Starting phenix.real_space_refine on Fri Mar 6 21:17:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q9f_13868/03_2026/7q9f_13868.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q9f_13868/03_2026/7q9f_13868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7q9f_13868/03_2026/7q9f_13868.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q9f_13868/03_2026/7q9f_13868.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q9f_13868/03_2026/7q9f_13868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q9f_13868/03_2026/7q9f_13868.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.020 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 148 5.16 5 C 21751 2.51 5 N 5609 2.21 5 O 6756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34264 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1009, 7874 Classifications: {'peptide': 1009} Link IDs: {'PTRANS': 50, 'TRANS': 958} Chain breaks: 7 Chain: "B" Number of atoms: 7848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 7848 Classifications: {'peptide': 1005} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 50, 'TRANS': 954} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 7926 Classifications: {'peptide': 1014} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 962} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1668 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 216, 1661 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 216, 1661 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1689 Chain: "H" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1578 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1668 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 216, 1661 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 216, 1661 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1689 Chain: "E" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1578 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 1668 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 216, 1661 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 216, 1661 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1689 Chain: "J" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1578 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 8.70, per 1000 atoms: 0.25 Number of scatterers: 34264 At special positions: 0 Unit cell: (160.72, 168.92, 215.66, 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 148 16.00 O 6756 8.00 N 5609 7.00 C 21751 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 137 " - pdb=" SG ACYS L 197 " distance=2.03 Simple disulfide: pdb=" SG CYS L 137 " - pdb=" SG BCYS L 197 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 201 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 137 " - pdb=" SG ACYS F 197 " distance=2.03 Simple disulfide: pdb=" SG CYS F 137 " - pdb=" SG BCYS F 197 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 137 " - pdb=" SG ACYS K 197 " distance=2.03 Simple disulfide: pdb=" SG CYS K 137 " - pdb=" SG BCYS K 197 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 145 " - pdb=" SG CYS J 201 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " BETA1-6 " NAG D 1 " - " FUC D 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG P 1 " - " FUC P 4 " " NAG V 1 " - " FUC V 4 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 279 " " NAG A1303 " - " ASN A 600 " " NAG A1304 " - " ASN A 613 " " NAG A1305 " - " ASN A 654 " " NAG A1306 " - " ASN A 706 " " NAG A1307 " - " ASN A1071 " " NAG A1308 " - " ASN A 328 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 279 " " NAG B1303 " - " ASN B 328 " " NAG B1304 " - " ASN B 600 " " NAG B1305 " - " ASN B 613 " " NAG B1306 " - " ASN B 654 " " NAG B1307 " - " ASN B 706 " " NAG B1308 " - " ASN B1071 " " NAG B1309 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 279 " " NAG C1303 " - " ASN C 600 " " NAG C1304 " - " ASN C 613 " " NAG C1305 " - " ASN C 654 " " NAG C1306 " - " ASN C 706 " " NAG C1307 " - " ASN C1071 " " NAG C1308 " - " ASN C 328 " " NAG D 1 " - " ASN A 340 " " NAG G 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 714 " " NAG M 1 " - " ASN A 798 " " NAG N 1 " - " ASN A1095 " " NAG O 1 " - " ASN A1131 " " NAG P 1 " - " ASN B 340 " " NAG Q 1 " - " ASN B 234 " " NAG R 1 " - " ASN B 714 " " NAG S 1 " - " ASN B 798 " " NAG T 1 " - " ASN B1095 " " NAG U 1 " - " ASN B1131 " " NAG V 1 " - " ASN C 340 " " NAG W 1 " - " ASN C 714 " " NAG X 1 " - " ASN C 798 " " NAG Y 1 " - " ASN C1095 " " NAG Z 1 " - " ASN C1131 " Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.6 seconds 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8046 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 85 sheets defined 20.3% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 362 through 368 removed outlier: 3.878A pdb=" N TYR A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.671A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 780 Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.679A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 906 removed outlier: 3.559A pdb=" N ALA A 900 " --> pdb=" O ALA A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 916 removed outlier: 4.122A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 915 " --> pdb=" O ASN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 942 through 962 Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 979 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 5.022A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 