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 90 optimal weight: 1.9990 chunk 144 optimal weight: 0.0010 chunk 145 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 191 optimal weight: 7.9990 chunk 195 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 276 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS D 111 HIS ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.106935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.075049 restraints weight = 65619.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.078947 restraints weight = 35810.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.079541 restraints weight = 20117.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.080029 restraints weight = 16762.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.080139 restraints weight = 16422.797| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24948 Z= 0.113 Angle : 0.624 15.800 33870 Z= 0.289 Chirality : 0.043 0.434 3934 Planarity : 0.003 0.048 4198 Dihedral : 6.517 59.955 4258 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 5.24 % Allowed : 28.41 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.16), residues: 2988 helix: 1.28 (0.15), residues: 1300 sheet: -1.80 (0.28), residues: 346 loop : -1.51 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 800 TYR 0.019 0.001 TYR A 566 PHE 0.016 0.001 PHE A 735 TRP 0.030 0.001 TRP C 368 HIS 0.011 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00262 (24894) covalent geometry : angle 0.60517 (33716) SS BOND : bond 0.00397 ( 8) SS BOND : angle 1.20020 ( 16) hydrogen bonds : bond 0.03143 ( 984) hydrogen bonds : angle 4.37187 ( 2832) link_BETA1-4 : bond 0.00460 ( 21) link_BETA1-4 : angle 2.05952 ( 63) link_NAG-ASN : bond 0.00481 ( 25) link_NAG-ASN : angle 2.71981 ( 75) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 269 time to evaluate : 0.930 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: A 90 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8423 (tp30) REVERT: A 316 MET cc_start: 0.9111 (mmm) cc_final: 0.8488 (tpt) REVERT: A 444 VAL cc_start: 0.8675 (t) cc_final: 0.8446 (t) REVERT: A 469 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8345 (tp30) REVERT: A 507 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8094 (t70) REVERT: A 645 LEU cc_start: 0.8848 (mt) cc_final: 0.8466 (mt) REVERT: A 691 MET cc_start: 0.8341 (ptt) cc_final: 0.7838 (ptt) REVERT: A 712 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8612 (ttm110) REVERT: A 754 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: B 84 ASN cc_start: 0.7750 (m-40) cc_final: 0.7475 (m110) REVERT: B 152 ASP cc_start: 0.8124 (t70) cc_final: 0.7692 (t0) REVERT: B 217 GLU cc_start: 0.8513 (tm-30) cc_final: 0.7967 (tm-30) REVERT: B 234 MET cc_start: 0.8165 (tpp) cc_final: 0.7802 (tpp) REVERT: B 335 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8739 (tt0) REVERT: B 433 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8028 (pp) REVERT: B 487 LYS cc_start: 0.6683 (OUTLIER) cc_final: 0.6337 (pttt) REVERT: B 635 ILE cc_start: 0.8878 (mm) cc_final: 0.8662 (mm) REVERT: B 649 SER cc_start: 0.9339 (p) cc_final: 0.9012 (t) REVERT: B 735 PHE cc_start: 0.7321 (t80) cc_final: 0.7017 (t80) REVERT: C 54 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6343 (tm-30) REVERT: C 116 ASN cc_start: 0.9222 (t0) cc_final: 0.8964 (t0) REVERT: C 520 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8962 (p) REVERT: C 564 TRP cc_start: 0.7975 (m-10) cc_final: 0.7774 (m-10) REVERT: C 565 MET cc_start: 0.8552 (mmp) cc_final: 0.8325 (mmm) REVERT: C 691 MET cc_start: 0.8770 (ppp) cc_final: 0.8349 (ppp) REVERT: C 709 MET cc_start: 0.8946 (mmm) cc_final: 0.8616 (mmm) REVERT: C 747 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.7856 (tp-100) REVERT: D 50 MET cc_start: 0.7901 (tmm) cc_final: 0.7482 (tmm) REVERT: D 87 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7689 (t0) REVERT: D 153 PHE cc_start: 0.9202 (OUTLIER) cc_final: 0.8373 (t80) REVERT: D 264 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8864 (tp) REVERT: D 316 MET cc_start: 0.9102 (mmm) cc_final: 0.8593 (tpt) REVERT: D 501 MET cc_start: 0.7515 (tpp) cc_final: 0.7251 (tpp) REVERT: D 505 LEU cc_start: 0.6278 (OUTLIER) cc_final: 0.6031 (mm) REVERT: D 579 PHE cc_start: 0.6942 (OUTLIER) cc_final: 0.6413 (p90) REVERT: D 691 MET cc_start: 0.8565 (mmm) cc_final: 0.8337 (mmm) REVERT: D 799 TRP cc_start: 0.6548 (OUTLIER) cc_final: 0.5703 (t-100) outliers start: 136 outliers final: 105 residues processed: 381 average time/residue: 0.1275 time to fit residues: 83.6944 Evaluate side-chains 376 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 