Starting phenix.real_space_refine on Thu Mar 5 13:17:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cyd_30497/03_2026/7cyd_30497.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cyd_30497/03_2026/7cyd_30497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cyd_30497/03_2026/7cyd_30497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cyd_30497/03_2026/7cyd_30497.map" model { file = "/net/cci-nas-00/data/ceres_data/7cyd_30497/03_2026/7cyd_30497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cyd_30497/03_2026/7cyd_30497.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 111 5.16 5 C 14052 2.51 5 N 3738 2.21 5 O 4419 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22320 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7122 Classifications: {'peptide': 964} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 33, 'TRANS': 930} Chain breaks: 4 Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 543 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 233 Chain: "B" Number of atoms: 7122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7122 Classifications: {'peptide': 964} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 33, 'TRANS': 930} Chain breaks: 4 Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 543 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 233 Chain: "C" Number of atoms: 7122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7122 Classifications: {'peptide': 964} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 33, 'TRANS': 930} Chain breaks: 4 Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 543 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 233 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 4.89, per 1000 atoms: 0.22 Number of scatterers: 22320 At special positions: 0 Unit cell: (133, 133, 151.2, 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 111 16.00 O 4419 8.00 N 3738 7.00 C 14052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 320 " distance=2.04 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 396 " distance=2.02 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 630 " distance=2.04 Simple disulfide: pdb=" SG CYS A 715 " - pdb=" SG CYS A 726 " distance=2.02 Simple disulfide: pdb=" SG CYS A 917 " - pdb=" SG CYS A 928 " distance=2.04 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 317 " - pdb=" SG CYS B 320 " distance=2.04 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 396 " distance=2.02 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 630 " distance=2.04 Simple disulfide: pdb=" SG CYS B 715 " - pdb=" SG CYS B 726 " distance=2.02 Simple disulfide: pdb=" SG CYS B 917 " - pdb=" SG CYS B 928 " distance=2.04 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 317 " - pdb=" SG CYS C 320 " distance=2.04 Simple disulfide: pdb=" SG CYS C 369 " - pdb=" SG CYS C 396 " distance=2.02 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 630 " distance=2.04 Simple disulfide: pdb=" SG CYS C 715 " - pdb=" SG CYS C 726 " distance=2.02 Simple disulfide: pdb=" SG CYS C 917 " - pdb=" SG CYS C 928 " 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 Atom "HETATM21940 O5 NAG B1201 .*. O " rejected from bonding due to valence issues. Atom "HETATM21744 O5 NAG A1201 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN F 4 " - " MAN F 5 " " MAN H 4 " - " MAN H 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " MAN D 6 " - " MAN D 7 " " BMA F 3 " - " MAN F 4 " " MAN F 6 " - " MAN F 7 " " BMA H 3 " - " MAN H 4 " " MAN H 6 " - " MAN H 7 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " " BMA F 3 " - " MAN F 6 " " BMA H 3 " - " MAN H 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG A1201 " - " ASN A 98 " " NAG A1202 " - " ASN A 122 " " NAG A1203 " - " ASN A 171 " " NAG A1204 " - " ASN A 220 " " NAG A1205 " - " ASN A 326 " " NAG A1206 " - " ASN A 518 " " NAG A1207 " - " ASN A 440 " " NAG A1208 " - " ASN A 663 " " NAG A1209 " - " ASN A 542 " " NAG A1210 " - " ASN A 568 " " NAG A1211 " - " ASN A 581 " " NAG A1212 " - " ASN A 587 " " NAG A1213 " - " ASN A 671 " " NAG A1214 " - " ASN A1015 " " NAG B1201 " - " ASN B 98 " " NAG B1202 " - " ASN B 122 " " NAG B1203 " - " ASN B 171 " " NAG B1204 " - " ASN B 220 " " NAG B1205 " - " ASN B 326 " " NAG B1206 " - " ASN B 518 " " NAG B1207 " - " ASN B 440 " " NAG B1208 " - " ASN B 663 " " NAG B1209 " - " ASN B 542 " " NAG B1210 " - " ASN B 568 " " NAG B1211 " - " ASN B 581 " " NAG B1212 " - " ASN B 587 " " NAG B1213 " - " ASN B 671 " " NAG B1214 " - " ASN B1015 " " NAG C1201 " - " ASN C 98 " " NAG C1202 " - " ASN C 122 " " NAG C1203 " - " ASN C 171 " " NAG C1204 " - " ASN C 220 " " NAG C1205 " - " ASN C 326 " " NAG C1206 " - " ASN C 518 " " NAG C1207 " - " ASN C 440 " " NAG C1208 " - " ASN C 663 " " NAG C1209 " - " ASN C 542 " " NAG C1210 " - " ASN C 568 " " NAG C1211 " - " ASN C 581 " " NAG C1212 " - " ASN C 587 " " NAG C1213 " - " ASN C 671 " " NAG C1214 " - " ASN C1015 " " NAG D 1 " - " ASN A 62 " " NAG E 1 " - " ASN A 243 " " NAG F 1 " - " ASN B 62 " " NAG G 1 " - " ASN B 243 " " NAG H 1 " - " ASN C 62 " " NAG I 1 " - " ASN C 243 " Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 959.5 milliseconds 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5394 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 39 sheets defined 25.5% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 257 through 266 Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 616 through 626 removed outlier: 3.919A pdb=" N GLN A 625 " --> pdb=" O GLU A 621 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 652 Processing helix chain 'A' and resid 655 through 661 removed outlier: 4.102A pdb=" N THR A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU A 661 " --> pdb=" O LYS A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 671 Processing helix chain 'A' and resid 690 through 699 Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 723 through 732 Processing helix chain 'A' and resid 741 through 757 removed outlier: 4.124A pdb=" N ALA A 757 " --> pdb=" O ILE A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 781 removed outlier: 3.982A pdb=" N GLN A 774 " --> pdb=" O SER A 770 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER A 775 " --> pdb=" O LEU A 771 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL A 780 " --> pdb=" O ARG A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 810 removed outlier: 4.152A pdb=" N LYS A 792 " --> pdb=" O GLN A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 853 Processing helix chain 'A' and resid 861 through 869 Processing helix chain 'A' and resid 870 through 915 removed outlier: 3.535A pdb=" N ASN A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1008 removed outlier: 3.593A pdb=" N ASP A1007 " --> pdb=" O THR A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1030 Processing helix chain 'B' and resid 257 through 266 Processing helix chain 'B' and resid 607 through 614 Processing helix chain 'B' and resid 616 through 626 removed outlier: 3.919A pdb=" N GLN B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 652 Processing helix chain 'B' and resid 655 through 661 removed outlier: 4.103A pdb=" N THR B 660 " --> pdb=" O LYS B 656 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU B 661 " --> pdb=" O LYS B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 671 Processing helix chain 'B' and resid 690 through 699 Processing helix chain 'B' and resid 711 through 715 Processing helix chain 'B' and resid 723 through 732 Processing helix chain 'B' and resid 741 through 757 removed outlier: 4.123A pdb=" N ALA B 757 " --> pdb=" O ILE B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 781 removed outlier: 3.982A pdb=" N GLN B 774 " --> pdb=" O SER B 770 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER B 775 " --> pdb=" O LEU B 771 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL B 780 " --> pdb=" O ARG B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 810 removed outlier: 4.152A pdb=" N LYS B 792 " --> pdb=" O GLN B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 853 Processing helix chain 'B' and resid 861 through 869 Processing helix chain 'B' and resid 870 through 915 removed outlier: 3.535A pdb=" N ASN B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1008 removed outlier: 3.594A pdb=" N ASP B1007 " --> pdb=" O THR B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1025 through 1030 Processing helix chain 'C' and resid 257 through 266 Processing helix chain 'C' and resid 607 through 614 Processing helix chain 'C' and resid 616 through 626 removed outlier: 3.919A pdb=" N GLN C 625 " --> pdb=" O GLU C 621 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR C 626 " --> pdb=" O LEU C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 652 Processing helix chain 'C' and resid 655 through 661 removed outlier: 4.103A pdb=" N THR C 660 " --> pdb=" O LYS C 656 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU C 661 " --> pdb=" O LYS C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 671 Processing helix chain 'C' and resid 690 through 699 Processing helix chain 'C' and resid 711 through 715 Processing helix chain 'C' and resid 723 through 732 Processing helix chain 'C' and resid 741 through 757 removed outlier: 4.123A pdb=" N ALA C 757 " --> pdb=" O ILE C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 781 removed outlier: 3.982A pdb=" N GLN C 774 " --> pdb=" O SER C 770 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER C 775 " --> pdb=" O LEU C 771 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG C 776 " --> pdb=" O ALA C 772 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL C 780 " --> pdb=" O ARG C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 810 removed outlier: 4.152A pdb=" N LYS C 792 " --> pdb=" O GLN C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 853 Processing helix chain 'C' and resid 861 through 869 Processing helix chain 'C' and resid 870 through 915 removed outlier: 3.535A pdb=" N ASN C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1008 removed outlier: 3.593A pdb=" N ASP C1007 " --> pdb=" O THR C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1025 through 1030 Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 81 removed outlier: 5.008A pdb=" N VAL A 70 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL A 244 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ARG A 72 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL A 242 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE A 74 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 240 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA A 238 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU A 234 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE A 117 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE A 195 " --> pdb=" O ILE A 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 