Starting phenix.real_space_refine on Sat Jul 4 18:21:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cyd_30497/07_2026/7cyd_30497.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cyd_30497/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7cyd_30497/07_2026/7cyd_30497.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cyd_30497/07_2026/7cyd_30497.cif" model { file = "/net/cci-nas-00/data/ceres_data/7cyd_30497/07_2026/7cyd_30497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cyd_30497/07_2026/7cyd_30497.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cyd_30497/07_2026/7cyd_30497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cyd_30497/07_2026/7cyd_30497.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 chiralities: 14 Time building chain proxies: 4.76, per 1000 atoms: 0.21 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: 1.64 Conformation dependent library (CDL) restraints added in 928.1 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: 0.86 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: 3.72 Time building geometry restraints manager: 2.26 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 - 17.46: 11792 17.46 - 34.92: 989 34.92 - 52.38: 267 52.38 - 69.84: 56 69.84 - 87.30: 9 Dihedral angle restraints: 13113 sinusoidal: 4698 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 13110 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.960 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 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 : 14.465 87.297 7665 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/Z covalent geometry : bond 0.00887 / 0.52 (22782) covalent geometry : angle 1.21396 / 0.73 (30666) SS BOND : bond 0.01066 / 0.72 ( 18) SS BOND : angle 4.15060 / 2.69 ( 36) hydrogen bonds : bond 0.17522 / 11.43 ( 753) hydrogen bonds : angle 9.36776 / 6.62 ( 2097) link_ALPHA1-2 : bond 0.00704 / 0.32 ( 3) link_ALPHA1-2 : angle 0.85389 / 0.46 ( 9) link_ALPHA1-3 : bond 0.00356 / 0.20 ( 6) link_ALPHA1-3 : angle 2.34090 / 2.03 ( 18) link_ALPHA1-6 : bond 0.00389 / 0.18 ( 3) link_ALPHA1-6 : angle 1.29986 / 0.70 ( 9) link_BETA1-4 : bond 0.00125 / 0.08 ( 12) link_BETA1-4 : angle 1.56698 / 1.00 ( 36) link_NAG-ASN : bond 0.14544 / 9.70 ( 48) link_NAG-ASN : angle 8.93165 / 6.48 ( 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 : 0.846 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: 0.1408 time to fit residues: 206.9866 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 : 0.754 ------------------------------------------------------------------------------- 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... A 80 ASN A 260 ASN A 498 ASN A 593 GLN 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 507 GLN C 593 GLN ** 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.130655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.119033 restraints weight = 58384.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.121751 restraints weight = 31467.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.123563 restraints weight = 19773.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.124812 restraints weight = 13724.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.125695 restraints weight = 10220.967| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22872 Z= 0.216 Angle : 0.931 16.035 30918 Z= 0.452 Chirality : 0.058 0.435 3288 Planarity : 0.005 0.077 4020 Dihedral : 9.105 58.454 3356 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.96 % Favored : 94.93 % Rotamer: Outliers : 6.44 % Allowed : 15.89 % Favored : 77.67 % 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: -2.65 (0.14), residues: 2862 helix: -0.83 (0.17), residues: 657 sheet: -1.59 (0.21), residues: 564 loop : -2.28 (0.13), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 638 TYR 0.031 0.002 TYR C 729 PHE 0.033 0.003 PHE A 182 TRP 0.015 0.002 TRP A 404 HIS 0.012 0.003 HIS C 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.22 (22782) covalent geometry : angle 0.86228 / 0.44 (30666) SS BOND : bond 0.00864 / 0.56 ( 18) SS BOND : angle 2.71869 / 1.82 ( 36) hydrogen bonds : bond 0.05976 / 4.09 ( 753) hydrogen bonds : angle 7.63342 / 5.36 ( 2097) link_ALPHA1-2 : bond 0.00358 / 0.17 ( 3) link_ALPHA1-2 : angle 2.24331 / 1.16 ( 9) link_ALPHA1-3 : bond 0.00528 / 0.26 ( 6) link_ALPHA1-3 : angle 2.39753 / 1.76 ( 18) link_ALPHA1-6 : bond 0.00312 / 0.14 ( 3) link_ALPHA1-6 : angle 1.94729 / 1.01 ( 9) link_BETA1-4 : bond 0.00718 / 0.39 ( 12) link_BETA1-4 : angle 2.08576 / 1.50 ( 36) link_NAG-ASN : bond 0.00645 / 0.38 ( 48) link_NAG-ASN : angle 4.86837 / 3.47 ( 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 851 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 710 time to evaluate : 0.765 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: symmetry clash REVERT: A 50 SER cc_start: 0.8543 (t) cc_final: 0.8298 (t) REVERT: A 129 ARG cc_start: 0.7677 (ptm160) cc_final: 0.7430 (ptm160) REVERT: A 403 ASN cc_start: 0.8313 (t0) cc_final: 0.8053 (t0) REVERT: A 650 GLU cc_start: 0.7514 (tp30) cc_final: 0.7113 (tp30) REVERT: A 719 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6802 (tt) REVERT: A 779 TYR cc_start: 0.8566 (t80) cc_final: 0.8218 (t80) REVERT: A 846 HIS cc_start: 0.8436 (t70) cc_final: 0.8160 (t-90) REVERT: A 850 GLN cc_start: 0.8235 (mt0) cc_final: 0.7876 (mt0) REVERT: A 854 ASN cc_start: 0.8677 (p0) cc_final: 0.8246 (p0) REVERT: A 869 LEU cc_start: 0.8451 (mt) cc_final: 0.8000 (mt) REVERT: A 922 SER cc_start: 0.8964 (t) cc_final: 0.8763 (t) REVERT: A 936 SER cc_start: 0.8085 (t) cc_final: 0.7804 (t) REVERT: A 939 ASN cc_start: 0.7795 (t0) cc_final: 0.7574 (t0) REVERT: B 192 GLU cc_start: 0.7829 (tt0) cc_final: 0.7520 (tt0) REVERT: B 433 GLU cc_start: 0.7374 (pt0) cc_final: 0.7123 (pm20) REVERT: B 863 GLN cc_start: 0.8219 (tp40) cc_final: 0.7913 (tp-100) REVERT: B 870 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8300 (t0) REVERT: B 875 ASP cc_start: 0.8901 (m-30) cc_final: 0.8215 (m-30) REVERT: B 879 ASP cc_start: 0.8854 (p0) cc_final: 0.8513 (p0) REVERT: B 1026 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8163 (mt) REVERT: C 286 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.7011 (tp) REVERT: C 619 CYS cc_start: 0.8331 (t) cc_final: 0.8059 (t) REVERT: C 638 ARG cc_start: 0.8915 (ttm110) cc_final: 0.8635 (ptm-80) REVERT: C 643 LEU cc_start: 0.8656 (mt) cc_final: 0.8326 (mt) REVERT: C 669 ASP cc_start: 0.7667 (t0) cc_final: 0.7270 (t70) REVERT: C 839 GLN cc_start: 0.7700 (pt0) cc_final: 0.7242 (pt0) REVERT: C 863 GLN cc_start: 0.8406 (tp40) cc_final: 0.8055 (tp-100) REVERT: C 885 ARG cc_start: 0.8536 (mtt180) cc_final: 0.8173 (mmt90) REVERT: C 886 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8760 (tp) REVERT: C 907 ARG cc_start: 0.8368 (ttm110) cc_final: 0.8114 (ttp80) REVERT: C 908 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7550 (mm-40) REVERT: C 935 PHE cc_start: 0.8190 (p90) cc_final: 0.7821 (p90) outliers start: 141 outliers final: 116 residues processed: 802 average time/residue: 0.1409 time to fit residues: 173.4489 Evaluate side-chains 777 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 656 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 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 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 303 VAL 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 552 SER 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 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 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 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 911 GLN 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 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 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 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 720 SER 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 886 LEU Chi-restraints excluded: chain C residue 922 SER Chi-restraints excluded: chain C residue 953 LEU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 8.9990 chunk 244 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 221 optimal weight: 10.0000 chunk 140 optimal weight: 0.6980 chunk 174 optimal weight: 7.9990 chunk 198 optimal weight: 0.0980 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 HIS A 213 ASN A 368 ASN A 498 ASN A 831 ASN A 863 GLN A 895 HIS 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** A 978 GLN 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 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 246 GLN C 507 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.129137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.117600 restraints weight = 58300.