254 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 754 GLN Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 764 TYR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 557 ASN Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 747 GLN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 802 CYS Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 549 ASN Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 579 PHE Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 744 PHE Chi-restraints excluded: chain D residue 794 MET Chi-restraints excluded: chain D residue 799 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 86 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 293 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 277 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 0.1980 chunk 154 optimal weight: 5.9990 chunk 270 optimal weight: 30.0000 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS D 111 HIS ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.105630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.073658 restraints weight = 67543.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.076048 restraints weight = 37256.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.076770 restraints weight = 23032.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.077099 restraints weight = 20892.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.077156 restraints weight = 18989.676| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24948 Z= 0.177 Angle : 0.658 15.998 33870 Z= 0.306 Chirality : 0.044 0.414 3934 Planarity : 0.003 0.048 4198 Dihedral : 6.590 59.874 4257 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 5.63 % Allowed : 28.41 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.16), residues: 2988 helix: 1.36 (0.15), residues: 1290 sheet: -1.86 (0.28), residues: 347 loop : -1.52 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 800 TYR 0.018 0.001 TYR A 566 PHE 0.020 0.001 PHE A 735 TRP 0.029 0.001 TRP C 368 HIS 0.010 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00408 (24894) covalent geometry : angle 0.63923 (33716) SS BOND : bond 0.00107 ( 8) SS BOND : angle 1.28185 ( 16) hydrogen bonds : bond 0.03247 ( 984) hydrogen bonds : angle 4.43623 ( 2832) link_BETA1-4 : bond 0.00408 ( 21) link_BETA1-4 : angle 2.09635 ( 63) link_NAG-ASN : bond 0.00531 ( 25) link_NAG-ASN : angle 2.78660 ( 75) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 253 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8509 (tp30) REVERT: A 155 SER cc_start: 0.9282 (OUTLIER) cc_final: 0.8863 (t) REVERT: A 316 MET cc_start: 0.9120 (mmm) cc_final: 0.8504 (tpt) REVERT: A 444 VAL cc_start: 0.8724 (t) cc_final: 0.8492 (t) REVERT: A 469 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8407 (tp30) REVERT: A 507 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.8118 (t70) REVERT: A 645 LEU cc_start: 0.8874 (mt) cc_final: 0.8469 (mt) REVERT: A 691 MET cc_start: 0.8527 (ptt) cc_final: 0.7999 (ptt) REVERT: A 712 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8673 (ttm110) REVERT: A 754 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: B 50 MET cc_start: 0.8015 (ppp) cc_final: 0.7193 (ppp) REVERT: B 84 ASN cc_start: 0.7846 (m-40) cc_final: 0.7526 (m110) REVERT: B 152 ASP cc_start: 0.8318 (t70) cc_final: 0.7848 (t0) REVERT: B 217 GLU cc_start: 0.8587 (tm-30) cc_final: 0.7987 (tm-30) REVERT: B 234 MET cc_start: 0.8306 (tpp) cc_final: 0.8055 (mmm) REVERT: B 335 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.8796 (tm-30) REVERT: B 433 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7973 (pp) REVERT: B 487 LYS cc_start: 0.6801 (OUTLIER) cc_final: 0.6435 (pttt) REVERT: B 635 ILE cc_start: 0.8901 (mm) cc_final: 0.8681 (mm) REVERT: B 735 PHE cc_start: 0.7555 (t80) cc_final: 0.7063 (t80) REVERT: C 116 ASN cc_start: 0.9290 (t0) cc_final: 0.9008 (t0) REVERT: C 270 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.7990 (ttp80) REVERT: C 323 MET cc_start: 0.9340 (tpp) cc_final: 0.9051 (tpp) REVERT: C 495 ASN cc_start: 0.9021 (p0) cc_final: 0.8663 (p0) REVERT: C 520 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8958 (p) REVERT: C 564 TRP cc_start: 0.7981 (m-10) cc_final: 0.7736 (m-10) REVERT: C 565 MET cc_start: 0.8599 (mmp) cc_final: 0.8351 (mmm) REVERT: C 691 MET cc_start: 0.8782 (ppp) cc_final: 0.8292 (ppp) REVERT: C 705 MET cc_start: 0.8667 (mmm) cc_final: 0.8341 (mmt) REVERT: C 709 MET cc_start: 0.9050 (mmm) cc_final: 0.8710 (mmm) REVERT: C 747 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.7843 (tp-100) REVERT: D 50 MET cc_start: 0.7852 (tmm) cc_final: 0.7458 (tmm) REVERT: D 87 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7684 (t0) REVERT: D 153 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8172 (t80) REVERT: D 264 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8883 (tp) REVERT: D 316 MET cc_start: 0.9113 (mmm) cc_final: 0.8590 (tpt) REVERT: D 501 MET cc_start: 0.7537 (tpp) cc_final: 0.7268 (tpp) REVERT: D 505 LEU cc_start: 0.6335 (OUTLIER) cc_final: 0.6077 (mm) REVERT: D 579 PHE cc_start: 0.6963 (OUTLIER) cc_final: 0.6428 (p90) REVERT: D 799 TRP cc_start: 0.6580 (OUTLIER) cc_final: 0.5728 (t-100) outliers start: 146 outliers final: 116 residues processed: 373 average time/residue: 0.1245 time to fit residues: 80.0491 Evaluate side-chains 384 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 250 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 463 CYS Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 754 GLN Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 764 TYR Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 641 TRP Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 802 CYS Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 557 ASN Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 747 GLN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 802 CYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 549 ASN Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 579 PHE Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 744 PHE Chi-restraints excluded: chain D residue 794 MET Chi-restraints excluded: chain D residue 799 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 22 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 297 optimal weight: 9.9990 chunk 146 optimal weight: 0.0060 chunk 164 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 11 optimal weight: 0.0040 chunk 86 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.8610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS D 111 HIS ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.107189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.075338 restraints weight = 65504.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.079119 restraints weight = 35659.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.079713 restraints weight = 20126.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.080149 restraints weight = 16927.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.080360 restraints weight = 16607.929| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24948 Z= 0.113 Angle : 0.648 16.552 33870 Z= 0.296 Chirality : 0.043 0.435 3934 Planarity : 0.003 0.048 4198 Dihedral : 6.455 59.158 4255 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.93 % Allowed : 29.07 % Favored : 66.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.16), residues: 2988 helix: 1.31 (0.15), residues: 1297 sheet: -1.66 (0.28), residues: 356 loop : -1.55 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 800 TYR 0.018 0.001 TYR A 566 PHE 0.021 0.001 PHE A 735 TRP 0.034 0.001 TRP C 368 HIS 0.005 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00263 (24894) covalent geometry : angle 0.62992 (33716) SS BOND : bond 0.00091 ( 8) SS BOND : angle 1.15508 ( 16) hydrogen bonds : bond 0.03112 ( 984) hydrogen bonds : angle 4.35111 ( 2832) link_BETA1-4 : bond 0.00458 ( 21) link_BETA1-4 : angle 2.04709 ( 63) link_NAG-ASN : bond 0.00483 ( 25) link_NAG-ASN : angle 2.70782 ( 75) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 268 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8379 (tp30) REVERT: A 316 MET cc_start: 0.9113 (mmm) cc_final: 0.8492 (tpt) REVERT: A 444 VAL cc_start: 0.8612 (t) cc_final: 0.8373 (t) REVERT: A 469 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8341 (tp30) REVERT: A 507 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8100 (t70) REVERT: A 565 MET cc_start: 0.8800 (pmm) cc_final: 0.7931 (pmm) REVERT: A 645 LEU cc_start: 0.8846 (mt) cc_final: 0.8466 (mt) REVERT: A 691 MET cc_start: 0.8403 (ptt) cc_final: 0.7874 (ptt) REVERT: A 712 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8661 (ttm110) REVERT: B 50 MET cc_start: 0.7965 (ppp) cc_final: 0.7308 (ppp) REVERT: B 84 ASN cc_start: 0.7742 (m-40) cc_final: 0.7448 (m110) REVERT: B 152 ASP cc_start: 0.8224 (t70) cc_final: 0.7803 (t0) REVERT: B 217 GLU cc_start: 0.8498 (tm-30) cc_final: 0.7928 (tm-30) REVERT: B 234 MET cc_start: 0.8137 (tpp) cc_final: 0.7929 (mmm) REVERT: B 335 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8757 (tm-30) REVERT: B 433 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8003 (pp) REVERT: B 487 LYS cc_start: 0.6626 (OUTLIER) cc_final: 0.6273 (pttt) REVERT: B 635 