81 removed outlier: 5.008A pdb=" N VAL A 70 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL A 244 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ARG A 72 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL A 242 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE A 74 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 240 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA A 238 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU A 234 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N ASP A 239 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR A 254 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 241 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ILE A 252 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASN A 243 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 177 through 182 removed outlier: 3.554A pdb=" N PHE A 143 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE A 132 " --> pdb=" O PHE A 143 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 133 " --> pdb=" O ASN A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 201 removed outlier: 4.126A pdb=" N PHE A 209 " --> pdb=" O PHE A 201 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 274 through 278 removed outlier: 3.766A pdb=" N GLN A 502 " --> pdb=" O MET A 514 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY A 512 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 290 through 291 removed outlier: 6.358A pdb=" N LEU A 481 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N TYR A 473 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 307 through 308 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 363 removed outlier: 3.684A pdb=" N SER A 361 " --> pdb=" O ASN A 403 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N MET A 398 " --> pdb=" O SER A 414 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A 414 " --> pdb=" O MET A 398 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 380 through 381 removed outlier: 3.548A pdb=" N VAL A 380 " --> pdb=" O GLY A 427 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 546 through 550 Processing sheet with id=AB2, first strand: chain 'A' and resid 580 through 585 Processing sheet with id=AB3, first strand: chain 'A' and resid 593 through 598 removed outlier: 4.211A pdb=" N GLN A 593 " --> pdb=" O HIS A 949 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS A 949 " --> pdb=" O GLN A 593 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY A 944 " --> pdb=" O ALA A 940 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA A 940 " --> pdb=" O GLY A 944 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL A 946 " --> pdb=" O VAL A 938 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL A 938 " --> pdb=" O VAL A 946 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU A 948 " --> pdb=" O SER A 936 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER A 936 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR A 950 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 604 through 606 Processing sheet with id=AB5, first strand: chain 'B' and resid 70 through 81 removed outlier: 5.008A pdb=" N VAL B 70 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL B 244 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ARG B 72 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL B 242 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N PHE B 74 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 240 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA B 238 " --> pdb=" O PRO B 76 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU B 234 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE B 117 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE B 195 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 70 through 81 removed outlier: 5.008A pdb=" N VAL B 70 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL B 244 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ARG B 72 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL B 242 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N PHE B 74 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 240 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA B 238 " --> pdb=" O PRO B 76 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU B 234 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N ASP B 239 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N TYR B 254 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU B 241 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASN B 243 " --> pdb=" O ALA B 250 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 177 through 182 removed outlier: 3.554A pdb=" N PHE B 143 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE B 132 " --> pdb=" O PHE B 143 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU B 133 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 200 through 201 removed outlier: 4.126A pdb=" N PHE B 209 " --> pdb=" O PHE B 201 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 274 through 278 removed outlier: 3.766A pdb=" N GLN B 502 " --> pdb=" O MET B 514 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY B 512 " --> pdb=" O VAL B 504 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 290 through 291 removed outlier: 6.358A pdb=" N LEU B 481 " --> pdb=" O ILE B 494 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N TYR B 473 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 307 through 308 Processing sheet with id=AC3, first strand: chain 'B' and resid 361 through 363 removed outlier: 3.684A pdb=" N SER B 361 " --> pdb=" O ASN B 403 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N MET B 398 " --> pdb=" O SER B 414 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER B 414 " --> pdb=" O MET B 398 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 380 through 381 removed outlier: 3.549A pdb=" N VAL B 380 " --> pdb=" O GLY B 427 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 546 through 550 Processing sheet with id=AC6, first strand: chain 'B' and resid 580 through 585 Processing sheet with id=AC7, first strand: chain 'B' and resid 593 through 598 removed outlier: 4.212A pdb=" N GLN B 593 " --> pdb=" O HIS B 949 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N HIS B 949 " --> pdb=" O GLN B 593 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY B 944 " --> pdb=" O ALA B 940 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ALA B 940 " --> pdb=" O GLY B 944 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 946 " --> pdb=" O VAL B 938 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL B 938 " --> pdb=" O VAL B 946 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU B 948 " --> pdb=" O SER B 936 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER B 936 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B 950 " --> pdb=" O ILE B 934 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 604 through 606 Processing sheet with id=AC9, first strand: chain 'C' and resid 70 through 81 removed outlier: 5.007A pdb=" N VAL C 70 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL C 244 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ARG C 72 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL C 242 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N PHE C 74 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL C 240 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA C 238 " --> pdb=" O PRO C 76 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU C 234 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE C 117 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE C 195 " --> pdb=" O ILE C 117 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 70 through 81 removed outlier: 5.007A pdb=" N VAL C 70 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL C 244 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ARG C 72 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL C 242 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N PHE C 74 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL C 240 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA C 238 " --> pdb=" O PRO C 76 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU C 234 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N ASP C 239 " --> pdb=" O TYR C 254 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N TYR C 254 " --> pdb=" O ASP C 239 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU C 241 " --> pdb=" O ILE C 252 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE C 252 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASN C 243 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 177 through 182 removed outlier: 3.554A pdb=" N PHE C 143 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ILE C 132 " --> pdb=" O PHE C 143 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU C 133 " --> pdb=" O ASN C 218 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 200 through 201 removed outlier: 4.126A pdb=" N PHE C 209 " --> pdb=" O PHE C 201 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 274 through 278 removed outlier: 3.766A pdb=" N GLN C 502 " --> pdb=" O MET C 514 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY C 512 " --> pdb=" O VAL C 504 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 290 through 291 removed outlier: 6.358A pdb=" N LEU C 481 " --> pdb=" O ILE C 494 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TYR C 473 " --> pdb=" O LEU C 481 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 307 through 308 Processing sheet with id=AD7, first strand: chain 'C' and resid 361 through 363 removed outlier: 3.685A pdb=" N SER C 361 " --> pdb=" O ASN C 403 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N MET C 398 " --> pdb=" O SER C 414 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER C 414 " --> pdb=" O MET C 398 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 380 through 381 removed outlier: 3.548A pdb=" N VAL C 380 " --> pdb=" O GLY C 427 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 546 through 550 Processing sheet with id=AE1, first strand: chain 'C' and resid 580 through 585 Processing sheet with id=AE2, first strand: chain 'C' and resid 593 through 598 removed outlier: 4.212A pdb=" N GLN C 593 " --> pdb=" O HIS C 949 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS C 949 " --> pdb=" O GLN C 593 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY C 944 " --> pdb=" O ALA C 940 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA C 940 " --> pdb=" O GLY C 944 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL C 946 " --> pdb=" O VAL C 938 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL C 938 " --> pdb=" O VAL C 946 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU C 948 " --> pdb=" O SER C 936 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER C 936 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR C 950 " --> pdb=" O ILE C 934 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 604 through 606 762 hydrogen bonds defined for protein. 