Starting phenix.real_space_refine on Tue Jun 24 17:25:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bj4_44629/06_2025/9bj4_44629.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bj4_44629/06_2025/9bj4_44629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bj4_44629/06_2025/9bj4_44629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bj4_44629/06_2025/9bj4_44629.map" model { file = "/net/cci-nas-00/data/ceres_data/9bj4_44629/06_2025/9bj4_44629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bj4_44629/06_2025/9bj4_44629.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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 129 5.16 5 C 18284 2.51 5 N 4762 2.21 5 O 5522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 1.52s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28697 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7825 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Chain: "B" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7825 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Chain: "C" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7825 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 53, 'TRANS': 948} Chain breaks: 7 Chain: "H" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 917 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "L" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 805 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "D" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 917 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "E" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 805 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "F" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 917 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "G" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 805 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "I" 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: "J" 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: 18.08, per 1000 atoms: 0.63 Number of scatterers: 28697 At special positions: 0 Unit cell: (140.567, 138.832, 205.645, 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 129 16.00 O 5522 8.00 N 4762 7.00 C 18284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 91 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 91 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 91 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG I 1 " - " ASN A 343 " " NAG J 1 " - " ASN B 343 " Time building additional restraints: 6.10 Conformation dependent library (CDL) restraints added in 3.4 seconds 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6846 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 57 sheets defined 22.8% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.77 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.004A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.054A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.076A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.290A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.714A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.551A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.140A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.326A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.585A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.485A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.969A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.954A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.052A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.030A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 408 removed outlier: 4.549A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.571A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.078A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.143A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.269A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.510A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.892A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.021A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.807A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.051A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.466A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.040A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.118A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.176A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.434A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.907A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.793A pdb=" N GLU H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.896A pdb=" N GLU L 86 " --> pdb=" O ALA L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 101 removed outlier: 3.871A pdb=" N LEU L 101 " --> pdb=" O LEU L 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 removed outlier: 3.719A pdb=" N GLU D 64 " --> pdb=" O PRO D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'E' and resid 82 through 86 removed outlier: 3.529A pdb=" N ASP E 85 " --> pdb=" O GLN E 82 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU E 86 " --> pdb=" O ALA E 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 82 through 86' Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.881A pdb=" N LEU E 101 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 64 removed outlier: 3.724A pdb=" N GLU F 64 " --> pdb=" O PRO F 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 64' Processing helix chain 'G' and resid 82 through 86 removed outlier: 3.520A pdb=" N ASP G 85 " --> pdb=" O GLN G 82 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU G 86 " --> pdb=" O ALA G 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 82 through 86' Processing helix chain 'G' and resid 97 through 101 removed outlier: 3.876A pdb=" N LEU G 101 " --> pdb=" O LEU G 98 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.301A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.826A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.602A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.931A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.397A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 