4.276A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 362 through 368 removed outlier: 3.663A pdb=" N TYR B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 4.100A pdb=" N ASN B 385 " --> pdb=" O PRO B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 3.994A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 759 through 780 Processing helix chain 'B' and resid 798 through 802 removed outlier: 4.433A pdb=" N GLN B 801 " --> pdb=" O ASN B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.776A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 907 Processing helix chain 'B' and resid 910 through 915 Processing helix chain 'B' and resid 916 through 938 removed outlier: 3.862A pdb=" N ASN B 922 " --> pdb=" O LYS B 918 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 962 removed outlier: 4.031A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1029 removed outlier: 4.442A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 3.983A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 362 through 368 removed outlier: 3.588A pdb=" N TYR C 366 " --> pdb=" O TYR C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 385 removed outlier: 3.954A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 4.318A pdb=" N ARG C 405 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 759 through 780 Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 863 through 882 removed outlier: 3.837A pdb=" N GLN C 869 " --> pdb=" O GLU C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 Processing helix chain 'C' and resid 894 through 906 removed outlier: 3.696A pdb=" N ALA C 900 " --> pdb=" O ALA C 896 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR C 901 " --> pdb=" O MET C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 938 removed outlier: 4.166A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU C 915 " --> pdb=" O ASN C 911 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LYS C 918 " --> pdb=" O TYR C 914 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU C 919 " --> pdb=" O GLU C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 941 No H-bonds generated for 'chain 'C' and resid 939 through 941' Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.912A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.650A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1029 removed outlier: 5.121A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 3.717A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.509A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 99 Processing helix chain 'L' and resid 124 through 130 removed outlier: 3.521A pdb=" N SER L 130 " --> pdb=" O GLU L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 191 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'F' and resid 95 through 99 Processing helix chain 'F' and resid 124 through 130 removed outlier: 3.608A pdb=" N SER F 130 " --> pdb=" O GLU F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 191 Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.555A pdb=" N GLN E 65 " --> pdb=" O GLN E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'K' and resid 80 through 84 removed outlier: 3.596A pdb=" N PHE K 84 " --> pdb=" O PRO K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 99 Processing helix chain 'K' and resid 124 through 130 Processing helix chain 'K' and resid 186 through 191 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'J' and resid 192 through 194 No H-bonds generated for 'chain 'J' and resid 192 through 194' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.576A pdb=" N THR A 63 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.198A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 141 removed outlier: 6.458A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 12.382A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.681A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 316 removed outlier: 3.570A pdb=" N TYR A 310 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 325 removed outlier: 3.770A pdb=" N PHE A 540 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AA9, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.937A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB2, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB3, first strand: chain 'A' and resid 651 through 652 removed outlier: 3.587A pdb=" N ALA A 691 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 672 " --> pdb=" O SER A 688 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR A 692 " --> pdb=" O CYS A 668 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 708 through 712 removed outlier: 3.574A pdb=" N THR A1073 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 716 through 725 removed outlier: 3.555A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AB7, first strand: chain 'A' and resid 785 through 787 removed outlier: 6.064A pdb=" N ILE A 785 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.378A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.729A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.534A pdb=" N ASP B 53 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.521A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 132 through 141 removed outlier: 6.129A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 12.788A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 308 through 314 removed outlier: 3.714A pdb=" N TYR B 310 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 322 through 325 Processing sheet with id=AC6, first strand: chain 'B' and resid 322 