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.120303 restraints weight = 31510.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.122124 restraints weight = 19787.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.123355 restraints weight = 13729.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.124250 restraints weight = 10230.804| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22872 Z= 0.191 Angle : 0.836 16.598 30918 Z= 0.406 Chirality : 0.054 0.417 3288 Planarity : 0.005 0.050 4020 Dihedral : 7.794 59.481 3257 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.52 % Favored : 94.37 % Rotamer: Outliers : 6.39 % Allowed : 19.59 % Favored : 74.02 % 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: -2.39 (0.14), residues: 2862 helix: -0.26 (0.18), residues: 660 sheet: -1.46 (0.20), residues: 570 loop : -2.28 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 72 TYR 0.027 0.002 TYR A 748 PHE 0.038 0.002 PHE A 697 TRP 0.040 0.002 TRP C 588 HIS 0.012 0.003 HIS B 895 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (22782) covalent geometry : angle 0.76941 / 0.39 (30666) SS BOND : bond 0.00797 / 0.51 ( 18) SS BOND : angle 2.13809 / 1.40 ( 36) hydrogen bonds : bond 0.05679 / 3.82 ( 753) hydrogen bonds : angle 7.20346 / 5.04 ( 2097) link_ALPHA1-2 : bond 0.00256 / 0.12 ( 3) link_ALPHA1-2 : angle 2.17925 / 1.16 ( 9) link_ALPHA1-3 : bond 0.00506 / 0.25 ( 6) link_ALPHA1-3 : angle 2.35395 / 1.85 ( 18) link_ALPHA1-6 : bond 0.00160 / 0.06 ( 3) link_ALPHA1-6 : angle 1.82389 / 0.97 ( 9) link_BETA1-4 : bond 0.00546 / 0.32 ( 12) link_BETA1-4 : angle 1.87748 / 1.27 ( 36) link_NAG-ASN : bond 0.00624 / 0.36 ( 48) link_NAG-ASN : angle 4.57324 / 3.25 ( 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 829 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 689 time to evaluate : 0.804 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: A 50 SER cc_start: 0.8656 (t) cc_final: 0.8404 (t) REVERT: A 349 LYS cc_start: 0.7575 (mtmt) cc_final: 0.7173 (mtmm) REVERT: A 391 ASP cc_start: 0.7303 (p0) cc_final: 0.7082 (p0) REVERT: A 403 ASN cc_start: 0.8294 (t0) cc_final: 0.8081 (t0) REVERT: A 439 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.7991 (mmm) REVERT: A 514 MET cc_start: 0.7256 (OUTLIER) cc_final: 0.6960 (mtm) REVERT: A 530 LEU cc_start: 0.8510 (mt) cc_final: 0.8247 (mp) REVERT: A 621 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7895 (mm-30) REVERT: A 719 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6538 (tt) REVERT: A 779 TYR cc_start: 0.8669 (t80) cc_final: 0.8367 (t80) REVERT: A 824 GLN cc_start: 0.8520 (mp10) cc_final: 0.8225 (mp10) REVERT: A 846 HIS cc_start: 0.8438 (t70) cc_final: 0.8174 (t-90) REVERT: A 850 GLN cc_start: 0.8292 (mt0) cc_final: 0.7939 (mt0) REVERT: A 852 ARG cc_start: 0.8291 (ttt-90) cc_final: 0.8053 (ttt-90) REVERT: A 854 ASN cc_start: 0.8721 (p0) cc_final: 0.8263 (p0) REVERT: A 856 GLN cc_start: 0.8221 (tp-100) cc_final: 0.7896 (tp-100) REVERT: A 869 LEU cc_start: 0.8584 (mt) cc_final: 0.8294 (mt) REVERT: A 997 MET cc_start: 0.5409 (tpt) cc_final: 0.5139 (tpt) REVERT: B 192 GLU cc_start: 0.7785 (tt0) cc_final: 0.7560 (tt0) REVERT: B 433 GLU cc_start: 0.7685 (pt0) cc_final: 0.7415 (pm20) REVERT: B 567 ARG cc_start: 0.7763 (tmm160) cc_final: 0.7466 (ptm-80) REVERT: B 621 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7696 (mt-10) REVERT: B 870 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8315 (t0) REVERT: C 305 TYR cc_start: 0.8502 (m-10) cc_final: 0.8159 (m-10) REVERT: C 619 CYS cc_start: 0.8439 (t) cc_final: 0.8144 (t) REVERT: C 643 LEU cc_start: 0.8577 (mt) cc_final: 0.8204 (mt) REVERT: C 824 GLN cc_start: 0.8320 (mp10) cc_final: 0.7960 (mp10) REVERT: C 863 GLN cc_start: 0.8404 (tp40) cc_final: 0.8026 (tp-100) REVERT: C 877 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8333 (mm-40) REVERT: C 885 ARG cc_start: 0.8591 (mtt180) cc_final: 0.8246 (mmt90) REVERT: C 886 LEU cc_start: 0.8996 (mm) cc_final: 0.8775 (tp) outliers start: 140 outliers final: 109 residues processed: 775 average time/residue: 0.1534 time to fit residues: 181.7451 Evaluate side-chains 765 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 652 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 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 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 439 MET 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 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 712 TYR 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 871 ILE Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1016 VAL 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 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 720 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 763 SER 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 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 967 CYS Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1002 ILE 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 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 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 435 VAL 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 604 ILE Chi-restraints excluded: chain C residue 617 VAL 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 733 ILE Chi-restraints excluded: chain C residue 763 SER Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 911 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 278 optimal weight: 8.9990 chunk 265 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 257 optimal weight: 1.9990 chunk 234 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 173 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN A 863 GLN ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN B 246 GLN B 479 ASN ** 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 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.129995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.119264 restraints weight = 56759.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.121908 restraints weight = 29814.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.123673 restraints weight = 18235.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.124892 restraints weight = 12354.