2097 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.36 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6776 1.33 - 1.46: 5720 1.46 - 1.58: 10145 1.58 - 1.71: 0 1.71 - 1.83: 141 Bond restraints: 22782 Sorted by residual: bond pdb=" C MET C 439 " pdb=" N ASN C 440 " ideal model delta sigma weight residual 1.332 1.471 -0.139 1.35e-02 5.49e+03 1.06e+02 bond pdb=" C MET A 439 " pdb=" N ASN A 440 " ideal model delta sigma weight residual 1.332 1.471 -0.139 1.35e-02 5.49e+03 1.06e+02 bond pdb=" C MET B 439 " pdb=" N ASN B 440 " ideal model delta sigma weight residual 1.332 1.470 -0.139 1.35e-02 5.49e+03 1.06e+02 bond pdb=" N LEU A 953 " pdb=" CA LEU A 953 " ideal model delta sigma weight residual 1.453 1.488 -0.034 8.30e-03 1.45e+04 1.72e+01 bond pdb=" N LEU C 953 " pdb=" CA LEU C 953 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.67e+01 ... (remaining 22777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 27107 1.77 - 3.55: 2924 3.55 - 5.32: 487 5.32 - 7.09: 106 7.09 - 8.87: 42 Bond angle restraints: 30666 Sorted by residual: angle pdb=" CA GLY C 93 " pdb=" C GLY C 93 " pdb=" O GLY C 93 " ideal model delta sigma weight residual 122.37 117.87 4.50 7.30e-01 1.88e+00 3.81e+01 angle pdb=" CA GLY A 93 " pdb=" C GLY A 93 " pdb=" O GLY A 93 " ideal model delta sigma weight residual 122.37 118.00 4.37 7.30e-01 1.88e+00 3.58e+01 angle pdb=" CA GLY B 93 " pdb=" C GLY B 93 " pdb=" O GLY B 93 " ideal model delta sigma weight residual 122.37 118.03 4.34 7.30e-01 1.88e+00 3.53e+01 angle pdb=" C PHE A 318 " pdb=" CA PHE A 318 " pdb=" CB PHE A 318 " ideal model delta sigma weight residual 110.88 102.86 8.02 1.57e+00 4.06e-01 2.61e+01 angle pdb=" C PHE B 318 " pdb=" CA PHE B 318 " pdb=" CB PHE B 318 " ideal model delta sigma weight residual 110.88 102.88 8.00 1.57e+00 4.06e-01 2.60e+01 ... (remaining 30661 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.48: 13552 24.48 - 48.96: 774 48.96 - 73.44: 164 73.44 - 97.92: 39 97.92 - 122.39: 60 Dihedral angle restraints: 14589 sinusoidal: 6174 harmonic: 8415 Sorted by residual: dihedral pdb=" CB CYS C 369 " pdb=" SG CYS C 369 " pdb=" SG CYS C 396 " pdb=" CB CYS C 396 " ideal model delta sinusoidal sigma weight residual 93.00 35.21 57.79 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" CB CYS B 369 " pdb=" SG CYS B 369 " pdb=" SG CYS B 396 " pdb=" CB CYS B 396 " ideal model delta sinusoidal sigma weight residual 93.00 35.25 57.75 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" CB CYS A 369 " pdb=" SG CYS A 369 " pdb=" SG CYS A 396 " pdb=" CB CYS A 396 " ideal model delta sinusoidal sigma weight residual 93.00 35.26 57.74 1 1.00e+01 1.00e-02 4.48e+01 ... (remaining 14586 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.190: 3187 0.190 - 0.380: 88 0.380 - 0.571: 5 0.571 - 0.761: 1 0.761 - 0.951: 7 Chirality restraints: 3288 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.53e+02 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.51e+02 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.47e+02 ... (remaining 3285 not shown) Planarity restraints: 4068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.300 2.00e-02 2.50e+03 2.53e-01 7.98e+02 pdb=" C7 NAG G 1 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.433 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " 0.300 2.00e-02 2.50e+03 2.53e-01 7.98e+02 pdb=" C7 NAG E 1 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " 0.188 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " -0.433 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " 0.300 2.00e-02 2.50e+03 2.52e-01 7.96e+02 pdb=" C7 NAG I 1 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " -0.432 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " 0.023 2.00e-02 2.50e+03 ... (remaining 4065 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 184 2.45 - 3.06: 17289 3.06 - 3.68: 34145 3.68 - 4.29: 47323 4.29 - 4.90: 73175 Nonbonded interactions: 172116 Sorted by model distance: nonbonded pdb=" CB SER C 245 " pdb=" O7 NAG I 2 " model vdw 1.838 3.440 nonbonded pdb=" CB SER A 245 " pdb=" O7 NAG E 2 " model vdw 1.903 3.440 nonbonded pdb=" OG SER C 245 " pdb=" O7 NAG I 2 " model vdw 1.958 3.040 nonbonded pdb=" OG SER A 245 " pdb=" O7 NAG E 2 " model vdw 1.993 3.040 nonbonded pdb=" CB SER B 245 " pdb=" O7 NAG G 2 " model vdw 2.032 3.440 ... (remaining 172111 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.400 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 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 : 0.011 0.393 22872 Z= 0.617 Angle : 1.364 31.753 30918 Z= 0.762 Chirality : 0.087 0.951 3288 Planarity : 0.012 0.253 4020 Dihedral : 17.869 122.395 9141 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 30.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.56 % Favored : 94.34 % Rotamer: Outliers : 9.09 % Allowed : 9.27 % Favored : 81.64 % Cbeta Deviations : 0.56 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.13), residues: 2862 helix: -2.65 (0.14), residues: 651 sheet: -1.66 (0.23), residues: 483 loop : -2.19 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG C 359 TYR 0.027 0.003 TYR A 144 PHE 0.030 0.003 PHE C 373 TRP 0.021 0.004 TRP B 404 HIS 0.026 0.005 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00887 (22782) covalent geometry : angle 1.21396 (30666) SS BOND : bond 0.01066 ( 18) SS BOND : angle 4.15060 ( 36) hydrogen bonds : bond 0.17522 ( 753) hydrogen bonds : angle 9.36776 ( 2097) link_ALPHA1-2 : bond 0.00704 ( 3) link_ALPHA1-2 : angle 0.85389 ( 9) link_ALPHA1-3 : bond 0.00356 ( 6) link_ALPHA1-3 : angle 2.34090 ( 18) link_ALPHA1-6 : bond 0.00389 ( 3) link_ALPHA1-6 : angle 1.29986 ( 9) link_BETA1-4 : bond 0.00125 ( 12) link_BETA1-4 : angle 1.56698 ( 36) link_NAG-ASN : bond 0.14544 ( 48) link_NAG-ASN : angle 8.93165 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 795 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8844 (t) cc_final: 0.8517 (t) REVERT: A 102 ARG cc_start: 0.7643 (mpt-90) cc_final: 0.7293 (ttp-170) REVERT: A 129 ARG cc_start: 0.7488 (ptm160) cc_final: 0.7241 (ptm160) REVERT: A 192 GLU cc_start: 0.7701 (tt0) cc_final: 0.7244 (tt0) REVERT: A 202 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7823 (m-80) REVERT: A 371 PHE cc_start: 0.7557 (p90) cc_final: 0.6942 (p90) REVERT: A 375 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7895 (mtmt) REVERT: A 396 CYS cc_start: 0.4177 (p) cc_final: 0.3150 (p) REVERT: A 403 ASN cc_start: 0.7595 (t0) cc_final: 0.7285 (t0) REVERT: A 479 ASN cc_start: 0.8054 (m110) cc_final: 0.7850 (m110) REVERT: A 638 ARG cc_start: 0.9071 (ttp-110) cc_final: 0.8863 (ttp-110) REVERT: A 642 MET cc_start: 0.9027 (mtm) cc_final: 0.8787 (mtp) REVERT: A 650 GLU cc_start: 0.8621 (tp30) cc_final: 0.8171 (tp30) REVERT: A 652 LEU cc_start: 0.7436 (mt) cc_final: 0.7142 (mt) REVERT: A 669 ASP cc_start: 0.7858 (t0) cc_final: 0.7487 (t0) REVERT: A 693 GLU cc_start: 0.7729 (pt0) cc_final: 0.7179 (pp20) REVERT: A 723 ASP cc_start: 0.8004 (t0) cc_final: 0.7727 (t0) REVERT: A 747 MET cc_start: 0.8806 (mtm) cc_final: 0.8565 (mtp) REVERT: A 824 GLN cc_start: 0.8768 (mp10) cc_final: 0.8022 (mp10) REVERT: A 846 HIS cc_start: 0.8932 (t70) cc_final: 0.8631 (t-90) REVERT: A 850 GLN cc_start: 0.8866 (mt0) cc_final: 0.8232 (mt0) REVERT: A 853 GLN cc_start: 0.8635 (pp30) cc_final: 0.8130 (pp30) REVERT: A 854 ASN cc_start: 0.8322 (p0) cc_final: 0.7801 (p0) REVERT: A 855 PHE cc_start: 0.9207 (m-80) cc_final: 0.8986 (m-80) REVERT: A 856 GLN cc_start: 0.8759 (tp-100) cc_final: 0.8418 (tp-100) REVERT: A 876 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7823 (tm-30) REVERT: A 908 GLN cc_start: 0.8828 (mm110) cc_final: 0.8401 (mm110) REVERT: A 924 ARG cc_start: 0.9027 (mtp180) cc_final: 0.8484 (mtp-110) REVERT: A 936 SER cc_start: 0.7185 (t) cc_final: 0.6860 (t) REVERT: A 939 ASN cc_start: 0.8514 (t0) cc_final: 0.8217 (t0) REVERT: A 943 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7982 (tp30) REVERT: A 949 HIS cc_start: 0.7510 (m-70) cc_final: 0.6931 (m90) REVERT: A 991 ARG cc_start: 0.8062 (mmt90) cc_final: 0.7233 (mmm-85) REVERT: B 156 HIS cc_start: 0.4095 (m90) cc_final: 0.3824 (m170) REVERT: B 192 GLU cc_start: 0.6489 (tt0) cc_final: 0.5802 (tt0) REVERT: B 387 PHE cc_start: 0.7522 (m-80) cc_final: 0.7224 (m-80) REVERT: B 506 TYR cc_start: 0.9332 (t80) cc_final: 0.9072 (t80) REVERT: B 519 PHE cc_start: 0.7715 (t80) cc_final: 0.7378 (t80) REVERT: B 567 ARG cc_start: 0.7683 (ttt180) cc_final: 0.7191 (ptt90) REVERT: B 595 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7566 (mp0) REVERT: B 621 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8277 (mt-10) REVERT: B 622 LEU cc_start: 0.9069 (mp) cc_final: 0.8857 (mp) REVERT: B 669 ASP cc_start: 0.7728 (t0) cc_final: 0.7489 (t0) REVERT: B 693 GLU cc_start: 0.7824 (pt0) cc_final: 0.7525 (pt0) REVERT: B 723 ASP cc_start: 0.8371 (t0) cc_final: 0.8047 (t70) REVERT: B 824 GLN cc_start: 0.8725 (mp10) cc_final: 0.8413 (mp10) REVERT: B 831 ASN cc_start: 0.8198 (t0) cc_final: 0.7846 (t0) REVERT: B 840 GLN cc_start: 0.8999 (tt0) cc_final: 0.8695 (tp40) REVERT: B 863 GLN cc_start: 0.8628 (tp40) cc_final: 0.8369 (tp-100) REVERT: B 875 ASP cc_start: 0.9277 (m-30) cc_final: 0.9036 (m-30) REVERT: B 879 ASP cc_start: 0.9236 (p0) cc_final: 0.8955 (p0) REVERT: B 885 ARG cc_start: 0.9047 (mtt180) cc_final: 0.8792 (mmt90) REVERT: B 924 ARG cc_start: 0.8571 (mtp180) cc_final: 0.8222 (mtp-110) REVERT: B 925 TYR cc_start: 0.7778 (p90) cc_final: 0.7543 (p90) REVERT: B 943 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7786 (tp30) REVERT: B 958 LYS cc_start: 0.8274 (tppt) cc_final: 0.8037 (tptm) REVERT: B 999 GLU cc_start: 0.8589 (tm-30) cc_final: 0.7954 (tm-30) REVERT: C 192 GLU cc_start: 0.5867 (tt0) cc_final: 0.4884 (tt0) REVERT: C 202 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.7718 (m-80) REVERT: C 264 CYS cc_start: 0.6007 (OUTLIER) cc_final: 0.5670 (t) REVERT: C 349 LYS cc_start: 0.8542 (mtmt) cc_final: 0.8127 (mttt) REVERT: C 588 TRP cc_start: 0.6994 (t-100) cc_final: 0.6534 (t-100) REVERT: C 597 LEU cc_start: 0.7855 (mt) cc_final: 0.7515 (mp) REVERT: C 613 CYS cc_start: 0.6983 (m) cc_final: 0.5491 (m) REVERT: C 616 ASN cc_start: 0.7257 (m-40) cc_final: 0.6611 (m-40) REVERT: C 619 CYS cc_start: 0.8576 (t) cc_final: 0.8237 (t) REVERT: C 642 MET cc_start: 0.9016 (mtm) cc_final: 0.8642 (mtp) REVERT: C 643 LEU cc_start: 0.9092 (mt) cc_final: 0.8677 (mt) REVERT: C 652 LEU cc_start: 0.7917 (mt) cc_final: 0.7679 (mt) REVERT: C 655 ASP cc_start: 0.8162 (m-30) cc_final: 0.7865 (t0) REVERT: C 824 GLN cc_start: 0.8390 (mp10) cc_final: 0.8119 (mp10) REVERT: C 850 GLN cc_start: 0.8995 (mt0) cc_final: 0.8778 (mt0) REVERT: C 863 GLN cc_start: 0.8596 (tp40) cc_final: 0.8188 (tp-100) REVERT: C 880 ARG cc_start: 0.7388 (ptp-170) cc_final: 0.7041 (ttm110) REVERT: C 885 ARG cc_start: 0.8911 (mtt180) cc_final: 0.8229 (mmt90) REVERT: C 912 GLN cc_start: 0.9086 (tt0) cc_final: 0.8381 (tp-100) REVERT: C 924 ARG cc_start: 0.9161 (mtp180) cc_final: 0.8773 (mtm-85) REVERT: C 999 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8282 (tm-30) REVERT: C 1001 ARG cc_start: 0.8879 (ttm170) cc_final: 0.8445 (ttm-80) outliers start: 199 outliers final: 164 residues processed: 946 average time/residue: 0.1524 time to fit residues: 222.1061 Evaluate side-chains 848 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 681 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 967 CYS Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1002 ILE Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 202 TYR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 575 SER Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 733 ILE Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 763 SER Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain C residue 773 ILE Chi-restraints excluded: chain C residue 779 TYR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 914 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1002 ILE Chi-restraints excluded: chain C residue 1016 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 0.4980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 ASN A 498 ASN A 834 GLN A 839 GLN A 890 ASN A 912 GLN ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 593 GLN ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 GLN ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 HIS ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 HIS ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 834 GLN C 838 ASN C 839 GLN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 933 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.130257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.118856 restraints weight = 57048.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.121545 restraints weight = 30312.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.123352 restraints weight = 18812.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.124589 restraints weight = 12920.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.125445 restraints weight = 9518.455| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 22872 Z= 0.223 Angle : 0.932 16.789 30918 Z= 0.449 Chirality : 0.057 0.451 3288 Planarity : 0.005 0.071 4020 Dihedral : 13.903 99.825 4832 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.03 % Favored : 94.86 % Rotamer: Outliers : 6.39 % Allowed : 16.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.14), residues: 2862 helix: -0.82 (0.17), residues: 657 sheet: -1.55 (0.21), residues: 564 loop : -2.25 (0.13), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG B 72 TYR 0.025 0.002 TYR C 729 PHE 0.031 0.003 PHE A 697 TRP 0.016 0.002 TRP A 404 HIS 0.012 0.003 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00461 (22782) covalent geometry : angle 0.84962 (30666) SS BOND : bond 0.00753 ( 18) SS BOND : angle 2.67533 ( 36) hydrogen bonds : bond 0.06134 ( 753) hydrogen bonds : angle 7.71823 ( 2097) link_ALPHA1-2 : bond 0.00328 ( 3) link_ALPHA1-2 : angle 2.69039 ( 9) link_ALPHA1-3 : bond 0.00474 ( 6) link_ALPHA1-3 : angle 3.25223 ( 18) link_ALPHA1-6 : bond 0.01232 ( 3) link_ALPHA1-6 : angle 2.55607 ( 9) link_BETA1-4 : bond 0.01068 ( 12) link_BETA1-4 : angle 2.20748 ( 36) link_NAG-ASN : bond 0.00731 ( 48) link_NAG-ASN : angle 5.23388 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 709 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8529 (t) cc_final: 0.8291 (t) REVERT: A 129 ARG cc_start: 0.7664 (ptm160) cc_final: 0.7444 (ptm160) REVERT: A 403 ASN cc_start: 0.8293 (t0) cc_final: 0.8036 (t0) REVERT: A 650 GLU cc_start: 0.7528 (tp30) cc_final: 0.7111 (tp30) REVERT: A 719 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6800 (tt) REVERT: A 779 TYR cc_start: 0.8548 (t80) cc_final: 0.8162 (t80) REVERT: A 824 GLN cc_start: 0.8502 (mp10) cc_final: 0.8273 (mp10) REVERT: A 846 HIS cc_start: 0.8463 (t70) cc_final: 0.8196 (t-90) REVERT: A 850 GLN cc_start: 0.8250 (mt0) cc_final: 0.7762 (mt0) REVERT: A 853 GLN cc_start: 0.8732 (pp30) cc_final: 0.8168 (pp30) REVERT: A 854 ASN cc_start: 0.8584 (p0) cc_final: 0.8056 (p0) REVERT: A 904 ARG cc_start: 0.7313 (tpt-90) cc_final: 0.6868 (tpt170) REVERT: A 936 SER cc_start: 0.7906 (t) cc_final: 0.7589 (t) REVERT: B 192 GLU cc_start: 0.7849 (tt0) cc_final: 0.7629 (tt0) REVERT: B 433 GLU cc_start: 0.7370 (pt0) cc_final: 0.7094 (pm20) REVERT: B 621 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8056 (mt-10) REVERT: B 863 GLN cc_start: 0.8208 (tp40) cc_final: 0.7904 (tp-100) REVERT: B 870 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8304 (t0) REVERT: B 875 ASP cc_start: 0.8875 (m-30) cc_final: 0.8169 (m-30) REVERT: B 879 ASP cc_start: 0.8861 (p0) cc_final: 0.8519 (p0) REVERT: B 1026 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8168 (mt) REVERT: C 192 GLU cc_start: 0.8117 (tt0) cc_final: 0.7894 (tt0) REVERT: C 597 LEU cc_start: 0.8116 (mt) cc_final: 0.7765 (mt) REVERT: C 616 ASN cc_start: 0.7937 (m-40) cc_final: 0.7713 (m110) REVERT: C 619 CYS cc_start: 0.8349 (t) cc_final: 0.8125 (t) REVERT: C 638 ARG cc_start: 0.8935 (ttm110) cc_final: 0.8538 (ptm-80) REVERT: C 669 ASP cc_start: 0.7675 (t0) cc_final: 0.7311 (t70) REVERT: C 839 GLN cc_start: 0.7756 (pt0) cc_final: 0.7032 (pt0) REVERT: C 863 GLN cc_start: 0.8393 (tp40) cc_final: 0.8053 (tp-100) REVERT: C 877 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8339 (mm-40) REVERT: C 885 ARG cc_start: 0.8552 (mtt180) cc_final: 0.7966 (mmt90) REVERT: C 886 LEU cc_start: 0.9041 (mm) cc_final: 0.8750 (tp) REVERT: C 907 ARG cc_start: 0.8381 (ttm110) cc_final: 0.8115 (ttp80) REVERT: C 908 GLN cc_start: 0.8442 (mm-40) cc_final: 0.7544 (mm-40) REVERT: C 935 PHE cc_start: 0.8268 (p90) cc_final: 0.7886 (p90) outliers start: 140 outliers final: 117 residues processed: 801 average time/residue: 0.1589 time to fit residues: 194.2376 Evaluate side-chains 776 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 656 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 800 LYS Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 625 GLN Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 712 TYR Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 870 ASP Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 967 CYS Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1002 ILE Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 712 TYR Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 733 ILE Chi-restraints excluded: chain C residue 763 SER Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain C residue 773 ILE Chi-restraints excluded: chain C residue 922 SER Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1016 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 110 optimal weight: 0.0970 chunk 221 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 198 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 0.0470 chunk 178 optimal weight: 6.9990 overall best weight: 1.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 HIS A 213 ASN A 368 ASN A 498 ASN A 593 GLN A 863 GLN A 895 HIS A 911 GLN A 912 GLN ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 831 ASN B 834 GLN B 838 ASN B 845 ASN ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 876 GLN ** B 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 HIS C 246 GLN C 507 GLN C 593 GLN ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 791 GLN ** C 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 912 GLN ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.130650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.118933 restraints weight = 58090.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.121643 restraints weight = 31506.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.123463 restraints weight = 19865.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.124706 restraints weight = 13808.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.125604 restraints weight = 10288.116| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22872 Z= 0.176 Angle : 0.856 16.674 30918 Z= 0.409 Chirality : 0.054 0.423 3288 Planarity : 0.005 0.054 4020 Dihedral : 11.664 85.797 4740 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.17 % Favored : 94.72 % Rotamer: Outliers : 6.35 % Allowed : 18.90 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.14), residues: 2862 helix: -0.24 (0.18), residues: 660 sheet: -1.45 (0.21), residues: 570 loop : -2.27 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 638 TYR 0.028 0.002 TYR A 748 PHE 0.041 0.002 PHE A 697 TRP 0.027 0.002 TRP B 588 HIS 0.017 0.003 HIS C 895 Details of bonding type rmsd covalent geometry : bond 0.00359 (22782) covalent geometry : angle 0.78060 (30666) SS BOND : bond 0.00721 ( 18) SS BOND : angle 2.17143 ( 36) hydrogen bonds : bond 0.05603 ( 753) hydrogen bonds : angle 7.17264 ( 2097) link_ALPHA1-2 : bond 0.00560 ( 3) link_ALPHA1-2 : angle 2.88005 ( 9) link_ALPHA1-3 : bond 0.00661 ( 6) link_ALPHA1-3 : angle 2.85060 ( 18) link_ALPHA1-6 : bond 0.00308 ( 3) link_ALPHA1-6 : angle 2.77635 ( 9) link_BETA1-4 : bond 0.00539 ( 12) link_BETA1-4 : angle 2.30056 ( 36) link_NAG-ASN : bond 0.00632 ( 48) link_NAG-ASN : angle 4.80697 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 696 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8637 (t) cc_final: 0.8387 (t) REVERT: A 349 LYS cc_start: 0.7532 (mtmt) cc_final: 0.7187 (mtmm) REVERT: A 391 ASP cc_start: 0.7255 (p0) cc_final: 0.7025 (p0) REVERT: A 403 ASN cc_start: 0.8415 (t0) cc_final: 0.8094 (t0) REVERT: A 439 MET cc_start: 0.8932 (mtp) cc_final: 0.8515 (mmm) REVERT: A 514 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6906 (mtm) REVERT: A 621 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7903 (mm-30) REVERT: A 719 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6474 (tt) REVERT: A 779 TYR cc_start: 0.8650 (t80) cc_final: 0.8367 (t80) REVERT: A 846 HIS cc_start: 0.8422 (t70) cc_final: 0.8146 (t-90) REVERT: A 850 GLN cc_start: 0.8301 (mt0) cc_final: 0.7880 (mt0) REVERT: A 854 ASN cc_start: 0.8738 (p0) cc_final: 0.8359 (p0) REVERT: A 856 GLN cc_start: 0.8127 (tp-100) cc_final: 0.7794 (tp-100) REVERT: A 869 LEU cc_start: 0.8538 (mt) cc_final: 0.8259 (mt) REVERT: A 997 MET cc_start: 0.5263 (tpt) cc_final: 0.5043 (tpt) REVERT: B 433 GLU cc_start: 0.7668 (pt0) cc_final: 0.7387 (pm20) REVERT: B 567 ARG cc_start: 0.7747 (tmm160) cc_final: 0.7482 (ptm-80) REVERT: B 870 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8275 (t0) REVERT: C 192 GLU cc_start: 0.8170 (tt0) cc_final: 0.7734 (tt0) REVERT: C 305 TYR cc_start: 0.8478 (m-10) cc_final: 