through 325 removed outlier: 3.802A pdb=" N THR B 585 " --> pdb=" O VAL B 548 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 550 " --> pdb=" O ASP B 583 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AC8, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.705A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AD1, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AD2, first strand: chain 'B' and resid 651 through 652 removed outlier: 3.743A pdb=" N TYR B 692 " --> pdb=" O CYS B 668 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 699 through 701 Processing sheet with id=AD4, first strand: chain 'B' and resid 708 through 712 Processing sheet with id=AD5, first strand: chain 'B' and resid 715 through 725 removed outlier: 6.925A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 715 through 725 Processing sheet with id=AD7, first strand: chain 'B' and resid 731 through 733 Processing sheet with id=AD8, first strand: chain 'B' and resid 1083 through 1087 removed outlier: 4.282A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.733A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 50 through 55 Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.176A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 135 through 142 removed outlier: 6.804A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.280A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.427A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 275 through 276 removed outlier: 7.083A pdb=" N LYS C 275 " --> pdb=" O THR C 283 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 308 through 316 removed outlier: 3.754A pdb=" N TYR C 310 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 321 through 322 removed outlier: 7.229A pdb=" N GLU C 321 " --> pdb=" O ASN C 537 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR C 585 " --> pdb=" O VAL C 548 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AE9, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.536A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AF2, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AF3, first strand: chain 'C' and resid 539 through 540 removed outlier: 3.828A pdb=" N PHE C 540 " --> pdb=" O LEU C 543 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.237A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN C 672 " --> pdb=" O SER C 688 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.783A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN C 714 " --> pdb=" O ALA C1067 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.783A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN C 714 " --> pdb=" O ALA C1067 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 731 through 733 Processing sheet with id=AF8, first strand: chain 'C' and resid 1117 through 1119 Processing sheet with id=AF9, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id=AG1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.250A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AG4, first strand: chain 'L' and resid 117 through 121 removed outlier: 5.290A pdb=" N SER L 134 " --> pdb=" O LEU L 184 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU L 184 " --> pdb=" O SER L 134 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N VAL L 136 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU L 182 " --> pdb=" O VAL L 136 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU L 138 " --> pdb=" O SER L 180 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N SER L 180 " --> pdb=" O LEU L 138 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASN L 140 " --> pdb=" O LEU L 178 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU L 178 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 156 through 158 removed outlier: 4.531A pdb=" N TRP L 151 " --> pdb=" O GLN L 158 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AG7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.590A pdb=" N VAL H 33 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY H 50 " --> pdb=" O PHE H 34 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AG9, first strand: chain 'H' and resid 125 through 129 removed outlier: 6.062A pdb=" N TYR H 181 " --> pdb=" O ASP H 149 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 125 through 129 removed outlier: 6.062A pdb=" N TYR H 181 " --> pdb=" O ASP H 149 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 156 through 159 removed outlier: 4.355A pdb=" N TYR H 199 " --> pdb=" O VAL H 216 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AH4, first strand: chain 'F' and resid 10 through 12 removed outlier: 7.122A pdb=" N LEU F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TYR F 50 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 117 through 121 removed outlier: 5.549A pdb=" N TYR F 176 " --> pdb=" O ASN F 141 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 157 through 158 removed outlier: 4.689A pdb=" N TRP F 151 " --> pdb=" O GLN F 158 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AH8, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.827A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AI1, first strand: chain 'E' and resid 125 through 129 removed outlier: 6.056A pdb=" N TYR E 181 " --> pdb=" O ASP E 149 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 125 through 129 removed outlier: 6.056A pdb=" N TYR E 181 " --> pdb=" O ASP E 149 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 155 through 159 removed outlier: 4.336A pdb=" N TYR E 199 " --> pdb=" O