5.887A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.367A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.835A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.525A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.251A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.764A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.764A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.768A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.721A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.525A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.554A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B 276 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.266A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.433A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 324 through 328 removed outlier: 5.794A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.342A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.795A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.158A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.664A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.916A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD1, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.077A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.011A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.603A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.680A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.468A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 610 " --> pdb=" O ILE C 651 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.343A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.816A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.357A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.780A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.854A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE4, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.449A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.449A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP H 101 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AE8, first strand: chain 'L' and resid 49 through 51 removed outlier: 6.342A pdb=" N LEU L 49 " --> pdb=" O GLN L 40 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N GLN L 40 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE L 51 " --> pdb=" O TRP L 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 49 through 51 removed outlier: 6.342A pdb=" N LEU L 49 " --> pdb=" O GLN L 40 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N GLN L 40 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE L 51 " --> pdb=" O TRP L 38 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AF2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.421A pdb=" N GLU D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL D 109 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA D 88 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.421A pdb=" N GLU D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL D 109 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA D 88 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG D 94 " --> pdb=" O LEU D 102 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 9 through 12 removed outlier: 3.666A pdb=" N ILE E 51 " --> pdb=" O TRP E 38 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N GLN E 40 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU E 49 " --> pdb=" O GLN E 40 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 9 through 12 Processing sheet with id=AF6, first strand: chain 'E' and resid 19 through 24 Processing sheet with id=AF7, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AF8, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.443A pdb=" N GLU F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL F 109 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA F 88 " --> pdb=" O VAL F 109 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.443A pdb=" N GLU F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL F 109 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA F 88 " --> pdb=" O VAL F 109 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N CYS F 92 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TRP F 103 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ARG F 94 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP F 101 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.678A pdb=" N ILE G 51 " --> pdb=" O TRP G 38 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLN G 40 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU G 49 " --> pdb=" O GLN G 40 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 9 through 12 Processing sheet with id=AG3, first strand: chain 'G' and resid 19 through 24 1146 hydrogen bonds defined for protein. 3072 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: 14.94 Time building geometry restraints manager: 7.42 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: 9246 1.34 - 1.46: 6569 1.46 - 1.58: 13380 1.58 - 1.70: 0 1.70 - 1.82: 165 Bond restraints: 29360 Sorted by residual: bond pdb=" N SER A 443 " pdb=" CA SER A 443 " ideal model delta sigma weight residual 1.453 1.485 -0.031 1.22e-02 6.72e+03 6.54e+00 bond pdb=" N ASP A 442 " pdb=" CA ASP A 442 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.31e-02 5.83e+03 6.36e+00 bond pdb=" N PHE B 342 " pdb=" CA PHE B 342 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.33e-02 5.65e+03 5.76e+00 bond pdb=" N LYS A 444 " pdb=" CA LYS A 444 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.23e-02 6.61e+03 5.53e+00 bond pdb=" N ASN A 343 " pdb=" CA ASN A 343 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.41e+00 ... (remaining 29355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 39391 2.04 - 4.08: 520 4.08 - 6.13: 48 6.13 - 8.17: 4 8.17 - 10.21: 4 Bond angle restraints: 39967 Sorted by residual: angle pdb=" C ASN C 87 " pdb=" CA ASN C 87 " pdb=" CB ASN C 87 " ideal model delta sigma weight residual 116.54 110.87 5.67 1.15e+00 7.56e-01 2.43e+01 angle pdb=" C ASN A 87 " pdb=" CA ASN A 87 " pdb=" CB ASN A 87 " ideal model delta sigma weight residual 117.23 110.82 6.41 1.36e+00 5.41e-01 2.22e+01 angle pdb=" CA CYS C 617 " pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " ideal model delta sigma weight residual 114.40 124.61 -10.21 2.30e+00 1.89e-01 1.97e+01 angle pdb=" CA CYS A 617 " pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " ideal model delta sigma weight residual 