0.8076 (m-10) REVERT: C 597 LEU cc_start: 0.7765 (mt) cc_final: 0.7453 (mt) REVERT: C 619 CYS cc_start: 0.8321 (t) cc_final: 0.8068 (t) REVERT: C 621 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7565 (mt-10) REVERT: C 824 GLN cc_start: 0.8350 (mp10) cc_final: 0.8002 (mp10) REVERT: C 863 GLN cc_start: 0.8348 (tp40) cc_final: 0.7952 (tp-100) REVERT: C 880 ARG cc_start: 0.6702 (ttm110) cc_final: 0.6457 (ttp-110) REVERT: C 885 ARG cc_start: 0.8583 (mtt180) cc_final: 0.8243 (mmt90) outliers start: 139 outliers final: 108 residues processed: 781 average time/residue: 0.1532 time to fit residues: 182.1809 Evaluate side-chains 765 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 654 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 800 LYS Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 922 SER Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 712 TYR Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 870 ASP Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 967 CYS Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1002 ILE Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 712 TYR Chi-restraints excluded: chain C residue 720 SER Chi-restraints excluded: chain C residue 733 ILE Chi-restraints excluded: chain C residue 763 SER Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 922 SER Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 968 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 278 optimal weight: 0.7980 chunk 265 optimal weight: 3.9990 chunk 197 optimal weight: 0.3980 chunk 261 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 257 optimal weight: 4.9990 chunk 234 optimal weight: 0.0870 chunk 70 optimal weight: 8.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN A 783 GLN A 863 GLN ** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN B 479 ASN B 728 GLN ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 831 ASN B 863 GLN ** B 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 507 GLN C 831 ASN ** C 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.130342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.119261 restraints weight = 56211.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.121950 restraints weight = 29274.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.123778 restraints weight = 17904.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.125022 restraints weight = 12126.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.125905 restraints weight = 8839.124| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22872 Z= 0.166 Angle : 0.859 16.588 30918 Z= 0.405 Chirality : 0.054 0.442 3288 Planarity : 0.004 0.052 4020 Dihedral : 10.558 72.132 4698 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.73 % Favored : 94.16 % Rotamer: Outliers : 5.80 % Allowed : 22.69 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.14), residues: 2862 helix: -0.08 (0.19), residues: 660 sheet: -1.34 (0.21), residues: 543 loop : -2.33 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1001 TYR 0.030 0.002 TYR A 748 PHE 0.027 0.002 PHE A 519 TRP 0.036 0.002 TRP B 588 HIS 0.024 0.002 HIS C 895 Details of bonding type rmsd covalent geometry : bond 0.00347 (22782) covalent geometry : angle 0.78232 (30666) SS BOND : bond 0.00826 ( 18) SS BOND : angle 1.90160 ( 36) hydrogen bonds : bond 0.05338 ( 753) hydrogen bonds : angle 6.90297 ( 2097) link_ALPHA1-2 : bond 0.00904 ( 3) link_ALPHA1-2 : angle 3.23147 ( 9) link_ALPHA1-3 : bond 0.00643 ( 6) link_ALPHA1-3 : angle 3.13421 ( 18) link_ALPHA1-6 : bond 0.00131 ( 3) link_ALPHA1-6 : angle 2.59847 ( 9) link_BETA1-4 : bond 0.00630 ( 12) link_BETA1-4 : angle 2.35677 ( 36) link_NAG-ASN : bond 0.00773 ( 48) link_NAG-ASN : angle 4.82941 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 677 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 LYS cc_start: 0.7606 (mtmt) cc_final: 0.7247 (mtmm) REVERT: A 371 PHE cc_start: 0.7960 (p90) cc_final: 0.7669 (p90) REVERT: A 391 ASP cc_start: 0.7315 (p0) cc_final: 0.7087 (p0) REVERT: A 403 ASN cc_start: 0.8148 (t0) cc_final: 0.7940 (t0) REVERT: A 439 MET cc_start: 0.8836 (mtp) cc_final: 0.8414 (mmm) REVERT: A 514 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6985 (mtm) REVERT: A 597 LEU cc_start: 0.8285 (mm) cc_final: 0.7993 (mt) REVERT: A 621 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7520 (mm-30) REVERT: A 719 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6521 (tt) REVERT: A 779 TYR cc_start: 0.8656 (t80) cc_final: 0.8428 (t80) REVERT: A 824 GLN cc_start: 0.8463 (mp10) cc_final: 0.8165 (mp10) REVERT: A 846 HIS cc_start: 0.8483 (t70) cc_final: 0.8221 (t-90) REVERT: A 850 GLN cc_start: 0.8345 (mt0) cc_final: 0.7999 (mt0) REVERT: A 852 ARG cc_start: 0.8291 (ttt-90) cc_final: 0.8056 (ttt-90) REVERT: A 854 ASN cc_start: 0.8817 (p0) cc_final: 0.8517 (p0) REVERT: A 856 GLN cc_start: 0.8188 (tp-100) cc_final: 0.7738 (tp-100) REVERT: A 868 ARG cc_start: 0.8453 (mmm160) cc_final: 0.8116 (mmm-85) REVERT: A 997 MET cc_start: 0.5158 (tpt) cc_final: 0.4814 (tpt) REVERT: B 74 PHE cc_start: 0.8120 (m-80) cc_final: 0.7825 (m-80) REVERT: B 207 ARG cc_start: 0.7098 (tmm-80) cc_final: 0.6863 (tmm-80) REVERT: B 433 GLU cc_start: 0.7658 (pt0) cc_final: 0.7369 (pm20) REVERT: B 567 ARG cc_start: 0.7790 (tmm160) cc_final: 0.7551 (ptm-80) REVERT: B 638 ARG cc_start: 0.9055 (ttp80) cc_final: 0.8752 (ttp80) REVERT: B 697 PHE cc_start: 0.8125 (m-80) cc_final: 0.7853 (m-80) REVERT: B 834 GLN cc_start: 0.8313 (tp40) cc_final: 0.7713 (tp40) REVERT: B 840 GLN cc_start: 0.8464 (tp40) cc_final: 0.8096 (tt0) REVERT: B 870 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8282 (t0) REVERT: B 879 ASP cc_start: 0.8892 (p0) cc_final: 0.8592 (p0) REVERT: B 913 LYS cc_start: 0.8673 (mmmt) cc_final: 0.8468 (mmmt) REVERT: C 286 LEU cc_start: 0.6832 (tp) cc_final: 0.6556 (tp) REVERT: C 305 TYR cc_start: 0.8537 (m-10) cc_final: 0.8003 (m-10) REVERT: C 621 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7529 (mt-10) REVERT: C 639 ASN cc_start: 0.8499 (t0) cc_final: 0.8095 (t0) REVERT: C 643 LEU cc_start: 0.8591 (mt) cc_final: 0.8200 (mt) REVERT: C 661 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6353 (mt) REVERT: C 824 GLN cc_start: 0.8286 (mp10) cc_final: 0.7830 (mp10) REVERT: C 863 GLN cc_start: 0.8284 (tp40) cc_final: 0.7860 (tp-100) REVERT: C 885 ARG cc_start: 0.8583 (mtt180) cc_final: 0.8157 (mmt90) REVERT: C 886 LEU cc_start: 0.9019 (mm) cc_final: 0.8740 (tp) REVERT: C 904 ARG cc_start: 0.7880 (tpt170) cc_final: 0.6661 (tpt170) outliers start: 127 outliers final: 107 residues processed: 759 average time/residue: 0.1608 time to fit residues: 186.0985 Evaluate side-chains 760 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 649 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 CYS Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 890 ASN Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 922 SER Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 712 TYR Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 870 ASP Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1002 ILE Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 712 TYR Chi-restraints excluded: chain C residue 733 ILE Chi-restraints excluded: chain C residue 890 ASN Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 922 SER Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 1002 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 134 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 216 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 845 ASN A 863 GLN ** A 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 933 HIS A 978 GLN B 507 GLN ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 ASN C 895 HIS ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.132977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.121549 restraints weight = 57548.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.124282 restraints weight = 30439.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.126100 restraints weight = 18890.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.127363 restraints weight = 12980.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.128269 restraints weight = 9601.337| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22872 Z= 0.149 Angle : 0.866 16.420 30918 Z= 0.407 Chirality : 0.065 1.420 3288 Planarity : 0.004 0.062 4020 Dihedral : 9.561 59.491 4682 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.80 % Favored : 94.10 % Rotamer: Outliers : 5.43 % Allowed : 23.97 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.14), residues: 2862 helix: 0.05 (0.19), residues: 648 sheet: -1.32 (0.22), residues: 513 loop : -2.28 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1001 TYR 0.023 0.002 TYR A 748 PHE 0.026 0.002 PHE A 519 TRP 0.016 0.001 TRP C 588 HIS 0.024 0.002 HIS B 895 Details of bonding type rmsd covalent geometry : bond 0.00299 (22782) covalent geometry : angle 0.78895 (30666) SS BOND : bond 0.00647 ( 18) SS BOND : angle 1.89778 ( 36) hydrogen bonds : bond 0.05111 ( 753) hydrogen bonds : angle 6.63769 ( 2097) link_ALPHA1-2 : bond 0.01456 ( 3) link_ALPHA1-2 : angle 2.78661 ( 9) link_ALPHA1-3 : bond 0.00793 ( 6) link_ALPHA1-3 : angle 3.02006 ( 18) link_ALPHA1-6 : bond 0.00238 ( 3) link_ALPHA1-6 : angle 2.28401 ( 9) link_BETA1-4 : bond 0.00656 ( 12) link_BETA1-4 : angle 2.37870 ( 36) link_NAG-ASN : bond 0.00784 ( 48) link_NAG-ASN : angle 4.92687 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 673 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 LYS cc_start: 0.7685 (mtmt) cc_final: 0.7259 (mtmm) REVERT: A 391 ASP cc_start: 0.7302 (p0) cc_final: 0.7072 (p0) REVERT: A 439 MET cc_start: 0.8817 (mtp) cc_final: 0.8378 (mmm) REVERT: A 614 ASN cc_start: 0.8663 (t0) cc_final: 0.8457 (t0) REVERT: A 621 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7641 (mm-30) REVERT: A 669 ASP cc_start: 0.7215 (t0) cc_final: 0.6854 (t70) REVERT: A 719 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6580 (tt) REVERT: A 824 GLN cc_start: 0.8449 (mp10) cc_final: 0.8092 (mp10) REVERT: A 846 HIS cc_start: 0.8352 (t70) cc_final: 0.8065 (t-90) REVERT: A 850 GLN cc_start: 0.8313 (mt0) cc_final: 0.7929 (mt0) REVERT: A 852 ARG cc_start: 0.8195 (ttt-90) cc_final: 0.7985 (ttt-90) REVERT: A 854 ASN cc_start: 0.8783 (p0) cc_final: 0.8523 (p0) REVERT: A 856 GLN cc_start: 0.8150 (tp-100) cc_final: 0.7672 (tp-100) REVERT: A 924 ARG cc_start: 0.8577 (ptp90) cc_final: 0.8354 (ptp90) REVERT: A 943 GLU cc_start: 0.8135 (tp30) cc_final: 0.7671 (tp30) REVERT: A 985 LYS cc_start: 0.8032 (tttt) cc_final: 0.7762 (tttp) REVERT: A 997 MET cc_start: 0.4901 (tpt) cc_final: 0.4661 (tpt) REVERT: B 433 GLU cc_start: 0.7719 (pt0) cc_final: 0.7375 (pm20) REVERT: B 655 ASP cc_start: 0.8061 (t0) cc_final: 0.7853 (t0) REVERT: B 697 PHE cc_start: 0.8207 (m-80) cc_final: 0.7682 (m-80) REVERT: B 747 MET cc_start: 0.8228 (ptp) cc_final: 0.7806 (ptp) REVERT: B 834 GLN cc_start: 0.8440 (tp40) cc_final: 0.8202 (tp40) REVERT: B 840 GLN cc_start: 0.8408 (tp40) cc_final: 0.8051 (tt0) REVERT: B 870 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8113 (t0) REVERT: B 879 ASP cc_start: 0.8814 (p0) cc_final: 0.8462 (p0) REVERT: B 936 SER cc_start: 0.8689 (t) cc_final: 0.8463 (p) REVERT: B 997 MET cc_start: 0.4502 (tpt) cc_final: 0.4173 (tpt) REVERT: B 1014 CYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7816 (m) REVERT: C 159 PHE cc_start: 0.7525 (m-80) cc_final: 0.7239 (m-10) REVERT: C 207 ARG cc_start: 0.7607 (tmm-80) cc_final: 0.7232 (tmm-80) REVERT: C 305 TYR cc_start: 0.8508 (m-10) cc_final: 0.7974 (m-10) REVERT: C 329 LEU cc_start: 0.8870 (tt) cc_final: 0.8565 (tp) REVERT: C 621 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7552 (mt-10) REVERT: C 638 ARG cc_start: 0.8955 (ttp80) cc_final: 0.8599 (ttp80) REVERT: C 661 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6313 (mt) REVERT: C 669 ASP cc_start: 0.7853 (t0) cc_final: 0.7575 (t0) REVERT: C 697 PHE cc_start: 0.8462 (m-80) cc_final: 0.8069 (m-80) REVERT: C 856 GLN cc_start: 0.7322 (tm-30) cc_final: 0.6349 (tm-30) REVERT: C 863 GLN cc_start: 0.8191 (tp40) cc_final: 0.7724 (tp-100) REVERT: C 877 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8034 (mm-40) REVERT: C 880 ARG cc_start: 0.6815 (ttm110) cc_final: 0.5932 (ttm110) REVERT: C 885 ARG cc_start: 0.8461 (mtt180) cc_final: 0.8050 (mmt90) REVERT: C 904 ARG cc_start: 0.7816 (tpt170) cc_final: 0.6951 (tpt170) REVERT: C 908 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7094 (mm-40) REVERT: C 935 PHE cc_start: 0.8022 (p90) cc_final: 0.7756 (p90) REVERT: C 1023 ARG cc_start: 0.8665 (tpt-90) cc_final: 0.8441 (mtp180) outliers start: 119 outliers final: 100 residues processed: 745 average time/residue: 0.1622 time to fit residues: 183.3221 Evaluate side-chains 746 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 642 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 CYS Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 890 ASN Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 856 GLN Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 870 ASP Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1014 CYS Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 712 TYR Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 890 ASN Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 283 optimal weight: 0.0070 chunk 156 optimal weight: 5.9990 chunk 6 optimal weight: 0.0050 chunk 79 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 221 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 185 optimal weight: 8.9990 chunk 179 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.8018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN A 246 GLN A 538 ASN ** A 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN B 200 HIS B 507 GLN B 804 ASN ** B 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 507 GLN C 831 ASN ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 876 GLN ** C 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.129263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.117926 restraints weight = 56375.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.120630 restraints weight = 29669.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.122450 restraints weight = 18300.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.123713 restraints weight = 12512.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.124606 restraints weight = 9206.317| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22872 Z= 0.176 Angle : 0.859 16.314 30918 Z= 0.406 Chirality : 0.053 0.457 3288 Planarity : 0.004 0.052 4020 Dihedral : 9.161 59.774 4657 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.36 % Favored : 93.54 % Rotamer: Outliers : 5.98 % Allowed : 24.84 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.15), residues: 2862 helix: 0.13 (0.19), residues: 648 sheet: -1.44 (0.22), residues: 528 loop : -2.31 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1001 TYR 0.031 0.002 TYR B 138 PHE 0.029 0.002 PHE C 123 TRP 0.044 0.002 TRP C 588 HIS 0.023 0.003 HIS B 895 Details of bonding type rmsd covalent geometry : bond 0.00361 (22782) covalent geometry : angle 0.79085 (30666) SS BOND : bond 0.00653 ( 18) SS BOND : angle 1.78717 ( 36) hydrogen bonds : bond 0.05290 ( 753) hydrogen bonds : angle 6.64969 ( 2097) link_ALPHA1-2 : bond 0.01255 ( 3) link_ALPHA1-2 : angle 2.06497 ( 9) link_ALPHA1-3 : bond 0.00662 ( 6) link_ALPHA1-3 : angle 3.04846 ( 18) link_ALPHA1-6 : bond 0.00143 ( 3) link_ALPHA1-6 : angle 2.59602 ( 9) link_BETA1-4 : bond 0.00582 ( 12) link_BETA1-4 : angle 2.51824 ( 36) link_NAG-ASN : bond 0.00917 ( 48) link_NAG-ASN : angle 4.59397 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 666 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 LYS cc_start: 0.7815 (mtmt) cc_final: 0.7261 (mtmm) REVERT: A 439 MET cc_start: 0.8857 (mtp) cc_final: 0.8419 (mmm) REVERT: A 515 LEU cc_start: 0.7910 (tp) cc_final: 0.7680 (tt) REVERT: A 597 LEU cc_start: 0.8335 (mm) cc_final: 0.8087 (mt) REVERT: A 614 ASN cc_start: 0.8720 (t0) cc_final: 0.8509 (t0) REVERT: A 621 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7765 (mm-30) REVERT: A 661 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.5983 (mt) REVERT: A 719 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6640 (tt) REVERT: A 779 TYR cc_start: 0.8641 (t80) cc_final: 0.8337 (t80) REVERT: A 824 GLN cc_start: 0.8426 (mp10) cc_final: 0.8051 (mp10) REVERT: A 854 ASN cc_start: 0.8803 (p0) cc_final: 0.8558 (p0) REVERT: A 943 GLU cc_start: 0.8224 (tp30) cc_final: 0.7922 (tp30) REVERT: A 985 LYS cc_start: 0.8122 (tttt) cc_final: 0.7774 (tttp) REVERT: A 997 MET cc_start: 0.5152 (tpt) cc_final: 0.4793 (tpt) REVERT: B 129 ARG cc_start: 0.7885 (ptm160) cc_final: 0.7488 (ptm160) REVERT: B 433 GLU cc_start: 0.7786 (pt0) cc_final: 0.7514 (pm20) REVERT: B 655 ASP cc_start: 0.8057 (t0) cc_final: 0.7821 (t0) REVERT: B 697 PHE cc_start: 0.8292 (m-80) cc_final: 0.8049 (m-80) REVERT: B 840 GLN cc_start: 0.8412 (tp40) cc_final: 0.8017 (tt0) REVERT: B 870 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8145 (t0) REVERT: B 879 ASP cc_start: 0.8841 (p0) cc_final: 0.8492 (p0) REVERT: B 936 SER cc_start: 0.8747 (t) cc_final: 0.8543 (p) REVERT: B 943 GLU cc_start: 0.8291 (tp30) cc_final: 0.8090 (tp30) REVERT: B 997 MET cc_start: 0.4580 (tpt) cc_final: 0.4075 (tpt) REVERT: C 159 PHE cc_start: 0.7705 (m-80) cc_final: 0.7384 (m-10) REVERT: C 305 TYR cc_start: 0.8615 (m-10) cc_final: 0.8378 (m-80) REVERT: C 445 LYS cc_start: 0.8726 (ttmt) cc_final: 0.8216 (ttmm) REVERT: C 621 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7586 (mt-10) REVERT: C 638 ARG cc_start: 0.9107 (ttp80) cc_final: 0.8779 (ttp80) REVERT: C 639 ASN cc_start: 0.8511 (t0) cc_final: 0.8249 (t0) REVERT: C 661 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6297 (mt) REVERT: C 697 PHE cc_start: 0.8490 (m-10) cc_final: 0.8225 (m-80) REVERT: C 824 GLN cc_start: 0.8161 (mp10) cc_final: 0.7884 (mp10) REVERT: C 856 GLN cc_start: 0.7429 (tm-30) cc_final: 0.6811 (tm-30) REVERT: C 863 GLN cc_start: 0.8180 (tp40) cc_final: 0.7697 (tp-100) REVERT: C 880 ARG cc_start: 0.6979 (ttm110) cc_final: 0.6437 (ttm110) REVERT: C 885 ARG cc_start: 0.8564 (mtt180) cc_final: 0.8114 (mmt90) REVERT: C 904 ARG cc_start: 0.7853 (tpt170) cc_final: 0.7052 (tpt170) REVERT: C 908 GLN cc_start: 0.8344 (mm-40) cc_final: 0.7597 (mm-40) REVERT: C 935 PHE cc_start: 0.8189 (p90) cc_final: 0.7912 (p90) outliers start: 131 outliers final: 117 residues processed: 752 average time/residue: 0.1587 time to fit residues: 181.9077 Evaluate side-chains 765 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 644 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 CYS Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 890 ASN Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 922 SER Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 870 ASP Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 925 TYR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 625 GLN Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 712 TYR Chi-restraints excluded: chain C residue 798 PHE Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 922 SER Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1002 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 266 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 210 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 HIS A 213 ASN A 246 GLN A 538 ASN A 593 GLN ** A 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 GLN ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 ASN ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 507 GLN C 731 ASN ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN ** C 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.123885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.112651 restraints weight = 56811.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.115300 restraints weight = 30291.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.117049 restraints weight = 18874.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.118259 restraints weight = 13026.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.119113 restraints weight = 9674.533| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 22872 Z= 0.260 Angle : 0.951 18.550 30918 Z= 0.456 Chirality : 0.059 1.027 3288 Planarity : 0.005 0.051 4020 Dihedral : 9.315 59.937 4657 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.07 % Favored : 91.82 % Rotamer: Outliers : 7.44 % Allowed : 25.02 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.14), residues: 2862 helix: -0.03 (0.19), residues: 642 sheet: -1.44 (0.23), residues: 489 loop : -2.46 (0.13), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1001 TYR 0.034 0.002 TYR A 900 PHE 0.028 0.003 PHE A 54 TRP 0.062 0.004 TRP C 588 HIS 0.020 0.003 HIS A 895 Details of bonding type rmsd covalent geometry : bond 0.00543 (22782) covalent geometry : angle 0.87174 (30666) SS BOND : bond 0.00774 ( 18) SS BOND : angle 1.95512 ( 36) hydrogen bonds : bond 0.05703 ( 753) hydrogen bonds : angle 6.94152 ( 2097) link_ALPHA1-2 : bond 0.01423 ( 3) link_ALPHA1-2 : angle 1.88505 ( 9) link_ALPHA1-3 : bond 0.00693 ( 6) link_ALPHA1-3 : angle 3.14945 ( 18) link_ALPHA1-6 : bond 0.00428 ( 3) link_ALPHA1-6 : angle 3.02403 ( 9) link_BETA1-4 : bond 0.00640 ( 12) link_BETA1-4 : angle 2.81533 ( 36) link_NAG-ASN : bond 0.00720 ( 48) link_NAG-ASN : angle 5.21521 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 662 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 SER cc_start: 0.9138 (OUTLIER) cc_final: 0.8929 (p) REVERT: A 349 LYS cc_start: 0.8059 (mtmt) cc_final: 0.7580 (mtmm) REVERT: A 398 MET cc_start: 0.6879 (mmm) cc_final: 0.6550 (mmm) REVERT: A 439 MET