VAL E 216 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AI5, first strand: chain 'K' and resid 10 through 12 removed outlier: 7.322A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AI7, first strand: chain 'K' and resid 117 through 121 removed outlier: 5.307A pdb=" N SER K 134 " --> pdb=" O LEU K 184 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU K 184 " --> pdb=" O SER K 134 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL K 136 " --> pdb=" O LEU K 182 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU K 182 " --> pdb=" O VAL K 136 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU K 138 " --> pdb=" O SER K 180 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N SER K 180 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASN K 140 " --> pdb=" O LEU K 178 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU K 178 " --> pdb=" O ASN K 140 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'K' and resid 156 through 158 removed outlier: 4.521A pdb=" N TRP K 151 " --> pdb=" O GLN K 158 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'J' and resid 5 through 6 Processing sheet with id=AJ1, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.778A pdb=" N PHE J 34 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY J 50 " --> pdb=" O PHE J 34 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'J' and resid 125 through 129 removed outlier: 6.134A pdb=" N TYR J 181 " --> pdb=" O ASP J 149 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'J' and resid 125 through 129 removed outlier: 6.134A pdb=" N TYR J 181 " --> pdb=" O ASP J 149 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'J' and resid 156 through 159 removed outlier: 4.377A pdb=" N TYR J 199 " --> pdb=" O VAL J 216 " (cutoff:3.500A) 1478 hydrogen bonds defined for protein. 3846 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: 8.25 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10853 1.34 - 1.46: 8539 1.46 - 1.58: 15460 1.58 - 1.70: 0 1.70 - 1.82: 188 Bond restraints: 35040 Sorted by residual: bond pdb=" N ASP K 1 " pdb=" CA ASP K 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.58e+00 bond pdb=" N ASP F 1 " pdb=" CA ASP F 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.56e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.49e+00 bond pdb=" C1 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.48e+00 bond pdb=" C1 BMA P 3 " pdb=" C2 BMA P 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.37e+00 ... (remaining 35035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 46334 1.27 - 2.53: 1035 2.53 - 3.80: 289 3.80 - 5.07: 34 5.07 - 6.33: 7 Bond angle restraints: 47699 Sorted by residual: angle pdb=" N THR C 615 " pdb=" CA THR C 615 " pdb=" C THR C 615 " ideal model delta sigma weight residual 114.62 110.79 3.83 1.14e+00 7.69e-01 1.13e+01 angle pdb=" N THR B 615 " pdb=" CA THR B 615 " pdb=" C THR B 615 " ideal model delta sigma weight residual 114.62 111.17 3.45 1.14e+00 7.69e-01 9.18e+00 angle pdb=" CA THR C 615 " pdb=" C THR C 615 " pdb=" N GLU C 616 " ideal model delta sigma weight residual 119.71 116.84 2.87 1.17e+00 7.31e-01 6.03e+00 angle pdb=" C GLY K 51 " pdb=" N ALA K 52 " pdb=" CA ALA K 52 " ideal model delta sigma weight residual 121.54 126.05 -4.51 1.91e+00 2.74e-01 5.58e+00 angle pdb=" C3 BMA P 3 " pdb=" C2 BMA P 3 " pdb=" O2 BMA P 3 " ideal model delta sigma weight residual 112.95 106.62 6.33 3.00e+00 1.11e-01 4.45e+00 ... (remaining 47694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.05: 21052 22.05 - 44.10: 554 44.10 - 66.15: 79 66.15 - 88.20: 31 88.20 - 110.24: 9 Dihedral angle restraints: 21725 sinusoidal: 9196 harmonic: 12529 Sorted by residual: dihedral pdb=" CB CYS B1079 " pdb=" SG CYS B1079 " pdb=" SG CYS B1123 " pdb=" CB CYS B1123 " ideal model delta sinusoidal sigma weight residual -86.00 -125.08 39.08 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" O4 BMA V 3 " pdb=" C4 BMA V 3 " pdb=" C5 BMA V 3 " pdb=" O5 BMA V 3 " ideal model delta sinusoidal sigma weight residual 288.71 178.47 110.24 1 3.00e+01 1.11e-03 1.44e+01 dihedral pdb=" O4 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C5 BMA P 3 " pdb=" O5 BMA P 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.66 109.05 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 21722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4763 0.055 - 0.111: 689 0.111 - 0.166: 153 0.166 - 0.222: 3 0.222 - 0.277: 2 Chirality restraints: 5610 Sorted by residual: chirality pdb=" C5 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C6 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C5 BMA V 3 " pdb=" C4 BMA V 3 " pdb=" C6 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.90e-01 ... (remaining 5607 not shown) Planarity restraints: 6107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU E 153 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.59e+00 pdb=" N PRO E 154 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 154 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 154 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU J 153 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO J 154 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO J 154 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO J 154 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 153 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO H 154 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO H 154 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 154 " -0.020 5.00e-02 