114.40 124.52 -10.12 2.30e+00 1.89e-01 1.94e+01 angle pdb=" N VAL B 130 " pdb=" CA VAL B 130 " pdb=" C VAL B 130 " ideal model delta sigma weight residual 112.43 108.63 3.80 9.20e-01 1.18e+00 1.71e+01 ... (remaining 39962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 15544 17.95 - 35.90: 1471 35.90 - 53.85: 386 53.85 - 71.79: 74 71.79 - 89.74: 33 Dihedral angle restraints: 17508 sinusoidal: 6837 harmonic: 10671 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 177.15 -84.15 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 175.67 -82.67 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -167.66 81.66 1 1.00e+01 1.00e-02 8.21e+01 ... (remaining 17505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4282 0.096 - 0.192: 251 0.192 - 0.288: 0 0.288 - 0.384: 1 0.384 - 0.480: 1 Chirality restraints: 4535 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.72e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 6.62e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.76e+00 ... (remaining 4532 not shown) Planarity restraints: 5172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.345 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG I 1 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " -0.100 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.530 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " -0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " -0.336 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG J 1 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " -0.141 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " 0.517 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " -0.304 2.00e-02 2.50e+03 2.57e-01 8.24e+02 pdb=" C7 NAG I 2 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " 0.442 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " -0.030 2.00e-02 2.50e+03 ... (remaining 5169 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 603 2.69 - 3.24: 26431 3.24 - 3.79: 41249 3.79 - 4.35: 51755 4.35 - 4.90: 90757 Nonbonded interactions: 210795 Sorted by model distance: nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.135 3.040 nonbonded pdb=" OG SER A 359 " pdb=" OD1 ASN A 394 " model vdw 2.147 3.040 nonbonded pdb=" O ILE C 742 " pdb=" NH1 ARG C1000 " model vdw 2.209 3.120 nonbonded pdb=" OG1 THR G 5 " pdb=" OG1 THR G 24 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR L 5 " pdb=" OG1 THR L 24 " model vdw 2.239 3.040 ... (remaining 210790 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' } 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=0.27 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 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: 1.250 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 67.950 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.180 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: 0.020 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 29409 Z= 0.164 Angle : 0.593 10.209 40069 Z= 0.321 Chirality : 0.045 0.480 4535 Planarity : 0.008 0.299 5170 Dihedral : 15.256 89.742 10527 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.58 % Favored : 96.25 % Rotamer: Outliers : 1.97 % Allowed : 15.90 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3630 helix: 1.81 (0.22), residues: 621 sheet: 0.76 (0.16), residues: 993 loop : -1.15 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 33 HIS 0.004 0.001 HIS A1064 PHE 0.028 0.001 PHE B 192 TYR 0.017 0.001 TYR A 170 ARG 0.005 0.000 ARG D 82A Details of bonding type rmsd link_NAG-ASN : bond 0.00869 ( 2) link_NAG-ASN : angle 4.06212 ( 6) link_BETA1-4 : bond 0.00329 ( 2) link_BETA1-4 : angle 1.00926 ( 6) hydrogen bonds : bond 0.14653 ( 1114) hydrogen bonds : angle 6.51688 ( 3072) SS BOND : bond 0.00463 ( 45) SS BOND : angle 1.84362 ( 90) covalent geometry : bond 0.00360 (29360) covalent geometry : angle 0.58484 (39967) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 271 time to evaluate : 2.966 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7449 (pm20) REVERT: A 220 PHE cc_start: 0.6584 (t80) cc_final: 0.6234 (t80) REVERT: A 238 PHE cc_start: 0.5303 (p90) cc_final: 0.5102 (p90) REVERT: A 473 TYR cc_start: 0.6735 (t80) cc_final: 0.6441 (t80) REVERT: H 38 ARG cc_start: 0.6158 (ptm160) cc_final: 0.5309 (mtp-110) REVERT: H 91 TYR cc_start: 0.6719 (m-10) cc_final: 0.6512 (m-80) REVERT: L 49 LEU cc_start: 0.6184 (tt) cc_final: 0.5939 (mp) REVERT: L 50 LEU cc_start: 0.6313 (tp) cc_final: 0.5881 (tt) REVERT: E 50 LEU cc_start: 0.6453 (tp) cc_final: 0.6066 (tt) REVERT: F 91 TYR cc_start: 0.6601 (m-10) cc_final: 0.6390 (m-10) outliers start: 63 outliers final: 54 residues processed: 325 average time/residue: 0.3636 time to fit residues: 195.0660 Evaluate side-chains 301 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 246 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 20.0000 chunk 277 optimal weight: 3.9990 chunk 153 optimal weight: 0.2980 chunk 94 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 286 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 174 optimal weight: 0.0570 chunk 213 optimal weight: 6.9990 chunk 332 optimal weight: 8.9990 overall best weight: 2.0704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN B 165 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN C 125 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 GLN E 40 GLN G 17 GLN G 54 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.159582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.103751 restraints weight = 46892.477| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.02 r_work: 0.3188 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29409 Z= 0.172 Angle : 0.596 10.534 40069 Z= 0.310 Chirality : 0.046 0.302 4535 Planarity : 0.004 0.038 5170 Dihedral : 5.790 59.307 4114 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.47 % Rotamer: Outliers : 3.44 % Allowed : 15.31 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 3630 helix: 1.97 (0.21), residues: 639 sheet: 0.65 (0.16), residues: 1029 loop : -1.17 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 33 HIS 0.005 0.001 HIS A1064 PHE 0.020 0.001 PHE A 86 TYR 0.018 0.001 TYR B1067 ARG 0.006 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 2) link_NAG-ASN : angle 5.16355 ( 6) link_BETA1-4 : bond 0.00851 ( 2) link_BETA1-4 : angle 3.17147 ( 6) hydrogen bonds : bond 0.06068 ( 1114) hydrogen bonds : angle 