cc_start: 0.8751 (mtp) cc_final: 0.8086 (mmm) REVERT: A 515 LEU cc_start: 0.8424 (tp) cc_final: 0.8141 (tt) REVERT: A 597 LEU cc_start: 0.8291 (mm) cc_final: 0.8051 (mt) REVERT: A 621 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7989 (mm-30) REVERT: A 719 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7009 (tt) REVERT: A 779 TYR cc_start: 0.8696 (t80) cc_final: 0.8208 (t80) REVERT: A 854 ASN cc_start: 0.8812 (p0) cc_final: 0.8605 (p0) REVERT: A 943 GLU cc_start: 0.8367 (tp30) cc_final: 0.8020 (tp30) REVERT: A 985 LYS cc_start: 0.8156 (tttt) cc_final: 0.7700 (tttp) REVERT: A 997 MET cc_start: 0.5228 (tpt) cc_final: 0.4777 (tpt) REVERT: A 1014 CYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7401 (m) REVERT: B 72 ARG cc_start: 0.8419 (ttp-110) cc_final: 0.8091 (ttm170) REVERT: B 129 ARG cc_start: 0.8034 (ptm160) cc_final: 0.7656 (ptm160) REVERT: B 207 ARG cc_start: 0.8210 (tmt170) cc_final: 0.7869 (ptm160) REVERT: B 391 ASP cc_start: 0.7650 (p0) cc_final: 0.7280 (p0) REVERT: B 506 TYR cc_start: 0.8638 (t80) cc_final: 0.8165 (t80) REVERT: B 507 GLN cc_start: 0.7595 (mt0) cc_final: 0.7329 (mp10) REVERT: B 614 ASN cc_start: 0.8939 (t0) cc_final: 0.8703 (t0) REVERT: B 655 ASP cc_start: 0.8152 (t0) cc_final: 0.7919 (t0) REVERT: B 697 PHE cc_start: 0.8428 (m-80) cc_final: 0.8104 (m-80) REVERT: B 736 LEU cc_start: 0.9100 (tp) cc_final: 0.8856 (tp) REVERT: B 747 MET cc_start: 0.8466 (ptp) cc_final: 0.8263 (ptm) REVERT: B 839 GLN cc_start: 0.8618 (pt0) cc_final: 0.8069 (pt0) REVERT: B 840 GLN cc_start: 0.8439 (tp40) cc_final: 0.8075 (tt0) REVERT: B 870 ASP cc_start: 0.8774 (OUTLIER) cc_final: 0.8434 (t0) REVERT: B 879 ASP cc_start: 0.8822 (p0) cc_final: 0.8540 (p0) REVERT: B 997 MET cc_start: 0.4941 (tpt) cc_final: 0.4239 (tpt) REVERT: B 1032 GLU cc_start: 0.8629 (pp20) cc_final: 0.7807 (pp20) REVERT: C 159 PHE cc_start: 0.7874 (m-80) cc_final: 0.7546 (m-10) REVERT: C 305 TYR cc_start: 0.8715 (m-10) cc_final: 0.8428 (m-10) REVERT: C 614 ASN cc_start: 0.8879 (t0) cc_final: 0.8375 (t0) REVERT: C 621 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7768 (mt-10) REVERT: C 639 ASN cc_start: 0.8739 (t0) cc_final: 0.8293 (t0) REVERT: C 643 LEU cc_start: 0.8692 (mt) cc_final: 0.8482 (tp) REVERT: C 661 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6623 (mt) REVERT: C 824 GLN cc_start: 0.8209 (mp10) cc_final: 0.7894 (mp10) REVERT: C 856 GLN cc_start: 0.7488 (tm-30) cc_final: 0.6360 (tm-30) REVERT: C 863 GLN cc_start: 0.8086 (tp40) cc_final: 0.7616 (tp-100) REVERT: C 880 ARG cc_start: 0.7016 (ttm110) cc_final: 0.6158 (ttm110) REVERT: C 995 ARG cc_start: 0.8687 (tpp80) cc_final: 0.8137 (ttm-80) outliers start: 163 outliers final: 142 residues processed: 768 average time/residue: 0.1554 time to fit residues: 180.9106 Evaluate side-chains 794 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 647 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 CYS Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 890 ASN Chi-restraints excluded: chain A residue 895 HIS Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 922 SER Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1014 CYS Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 870 ASP Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 895 HIS Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 925 TYR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 977 ARG Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 625 GLN Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 712 TYR Chi-restraints excluded: chain C residue 720 SER Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 798 PHE Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 922 SER Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1002 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 215 optimal weight: 0.0970 chunk 285 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 242 optimal weight: 5.9990 chunk 206 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 HIS A 246 GLN ** A 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 GLN ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 911 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 = 0.3880 r_free = 0.3880 target = 0.126521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.115369 restraints weight = 57419.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.118059 restraints weight = 30634.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.119859 restraints weight = 18978.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.121077 restraints weight = 12987.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.121972 restraints weight = 9563.422| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22872 Z= 0.202 Angle : 0.937 20.856 30918 Z= 0.445 Chirality : 0.059 0.957 3288 Planarity : 0.005 0.051 4020 Dihedral : 8.914 59.897 4657 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.72 % Favored : 92.17 % Rotamer: Outliers : 6.39 % Allowed : 27.35 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.14), residues: 2862 helix: -0.18 (0.19), residues: 654 sheet: -1.56 (0.25), residues: 417 loop : -2.43 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 102 TYR 0.041 0.002 TYR A 748 PHE 0.027 0.002 PHE A 54 TRP 0.061 0.003 TRP C 588 HIS 0.024 0.003 HIS C 895 Details of bonding type rmsd covalent geometry : bond 0.00423 (22782) covalent geometry : angle 0.86115 (30666) SS BOND : bond 0.00822 ( 18) SS BOND : angle 1.97438 ( 36) hydrogen bonds : bond 0.05503 ( 753) hydrogen bonds : angle 6.86789 ( 2097) link_ALPHA1-2 : bond 0.01109 ( 3) link_ALPHA1-2 : angle 2.09766 ( 9) link_ALPHA1-3 : bond 0.00804 ( 6) link_ALPHA1-3 : angle 3.01175 ( 18) link_ALPHA1-6 : bond 0.00232 ( 3) link_ALPHA1-6 : angle 2.61444 ( 9) link_BETA1-4 : bond 0.00644 ( 12) link_BETA1-4 : angle 2.72217 ( 36) link_NAG-ASN : bond 0.00802 ( 48) link_NAG-ASN : angle 5.10387 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 667 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 LYS cc_start: 0.8061 (mtmt) cc_final: 0.7580 (mtmm) REVERT: A 515 LEU cc_start: 0.8393 (tp) cc_final: 0.8096 (tt) REVERT: A 597 LEU cc_start: 0.8201 (mm) cc_final: 0.7967 (mt) REVERT: A 621 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7885 (mm-30) REVERT: A 626 TYR cc_start: 0.8275 (m-10) cc_final: 0.8055 (m-10) REVERT: A 719 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7189 (tt) REVERT: A 779 TYR cc_start: 0.8654 (t80) cc_final: 0.8404 (t80) REVERT: A 824 GLN cc_start: 0.8380 (mp10) cc_final: 0.8006 (mp10) REVERT: A 854 ASN cc_start: 0.8819 (p0) cc_final: 0.8584 (p0) REVERT: A 943 GLU cc_start: 0.8330 (tp30) cc_final: 0.7996 (tp30) REVERT: A 997 MET cc_start: 0.5090 (tpt) cc_final: 0.4689 (tpt) REVERT: B 72 ARG cc_start: 0.8430 (ttp-110) cc_final: 0.8110 (ttm170) REVERT: B 129 ARG cc_start: 0.7988 (ptm160) cc_final: 0.7581 (ptm160) REVERT: B 207 ARG cc_start: 0.8228 (tmt170) cc_final: 0.7921 (ptm160) REVERT: B 391 ASP cc_start: 0.7650 (p0) cc_final: 0.7153 (p0) REVERT: B 506 TYR cc_start: 0.8583 (t80) cc_final: 0.8076 (t80) REVERT: B 507 GLN cc_start: 0.7644 (mt0) cc_final: 0.7367 (mt0) REVERT: B 567 ARG cc_start: 0.7839 (ptm-80) cc_final: 0.7626 (ptm-80) REVERT: B 614 ASN cc_start: 0.8923 (t0) cc_final: 0.8688 (t0) REVERT: B 697 PHE cc_start: 0.8441 (m-80) cc_final: 0.8071 (m-80) REVERT: B 747 MET cc_start: 0.8530 (ptp) cc_final: 0.8257 (ptm) REVERT: B 839 GLN cc_start: 0.8515 (pt0) cc_final: 0.8050 (pt0) REVERT: B 870 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8261 (t0) REVERT: B 879 ASP cc_start: 0.8803 (p0) cc_final: 0.8521 (p0) REVERT: B 943 GLU cc_start: 0.8553 (tp30) cc_final: 0.8156 (tp30) REVERT: B 997 MET cc_start: 0.4896 (tpt) cc_final: 0.4383 (tpt) REVERT: B 1032 GLU cc_start: 0.8535 (pp20) cc_final: 0.8204 (pp20) REVERT: C 305 TYR cc_start: 0.8688 (m-10) cc_final: 0.8431 (m-10) REVERT: C 614 ASN cc_start: 0.8919 (t0) cc_final: 0.8459 (t0) REVERT: C 621 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7708 (mt-10) REVERT: C 638 ARG cc_start: 0.9096 (ttp80) cc_final: 0.8818 (ttm110) REVERT: C 639 ASN cc_start: 0.8733 (t0) cc_final: 0.8251 (t0) REVERT: C 661 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6472 (mt) REVERT: C 824 GLN cc_start: 0.8176 (mp10) cc_final: 0.7851 (mp10) REVERT: C 856 GLN cc_start: 0.7451 (tm-30) cc_final: 0.6280 (tm-30) REVERT: C 863 GLN cc_start: 0.8108 (tp40) cc_final: 0.7583 (tp-100) REVERT: C 880 ARG cc_start: 0.7102 (ttm110) cc_final: 0.6327 (ttm110) REVERT: C 885 ARG cc_start: 0.8585 (mtt180) cc_final: 0.7887 (mtt180) REVERT: C 908 GLN cc_start: 0.8239 (mm-40) cc_final: 0.5918 (mm-40) REVERT: C 995 ARG cc_start: 0.8764 (tpp80) cc_final: 0.8230 (ttm-80) outliers start: 140 outliers final: 126 residues processed: 762 average time/residue: 0.1582 time to fit residues: 183.3447 Evaluate side-chains 780 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 651 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 CYS Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 890 ASN Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 922 SER Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 870 ASP Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 925 TYR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 798 PHE Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1002 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 150 optimal weight: 2.9990 chunk 214 optimal weight: 0.0770 chunk 158 optimal weight: 0.1980 chunk 287 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 246 GLN A 625 GLN ** A 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 GLN ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN B 246 GLN ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 GLN ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.129659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.118187 restraints weight = 57702.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.120899 restraints weight = 31301.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.122700 restraints weight = 19709.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.123910 restraints weight = 13708.