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.125768 restraints weight = 8996.566| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4031 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= 0.163 Angle : 0.834 17.828 30918 Z= 0.400 Chirality : 0.057 0.981 3288 Planarity : 0.004 0.059 4020 Dihedral : 7.320 58.742 3223 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.70 % Favored : 94.20 % Rotamer: Outliers : 5.57 % Allowed : 22.65 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.14), residues: 2862 helix: -0.04 (0.19), residues: 651 sheet: -1.30 (0.21), residues: 543 loop : -2.32 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 72 TYR 0.030 0.002 TYR A 748 PHE 0.027 0.002 PHE A 519 TRP 0.015 0.002 TRP C 588 HIS 0.008 0.002 HIS B 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (22782) covalent geometry : angle 0.76635 / 0.38 (30666) SS BOND : bond 0.00944 / 0.65 ( 18) SS BOND : angle 1.94938 / 1.32 ( 36) hydrogen bonds : bond 0.05346 / 3.62 ( 753) hydrogen bonds : angle 6.91286 / 4.81 ( 2097) link_ALPHA1-2 : bond 0.00299 / 0.13 ( 3) link_ALPHA1-2 : angle 2.07597 / 1.10 ( 9) link_ALPHA1-3 : bond 0.00575 / 0.30 ( 6) link_ALPHA1-3 : angle 2.38225 / 1.86 ( 18) link_ALPHA1-6 : bond 0.00194 / 0.08 ( 3) link_ALPHA1-6 : angle 1.58657 / 0.83 ( 9) link_BETA1-4 : bond 0.00679 / 0.43 ( 12) link_BETA1-4 : angle 1.75077 / 1.19 ( 36) link_NAG-ASN : bond 0.00823 / 0.40 ( 48) link_NAG-ASN : angle 4.62667 / 3.41 ( 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 805 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 683 time to evaluate : 0.753 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: A 50 SER cc_start: 0.8773 (t) cc_final: 0.8569 (t) REVERT: A 72 ARG cc_start: 0.8167 (ptm-80) cc_final: 0.7349 (ptm-80) REVERT: A 261 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8254 (ttm110) REVERT: A 349 LYS cc_start: 0.7636 (mtmt) cc_final: 0.7259 (mtmm) REVERT: A 391 ASP cc_start: 0.7326 (p0) cc_final: 0.7104 (p0) REVERT: A 403 ASN cc_start: 0.8202 (t0) cc_final: 0.7980 (t0) REVERT: A 439 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7812 (mmm) REVERT: A 468 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7953 (tt) REVERT: A 514 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6998 (mtm) REVERT: A 621 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7500 (mm-30) REVERT: A 719 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6548 (tt) REVERT: A 779 TYR cc_start: 0.8631 (t80) cc_final: 0.8420 (t80) REVERT: A 824 GLN cc_start: 0.8497 (mp10) cc_final: 0.8124 (mp10) REVERT: A 846 HIS cc_start: 0.8513 (t70) cc_final: 0.8229 (t-90) REVERT: A 850 GLN cc_start: 0.8359 (mt0) cc_final: 0.7962 (mt0) REVERT: A 852 ARG cc_start: 0.8265 (ttt-90) cc_final: 0.8056 (ttt-90) REVERT: A 854 ASN cc_start: 0.8739 (p0) cc_final: 0.8287 (p0) REVERT: A 856 GLN cc_start: 0.8253 (tp-100) cc_final: 0.7777 (tp-100) REVERT: A 868 ARG cc_start: 0.8317 (mmm160) cc_final: 0.8029 (mmm-85) REVERT: A 877 GLN cc_start: 0.8303 (mm110) cc_final: 0.7484 (mm-40) REVERT: A 997 MET cc_start: 0.5000 (tpt) cc_final: 0.4654 (tpt) REVERT: B 74 PHE cc_start: 0.8215 (m-80) cc_final: 0.8007 (m-80) REVERT: B 433 GLU cc_start: 0.7727 (pt0) cc_final: 0.7382 (pm20) REVERT: B 506 TYR cc_start: 0.8451 (t80) cc_final: 0.7647 (t80) REVERT: B 507 GLN cc_start: 0.7574 (mt0) cc_final: 0.7373 (mt0) REVERT: B 567 ARG cc_start: 0.7802 (tmm160) cc_final: 0.7573 (ptm-80) REVERT: B 621 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7612 (mt-10) REVERT: B 834 GLN cc_start: 0.8369 (tp40) cc_final: 0.7749 (tp40) REVERT: B 838 ASN cc_start: 0.7554 (m-40) cc_final: 0.7265 (m-40) REVERT: B 840 GLN cc_start: 0.8435 (tp40) cc_final: 0.8056 (tt0) REVERT: B 870 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8395 (t0) REVERT: B 879 ASP cc_start: 0.8878 (p0) cc_final: 0.8558 (p0) REVERT: C 305 TYR cc_start: 0.8550 (m-10) cc_final: 0.7978 (m-10) REVERT: C 619 CYS cc_start: 0.8504 (t) cc_final: 0.8300 (t) REVERT: C 638 ARG cc_start: 0.8757 (ttp80) cc_final: 0.7953 (ttp80) REVERT: C 661 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6256 (mt) REVERT: C 863 GLN cc_start: 0.8234 (tp40) cc_final: 0.7828 (tp-100) REVERT: C 877 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8363 (mm-40) REVERT: C 885 ARG cc_start: 0.8627 (mtt180) cc_final: 0.8214 (mmt90) REVERT: C 904 ARG cc_start: 0.7930 (tpt170) cc_final: 0.7518 (tpt170) REVERT: C 908 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7811 (mm-40) outliers start: 122 outliers final: 100 residues processed: 759 average time/residue: 0.1550 time to fit residues: 179.5392 Evaluate side-chains 761 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 654 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 261 ARG 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 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 439 MET Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 468 LEU 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 871 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 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 290 ILE 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 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 700 LEU 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 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 992 ILE 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 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 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 712 TYR Chi-restraints excluded: chain C residue 733 ILE Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 911 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 13 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 chunk 134 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 216 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 HIS A 213 ASN A 538 ASN A 845 ASN A 863 GLN ** A 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 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 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 ASN B 908 GLN ** B 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 ASN C 890 ASN C 908 GLN ** 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 = 0.3890 r_free = 0.3890 target = 0.128217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.117213 restraints weight = 55976.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.119893 restraints weight = 29315.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.121667 restraints weight = 17929.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.122915 restraints weight = 12186.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.123768 restraints weight = 8900.557| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4402 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= 0.177 Angle : 0.865 16.395 30918 Z= 0.411 Chirality : 0.069 1.704 3288 Planarity : 0.005 0.071 4020 Dihedral : 6.987 56.940 3206 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.53 % Favored : 93.36 % Rotamer: Outliers : 6.48 % Allowed : 23.56 % Favored : 69.95 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.31 (0.14), residues: 2862 helix: 0.05 (0.19), residues: 651 sheet: -1.32 (0.21), residues: 543 loop : -2.37 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 118 TYR 0.027 0.002 TYR A 206 PHE 0.026 0.002 PHE A 519 TRP 0.013 0.002 TRP B 588 HIS 0.024 0.002 HIS B 895 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.18 (22782) covalent geometry : angle 0.79756 / 0.40 (30666) SS BOND : bond 0.00755 / 0.51 ( 18) SS BOND : angle 1.77890 / 1.21 ( 36) hydrogen bonds : bond 0.05242 / 3.57 ( 753) hydrogen bonds : angle 6.79101 / 4.71 ( 2097) link_ALPHA1-2 : bond 0.00179 / 0.07 ( 3) link_ALPHA1-2 : angle 2.19665 / 1.15 ( 9) link_ALPHA1-3 : bond 0.00477 / 0.23 ( 6) link_ALPHA1-3 : angle 2.31009 / 1.80 ( 18) link_ALPHA1-6 : bond 0.00103 / 0.05 ( 3) link_ALPHA1-6 : angle 1.71355 / 0.89 ( 9) link_BETA1-4 : bond 0.00469 / 0.28 ( 12) link_BETA1-4 : angle 1.84756 / 1.26 ( 36) link_NAG-ASN : bond 0.00847 / 0.43 ( 48) link_NAG-ASN : angle 4.72943 / 3.23 ( 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 813 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 671 time to evaluate : 0.749 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: A 349 LYS cc_start: 0.7861 (mtmt) cc_final: 0.7407 (mtmm) REVERT: A 403 ASN cc_start: 0.8326 (t0) cc_final: 0.8105 (t0) REVERT: A 439 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.7862 (mmm) REVERT: A 514 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6989 (mtm) REVERT: A 621 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7669 (mm-30) REVERT: A 719 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6648 (tt) REVERT: A 824 GLN cc_start: 0.8478 (mp10) cc_final: 0.8106 (mp10) REVERT: A 846 HIS cc_start: 0.8428 (t70) cc_final: 0.8131 (t-90) REVERT: A 850 GLN cc_start: 0.8383 (mt0) cc_final: 0.7984 (mt0) REVERT: A 852 ARG cc_start: 0.8275 (ttt-90) cc_final: 0.8071 (ttt-90) REVERT: A 854 ASN cc_start: 0.8742 (p0) cc_final: 0.8308 (p0) REVERT: A 856 GLN cc_start: 0.8306 (tp-100) cc_final: 0.7805 (tp-100) REVERT: A 868 ARG cc_start: 0.8301 (mmm160) cc_final: 0.7995 (mmm-85) REVERT: A 985 LYS cc_start: 0.8111 (tttt) cc_final: 0.7790 (tttp) REVERT: A 997 MET cc_start: 0.5175 (tpt) cc_final: 0.4711 (tpt) REVERT: B 433 GLU cc_start: 0.7779 (pt0) cc_final: 0.7415 (pm20) REVERT: B 506 TYR cc_start: 0.8635 (t80) cc_final: 0.7961 (t80) REVERT: B 621 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7695 (mt-10) REVERT: B 635 ASP cc_start: 0.8186 (t70) cc_final: 0.7760 (t0) REVERT: B 638 ARG cc_start: 0.9078 (ttp80) cc_final: 0.8599 (ttp80) REVERT: B 747 MET cc_start: 0.8316 (ptp) cc_final: 0.7868 (ptp) REVERT: B 840 GLN cc_start: 0.8409 (tp40) cc_final: 0.8036 (tt0) REVERT: B 863 GLN cc_start: 0.8216 (tp-100) cc_final: 0.7702 (tp-100) REVERT: B 870 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8247 (t0) REVERT: B 879 ASP cc_start: 0.8843 (p0) cc_final: 0.8499 (p0) REVERT: B 913 LYS cc_start: 0.8659 (mmmt) cc_final: 0.8449 (mmmt) REVERT: B 924 ARG cc_start: 0.8417 (ptp90) cc_final: 0.7963 (ptp90) REVERT: B 997 MET cc_start: 0.4430 (tpt) cc_final: 0.3927 (tpt) REVERT: B 1032 GLU cc_start: 0.8479 (pp20) cc_final: 0.8128 (pp20) REVERT: C 55 ASN cc_start: 0.8323 (p0) cc_final: 0.8084 (p0) REVERT: C 305 TYR cc_start: 0.8596 (m-10) cc_final: 0.8324 (m-80) REVERT: C 329 LEU cc_start: 0.8907 (tt) cc_final: 0.8561 (tp) REVERT: C 597 LEU cc_start: 0.7867 (mt) cc_final: 0.7608 (mt) REVERT: C 697 PHE cc_start: 0.8501 (m-80) cc_final: 0.8248 (m-80) REVERT: C 824 GLN cc_start: 0.8280 (mp10) cc_final: 0.7994 (mp10) REVERT: C 863 GLN cc_start: 0.8169 (tp40) cc_final: 0.7711 (tp-100) REVERT: C 875 ASP cc_start: 0.8648 (m-30) cc_final: 0.8287 (p0) REVERT: C 877 GLN cc_start: 0.8682 (mm-40) cc_final: 0.6709 (mm-40) REVERT: C 885 ARG cc_start: 0.8725 (mtt180) cc_final: 0.8196 (mmt90) REVERT: C 935 PHE cc_start: 0.8180 (p90) cc_final: 0.7907 (p90) outliers start: 142 outliers final: 119 residues processed: 756 average time/residue: 0.1441 time to fit residues: 167.7018 Evaluate side-chains 766 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 643 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 123 PHE 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 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 439 MET 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 538 ASN 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 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 712 TYR 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 767 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 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 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 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 595 GLU 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 712 TYR Chi-restraints excluded: chain B residue 719 LEU 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 889 LEU 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 1016 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain C residue 152 SER 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 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 451 ILE Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 564 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 650 GLU 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 893 VAL Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 953 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 283 optimal weight: 0.3980 chunk 156 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 221 optimal weight: 20.0000 chunk 149 optimal weight: 2.9990 chunk 185 optimal weight: 0.7980 chunk 179 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN A 246 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 933 HIS ** 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 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 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 = 0.3904 r_free = 0.3904 target = 0.129337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.118296 restraints weight = 56492.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.121033 restraints weight = 29433.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.122858 restraints weight = 17923.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.124115 restraints weight = 12109.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.125024 restraints weight = 8814.767| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22872 Z= 0.152 Angle : 0.844 18.465 30918 Z= 0.399 Chirality : 0.058 1.376 3288 Planarity : 0.004 0.048 4020 Dihedral : 6.642 58.519 3187 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.71 % Favored : 93.19 % Rotamer: Outliers : 5.94 % Allowed : 25.16 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.27 (0.15), residues: 2862 helix: 0.21 (0.19), residues: 648 sheet: -1.42 (0.22), residues: 528 loop : -2.35 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1001 TYR 0.030 0.002 TYR A 206 PHE 0.033 0.002 PHE B 697 TRP 0.028 0.002 TRP A 588 HIS 0.023 0.002 HIS B 895 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (22782) covalent geometry : angle 0.77583 / 0.38 (30666) SS BOND : bond 0.00743 / 0.50 ( 18) SS BOND : angle 1.86141 / 1.31 ( 36) hydrogen bonds : bond 0.05188 / 3.52 ( 753) hydrogen bonds : angle 6.61637 / 4.60 ( 2097) link_ALPHA1-2 : bond 0.00324 / 0.14 ( 3) link_ALPHA1-2 : angle 2.17221 / 1.14 ( 9) link_ALPHA1-3 : bond 0.00533 / 0.27 ( 6) link_ALPHA1-3 : angle 2.30534 / 1.83 ( 18) link_ALPHA1-6 : bond 0.00171 / 0.07 ( 3) link_ALPHA1-6 : angle 1.62605 / 0.84 ( 9) link_BETA1-4 : bond 0.00501 / 0.30 ( 12) link_BETA1-4 : angle 1.75043 / 1.20 ( 36) link_NAG-ASN : bond 0.00747 / 0.42 ( 48) link_NAG-ASN : angle 4.70138 / 3.21 ( 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 796 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 666 time to evaluate : 0.685 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 349 LYS cc_start: 0.7821 (mtmt) cc_final: 0.7365 (mtmm) REVERT: A 403 ASN cc_start: 0.8299 (t0) cc_final: 0.8076 (t0) REVERT: A 439 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.7934 (mmm) REVERT: A 597 LEU cc_start: 0.8381 (mm) cc_final: 0.8077 (mt) REVERT: A 614 ASN cc_start: 0.8602 (t0) cc_final: 0.8399 (t0) REVERT: A 621 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7762 (mm-30) REVERT: A 661 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.5919 (mt) REVERT: A 719 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.6703 (tt) REVERT: A 779 TYR cc_start: 0.8607 (t80) cc_final: 0.8295 (t80) REVERT: A 854 ASN cc_start: 0.8848 (p0) cc_final: 0.8480 (p0) REVERT: A 985 LYS cc_start: 0.8056 (tttt) cc_final: 0.7746 (tttp) REVERT: A 997 MET cc_start: 0.5117 (tpt) cc_final: 0.4658 (tpt) REVERT: B 433 GLU cc_start: 0.7764 (pt0) cc_final: 0.7422 (pm20) REVERT: B 506 TYR cc_start: 0.8635 (t80) cc_final: 0.8434 (t80) REVERT: B 621 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7735 (mt-10) REVERT: B 834 GLN cc_start: 0.8419 (tp40) cc_final: 0.7743 (tp40) REVERT: B 838 ASN cc_start: 0.7591 (m-40) cc_final: 0.7283 (m-40) REVERT: B 840 GLN cc_start: 0.8412 (tp40) cc_final: 0.8028 (tt0) REVERT: B 870 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8180 (t0) REVERT: B 879 ASP cc_start: 0.8822 (p0) cc_final: 0.8475 (p0) REVERT: B 924 ARG cc_start: 0.8419 (ptp90) cc_final: 0.8027 (ptp90) REVERT: B 997 MET cc_start: 0.4510 (tpt) cc_final: 0.3948 (tpt) REVERT: B 1032 GLU cc_start: 0.8448 (pp20) cc_final: 0.8103 (pp20) REVERT: C 207 ARG cc_start: 0.7738 (tmm-80) cc_final: 0.7167 (tmm-80) REVERT: C 305 TYR cc_start: 0.8567 (m-10) cc_final: 0.8298 (m-80) REVERT: C 334 GLU cc_start: 0.8118 (pm20) cc_final: 0.7858 (pm20) REVERT: C 595 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7153 (tm-30) REVERT: C 614 ASN cc_start: 0.8758 (t0) cc_final: 0.8540 (t0) REVERT: C 661 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6311 (mt) REVERT: C 697 PHE cc_start: 0.8506 (m-80) cc_final: 0.8278 (m-80) REVERT: C 824 GLN cc_start: 0.8258 (mp10) cc_final: 0.7892 (mp10) REVERT: C 863 GLN cc_start: 0.8135 (tp40) cc_final: 0.7660 (tp-100) REVERT: C 885 ARG cc_start: 0.8666 (mtt180) cc_final: 0.8151 (mmt90) REVERT: C 935 PHE cc_start: 0.8180 (p90) cc_final: 0.7900 (p90) outliers start: 130 outliers final: 115 residues processed: 748 average time/residue: 0.1473 time to fit residues: 168.4448 Evaluate side-chains 771 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 651 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 420 SER Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 451 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 570 SER Chi-restraints excluded: chain A residue 584 ILE 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 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 994 SER Chi-restraints excluded: chain A residue 1022 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 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 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 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 595 GLU 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 712 TYR Chi-restraints excluded: chain B residue 719 LEU 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 889 LEU 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 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 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 451 ILE Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 491 ILE 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 701 VAL Chi-restraints excluded: chain C residue 712 TYR Chi-restraints excluded: chain C residue 798 PHE Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 893 VAL Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 953 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 chunk 182 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 246 optimal weight: 0.9990 chunk 266 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 210 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN A 246 GLN A 625 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 933 HIS ** 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 731 ASN C 850 GLN ** C 877 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 = 0.3895 r_free = 0.3895 target = 0.127644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.116459 restraints weight = 57589.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.119147 restraints weight = 30754.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.120989 restraints weight = 19114.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.122245 restraints weight = 13075.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.123136 restraints weight = 9607.990| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22872 Z= 0.192 Angle : 0.854 16.375 30918 Z= 0.410 Chirality : 0.055 0.542 3288 Planarity : 0.005 0.119 4020 Dihedral : 6.589 59.261 3182 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.62 % Favored : 92.28 % Rotamer: Outliers : 6.48 % Allowed : 25.75 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.40 (0.14), residues: 2862 helix: 0.05 (0.19), residues: 648 sheet: -1.42 (0.22), residues: 507 loop : -2.43 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1001 TYR 0.032 0.002 TYR A 900 PHE 0.032 0.002 PHE A 798 TRP 0.051 0.002 TRP A 588 HIS 0.009 0.002 HIS B 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 (22782) covalent geometry : angle 0.79544 / 0.40 (30666) SS BOND : bond 0.00826 / 0.55 ( 18) SS BOND : angle 1.78799 / 1.23 ( 36) hydrogen bonds : bond 0.05340 / 3.61 ( 753) hydrogen bonds : angle 6.67474 / 4.63 ( 2097) link_ALPHA1-2 : bond 0.00217 / 0.08 ( 3) link_ALPHA1-2 : angle 2.21603 / 1.18 ( 9) link_ALPHA1-3 : bond 0.00502 / 0.25 ( 6) link_ALPHA1-3 : angle 2.33760 / 1.76 ( 18) link_ALPHA1-6 : bond 0.00210 / 0.10 ( 3) link_ALPHA1-6 : angle 1.68905 / 0.86 ( 9) link_BETA1-4 : bond 0.00405 / 0.23 ( 12) link_BETA1-4 : angle 2.00258 / 1.37 ( 36) link_NAG-ASN : bond 0.00646 / 0.36 ( 48) link_NAG-ASN : angle 4.32872 / 3.06 ( 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 799 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 657 time to evaluate : 0.725 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 349 LYS cc_start: 0.7969 (mtmt) cc_final: 0.7385 (mtmm) REVERT: A 403 ASN cc_start: 0.8509 (t0) cc_final: 0.8177 (t0) REVERT: A 439 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.7919 (mmm) REVERT: A 621 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7750 (mm-30) REVERT: A 626 TYR cc_start: 0.8335 (m-10) cc_final: 0.8096 (m-10) REVERT: A 719 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.6716 (tt) REVERT: A 779 TYR cc_start: 0.8624 (t80) cc_final: 0.8330 (t80) REVERT: A 824 GLN cc_start: 0.8467 (mp10) cc_final: 0.8112 (mp10) REVERT: A 854 ASN cc_start: 0.8766 (p0) cc_final: 0.8416 (p0) REVERT: A 856 GLN cc_start: 0.8315 (tp-100) cc_final: 0.7842 (tp-100) REVERT: A 985 LYS cc_start: 0.8085 (tttt) cc_final: 0.7731 (tttp) REVERT: A 997 MET cc_start: 0.5227 (tpt) cc_final: 0.4584 (tpt) REVERT: B 207 ARG cc_start: 0.8261 (tmt170) cc_final: 0.7740 (ptm160) REVERT: B 433 GLU cc_start: 0.7777 (pt0) cc_final: 0.7452 (pm20) REVERT: B 614 ASN cc_start: 0.8895 (t0) cc_final: 0.8650 (t0) REVERT: B 621 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7800 (mt-10) REVERT: B 736 LEU cc_start: 0.9075 (tp) cc_final: 0.8762 (tp) REVERT: B 747 MET cc_start: 0.8553 (ptp) cc_final: 0.8323 (ptm) REVERT: B 834 GLN cc_start: 0.8452 (tp40) cc_final: 0.7746 (tp40) REVERT: B 839 GLN cc_start: 0.8609 (pt0) cc_final: 0.8071 (pt0) REVERT: B 870 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8264 (t0) REVERT: B 879 ASP cc_start: 0.8823 (p0) cc_final: 0.8486 (p0) REVERT: B 908 GLN cc_start: 0.8331 (tp40) cc_final: 0.8087 (tm-30) REVERT: B 924 ARG cc_start: 0.8351 (ptp90) cc_final: 0.7945 (ptp90) REVERT: B 997 MET cc_start: 0.4750 (tpt) cc_final: 0.4042 (tpt) REVERT: B 1032 GLU cc_start: 0.8504 (pp20) cc_final: 0.8155 (pp20) REVERT: C 305 TYR cc_start: 0.8665 (m-10) cc_final: 0.8414 (m-80) REVERT: C 597 LEU cc_start: 0.8061 (mt) cc_final: 0.7710 (mt) REVERT: C 614 ASN cc_start: 0.8831 (t0) cc_final: 0.8369 (t0) REVERT: C 621 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6731 (mt-10) REVERT: C 697 PHE cc_start: 0.8561 (m-80) cc_final: 0.8354 (m-80) REVERT: C 824 GLN cc_start: 0.8261 (mp10) cc_final: 0.7903 (mp10) REVERT: C 863 GLN cc_start: 0.8096 (tp40) cc_final: 0.7629 (tp-100) REVERT: C 935 PHE cc_start: 0.8337 (p90) cc_final: 0.8035 (p90) outliers start: 142 outliers final: 130 residues processed: 750 average time/residue: 0.1418 time to fit residues: 162.5768 Evaluate side-chains 780 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 647 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 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 439 MET Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 486 VAL 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 570 SER Chi-restraints excluded: chain A residue 584 ILE 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 719 LEU Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 780 VAL 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 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 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 