4.00e+02 ... (remaining 6104 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 305 2.53 - 3.12: 27264 3.12 - 3.72: 51836 3.72 - 4.31: 75264 4.31 - 4.90: 126249 Nonbonded interactions: 280918 Sorted by model distance: nonbonded pdb=" OG1 THR A 390 " pdb=" O GLU A 513 " model vdw 1.941 3.040 nonbonded pdb=" OG1 THR B 390 " pdb=" O GLU B 513 " model vdw 2.012 3.040 nonbonded pdb=" OG SER B 356 " pdb=" OD1 ASN B 391 " model vdw 2.037 3.040 nonbonded pdb=" O TYR F 189 " pdb=" OH TYR F 195 " model vdw 2.060 3.040 nonbonded pdb=" OD1 ASP B 361 " pdb=" N TYR B 362 " model vdw 2.110 3.120 ... (remaining 280913 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 242 or (resid 243 and (name N or name CA or nam \ e C or name O or name CB )) or resid 262 through 617 or resid 638 through 1308)) \ selection = (chain 'B' and resid 25 through 1308) selection = (chain 'C' and (resid 25 through 143 or resid 156 through 617 or resid 638 throu \ gh 1308)) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = (chain 'F' and (resid 1 through 165 or resid 167 through 196 or resid 198 throug \ h 216)) selection = (chain 'K' and (resid 1 through 165 or resid 167 through 196 or resid 198 throug \ h 216)) selection = (chain 'L' and (resid 1 through 165 or resid 167 through 196 or resid 198 throug \ h 216)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'P' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 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: 5.660 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: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 34.390 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 35158 Z= 0.168 Angle : 0.516 7.090 47999 Z= 0.255 Chirality : 0.044 0.277 5610 Planarity : 0.003 0.047 6065 Dihedral : 10.299 110.244 13517 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.45 % Allowed : 3.77 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.13), residues: 4252 helix: 0.93 (0.20), residues: 730 sheet: 0.37 (0.15), residues: 1276 loop : -0.27 (0.14), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 98 TYR 0.015 0.001 TYR B1064 PHE 0.009 0.001 PHE B 92 TRP 0.006 0.001 TRP E 102 HIS 0.003 0.001 HIS A 652 Details of bonding type rmsd covalent geometry : bond 0.00353 (35040) covalent geometry : angle 0.50868 (47699) SS BOND : bond 0.00219 ( 54) SS BOND : angle 0.65372 ( 108) hydrogen bonds : bond 0.12485 ( 1387) hydrogen bonds : angle 6.61575 ( 3846) link_BETA1-4 : bond 0.00237 ( 19) link_BETA1-4 : angle 1.11207 ( 57) link_BETA1-6 : bond 0.00266 ( 3) link_BETA1-6 : angle 2.18120 ( 9) link_NAG-ASN : bond 0.00226 ( 42) link_NAG-ASN : angle 1.50384 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 387 time to evaluate : 1.227 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 486 TYR cc_start: 0.8782 (m-80) cc_final: 0.8335 (m-80) REVERT: B 220 PHE cc_start: 0.7251 (t80) cc_final: 0.6613 (t80) REVERT: B 520 THR cc_start: 0.7611 (p) cc_final: 0.7327 (p) REVERT: B 899 MET cc_start: 0.9067 (mmm) cc_final: 0.8650 (tpt) REVERT: C 168 PHE cc_start: 0.8345 (t80) cc_final: 0.8144 (t80) REVERT: C 267 LEU cc_start: 0.8583 (mt) cc_final: 0.7929 (mt) REVERT: C 350 TRP cc_start: 0.8205 (p-90) cc_final: 0.7678 (p-90) REVERT: C 399 ILE cc_start: 0.8366 (pt) cc_final: 0.8083 (pt) REVERT: C 449 LEU cc_start: 0.9260 (mt) cc_final: 0.9053 (mm) REVERT: C 502 TYR cc_start: 0.9028 (m-80) cc_final: 0.8717 (m-10) REVERT: C 866 MET cc_start: 0.8831 (mtt) cc_final: 0.8515 (ttm) REVERT: C 899 MET cc_start: 0.8942 (mmm) cc_final: 0.8633 (tpt) REVERT: L 33 TYR cc_start: 0.8672 (m-80) cc_final: 0.8029 (m-80) REVERT: L 91 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8736 (pp30) REVERT: L 119 PHE cc_start: 0.8395 (m-80) cc_final: 0.8187 (t80) REVERT: H 32 TYR cc_start: 0.8840 (m-10) cc_final: 0.8580 (m-80) REVERT: H 48 MET cc_start: 0.8615 (mtp) cc_final: 0.8297 (mtp) REVERT: H 82 GLU cc_start: 0.9207 (tt0) cc_final: 0.8988 (tp30) REVERT: H 107 MET cc_start: 0.9106 (mmm) cc_final: 0.8888 (mmm) REVERT: F 4 MET cc_start: 0.7907 (mmm) cc_final: 0.7292 (mmm) REVERT: F 36 TRP cc_start: 0.8321 (m100) cc_final: 0.7932 (m100) REVERT: E 46 GLU cc_start: 0.8533 (tt0) cc_final: 0.8042 (pt0) REVERT: E 48 MET cc_start: 0.8650 (mtp) cc_final: 0.8268 (mtp) REVERT: E 197 GLN cc_start: 0.8337 (tp40) cc_final: 0.7744 (tm-30) REVERT: E 211 LYS cc_start: 0.9169 (mttm) cc_final: 0.8915 (tptp) REVERT: K 61 ASP cc_start: 0.9140 (p0) cc_final: 0.8811 (p0) outliers start: 17 outliers final: 7 residues processed: 404 average time/residue: 0.2783 time to fit residues: 166.9610 Evaluate side-chains 201 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 193 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain J residue 98 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 197 optimal weight: 0.3980 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 0.7980 chunk 424 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN A 560 GLN A 610 GLN A 962 GLN B 196 ASN B 447 ASN C 484 ASN C 801 GLN C 904 ASN C1008 GLN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN E 65 GLN E 176 GLN ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 176 GLN J 204 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.119512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3511 r_free = 0.3511 target = 0.078375 restraints weight = 117073.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.078639 restraints weight = 74755.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.077886 restraints weight = 71572.