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.124814 restraints weight = 10262.842| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22872 Z= 0.153 Angle : 0.919 18.136 30918 Z= 0.437 Chirality : 0.057 0.855 3288 Planarity : 0.004 0.051 4020 Dihedral : 8.305 59.821 4655 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.41 % Favored : 92.49 % Rotamer: Outliers : 5.62 % Allowed : 28.22 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.14), residues: 2862 helix: -0.23 (0.19), residues: 654 sheet: -1.33 (0.23), residues: 513 loop : -2.48 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1001 TYR 0.034 0.002 TYR A 748 PHE 0.026 0.002 PHE A 54 TRP 0.058 0.002 TRP C 588 HIS 0.025 0.003 HIS A 895 Details of bonding type rmsd covalent geometry : bond 0.00318 (22782) covalent geometry : angle 0.84809 (30666) SS BOND : bond 0.00670 ( 18) SS BOND : angle 1.91587 ( 36) hydrogen bonds : bond 0.05235 ( 753) hydrogen bonds : angle 6.65644 ( 2097) link_ALPHA1-2 : bond 0.01020 ( 3) link_ALPHA1-2 : angle 2.38608 ( 9) link_ALPHA1-3 : bond 0.00869 ( 6) link_ALPHA1-3 : angle 2.81781 ( 18) link_ALPHA1-6 : bond 0.00378 ( 3) link_ALPHA1-6 : angle 1.99892 ( 9) link_BETA1-4 : bond 0.00687 ( 12) link_BETA1-4 : angle 2.54321 ( 36) link_NAG-ASN : bond 0.00788 ( 48) link_NAG-ASN : angle 4.89115 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 664 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 TYR cc_start: 0.8528 (m-10) cc_final: 0.8320 (m-10) REVERT: A 349 LYS cc_start: 0.7891 (mtmt) cc_final: 0.7321 (mtmm) REVERT: A 439 MET cc_start: 0.8348 (mmm) cc_final: 0.7977 (mmm) REVERT: A 515 LEU cc_start: 0.8391 (tp) cc_final: 0.8079 (tt) REVERT: A 621 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7802 (mm-30) REVERT: A 719 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.6889 (tt) REVERT: A 779 TYR cc_start: 0.8645 (t80) cc_final: 0.8444 (t80) REVERT: A 838 ASN cc_start: 0.7431 (m-40) cc_final: 0.7153 (m-40) REVERT: A 943 GLU cc_start: 0.8159 (tp30) cc_final: 0.7812 (tp30) REVERT: A 997 MET cc_start: 0.5100 (tpt) cc_final: 0.4869 (tpt) REVERT: B 207 ARG cc_start: 0.8148 (tmt170) cc_final: 0.7746 (tmm-80) REVERT: B 567 ARG cc_start: 0.7901 (ptm-80) cc_final: 0.7600 (ptm-80) REVERT: B 614 ASN cc_start: 0.8811 (t0) cc_final: 0.8593 (t0) REVERT: B 697 PHE cc_start: 0.8379 (m-80) cc_final: 0.8117 (m-80) REVERT: B 747 MET cc_start: 0.8491 (ptp) cc_final: 0.8168 (ptm) REVERT: B 839 GLN cc_start: 0.8471 (pt0) cc_final: 0.8027 (pt0) REVERT: B 870 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8212 (t0) REVERT: B 879 ASP cc_start: 0.8751 (p0) cc_final: 0.8434 (p0) REVERT: B 997 MET cc_start: 0.4908 (tpt) cc_final: 0.4459 (tpt) REVERT: B 1026 LEU cc_start: 0.8031 (mt) cc_final: 0.7693 (mp) REVERT: B 1032 GLU cc_start: 0.8360 (pp20) cc_final: 0.8102 (pp20) REVERT: C 614 ASN cc_start: 0.8795 (t0) cc_final: 0.8336 (t0) REVERT: C 621 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7698 (mt-10) REVERT: C 638 ARG cc_start: 0.9070 (ttp80) cc_final: 0.8621 (ttp80) REVERT: C 661 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6559 (mt) REVERT: C 824 GLN cc_start: 0.8164 (mp10) cc_final: 0.7810 (mp10) REVERT: C 856 GLN cc_start: 0.7269 (tm-30) cc_final: 0.6753 (tm-30) REVERT: C 863 GLN cc_start: 0.8050 (tp40) cc_final: 0.7540 (tp-100) REVERT: C 995 ARG cc_start: 0.8745 (tpp80) cc_final: 0.8240 (ttm-80) REVERT: C 1023 ARG cc_start: 0.8808 (tpt-90) cc_final: 0.8549 (mtp180) outliers start: 123 outliers final: 111 residues processed: 744 average time/residue: 0.1583 time to fit residues: 178.4615 Evaluate side-chains 760 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 646 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 588 TRP Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 630 CYS Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 890 ASN Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 922 SER Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 870 ASP Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 925 TYR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 712 TYR Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 798 PHE Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 70 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 269 optimal weight: 0.9980 chunk 271 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 184 optimal weight: 0.0870 chunk 174 optimal weight: 0.0670 chunk 262 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.4300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 854 ASN ** A 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 GLN ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 912 GLN ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.127459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.116415 restraints weight = 56278.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.119104 restraints weight = 29352.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.120914 restraints weight = 17974.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.122124 restraints weight = 12190.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.123048 restraints weight = 8959.844| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22872 Z= 0.170 Angle : 0.959 17.322 30918 Z= 0.455 Chirality : 0.060 1.251 3288 Planarity : 0.005 0.083 4020 Dihedral : 8.206 59.212 4651 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.76 % Favored : 92.14 % Rotamer: Outliers : 5.34 % Allowed : 28.58 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.15), residues: 2862 helix: -0.19 (0.19), residues: 663 sheet: -1.37 (0.23), residues: 525 loop : -2.51 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 977 TYR 0.033 0.002 TYR A 748 PHE 0.028 0.002 PHE A 54 TRP 0.053 0.002 TRP C 588 HIS 0.023 0.003 HIS C 895 Details of bonding type rmsd covalent geometry : bond 0.00359 (22782) covalent geometry : angle 0.88944 (30666) SS BOND : bond 0.00736 ( 18) SS BOND : angle 2.07278 ( 36) hydrogen bonds : bond 0.05291 ( 753) hydrogen bonds : angle 6.66040 ( 2097) link_ALPHA1-2 : bond 0.00973 ( 3) link_ALPHA1-2 : angle 2.24987 ( 9) link_ALPHA1-3 : bond 0.00782 ( 6) link_ALPHA1-3 : angle 2.81816 ( 18) link_ALPHA1-6 : bond 0.00250 ( 3) link_ALPHA1-6 : angle 2.19262 ( 9) link_BETA1-4 : bond 0.00654 ( 12) link_BETA1-4 : angle 2.63795 ( 36) link_NAG-ASN : bond 0.00738 ( 48) link_NAG-ASN : angle 4.96735 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 654 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 TYR cc_start: 0.8273 (p90) cc_final: 0.8059 (p90) REVERT: A 213 ASN cc_start: 0.7385 (m110) cc_final: 0.6694 (t0) REVERT: A 349 LYS cc_start: 0.7989 (mtmt) cc_final: 0.7533 (mtmm) REVERT: A 389 LEU cc_start: 0.8784 (mt) cc_final: 0.8508 (mt) REVERT: A 419 TRP cc_start: 0.8951 (OUTLIER) cc_final: 0.8659 (p90) REVERT: A 439 MET cc_start: 0.8406 (mmm) cc_final: 0.8099 (mmm) REVERT: A 515 LEU cc_start: 0.8449 (tp) cc_final: 0.8127 (tt) REVERT: A 621 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8084 (mm-30) REVERT: A 719 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.6541 (tp) REVERT: A 779 TYR cc_start: 0.8686 (t80) cc_final: 0.8474 (t80) REVERT: A 824 GLN cc_start: 0.8285 (mp10) cc_final: 0.7961 (mp10) REVERT: A 943 GLU cc_start: 0.8282 (tp30) cc_final: 0.7909 (tp30) REVERT: A 997 MET cc_start: 0.5117 (tpt) cc_final: 0.4711 (tpt) REVERT: B 129 ARG cc_start: 0.7820 (ptm160) cc_final: 0.7298 (ptm160) REVERT: B 207 ARG cc_start: 0.8204 (tmt170) cc_final: 0.7948 (ptm160) REVERT: B 567 ARG cc_start: 0.7862 (ptm-80) cc_final: 0.7552 (ptm-80) REVERT: B 614 ASN cc_start: 0.8864 (t0) cc_final: 0.8621 (t0) REVERT: B 622 LEU cc_start: 0.9146 (mp) cc_final: 0.8343 (mp) REVERT: B 734 MET cc_start: 0.8366 (ttt) cc_final: 0.8009 (ttt) REVERT: B 747 MET cc_start: 0.8515 (ptp) cc_final: 0.8109 (ptm) REVERT: B 839 GLN cc_start: 0.8486 (pt0) cc_final: 0.8072 (pt0) REVERT: B 870 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.8210 (t0) REVERT: B 879 ASP cc_start: 0.8824 (p0) cc_final: 0.8482 (p0) REVERT: B 943 GLU cc_start: 0.8494 (tp30) cc_final: 0.8124 (tp30) REVERT: B 997 MET cc_start: 0.4839 (tpt) cc_final: 0.4269 (tpt) REVERT: B 1032 GLU cc_start: 0.8496 (pp20) cc_final: 0.8184 (pp20) REVERT: C 197 ARG cc_start: 0.6644 (ptp-110) cc_final: 0.6366 (ptp-110) REVERT: C 614 ASN cc_start: 0.8812 (t0) cc_final: 0.8398 (t0) REVERT: C 621 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7712 (mt-10) REVERT: C 661 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6533 (mt) REVERT: C 789 GLU cc_start: 0.7908 (tp30) cc_final: 0.7686 (pt0) REVERT: C 856 GLN cc_start: 0.7221 (tm-30) cc_final: 0.6922 (tm-30) REVERT: C 863 GLN cc_start: 0.8163 (tp40) cc_final: 0.7572 (tp-100) REVERT: C 1023 ARG cc_start: 0.8792 (tpt-90) cc_final: 0.8556 (mtp180) outliers start: 117 outliers final: 110 residues processed: 736 average time/residue: 0.1617 time to fit residues: 180.4434 Evaluate side-chains 764 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 650 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 588 TRP Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 630 CYS Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 854 ASN Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 890 ASN Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 922 SER Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 625 GLN Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 870 ASP Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 925 TYR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 798 PHE Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 23 optimal weight: 9.9990 chunk 218 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 978 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN B 774 GLN ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.122038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.110932 restraints weight = 57256.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.113572 restraints weight = 30152.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.115341 restraints weight = 18701.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.116550 restraints weight = 12845.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.117400 restraints weight = 9475.755| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.5668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 22872 Z= 0.288 Angle : 1.032 17.915 30918 Z= 0.498 Chirality : 0.061 1.310 3288 Planarity : 0.005 0.069 4020 Dihedral : 8.852 59.396 4647 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.75 % Favored : 90.15 % Rotamer: Outliers : 5.57 % Allowed : 28.90 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.14), residues: 2862 helix: -0.32 (0.19), residues: 675 sheet: -1.68 (0.24), residues: 453 loop : -2.61 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1001 TYR 0.035 0.003 TYR A 748 PHE 0.035 0.003 PHE B 90 TRP 0.071 0.003 TRP C 588 HIS 0.022 0.003 HIS C 895 Details of bonding type rmsd covalent geometry : bond 0.00606 (22782) covalent geometry : angle 0.96326 (30666) SS BOND : bond 0.01007 ( 18) SS BOND : angle 2.11816 ( 36) hydrogen bonds : bond 0.05886 ( 753) hydrogen bonds : angle 7.08124 ( 2097) link_ALPHA1-2 : bond 0.00794 ( 3) link_ALPHA1-2 : angle 1.87860 ( 9) link_ALPHA1-3 : bond 0.00695 ( 6) link_ALPHA1-3 : angle 3.11224 ( 18) link_ALPHA1-6 : bond 0.00387 ( 3) link_ALPHA1-6 : angle 2.96615 ( 9) link_BETA1-4 : bond 0.00648 ( 12) link_BETA1-4 : angle 3.03025 ( 36) link_NAG-ASN : bond 0.00832 ( 48) link_NAG-ASN : angle 5.05078 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4120.11 seconds wall clock time: 71 minutes 54.03 seconds (4314.03 seconds total)