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 491 ILE Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 GLU 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 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 889 LEU 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 977 ARG Chi-restraints excluded: chain B residue 1002 ILE Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 152 SER 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 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 451 ILE Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 491 ILE 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 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 893 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 215 optimal weight: 0.8980 chunk 285 optimal weight: 0.0370 chunk 164 optimal weight: 0.9980 chunk 237 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 242 optimal weight: 4.9990 chunk 206 optimal weight: 6.9990 chunk 202 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN A 246 GLN A 538 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 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN B 246 GLN B 838 ASN ** B 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 507 GLN ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 877 GLN ** 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 = 0.3909 r_free = 0.3909 target = 0.129666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.118750 restraints weight = 55832.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.121449 restraints weight = 29218.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.123249 restraints weight = 17838.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.124496 restraints weight = 12056.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.125366 restraints weight = 8761.163| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22872 Z= 0.147 Angle : 0.862 19.484 30918 Z= 0.411 Chirality : 0.055 0.460 3288 Planarity : 0.004 0.052 4020 Dihedral : 6.405 58.476 3182 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.67 % Favored : 93.22 % Rotamer: Outliers : 6.03 % Allowed : 26.62 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.15), residues: 2862 helix: -0.05 (0.19), residues: 654 sheet: -1.22 (0.23), residues: 477 loop : -2.39 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1001 TYR 0.029 0.002 TYR A 206 PHE 0.031 0.002 PHE B 697 TRP 0.043 0.002 TRP C 588 HIS 0.018 0.002 HIS A 895 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (22782) covalent geometry : angle 0.81100 / 0.40 (30666) SS BOND : bond 0.00633 / 0.42 ( 18) SS BOND : angle 1.78502 / 1.29 ( 36) hydrogen bonds : bond 0.05131 / 3.49 ( 753) hydrogen bonds : angle 6.56304 / 4.57 ( 2097) link_ALPHA1-2 : bond 0.00431 / 0.19 ( 3) link_ALPHA1-2 : angle 2.16439 / 1.13 ( 9) link_ALPHA1-3 : bond 0.00572 / 0.29 ( 6) link_ALPHA1-3 : angle 2.27076 / 1.84 ( 18) link_ALPHA1-6 : bond 0.00227 / 0.10 ( 3) link_ALPHA1-6 : angle 1.50708 / 0.78 ( 9) link_BETA1-4 : bond 0.00491 / 0.30 ( 12) link_BETA1-4 : angle 1.72944 / 1.20 ( 36) link_NAG-ASN : bond 0.00687 / 0.37 ( 48) link_NAG-ASN : angle 4.08438 / 2.91 ( 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 809 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 677 time to evaluate : 0.893 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 349 LYS cc_start: 0.7860 (mtmt) cc_final: 0.7302 (mtmm) REVERT: A 403 ASN cc_start: 0.8208 (t0) cc_final: 0.7961 (t0) REVERT: A 439 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.7939 (mmm) REVERT: A 614 ASN cc_start: 0.8442 (t0) cc_final: 0.8236 (t0) REVERT: A 621 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7721 (mm-30) REVERT: A 626 TYR cc_start: 0.8260 (m-10) cc_final: 0.8033 (m-10) REVERT: A 661 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.5980 (mt) REVERT: A 719 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.6845 (tt) REVERT: A 779 TYR cc_start: 0.8587 (t80) cc_final: 0.8335 (t80) REVERT: A 854 ASN cc_start: 0.8847 (p0) cc_final: 0.8527 (p0) REVERT: A 856 GLN cc_start: 0.8306 (tp-100) cc_final: 0.7876 (tp-100) REVERT: A 985 LYS cc_start: 0.8053 (tttt) cc_final: 0.7817 (tttp) REVERT: A 997 MET cc_start: 0.5176 (tpt) cc_final: 0.4813 (tpt) REVERT: B 207 ARG cc_start: 0.8229 (tmt170) cc_final: 0.7724 (ptm160) REVERT: B 433 GLU cc_start: 0.7729 (pt0) cc_final: 0.7450 (pm20) REVERT: B 567 ARG cc_start: 0.7865 (ptm-80) cc_final: 0.7619 (ptm-80) REVERT: B 614 ASN cc_start: 0.8816 (t0) cc_final: 0.8584 (t0) REVERT: B 621 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7773 (mt-10) REVERT: B 669 ASP cc_start: 0.7411 (t0) cc_final: 0.7193 (t70) REVERT: B 736 LEU cc_start: 0.9140 (tp) cc_final: 0.8916 (tp) REVERT: B 747 MET cc_start: 0.8514 (ptp) cc_final: 0.8251 (ptm) REVERT: B 834 GLN cc_start: 0.8511 (tp40) cc_final: 0.8165 (tp40) REVERT: B 838 ASN cc_start: 0.7926 (m110) cc_final: 0.7517 (m110) REVERT: B 870 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8168 (t0) REVERT: B 879 ASP cc_start: 0.8787 (p0) cc_final: 0.8466 (p0) REVERT: B 924 ARG cc_start: 0.8220 (ptp90) cc_final: 0.7906 (ptp90) REVERT: B 943 GLU cc_start: 0.8465 (tp30) cc_final: 0.7996 (tp30) REVERT: B 997 MET cc_start: 0.4628 (tpt) cc_final: 0.3913 (tpt) REVERT: B 1032 GLU cc_start: 0.8374 (pp20) cc_final: 0.8072 (pp20) REVERT: C 159 PHE cc_start: 0.7273 (m-80) cc_final: 0.7046 (m-80) REVERT: C 305 TYR cc_start: 0.8584 (m-10) cc_final: 0.8334 (m-10) REVERT: C 334 GLU cc_start: 0.8230 (pm20) cc_final: 0.8019 (pm20) REVERT: C 614 ASN cc_start: 0.8783 (t0) cc_final: 0.8342 (t0) REVERT: C 621 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6646 (mt-10) REVERT: C 824 GLN cc_start: 0.8211 (mp10) cc_final: 0.7831 (mp10) REVERT: C 863 GLN cc_start: 0.8055 (tp40) cc_final: 0.7547 (tp-100) REVERT: C 935 PHE cc_start: 0.8185 (p90) cc_final: 0.7894 (p90) REVERT: C 1023 ARG cc_start: 0.8770 (tpt-90) cc_final: 0.8512 (mtp180) outliers start: 132 outliers final: 116 residues processed: 760 average time/residue: 0.1618 time to fit residues: 187.5648 Evaluate side-chains 784 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 664 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 412 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 451 ILE 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 569 VAL Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 584 ILE 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 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 994 SER 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 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 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 491 ILE Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 GLU 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 724 LEU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 847 LEU 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 1002 ILE Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain C residue 108 PHE 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 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 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 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 870 ASP 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 913 LYS 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: 8.9990 chunk 214 optimal weight: 0.2980 chunk 158 optimal weight: 0.4980 chunk 287 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 120 optimal weight: 0.0570 chunk 30 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 156 optimal weight: 0.1980 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN A 246 GLN A 538 ASN ** 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 ** 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 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 GLN ** B 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 876 GLN ** C 921 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 = 0.3938 r_free = 0.3938 target = 0.131985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.120871 restraints weight = 55923.