5.52357 ( 3072) SS BOND : bond 0.00422 ( 45) SS BOND : angle 1.73068 ( 90) covalent geometry : bond 0.00416 (29360) covalent geometry : angle 0.58641 (39967) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 274 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8015 (pt0) cc_final: 0.7582 (pm20) REVERT: A 220 PHE cc_start: 0.6508 (t80) cc_final: 0.6044 (t80) REVERT: A 473 TYR cc_start: 0.6818 (t80) cc_final: 0.6534 (t80) REVERT: A 752 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8519 (mm) REVERT: B 918 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7804 (mt-10) REVERT: H 38 ARG cc_start: 0.7072 (ptm160) cc_final: 0.6219 (mtp-110) REVERT: H 52 TYR cc_start: 0.7772 (t80) cc_final: 0.7348 (t80) REVERT: H 89 MET cc_start: 0.3694 (tpt) cc_final: 0.3114 (tpt) REVERT: H 91 TYR cc_start: 0.6254 (m-10) cc_final: 0.5832 (m-10) REVERT: L 40 GLN cc_start: 0.5726 (mm-40) cc_final: 0.5277 (mp10) REVERT: D 48 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7597 (tpp) REVERT: D 52 TYR cc_start: 0.7767 (t80) cc_final: 0.7480 (t80) REVERT: F 38 ARG cc_start: 0.5596 (ptm-80) cc_final: 0.5040 (mtp-110) REVERT: F 89 MET cc_start: 0.4006 (tpt) cc_final: 0.3802 (tpt) REVERT: G 40 GLN cc_start: 0.6958 (pp30) cc_final: 0.5513 (tp40) REVERT: G 50 LEU cc_start: 0.7128 (mp) cc_final: 0.6309 (tt) outliers start: 110 outliers final: 71 residues processed: 360 average time/residue: 0.3677 time to fit residues: 219.3352 Evaluate side-chains 325 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 251 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 103 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 24 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 287 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN C 439 ASN C 506 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 GLN E 29 ASN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.157153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.102139 restraints weight = 46943.080| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.12 r_work: 0.3150 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 29409 Z= 0.203 Angle : 0.610 8.794 40069 Z= 0.318 Chirality : 0.046 0.277 4535 Planarity : 0.004 0.044 5170 Dihedral : 5.420 59.052 4070 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.97 % Favored : 95.98 % Rotamer: Outliers : 4.34 % Allowed : 16.21 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.14), residues: 3630 helix: 1.88 (0.21), residues: 642 sheet: 0.66 (0.16), residues: 1014 loop : -1.26 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 33 HIS 0.005 0.001 HIS A1064 PHE 0.018 0.002 PHE A 543 TYR 0.019 0.001 TYR B1067 ARG 0.005 0.000 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00802 ( 2) link_NAG-ASN : angle 3.48190 ( 6) link_BETA1-4 : bond 0.00313 ( 2) link_BETA1-4 : angle 1.52931 ( 6) hydrogen bonds : bond 0.06478 ( 1114) hydrogen bonds : angle 5.50988 ( 3072) SS BOND : bond 0.00494 ( 45) SS BOND : angle 1.72458 ( 90) covalent geometry : bond 0.00497 (29360) covalent geometry : angle 0.60298 (39967) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 259 time to evaluate : 3.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7570 (pm20) REVERT: A 220 PHE cc_start: 0.6599 (t80) cc_final: 0.6143 (t80) REVERT: A 276 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7526 (tt) REVERT: A 473 TYR cc_start: 0.6833 (t80) cc_final: 0.6569 (t80) REVERT: A 752 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8526 (mm) REVERT: B 918 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: C 129 LYS cc_start: 0.6498 (tmtt) cc_final: 0.6108 (tptp) REVERT: H 32 TYR cc_start: 0.8322 (m-10) cc_final: 0.7974 (m-10) REVERT: H 38 ARG cc_start: 0.6675 (ptm160) cc_final: 0.5361 (mtm110) REVERT: H 89 MET cc_start: 0.4066 (tpt) cc_final: 0.3513 (tpt) REVERT: H 91 TYR cc_start: 0.6376 (m-10) cc_final: 0.6018 (m-10) REVERT: D 48 MET cc_start: 0.8252 (ttm) cc_final: 0.7641 (tpp) REVERT: D 52 TYR cc_start: 0.7833 (t80) cc_final: 0.7396 (t80) REVERT: F 40 MET cc_start: 0.8388 (mmm) cc_final: 0.7046 (ttt) REVERT: F 48 MET cc_start: 0.8460 (ttt) cc_final: 0.7953 (tpp) REVERT: G 40 GLN cc_start: 0.6795 (pp30) cc_final: 0.5332 (tp40) REVERT: G 50 LEU cc_start: 0.7185 (mp) cc_final: 0.6364 (tt) outliers start: 139 outliers final: 97 residues processed: 379 average time/residue: 0.3542 time to fit residues: 222.0510 Evaluate side-chains 352 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 251 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 103 TRP Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 42 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 158 optimal weight: 2.9990 chunk 320 optimal weight: 7.9990 chunk 269 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 184 optimal weight: 0.8980 chunk 364 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 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 = 0.4029 r_free = 0.4029 target = 0.159267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.105757 restraints weight = 47253.548| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.89 r_work: 0.3222 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 29409 Z= 0.111 Angle : 0.527 7.959 40069 Z= 0.274 Chirality : 0.044 0.284 4535 Planarity : 0.004 0.036 5170 Dihedral : 5.120 58.716 4064 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.00 % Allowed : 17.81 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3630 helix: 2.18 (0.21), residues: 642 sheet: 0.71 (0.16), residues: 1023 loop : -1.12 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 104 HIS 0.003 0.000 HIS B 519 PHE 0.018 0.001 PHE C 192 TYR 0.018 0.001 TYR B1067 ARG 0.003 0.000 ARG C1000 Details of bonding type rmsd link_NAG-ASN : bond 0.01094 ( 2) link_NAG-ASN : angle 3.94241 ( 6) link_BETA1-4 : bond 0.00393 ( 2) link_BETA1-4 : angle 1.71480 ( 6) hydrogen bonds : bond 0.05306 ( 1114) hydrogen bonds : angle 5.23434 ( 3072) SS BOND : bond 0.00433 ( 45) SS BOND : angle 1.41114 ( 90) covalent geometry : bond 0.00246 (29360) covalent geometry : angle 0.52036 (39967) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 274 time to evaluate : 3.