ILE cc_start: 0.8875 (mm) cc_final: 0.8656 (mm) REVERT: B 649 SER cc_start: 0.9357 (p) cc_final: 0.8984 (t) REVERT: B 735 PHE cc_start: 0.7438 (t80) cc_final: 0.7043 (t80) REVERT: C 42 PHE cc_start: 0.7994 (m-10) cc_final: 0.7769 (m-10) REVERT: C 116 ASN cc_start: 0.9250 (t0) cc_final: 0.8983 (t0) REVERT: C 245 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7603 (ptp) REVERT: C 520 THR cc_start: 0.9191 (OUTLIER) cc_final: 0.8959 (p) REVERT: C 565 MET cc_start: 0.8542 (mmp) cc_final: 0.8292 (mmm) REVERT: C 691 MET cc_start: 0.8794 (ppp) cc_final: 0.8382 (ppp) REVERT: C 705 MET cc_start: 0.8678 (mmm) cc_final: 0.8361 (mmt) REVERT: C 709 MET cc_start: 0.9005 (mmm) cc_final: 0.8666 (mmm) REVERT: C 747 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.7738 (tp-100) REVERT: D 50 MET cc_start: 0.7848 (tmm) cc_final: 0.7448 (tmm) REVERT: D 87 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7686 (t0) REVERT: D 153 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8288 (t80) REVERT: D 264 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8853 (tp) REVERT: D 316 MET cc_start: 0.9096 (mmm) cc_final: 0.8569 (tpt) REVERT: D 360 MET cc_start: 0.8933 (mmm) cc_final: 0.7952 (mmm) REVERT: D 501 MET cc_start: 0.7570 (tpp) cc_final: 0.7305 (tpp) REVERT: D 505 LEU cc_start: 0.6249 (OUTLIER) cc_final: 0.5990 (mm) REVERT: D 579 PHE cc_start: 0.6921 (OUTLIER) cc_final: 0.6401 (p90) REVERT: D 691 MET cc_start: 0.8549 (mmm) cc_final: 0.8266 (mmm) REVERT: D 799 TRP cc_start: 0.6453 (OUTLIER) cc_final: 0.5607 (t-100) outliers start: 128 outliers final: 106 residues processed: 372 average time/residue: 0.1281 time to fit residues: 82.0508 Evaluate side-chains 380 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 258 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 566 TYR Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 764 TYR Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 487 LYS Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 802 CYS Chi-restraints excluded: chain B residue 823 ILE Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 493 ASP Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 557 ASN Chi-restraints excluded: chain C residue 648 ILE Chi-restraints excluded: chain C residue 747 GLN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 772 SER Chi-restraints excluded: chain C residue 802 CYS Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 549 ASN Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 579 PHE Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 744 PHE Chi-restraints excluded: chain D residue 794 MET Chi-restraints excluded: chain D residue 799 TRP Chi-restraints excluded: chain D residue 815 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 214 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 264 optimal weight: 0.5980 chunk 45 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 184 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 239 optimal weight: 0.9980 chunk 256 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS D 111 HIS ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.106575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.074618 restraints weight = 65857.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.078394 restraints weight = 35688.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.079107 restraints weight = 19925.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.079367 restraints weight = 16839.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.079514 restraints weight = 16475.133| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24948 Z= 0.137 Angle : 0.656 16.232 33870 Z= 0.301 Chirality : 0.043 0.423 3934 Planarity : 0.003 0.048 4198 Dihedral : 6.452 59.245 4255 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 5.17 % Allowed : 28.87 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.16), residues: 2988 helix: 1.34 (0.15), residues: 1296 sheet: -1.75 (0.28), residues: 356 loop : -1.56 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 800 TYR 0.018 0.001 TYR A 566 PHE 0.022 0.001 PHE A 735 TRP 0.039 0.001 TRP C 564 HIS 0.005 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00322 (24894) covalent geometry : angle 0.63792 (33716) SS BOND : bond 0.00111 ( 8) SS BOND : angle 1.18903 ( 16) hydrogen bonds : bond 0.03098 ( 984) hydrogen bonds : angle 4.35339 ( 2832) link_BETA1-4 : bond 0.00428 ( 21) link_BETA1-4 : angle 2.05574 ( 63) link_NAG-ASN : bond 0.00488 ( 25) link_NAG-ASN : angle 2.70473 ( 75) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3944.10 seconds wall clock time: 69 minutes 13.76 seconds (4153.76 seconds total)