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.123613 restraints weight = 29419.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.125460 restraints weight = 18035.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.126734 restraints weight = 12199.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.127662 restraints weight = 8863.536| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22872 Z= 0.146 Angle : 0.876 16.647 30918 Z= 0.420 Chirality : 0.055 0.430 3288 Planarity : 0.004 0.055 4020 Dihedral : 6.278 59.169 3182 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.67 % Favored : 93.22 % Rotamer: Outliers : 5.21 % Allowed : 27.99 % Favored : 66.80 % 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: -2.40 (0.15), residues: 2862 helix: -0.11 (0.19), residues: 654 sheet: -1.33 (0.24), residues: 441 loop : -2.37 (0.13), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1001 TYR 0.029 0.001 TYR A 206 PHE 0.029 0.001 PHE B 697 TRP 0.052 0.002 TRP C 588 HIS 0.022 0.002 HIS A 895 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (22782) covalent geometry : angle 0.82908 / 0.41 (30666) SS BOND : bond 0.00647 / 0.45 ( 18) SS BOND : angle 1.85208 / 1.32 ( 36) hydrogen bonds : bond 0.05055 / 3.46 ( 753) hydrogen bonds : angle 6.42953 / 4.47 ( 2097) link_ALPHA1-2 : bond 0.00434 / 0.19 ( 3) link_ALPHA1-2 : angle 2.08302 / 1.09 ( 9) link_ALPHA1-3 : bond 0.00637 / 0.33 ( 6) link_ALPHA1-3 : angle 2.24454 / 1.85 ( 18) link_ALPHA1-6 : bond 0.00311 / 0.14 ( 3) link_ALPHA1-6 : angle 1.32829 / 0.69 ( 9) link_BETA1-4 : bond 0.00533 / 0.34 ( 12) link_BETA1-4 : angle 1.64743 / 1.15 ( 36) link_NAG-ASN : bond 0.00741 / 0.41 ( 48) link_NAG-ASN : angle 3.97834 / 2.83 ( 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 791 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 677 time to evaluate : 0.786 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: 0.7761 (mtmt) cc_final: 0.7217 (mtmm) REVERT: A 439 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7943 (mmm) REVERT: A 597 LEU cc_start: 0.8318 (mm) cc_final: 0.8075 (mt) REVERT: A 621 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7841 (mm-30) REVERT: A 661 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.5971 (mt) REVERT: A 719 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.6822 (tt) REVERT: A 824 GLN cc_start: 0.8276 (mp10) cc_final: 0.7944 (mp10) REVERT: A 854 ASN cc_start: 0.8800 (p0) cc_final: 0.8460 (p0) REVERT: A 943 GLU cc_start: 0.8265 (tp30) cc_final: 0.7677 (tp30) REVERT: A 985 LYS cc_start: 0.8079 (tttt) cc_final: 0.7854 (tttp) REVERT: A 997 MET cc_start: 0.5069 (tpt) cc_final: 0.4731 (tpt) REVERT: B 207 ARG cc_start: 0.8248 (tmt170) cc_final: 0.7693 (ptm160) REVERT: B 567 ARG cc_start: 0.7595 (ptm-80) cc_final: 0.7320 (ptm-80) REVERT: B 616 ASN cc_start: 0.8580 (m-40) cc_final: 0.8140 (t0) REVERT: B 621 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7791 (mt-10) REVERT: B 734 MET cc_start: 0.8374 (ttt) cc_final: 0.8006 (ttt) REVERT: B 736 LEU cc_start: 0.9141 (tp) cc_final: 0.8895 (tp) REVERT: B 747 MET cc_start: 0.8518 (ptp) cc_final: 0.8213 (ptm) REVERT: B 802 MET cc_start: 0.6463 (mmp) cc_final: 0.6198 (mtt) REVERT: B 834 GLN cc_start: 0.8581 (tp40) cc_final: 0.8221 (tp40) REVERT: B 838 ASN cc_start: 0.7941 (m110) cc_final: 0.7692 (m110) REVERT: B 870 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8075 (t0) REVERT: B 879 ASP cc_start: 0.8676 (p0) cc_final: 0.8379 (p0) REVERT: B 943 GLU cc_start: 0.8457 (tp30) cc_final: 0.7950 (tp30) REVERT: B 997 MET cc_start: 0.4759 (tpt) cc_final: 0.4303 (tpt) REVERT: B 1026 LEU cc_start: 0.8031 (mt) cc_final: 0.7659 (mp) REVERT: B 1032 GLU cc_start: 0.8387 (pp20) cc_final: 0.8104 (pp20) REVERT: C 305 TYR cc_start: 0.8532 (m-10) cc_final: 0.8294 (m-10) REVERT: C 614 ASN cc_start: 0.8664 (t0) cc_final: 0.8448 (t0) REVERT: C 621 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6819 (mt-10) REVERT: C 856 GLN cc_start: 0.7702 (tm-30) cc_final: 0.6568 (tm-30) REVERT: C 863 GLN cc_start: 0.8151 (tp40) cc_final: 0.7661 (tp-100) REVERT: C 885 ARG cc_start: 0.8642 (mtt180) cc_final: 0.8085 (mmt90) REVERT: C 886 LEU cc_start: 0.8976 (mm) cc_final: 0.8641 (tp) REVERT: C 908 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8097 (mm-40) REVERT: C 1023 ARG cc_start: 0.8745 (tpt-90) cc_final: 0.8493 (mtp180) outliers start: 114 outliers final: 108 residues processed: 751 average time/residue: 0.1566 time to fit residues: 178.5626 Evaluate side-chains 758 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 646 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 435 VAL Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 459 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 569 VAL Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 584 ILE 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 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 968 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 994 SER 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 203 ILE Chi-restraints excluded: chain B residue 246 GLN 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 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 491 ILE Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 584 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 724 LEU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 847 LEU 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 882 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 948 LEU Chi-restraints excluded: chain B residue 1002 ILE Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain C residue 108 PHE 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 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 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 491 ILE 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 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 871 ILE Chi-restraints excluded: chain C residue 876 GLN 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 968 VAL Chi-restraints excluded: chain C residue 985 LYS Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1002 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 70 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 269 optimal weight: 0.8980 chunk 271 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 184 optimal weight: 0.7980 chunk 174 optimal weight: 0.7980 chunk 262 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN ** A 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 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 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B 507 GLN ** B 908 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 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 876 GLN ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.130387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.119368 restraints weight = 55752.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.122112 restraints weight = 29098.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.123939 restraints weight = 17739.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.125200 restraints weight = 11971.