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8120 (pt0) cc_final: 0.7735 (pm20) REVERT: A 473 TYR cc_start: 0.6915 (t80) cc_final: 0.6656 (t80) REVERT: B 52 GLN cc_start: 0.8239 (pm20) cc_final: 0.7980 (pm20) REVERT: B 918 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: C 129 LYS cc_start: 0.6820 (OUTLIER) cc_final: 0.6428 (tptp) REVERT: H 32 TYR cc_start: 0.8360 (m-10) cc_final: 0.7897 (m-80) REVERT: H 36 TRP cc_start: 0.6956 (m100) cc_final: 0.5513 (m100) REVERT: H 38 ARG cc_start: 0.6633 (ptm160) cc_final: 0.5389 (mtm110) REVERT: H 52 TYR cc_start: 0.8177 (t80) cc_final: 0.7591 (t80) REVERT: H 89 MET cc_start: 0.4214 (tpt) cc_final: 0.3682 (tpt) REVERT: H 91 TYR cc_start: 0.6615 (m-10) cc_final: 0.5725 (m-10) REVERT: D 36 TRP cc_start: 0.7080 (m100) cc_final: 0.6501 (m-90) REVERT: D 48 MET cc_start: 0.8399 (ttm) cc_final: 0.7815 (tpp) REVERT: D 52 TYR cc_start: 0.8089 (t80) cc_final: 0.7604 (t80) REVERT: D 89 MET cc_start: 0.3827 (tpt) cc_final: 0.3563 (tpt) REVERT: F 38 ARG cc_start: 0.6793 (ptm-80) cc_final: 0.6032 (ptm-80) REVERT: F 40 MET cc_start: 0.8317 (mmm) cc_final: 0.7148 (ttt) REVERT: F 48 MET cc_start: 0.8615 (ttt) cc_final: 0.8199 (tpp) REVERT: F 52 TYR cc_start: 0.8169 (t80) cc_final: 0.7629 (t80) REVERT: G 40 GLN cc_start: 0.6840 (pp30) cc_final: 0.5376 (tp40) REVERT: G 50 LEU cc_start: 0.7184 (mp) cc_final: 0.6350 (tt) outliers start: 96 outliers final: 66 residues processed: 352 average time/residue: 0.3779 time to fit residues: 218.8567 Evaluate side-chains 320 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 252 time to evaluate : 2.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 103 TRP Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 42 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 58 optimal weight: 5.9990 chunk 252 optimal weight: 4.9990 chunk 230 optimal weight: 4.9990 chunk 364 optimal weight: 10.0000 chunk 263 optimal weight: 0.8980 chunk 297 optimal weight: 2.9990 chunk 322 optimal weight: 20.0000 chunk 167 optimal weight: 0.0070 chunk 327 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 overall best weight: 2.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 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 = 0.3993 r_free = 0.3993 target = 0.156223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.100837 restraints weight = 47190.508| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.95 r_work: 0.3148 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 29409 Z= 0.216 Angle : 0.606 9.051 40069 Z= 0.317 Chirality : 0.046 0.308 4535 Planarity : 0.004 0.040 5170 Dihedral : 5.274 59.615 4060 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.52 % Favored : 95.45 % Rotamer: Outliers : 3.87 % Allowed : 17.46 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.14), residues: 3630 helix: 1.93 (0.21), residues: 642 sheet: 0.63 (0.16), residues: 1014 loop : -1.26 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 33 HIS 0.006 0.001 HIS A1064 PHE 0.020 0.002 PHE A 543 TYR 0.018 0.001 TYR B1067 ARG 0.004 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.01054 ( 2) link_NAG-ASN : angle 3.99314 ( 6) link_BETA1-4 : bond 0.00235 ( 2) link_BETA1-4 : angle 1.58671 ( 6) hydrogen bonds : bond 0.06428 ( 1114) hydrogen bonds : angle 5.39500 ( 3072) SS BOND : bond 0.00474 ( 45) SS BOND : angle 1.69083 ( 90) covalent geometry : bond 0.00540 (29360) covalent geometry : angle 0.59960 (39967) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 261 time to evaluate : 2.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7968 (pt0) cc_final: 0.7580 (pm20) REVERT: A 276 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7575 (tt) REVERT: A 473 TYR cc_start: 0.6939 (t80) cc_final: 0.6703 (t80) REVERT: A 516 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7801 (mp0) REVERT: A 752 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8580 (mm) REVERT: B 52 GLN cc_start: 0.8159 (pm20) cc_final: 0.7886 (pm20) REVERT: B 912 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8208 (p) REVERT: B 918 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7952 (mt-10) REVERT: C 129 LYS cc_start: 0.6650 (OUTLIER) cc_final: 0.6225 (tptp) REVERT: C 912 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8108 (p) REVERT: H 38 ARG cc_start: 0.6841 (ptm160) cc_final: 0.5312 (mtm110) REVERT: H 89 MET cc_start: 0.3976 (tpt) cc_final: 0.3561 (tpt) REVERT: H 91 TYR cc_start: 0.6559 (m-10) cc_final: 0.6164 (m-80) REVERT: D 36 TRP cc_start: 0.6843 (m100) cc_final: 0.6301 (m-90) REVERT: D 48 MET cc_start: 0.8267 (ttm) cc_final: 0.7686 (tpp) REVERT: F 38 ARG cc_start: 0.6858 (ptm-80) cc_final: 0.5561 (ptm-80) REVERT: F 40 MET cc_start: 0.8390 (mmm) cc_final: 0.7023 (ttt) REVERT: F 48 MET cc_start: 0.8470 (ttt) cc_final: 0.7663 (tpp) REVERT: F 52 TYR cc_start: 0.8014 (t80) cc_final: 0.7456 (t80) REVERT: G 40 GLN cc_start: 0.6749 (pp30) cc_final: 0.5403 (tp40) REVERT: G 50 LEU cc_start: 0.7400 (mp) cc_final: 0.6549 (tt) outliers start: 124 outliers final: 87 residues processed: 364 average time/residue: 0.3805 time to fit residues: 227.8630 Evaluate side-chains 345 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 252 time to evaluate : 3.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 103 TRP Chi-restraints excluded: chain F residue 111 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 249 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 260 optimal weight: 2.9990 chunk 353 optimal weight: 20.0000 chunk 312 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 ASN ** 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 = 0.4021 r_free = 0.4021 target = 0.158749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.103509 restraints weight = 47242.205| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.97 r_work: 0.3184 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29409 Z= 0.128 Angle : 0.536 7.995 40069 Z= 0.279 Chirality : 0.044 0.298 4535 Planarity : 0.004 0.037 5170 Dihedral : 5.077 59.010 4058 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.14 % Favored : 96.83 % Rotamer: Outliers : 3.06 % Allowed : 18.84 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 3630 helix: 2.16 (0.21), residues: 642 sheet: 0.60 (0.17), residues: 987 loop : -1.10 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.003 0.000 HIS C1064 PHE 0.017 0.001 PHE B 140 TYR 0.018 0.001 TYR B1067 ARG 0.003 0.000 ARG C1000 Details of bonding type rmsd link_NAG-ASN : bond 0.01078 ( 2) link_NAG-ASN : angle 3.54601 ( 6) link_BETA1-4 : bond 0.00269 ( 2) link_BETA1-4 : angle 1.62783 ( 6) hydrogen bonds : bond 0.05493 ( 1114) hydrogen bonds : angle 5.19432 ( 3072) SS BOND : bond 0.00386 ( 45) SS BOND : angle 1.40222 ( 90) covalent geometry : bond 0.00296 (29360) covalent geometry : angle 0.53040 (39967) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 268 time to evaluate : 3.