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.077981 restraints weight = 69356.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.078216 restraints weight = 61998.492| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 35158 Z= 0.165 Angle : 0.584 9.910 47999 Z= 0.297 Chirality : 0.044 0.184 5610 Planarity : 0.004 0.052 6065 Dihedral : 7.216 69.275 5971 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.42 % Allowed : 7.29 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.13), residues: 4252 helix: 1.41 (0.19), residues: 757 sheet: 0.43 (0.14), residues: 1307 loop : -0.33 (0.14), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 87 TYR 0.023 0.001 TYR B1064 PHE 0.041 0.002 PHE C 135 TRP 0.012 0.001 TRP H 108 HIS 0.006 0.001 HIS F 192 Details of bonding type rmsd covalent geometry : bond 0.00383 (35040) covalent geometry : angle 0.57437 (47699) SS BOND : bond 0.00251 ( 54) SS BOND : angle 1.31715 ( 108) hydrogen bonds : bond 0.04074 ( 1387) hydrogen bonds : angle 5.61358 ( 3846) link_BETA1-4 : bond 0.00349 ( 19) link_BETA1-4 : angle 1.37417 ( 57) link_BETA1-6 : bond 0.00097 ( 3) link_BETA1-6 : angle 1.74956 ( 9) link_NAG-ASN : bond 0.00231 ( 42) link_NAG-ASN : angle 1.57797 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 247 time to evaluate : 1.186 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: symmetry clash revert: 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 118 LEU cc_start: 0.9789 (tp) cc_final: 0.9467 (mp) REVERT: A 486 TYR cc_start: 0.9061 (m-80) cc_final: 0.8502 (m-10) REVERT: A 513 GLU cc_start: 0.8240 (mm-30) cc_final: 0.8015 (mp0) REVERT: A 1026 MET cc_start: 0.9073 (tpp) cc_final: 0.8317 (ttm) REVERT: B 133 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.7498 (m-80) REVERT: B 210 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8566 (tp) REVERT: B 220 PHE cc_start: 0.7370 (t80) cc_final: 0.6727 (t80) REVERT: B 875 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8943 (tt) REVERT: B 897 MET cc_start: 0.8821 (mtp) cc_final: 0.8548 (mtp) REVERT: B 899 MET cc_start: 0.9043 (mmm) cc_final: 0.8483 (tpt) REVERT: C 229 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.7954 (tp) REVERT: C 350 TRP cc_start: 0.8401 (p-90) cc_final: 0.7958 (p-90) REVERT: C 399 ILE cc_start: 0.8356 (pt) cc_final: 0.8041 (pt) REVERT: C 502 TYR cc_start: 0.9438 (m-80) cc_final: 0.9132 (m-10) REVERT: C 737 MET cc_start: 0.8026 (tpp) cc_final: 0.7709 (tpt) REVERT: C 1047 MET cc_start: 0.8898 (ptm) cc_final: 0.8693 (ptm) REVERT: L 119 PHE cc_start: 0.9190 (m-80) cc_final: 0.8597 (t80) REVERT: H 10 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7171 (mm-30) REVERT: H 48 MET cc_start: 0.8622 (mtp) cc_final: 0.8322 (mtp) REVERT: H 65 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7920 (mm-40) REVERT: H 80 TYR cc_start: 0.9169 (m-80) cc_final: 0.8748 (m-10) REVERT: H 81 MET cc_start: 0.8197 (ppp) cc_final: 0.7686 (ppp) REVERT: H 82 GLU cc_start: 0.9400 (tt0) cc_final: 0.8985 (tp30) REVERT: H 181 TYR cc_start: 0.9375 (m-80) cc_final: 0.9097 (m-80) REVERT: F 4 MET cc_start: 0.8253 (mmm) cc_final: 0.7203 (mmm) REVERT: F 36 TRP cc_start: 0.8498 (m100) cc_final: 0.8096 (m100) REVERT: E 46 GLU cc_start: 0.9028 (tt0) cc_final: 0.8721 (pt0) REVERT: E 48 MET cc_start: 0.8889 (mtp) cc_final: 0.8138 (mtp) REVERT: E 67 ARG cc_start: 0.8575 (mtp180) cc_final: 0.7364 (mtp180) REVERT: E 94 TYR cc_start: 0.8949 (m-80) cc_final: 0.8631 (m-80) REVERT: E 107 MET cc_start: 0.8683 (mmt) cc_final: 0.8474 (mmm) REVERT: E 211 LYS cc_start: 0.9296 (mttm) cc_final: 0.9089 (tptp) REVERT: K 61 ASP cc_start: 0.9472 (p0) cc_final: 0.9175 (p0) REVERT: K 198 GLU cc_start: 0.9722 (tt0) cc_final: 0.9501 (tm-30) REVERT: J 10 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8144 (mm-30) REVERT: J 48 MET cc_start: 0.8872 (mtt) cc_final: 0.8391 (tpp) REVERT: J 107 MET cc_start: 0.8255 (mtt) cc_final: 0.8027 (mtt) REVERT: J 213 ASP cc_start: 0.9245 (OUTLIER) cc_final: 0.8889 (t0) outliers start: 53 outliers final: 25 residues processed: 289 average time/residue: 0.2726 time to fit residues: 118.0814 Evaluate side-chains 225 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain J residue 98 ARG Chi-restraints excluded: chain J residue 213 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 107 optimal weight: 30.0000 chunk 250 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 391 optimal weight: 20.0000 chunk 146 optimal weight: 0.9990 chunk 143 optimal weight: 9.9990 chunk 363 optimal weight: 3.9990 chunk 217 optimal weight: 8.9990 chunk 180 optimal weight: 1.9990 chunk 253 optimal weight: 0.6980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 946 GLN C 447 ASN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** K 192 HIS ** 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 = 0.4206 r_free = 0.4206 target = 0.114434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.072494 restraints weight = 110496.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.074688 restraints weight = 70146.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.074380 restraints weight = 45363.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.074501 restraints weight = 47695.