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.126100 restraints weight = 8705.229| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.5431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22872 Z= 0.155 Angle : 0.923 15.883 30918 Z= 0.445 Chirality : 0.059 1.078 3288 Planarity : 0.004 0.060 4020 Dihedral : 5.983 58.550 3167 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.88 % Favored : 93.01 % Rotamer: Outliers : 5.62 % Allowed : 28.54 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.38 (0.15), residues: 2862 helix: -0.15 (0.19), residues: 654 sheet: -1.29 (0.24), residues: 468 loop : -2.35 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B1001 TYR 0.030 0.002 TYR A 206 PHE 0.048 0.002 PHE C 697 TRP 0.057 0.002 TRP C 588 HIS 0.022 0.002 HIS A 895 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (22782) covalent geometry : angle 0.87054 / 0.43 (30666) SS BOND : bond 0.00633 / 0.42 ( 18) SS BOND : angle 1.86289 / 1.29 ( 36) hydrogen bonds : bond 0.05163 / 3.51 ( 753) hydrogen bonds : angle 6.44196 / 4.48 ( 2097) link_ALPHA1-2 : bond 0.00370 / 0.16 ( 3) link_ALPHA1-2 : angle 2.04253 / 1.07 ( 9) link_ALPHA1-3 : bond 0.00560 / 0.28 ( 6) link_ALPHA1-3 : angle 2.22956 / 1.81 ( 18) link_ALPHA1-6 : bond 0.00195 / 0.09 ( 3) link_ALPHA1-6 : angle 1.45262 / 0.75 ( 9) link_BETA1-4 : bond 0.00480 / 0.30 ( 12) link_BETA1-4 : angle 1.72507 / 1.20 ( 36) link_NAG-ASN : bond 0.00783 / 0.48 ( 48) link_NAG-ASN : angle 4.36882 / 3.06 ( 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 782 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 659 time to evaluate : 0.786 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: 0.8348 (p90) cc_final: 0.8089 (p90) REVERT: A 213 ASN cc_start: 0.7124 (m110) cc_final: 0.6339 (t0) REVERT: A 349 LYS cc_start: 0.7795 (mtmt) cc_final: 0.7284 (mtmm) REVERT: A 439 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8064 (mmm) REVERT: A 597 LEU cc_start: 0.8269 (mm) cc_final: 0.7987 (mt) REVERT: A 621 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8079 (mm-30) REVERT: A 661 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.6329 (mt) REVERT: A 719 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.6804 (tt) REVERT: A 832 LYS cc_start: 0.8667 (tttm) cc_final: 0.8438 (tttm) REVERT: A 854 ASN cc_start: 0.8862 (p0) cc_final: 0.8630 (p0) REVERT: A 943 GLU cc_start: 0.8194 (tp30) cc_final: 0.7571 (tp30) REVERT: A 985 LYS cc_start: 0.8132 (tttt) cc_final: 0.7886 (tttp) REVERT: A 997 MET cc_start: 0.5110 (tpt) cc_final: 0.4737 (tpt) REVERT: B 207 ARG cc_start: 0.8216 (tmt170) cc_final: 0.7679 (ptm160) REVERT: B 567 ARG cc_start: 0.7614 (ptm-80) cc_final: 0.7280 (ptm-80) REVERT: B 616 ASN cc_start: 0.8467 (m-40) cc_final: 0.8046 (t0) REVERT: B 621 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7866 (mt-10) REVERT: B 734 MET cc_start: 0.8358 (ttt) cc_final: 0.8006 (ttt) REVERT: B 736 LEU cc_start: 0.9146 (tp) cc_final: 0.8909 (tp) REVERT: B 747 MET cc_start: 0.8634 (ptp) cc_final: 0.8354 (ptm) REVERT: B 834 GLN cc_start: 0.8615 (tp40) cc_final: 0.8248 (tp40) REVERT: B 838 ASN cc_start: 0.8090 (m110) cc_final: 0.7763 (m110) REVERT: B 870 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8115 (t0) REVERT: B 879 ASP cc_start: 0.8667 (p0) cc_final: 0.8371 (p0) REVERT: B 997 MET cc_start: 0.4702 (tpt) cc_final: 0.4135 (tpt) REVERT: B 1032 GLU cc_start: 0.8350 (pp20) cc_final: 0.8064 (pp20) REVERT: C 305 TYR cc_start: 0.8556 (m-10) cc_final: 0.8304 (m-10) REVERT: C 614 ASN cc_start: 0.8667 (t0) cc_final: 0.8447 (t0) REVERT: C 621 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6904 (mt-10) REVERT: C 661 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6531 (mt) REVERT: C 824 GLN cc_start: 0.8129 (mp10) cc_final: 0.7846 (mp10) REVERT: C 863 GLN cc_start: 0.8195 (tp40) cc_final: 0.7683 (tp-100) REVERT: C 880 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7487 (ptp90) REVERT: C 1023 ARG cc_start: 0.8745 (tpt-90) cc_final: 0.8536 (mtp180) outliers start: 123 outliers final: 109 residues processed: 736 average time/residue: 0.1571 time to fit residues: 176.6984 Evaluate side-chains 764 residues out of total 2505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 649 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN 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 435 VAL Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 588 TRP 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 724 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 863 GLN 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 992 ILE Chi-restraints excluded: chain A residue 994 SER 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 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 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 491 ILE Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 642 MET Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 847 LEU 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 882 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 925 TYR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1002 ILE Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain C residue 108 PHE 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 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 491 ILE 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 650 GLU 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 871 ILE Chi-restraints excluded: chain C residue 876 GLN Chi-restraints excluded: chain C residue 880 ARG 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 953 LEU Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 985 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 23 optimal weight: 7.9990 chunk 218 optimal weight: 0.0470 chunk 114 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 180 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 29 optimal weight: 0.2980 chunk 126 optimal weight: 8.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN ** A 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 GLN A 876 GLN A 908 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** A 978 GLN B 246 GLN ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 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 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 876 GLN ** 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 = 0.3942 r_free = 0.3942 target = 0.132128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.121258 restraints weight = 56519.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.123923 restraints weight = 30004.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.125729 restraints weight = 18508.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.126977 restraints weight = 12563.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.127882 restraints weight = 9151.734| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.320 22872 Z= 0.296 Angle : 1.079 59.199 30918 Z= 0.548 Chirality : 0.068 2.262 3288 Planarity : 0.005 0.131 4020 Dihedral : 5.972 58.475 3163 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.92 % Favored : 92.98 % Rotamer: Outliers : 5.57 % Allowed : 28.63 % Favored : 65.80 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.40 (0.15), residues: 2862 helix: -0.20 (0.19), residues: 654 sheet: -1.30 (0.24), residues: 468 loop : -2.35 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG A 977 TYR 0.037 0.002 TYR C 506 PHE 0.068 0.002 PHE B 332 TRP 0.152 0.004 TRP C 588 HIS 0.020 0.002 HIS A 895 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.30 (22782) covalent geometry : angle 1.03070 / 0.54 (30666) SS BOND : bond 0.00685 / 0.47 ( 18) SS BOND : angle 2.10210 / 1.65 ( 36) hydrogen bonds : bond 0.05203 / 3.55 ( 753) hydrogen bonds : angle 6.47172 / 4.50 ( 2097) link_ALPHA1-2 : bond 0.00358 / 0.16 ( 3) link_ALPHA1-2 : angle 2.05038 / 1.08 ( 9) link_ALPHA1-3 : bond 0.00562 / 0.29 ( 6) link_ALPHA1-3 : angle 2.23938 / 1.81 ( 18) link_ALPHA1-6 : bond 0.00199 / 0.09 ( 3) link_ALPHA1-6 : angle 1.45418 / 0.75 ( 9) link_BETA1-4 : bond 0.00485 / 0.30 ( 12) link_BETA1-4 : angle 1.74657 / 1.21 ( 36) link_NAG-ASN : bond 0.00795 / 0.49 ( 48) link_NAG-ASN : angle 4.54692 / 3.19 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4055.42 seconds wall clock time: 70 minutes 47.16 seconds (4247.16 seconds total)