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7936 (pt0) cc_final: 0.7555 (pm20) REVERT: A 220 PHE cc_start: 0.6114 (t80) cc_final: 0.5644 (t80) REVERT: A 473 TYR cc_start: 0.6739 (t80) cc_final: 0.6429 (t80) REVERT: A 912 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.7667 (p) REVERT: B 52 GLN cc_start: 0.8127 (pm20) cc_final: 0.7860 (pm20) REVERT: B 912 THR cc_start: 0.8292 (OUTLIER) cc_final: 0.7960 (p) REVERT: B 918 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7946 (mt-10) REVERT: C 129 LYS cc_start: 0.6546 (OUTLIER) cc_final: 0.6217 (tptp) REVERT: H 32 TYR cc_start: 0.8323 (m-10) cc_final: 0.8002 (m-10) REVERT: H 36 TRP cc_start: 0.6713 (m100) cc_final: 0.5213 (m100) REVERT: H 38 ARG cc_start: 0.6556 (ptm160) cc_final: 0.4946 (mtm110) REVERT: H 58 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6520 (mmt90) REVERT: H 89 MET cc_start: 0.4039 (tpt) cc_final: 0.3614 (tpt) REVERT: H 91 TYR cc_start: 0.6408 (m-10) cc_final: 0.5589 (m-80) REVERT: D 36 TRP cc_start: 0.6845 (m100) cc_final: 0.6328 (m-90) REVERT: D 48 MET cc_start: 0.8241 (ttm) cc_final: 0.7664 (tpp) REVERT: D 50 MET cc_start: 0.6169 (ttm) cc_final: 0.5915 (ttp) REVERT: D 52 TYR cc_start: 0.7959 (t80) cc_final: 0.7437 (t80) REVERT: F 38 ARG cc_start: 0.6753 (ptm-80) cc_final: 0.5642 (ptm-80) REVERT: F 40 MET cc_start: 0.8405 (mmm) cc_final: 0.7064 (ttt) REVERT: F 48 MET cc_start: 0.8481 (ttt) cc_final: 0.7673 (tpp) REVERT: F 52 TYR cc_start: 0.7980 (t80) cc_final: 0.7444 (t80) REVERT: F 89 MET cc_start: 0.3773 (tpt) cc_final: 0.3572 (tpt) REVERT: G 40 GLN cc_start: 0.6795 (pp30) cc_final: 0.5464 (tp40) REVERT: G 50 LEU cc_start: 0.7426 (mp) cc_final: 0.6645 (tt) outliers start: 98 outliers final: 79 residues processed: 349 average time/residue: 0.3939 time to fit residues: 224.9582 Evaluate side-chains 340 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 256 time to evaluate : 3.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 103 TRP Chi-restraints excluded: chain F residue 111 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 317 optimal weight: 0.0770 chunk 52 optimal weight: 0.7980 chunk 250 optimal weight: 1.9990 chunk 359 optimal weight: 20.0000 chunk 141 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 287 optimal weight: 3.9990 chunk 337 optimal weight: 9.9990 chunk 321 optimal weight: 20.0000 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.158702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.103547 restraints weight = 47305.400| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.95 r_work: 0.3187 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29409 Z= 0.130 Angle : 0.536 8.081 40069 Z= 0.278 Chirality : 0.044 0.300 4535 Planarity : 0.004 0.037 5170 Dihedral : 5.009 58.084 4058 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.77 % Favored : 96.17 % Rotamer: Outliers : 3.31 % Allowed : 19.06 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3630 helix: 2.23 (0.21), residues: 642 sheet: 0.61 (0.17), residues: 987 loop : -1.09 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.003 0.001 HIS A1064 PHE 0.018 0.001 PHE A 238 TYR 0.017 0.001 TYR B1067 ARG 0.002 0.000 ARG C1000 Details of bonding type rmsd link_NAG-ASN : bond 0.01091 ( 2) link_NAG-ASN : angle 3.35361 ( 6) link_BETA1-4 : bond 0.00264 ( 2) link_BETA1-4 : angle 1.59196 ( 6) hydrogen bonds : bond 0.05343 ( 1114) hydrogen bonds : angle 5.10937 ( 3072) SS BOND : bond 0.00364 ( 45) SS BOND : angle 1.35368 ( 90) covalent geometry : bond 0.00306 (29360) covalent geometry : angle 0.53095 (39967) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 268 time to evaluate : 3.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7602 (pm20) REVERT: A 220 PHE cc_start: 0.6301 (t80) cc_final: 0.5872 (t80) REVERT: A 473 TYR cc_start: 0.6839 (t80) cc_final: 0.6554 (t80) REVERT: A 516 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7693 (pm20) REVERT: A 912 THR cc_start: 0.8229 (OUTLIER) cc_final: 0.7647 (p) REVERT: B 52 GLN cc_start: 0.8139 (pm20) cc_final: 0.7876 (pm20) REVERT: B 409 GLN cc_start: 0.8437 (mp10) cc_final: 0.8093 (mp10) REVERT: B 912 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.7948 (p) REVERT: B 918 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8016 (mt-10) REVERT: C 129 LYS cc_start: 0.6571 (OUTLIER) cc_final: 0.6246 (tptp) REVERT: C 912 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.7838 (p) REVERT: H 32 TYR cc_start: 0.8348 (m-10) cc_final: 0.7989 (m-10) REVERT: H 36 TRP cc_start: 0.6731 (m100) cc_final: 0.5976 (m-90) REVERT: H 38 ARG cc_start: 0.6521 (ptm160) cc_final: 0.4865 (mtm110) REVERT: H 58 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.6481 (mmt90) REVERT: H 89 MET cc_start: 0.4093 (tpt) cc_final: 0.3664 (tpt) REVERT: H 91 TYR cc_start: 0.6452 (m-10) cc_final: 0.6112 (m-80) REVERT: D 36 TRP cc_start: 0.6890 (m100) cc_final: 0.6449 (m-90) REVERT: D 48 MET cc_start: 0.8236 (ttm) cc_final: 0.7676 (tpp) REVERT: D 50 MET cc_start: 0.6220 (ttm) cc_final: 0.5970 (ttp) REVERT: E 17 GLN cc_start: 0.0905 (OUTLIER) cc_final: 0.0584 (pm20) REVERT: F 38 ARG cc_start: 0.6673 (ptm-80) cc_final: 0.5397 (ptm-80) REVERT: F 40 MET cc_start: 0.8358 (mmm) cc_final: 0.6927 (ttt) REVERT: F 48 MET cc_start: 0.8492 (ttt) cc_final: 0.7662 (tpp) REVERT: F 52 TYR cc_start: 0.7989 (t80) cc_final: 0.7439 (t80) REVERT: G 40 GLN cc_start: 0.6750 (pp30) cc_final: 0.5458 (tp40) REVERT: G 50 LEU cc_start: 0.7455 (mp) cc_final: 0.6696 (tt) outliers start: 106 outliers final: 85 residues processed: 359 average time/residue: 0.4463 time to fit residues: 266.1790 Evaluate side-chains 351 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 257 time to evaluate : 2.