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.074594 restraints weight = 42992.328| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35158 Z= 0.123 Angle : 0.547 11.841 47999 Z= 0.275 Chirality : 0.044 0.232 5610 Planarity : 0.004 0.058 6065 Dihedral : 6.131 59.039 5965 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.26 % Allowed : 8.57 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.13), residues: 4252 helix: 1.71 (0.20), residues: 741 sheet: 0.41 (0.15), residues: 1274 loop : -0.39 (0.13), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 55 TYR 0.032 0.001 TYR L 99 PHE 0.039 0.001 PHE C 135 TRP 0.011 0.001 TRP E 102 HIS 0.003 0.001 HIS F 201 Details of bonding type rmsd covalent geometry : bond 0.00282 (35040) covalent geometry : angle 0.53626 (47699) SS BOND : bond 0.00290 ( 54) SS BOND : angle 1.53091 ( 108) hydrogen bonds : bond 0.03598 ( 1387) hydrogen bonds : angle 5.36658 ( 3846) link_BETA1-4 : bond 0.00329 ( 19) link_BETA1-4 : angle 1.40689 ( 57) link_BETA1-6 : bond 0.00132 ( 3) link_BETA1-6 : angle 1.55627 ( 9) link_NAG-ASN : bond 0.00227 ( 42) link_NAG-ASN : angle 1.46090 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 226 time to evaluate : 1.323 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7591 (t80) cc_final: 0.7073 (t80) REVERT: A 118 LEU cc_start: 0.9730 (tp) cc_final: 0.9392 (mp) REVERT: A 486 TYR cc_start: 0.8904 (m-80) cc_final: 0.8352 (m-80) REVERT: A 1026 MET cc_start: 0.9091 (tpp) cc_final: 0.8391 (ttm) REVERT: A 1047 MET cc_start: 0.9080 (ptm) cc_final: 0.8849 (ptm) REVERT: B 133 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.7034 (m-80) REVERT: B 210 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8207 (tp) REVERT: B 220 PHE cc_start: 0.7244 (t80) cc_final: 0.6632 (t80) REVERT: B 422 LEU cc_start: 0.9282 (tp) cc_final: 0.9064 (tp) REVERT: B 897 MET cc_start: 0.8771 (mtp) cc_final: 0.8527 (mtp) REVERT: B 899 MET cc_start: 0.9065 (mmm) cc_final: 0.8595 (tpt) REVERT: C 229 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.7921 (tp) REVERT: C 350 TRP cc_start: 0.8399 (p-90) cc_final: 0.8021 (p-90) REVERT: C 399 ILE cc_start: 0.8313 (pt) cc_final: 0.8011 (pt) REVERT: C 502 TYR cc_start: 0.9166 (m-80) cc_final: 0.8900 (m-10) REVERT: C 737 MET cc_start: 0.7977 (tpp) cc_final: 0.7687 (tpt) REVERT: C 1047 MET cc_start: 0.8855 (ptm) cc_final: 0.8614 (ptm) REVERT: L 55 ARG cc_start: 0.9091 (ttp80) cc_final: 0.8842 (tmt170) REVERT: H 10 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6976 (mm-30) REVERT: H 32 TYR cc_start: 0.8703 (m-80) cc_final: 0.8193 (m-80) REVERT: H 48 MET cc_start: 0.8464 (mtp) cc_final: 0.8165 (mtp) REVERT: H 80 TYR cc_start: 0.8956 (m-80) cc_final: 0.8423 (m-10) REVERT: H 82 GLU cc_start: 0.9217 (tt0) cc_final: 0.9010 (tp30) REVERT: H 148 LYS cc_start: 0.9656 (pptt) cc_final: 0.9158 (pptt) REVERT: F 4 MET cc_start: 0.8180 (mmm) cc_final: 0.7438 (mmm) REVERT: F 36 TRP cc_start: 0.8272 (m100) cc_final: 0.8062 (m100) REVERT: F 97 ARG cc_start: 0.8808 (mtp-110) cc_final: 0.8475 (mtp85) REVERT: E 46 GLU cc_start: 0.9058 (tt0) cc_final: 0.8782 (pt0) REVERT: E 48 MET cc_start: 0.8716 (mtp) cc_final: 0.7850 (mtp) REVERT: E 68 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8188 (p) REVERT: E 107 MET cc_start: 0.8531 (mmt) cc_final: 0.8289 (mmm) REVERT: E 211 LYS cc_start: 0.9166 (mttm) cc_final: 0.8957 (tptp) REVERT: K 61 ASP cc_start: 0.9313 (p0) cc_final: 0.9022 (p0) REVERT: J 10 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7864 (mm-30) REVERT: J 48 MET cc_start: 0.8670 (mtt) cc_final: 0.8377 (mmt) REVERT: J 107 MET cc_start: 0.8307 (mtt) cc_final: 0.8065 (mtt) outliers start: 47 outliers final: 27 residues processed: 266 average time/residue: 0.2671 time to fit residues: 107.1188 Evaluate side-chains 221 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain H residue 213 ASP Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain J residue 98 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 271 optimal weight: 3.9990 chunk 412 optimal weight: 8.9990 chunk 312 optimal weight: 30.0000 chunk 261 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 687 GLN B 484 ASN B 771 GLN B1002 GLN H 65 GLN H 101 GLN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** 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 = 0.4137 r_free = 0.4137 target = 0.112301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.068955 restraints weight = 108842.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.069341 restraints weight = 67482.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.068454 restraints weight = 49933.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.068782 restraints weight = 48619.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.068901 restraints weight = 44469.855| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 35158 Z= 0.277 Angle : 0.621 10.466 47999 Z= 0.314 Chirality : 0.045 0.249 5610 Planarity : 0.004 0.053 6065 Dihedral : 5.734 58.450 5965 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.87 % Allowed : 9.08 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.13), residues: 4252 helix: 1.22 (0.19), residues: 745 sheet: 0.37 (0.15), residues: 1286 loop : -0.54 (0.13), residues: 2221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 62 TYR 0.044 0.002 TYR L 99 PHE 0.034 0.002 PHE C 135 TRP 0.011 0.001 TRP F 36 HIS 0.008 0.001 HIS A 652 Details of bonding type rmsd covalent geometry : bond 0.00659 (35040) covalent geometry : angle 0.61222 (47699) SS BOND : bond 0.00354 ( 54) SS BOND : angle 1.20534 ( 108) hydrogen bonds : bond 0.04199 ( 1387) hydrogen bonds : angle 5.59245 ( 3846) link_BETA1-4 : bond 0.00258 ( 19) link_BETA1-4 : angle 1.53050 ( 57) link_BETA1-6 : bond 0.00301 ( 3) link_BETA1-6 : angle 1.64586 ( 9) link_NAG-ASN : bond 0.00363 ( 42) link_NAG-ASN : angle 1.63384 