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 103 TRP Chi-restraints excluded: chain F residue 111 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 150 optimal weight: 9.9990 chunk 301 optimal weight: 1.9990 chunk 291 optimal weight: 0.7980 chunk 177 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 312 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 357 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 295 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN E 40 GLN G 29 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.158172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.102752 restraints weight = 47738.106| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.36 r_work: 0.3157 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29409 Z= 0.118 Angle : 0.525 7.682 40069 Z= 0.273 Chirality : 0.044 0.292 4535 Planarity : 0.004 0.037 5170 Dihedral : 5.002 57.058 4058 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 3.06 % Allowed : 19.71 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 3630 helix: 2.31 (0.21), residues: 642 sheet: 0.61 (0.17), residues: 1002 loop : -1.02 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 104 HIS 0.003 0.000 HIS A1064 PHE 0.023 0.001 PHE B 192 TYR 0.017 0.001 TYR B1067 ARG 0.002 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.01050 ( 2) link_NAG-ASN : angle 3.23611 ( 6) link_BETA1-4 : bond 0.00286 ( 2) link_BETA1-4 : angle 1.65043 ( 6) hydrogen bonds : bond 0.05066 ( 1114) hydrogen bonds : angle 5.01977 ( 3072) SS BOND : bond 0.00327 ( 45) SS BOND : angle 1.26628 ( 90) covalent geometry : bond 0.00274 (29360) covalent geometry : angle 0.52012 (39967) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 268 time to evaluate : 3.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7437 (pm20) REVERT: A 220 PHE cc_start: 0.6017 (t80) cc_final: 0.5492 (t80) REVERT: A 473 TYR cc_start: 0.6635 (t80) cc_final: 0.6387 (t80) REVERT: A 912 THR cc_start: 0.7985 (OUTLIER) cc_final: 0.7317 (p) REVERT: B 52 GLN cc_start: 0.7953 (pm20) cc_final: 0.7684 (pm20) REVERT: B 409 GLN cc_start: 0.8360 (mp10) cc_final: 0.7948 (mp10) REVERT: B 912 THR cc_start: 0.8035 (OUTLIER) cc_final: 0.7607 (p) REVERT: B 918 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: C 129 LYS cc_start: 0.6325 (OUTLIER) cc_final: 0.6054 (tptp) REVERT: C 912 THR cc_start: 0.8014 (OUTLIER) cc_final: 0.7559 (p) REVERT: H 32 TYR cc_start: 0.8304 (m-10) cc_final: 0.7950 (m-10) REVERT: H 36 TRP cc_start: 0.6429 (m100) cc_final: 0.5729 (m-90) REVERT: H 38 ARG cc_start: 0.6366 (ptm160) cc_final: 0.4720 (mtm110) REVERT: H 58 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6297 (mmt90) REVERT: H 89 MET cc_start: 0.4008 (tpt) cc_final: 0.3522 (tpt) REVERT: H 91 TYR cc_start: 0.6126 (m-10) cc_final: 0.5824 (m-80) REVERT: D 36 TRP cc_start: 0.6671 (m100) cc_final: 0.6227 (m-90) REVERT: D 48 MET cc_start: 0.8123 (ttm) cc_final: 0.7560 (tpp) REVERT: D 50 MET cc_start: 0.5896 (ttm) cc_final: 0.5666 (ttp) REVERT: E 17 GLN cc_start: 0.0994 (OUTLIER) cc_final: 0.0736 (pm20) REVERT: F 38 ARG cc_start: 0.6466 (ptm-80) cc_final: 0.5213 (ptm-80) REVERT: F 40 MET cc_start: 0.8431 (mmm) cc_final: 0.6916 (ttt) REVERT: F 48 MET cc_start: 0.8368 (ttt) cc_final: 0.7505 (tpp) REVERT: F 52 TYR cc_start: 0.7684 (t80) cc_final: 0.7207 (t80) REVERT: G 40 GLN cc_start: 0.6710 (pp30) cc_final: 0.5412 (tp40) REVERT: G 50 LEU cc_start: 0.7530 (mp) cc_final: 0.6878 (tt) outliers start: 98 outliers final: 84 residues processed: 350 average time/residue: 0.3904 time to fit residues: 224.1065 Evaluate side-chains 349 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 257 time to evaluate : 3.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 103 TRP Chi-restraints excluded: chain F residue 111 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 333 optimal weight: 6.9990 chunk 231 optimal weight: 2.9990 chunk 262 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 362 optimal weight: 10.0000 chunk 301 optimal weight: 0.7980 chunk 313 optimal weight: 4.9990 chunk 221 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 325 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 409 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN E 29 ASN G 29 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.156160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.100703 restraints weight = 47573.892| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.33 r_work: 0.3133 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 29409 Z= 0.172 Angle : 0.587 15.359 40069 Z= 0.305 Chirality : 0.045 0.298 4535 Planarity : 0.004 0.037 5170 Dihedral : 5.081 56.722 4056 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.97 % Favored : 95.95 % Rotamer: Outliers : 3.50 % Allowed : 19.62 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 3630 helix: 2.13 (0.21), residues: 642 sheet: 0.60 (0.17), residues: 987 loop : -1.11 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 33 HIS 0.005 0.001 HIS A1064 PHE 0.027 0.001 PHE B 92 TYR 0.019 0.001 TYR B 508 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.01013 ( 2) link_NAG-ASN : angle 3.37441 ( 6) link_BETA1-4 : bond 0.00156 ( 2) link_BETA1-4 : angle 1.67724 ( 6) hydrogen bonds : bond 0.05675 ( 1114) hydrogen bonds : angle 5.14857 ( 3072) SS BOND : bond 0.00417 ( 45) SS BOND : angle 2.63216 ( 90) covalent geometry : bond 0.00424 (29360) covalent geometry : angle 0.57234 (39967) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 257 time to evaluate : 3.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7471 (pm20) REVERT: A 220 PHE cc_start: 0.6210 (t80) cc_final: 0.5649 (t80) REVERT: A 461 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8492 (tt) REVERT: A 473 TYR cc_start: 0.6671 (t80) cc_final: 0.6448 (t80) REVERT: A 516 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7549 (pm20) REVERT: A 912 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7465 (p) REVERT: B 52 GLN cc_start: 0.7991 (pm20) cc_final: 0.7726 (pm20) REVERT: B 409 GLN cc_start: 0.8347 (mp10) cc_final: 0.7943 (mp10) REVERT: B 912 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7848 (p) REVERT: B 918 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: C 129 LYS cc_start: 0.6349 (OUTLIER) cc_final: 0.6007 (tptp) REVERT: C 912 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7778 (p) REVERT: H 32 TYR cc_start: 0.8305 (m-10) cc_final: 0.7930 (m-10) REVERT: H 38 ARG cc_start: 0.6249 (ptm160) cc_final: 0.4624 (mtm110) REVERT: H 58 ARG cc_start: 0.6980 (OUTLIER) cc_final: 0.6296 (mmt90) REVERT: H 89 MET cc_start: 0.3895 (tpt) cc_final: 0.3337 (tpt) REVERT: H 91 TYR cc_start: 0.6299 (m-10) cc_final: 0.5859 (m-80) REVERT: D 36 TRP cc_start: 0.6692 (m100) cc_final: 0.6239 (m-90) REVERT: D 48 MET cc_start: 0.8124 (ttm) cc_final: 0.7565 (tpp) REVERT: D 50 MET cc_start: 0.5938 (ttm) cc_final: 0.5733 (ttp) REVERT: E 17 GLN cc_start: 0.0990 (OUTLIER) cc_final: 0.0709 (pm20) REVERT: F 48 MET cc_start: 0.8369 (ttt) cc_final: 0.8044 (tpp) REVERT: F 52 TYR cc_start: 0.7709 (t80) cc_final: 0.7219 (t80) REVERT: G 40 GLN cc_start: 0.6788 (pp30) cc_final: 0.5478 (tp40) REVERT: G 50 LEU cc_start: 0.7550 (mp) cc_final: 0.6907 (tt) outliers start: 112 outliers final: 93 residues processed: 350 average time/residue: 0.3807 time to fit residues: 219.0584 Evaluate side-chains 354 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 251 time to evaluate : 2.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 103 TRP Chi-restraints excluded: chain F residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 192 optimal weight: 2.9990 chunk 327 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 362 optimal weight: 30.0000 chunk 339 optimal weight: 10.0000 chunk 154 optimal weight: 0.0570 chunk 58 optimal weight: 0.3980 chunk 94 optimal weight: 0.0010 chunk 163 optimal weight: 1.9990 chunk 336 optimal weight: 8.9990 chunk 146 optimal weight: 0.5980 overall best weight: 0.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 409 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN E 29 ASN E 40 GLN G 29 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.158599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.103476 restraints weight = 47555.420| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.35 r_work: 0.3167 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 29409 Z= 0.107 Angle : 0.544 11.649 40069 Z= 0.281 Chirality : 0.044 0.308 4535 Planarity : 0.004 0.037 5170 Dihedral : 4.982 55.889 4056 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.78 % Favored : 97.16 % Rotamer: Outliers : 2.84 % Allowed : 20.37 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.14), residues: 3630 helix: 2.31 (0.21), residues: 642 sheet: 0.67 (0.17), residues: 1002 loop : -0.98 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 104 HIS 0.010 0.001 HIS A 207 PHE 0.027 0.001 PHE B 92 TYR 0.017 0.001 TYR B1067 ARG 0.003 0.000 ARG D 94 Details of bonding type rmsd link_NAG-ASN : bond 0.01071 ( 2) link_NAG-ASN : angle 3.25816 ( 6) link_BETA1-4 : bond 0.00265 ( 2) link_BETA1-4 : angle 1.68752 ( 6) hydrogen bonds : bond 0.04946 ( 1114) hydrogen bonds : angle 5.00826 ( 3072) SS BOND : bond 0.00299 ( 45) SS BOND : angle 2.06341 ( 90) covalent geometry : bond 0.00238 (29360) covalent geometry : angle 0.53358 (39967) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7260 Ramachandran restraints generated. 3630 Oldfield, 0 Emsley, 3630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 267 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7516 (pm20) REVERT: A 220 PHE cc_start: 0.6048 (t80) cc_final: 0.5546 (t80) REVERT: A 461 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8464 (tt) REVERT: A 473 TYR cc_start: 0.6644 (t80) cc_final: 0.6380 (t80) REVERT: A 516 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7546 (pm20) REVERT: A 912 THR cc_start: 0.7976 (OUTLIER) cc_final: 0.7307 (p) REVERT: A 1017 GLU cc_start: 0.7939 (tp30) cc_final: 0.7701 (tt0) REVERT: B 52 GLN cc_start: 0.7953 (pm20) cc_final: 0.7687 (pm20) REVERT: B 409 GLN cc_start: 0.8332 (mp10) cc_final: 0.7929 (mp10) REVERT: B 912 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7600 (p) REVERT: B 918 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: C 129 LYS cc_start: 0.6305 (OUTLIER) cc_final: 0.6022 (tptp) REVERT: H 32 TYR cc_start: 0.8314 (m-10) cc_final: 0.7955 (m-10) REVERT: H 36 TRP cc_start: 0.6380 (m100) cc_final: 0.5705 (m-90) REVERT: H 38 ARG cc_start: 0.6255 (ptm160) cc_final: 0.4657 (mtm110) REVERT: H 58 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.6290 (mmt90) REVERT: H 89 MET cc_start: 0.3962 (tpt) cc_final: 0.3399 (tpt) REVERT: H 91 TYR cc_start: 0.6116 (m-10) cc_final: 0.5796 (m-80) REVERT: D 36 TRP cc_start: 0.6732 (m100) cc_final: 0.6289 (m-90) REVERT: D 48 MET cc_start: 0.8111 (ttm) cc_final: 0.7559 (tpp) REVERT: D 50 MET cc_start: 0.5851 (ttm) cc_final: 0.5641 (ttp) REVERT: E 17 GLN cc_start: 0.0958 (OUTLIER) cc_final: 0.0688 (pm20) REVERT: F 40 MET cc_start: 0.7763 (mmp) cc_final: 0.5685 (ttt) REVERT: F 48 MET cc_start: 0.8372 (ttt) cc_final: 0.7517 (tpp) REVERT: F 52 TYR cc_start: 0.7670 (t80) cc_final: 0.7185 (t80) REVERT: G 40 GLN cc_start: 0.6820 (pp30) cc_final: 0.5592 (tp40) REVERT: G 50 LEU cc_start: 0.7503 (mp) cc_final: 0.6852 (tt) outliers start: 91 outliers final: 69 residues processed: 341 average time/residue: 0.3807 time to fit residues: 212.7169 Evaluate side-chains 336 residues out of total 3201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 258 time to evaluate : 3.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 103 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 266 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 217 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A 519 HIS B 196 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN G 29 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.154158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.098653 restraints weight = 47775.445| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.31 r_work: 0.3103 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 29409 Z= 0.227 Angle : 0.632 9.405 40069 Z= 0.330 Chirality : 0.047 0.301 4535 Planarity : 0.004 0.048 5170 Dihedral : 5.095 55.477 4051 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.88 % Favored : 95.07 % Rotamer: Outliers : 3.16 % Allowed : 19.99 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.14), residues: 3630 helix: 1.91 (0.21), residues: 642 sheet: 0.55 (0.17), residues: 945 loop : -1.16 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 33 HIS 0.006 0.001 HIS A1064 PHE 0.024 0.002 PHE A 543 TYR 0.022 0.001 TYR F 32 ARG 0.007 0.000 ARG F 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00942 ( 2) link_NAG-ASN : angle 3.70666 ( 6) link_BETA1-4 : bond 0.00225 ( 2) link_BETA1-4 : angle 1.86505 ( 6) hydrogen bonds : bond 0.06416 ( 1114) hydrogen bonds : angle 5.28627 ( 3072) SS BOND : bond 0.00468 ( 45) SS BOND : angle 2.25267 ( 90) covalent geometry : bond 0.00561 (29360) covalent geometry : angle 0.62128 (39967) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16433.50 seconds wall clock time: 282 minutes 59.31 seconds (16979.31 seconds total)