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 210 time to evaluate : 1.395 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: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7814 (t80) cc_final: 0.7325 (t80) REVERT: A 118 LEU cc_start: 0.9663 (tp) cc_final: 0.9346 (mp) REVERT: A 461 PHE cc_start: 0.8542 (m-80) cc_final: 0.8285 (t80) REVERT: A 486 TYR cc_start: 0.8660 (m-80) cc_final: 0.8090 (m-80) REVERT: B 133 PHE cc_start: 0.7218 (OUTLIER) cc_final: 0.6599 (m-80) REVERT: B 210 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.7948 (tp) REVERT: B 220 PHE cc_start: 0.7343 (t80) cc_final: 0.6741 (t80) REVERT: B 422 LEU cc_start: 0.9297 (tp) cc_final: 0.9082 (tp) REVERT: B 899 MET cc_start: 0.9083 (mmm) cc_final: 0.8495 (tpt) REVERT: C 229 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8077 (tp) REVERT: C 350 TRP cc_start: 0.8508 (p-90) cc_final: 0.8059 (p-90) REVERT: C 399 ILE cc_start: 0.8332 (pt) cc_final: 0.8051 (pt) REVERT: C 502 TYR cc_start: 0.8933 (m-80) cc_final: 0.8665 (m-10) REVERT: C 737 MET cc_start: 0.8061 (tpp) cc_final: 0.7768 (tpt) REVERT: L 55 ARG cc_start: 0.8992 (ttp80) cc_final: 0.8786 (tmt170) REVERT: H 10 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6788 (mm-30) REVERT: H 32 TYR cc_start: 0.8718 (m-80) cc_final: 0.8192 (m-80) REVERT: H 80 TYR cc_start: 0.8798 (m-80) cc_final: 0.8272 (m-10) REVERT: F 4 MET cc_start: 0.8148 (mmm) cc_final: 0.7454 (mmm) REVERT: F 36 TRP cc_start: 0.8271 (m100) cc_final: 0.7895 (m100) REVERT: E 48 MET cc_start: 0.8536 (mtp) cc_final: 0.7926 (mtp) REVERT: E 197 GLN cc_start: 0.8375 (tp40) cc_final: 0.7816 (tm-30) REVERT: K 148 LYS cc_start: 0.6462 (tmmt) cc_final: 0.5907 (tmmt) REVERT: J 10 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7617 (mm-30) REVERT: J 107 MET cc_start: 0.8345 (mtt) cc_final: 0.8001 (mtt) outliers start: 70 outliers final: 45 residues processed: 272 average time/residue: 0.2587 time to fit residues: 107.9445 Evaluate side-chains 233 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 185 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain H residue 202 ASN Chi-restraints excluded: chain F residue 145 ARG Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain J residue 98 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 173 optimal weight: 0.7980 chunk 371 optimal weight: 10.0000 chunk 260 optimal weight: 0.9980 chunk 310 optimal weight: 10.0000 chunk 367 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 chunk 327 optimal weight: 0.0970 chunk 63 optimal weight: 0.8980 chunk 346 optimal weight: 2.9990 chunk 279 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 771 GLN C 952 ASN H 65 GLN H 101 GLN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 163 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 GLN ** K 192 HIS ** 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 = 0.4206 r_free = 0.4206 target = 0.114384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.073337 restraints weight = 110855.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.074702 restraints weight = 71741.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.074198 restraints weight = 52361.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.074417 restraints weight = 49353.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.074525 restraints weight = 46058.960| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 35158 Z= 0.109 Angle : 0.525 10.134 47999 Z= 0.268 Chirality : 0.043 0.187 5610 Planarity : 0.004 0.052 6065 Dihedral : 5.186 55.860 5965 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.44 % Allowed : 9.80 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.13), residues: 4252 helix: 1.62 (0.20), residues: 746 sheet: 0.42 (0.15), residues: 1288 loop : -0.46 (0.13), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 24 TYR 0.044 0.001 TYR L 99 PHE 0.033 0.001 PHE E 29 TRP 0.012 0.001 TRP E 102 HIS 0.003 0.001 HIS F 201 Details of bonding type rmsd covalent geometry : bond 0.00242 (35040) covalent geometry : angle 0.51817 (47699) SS BOND : bond 0.00270 ( 54) SS BOND : angle 0.78012 ( 108) hydrogen bonds : bond 0.03446 ( 1387) hydrogen bonds : angle 5.24976 ( 3846) link_BETA1-4 : bond 0.00349 ( 19) link_BETA1-4 : angle 1.24473 ( 57) link_BETA1-6 : bond 0.00188 ( 3) link_BETA1-6 : angle 1.54740 ( 9) link_NAG-ASN : bond 0.00209 ( 42) link_NAG-ASN : angle 1.34044 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 209 time to evaluate : 1.225 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 92 PHE cc_start: 0.7560 (t80) cc_final: 0.6990 (t80) REVERT: A 118 LEU cc_start: 0.9720 (tp) cc_final: 0.9392 (mp) REVERT: A 461 PHE cc_start: 0.8699 (m-80) cc_final: 0.8333 (t80) REVERT: A 486 TYR cc_start: 0.8784 (m-80) cc_final: 0.8191 (m-80) REVERT: A 899 MET cc_start: 0.9130 (tpp) cc_final: 0.8896 (tpp) REVERT: A 914 TYR cc_start: 0.9209 (m-80) cc_final: 0.8845 (m-10) REVERT: A 1026 MET cc_start: 0.8925 (tpp) cc_final: 0.8364 (ttm) REVERT: B 133 PHE cc_start: 0.7358 (OUTLIER) cc_final: 0.6876 (m-80) REVERT: B 210 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8174 (tp) REVERT: B 422 LEU cc_start: 0.9284 (tp) cc_final: 0.9041 (tp) REVERT: B 899 MET cc_start: 0.9046 (mmm) cc_final: 0.8529 (tpt) REVERT: C 229 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7903 (tp) REVERT: C 350 TRP cc_start: 0.8474 (p-90) cc_final: 0.8076 (p-90) REVERT: C 399 ILE cc_start: 0.8318 (pt) cc_final: 0.8020 (pt) REVERT: C 502 TYR cc_start: 0.9086 (m-80) cc_final: 0.8792 (m-10) REVERT: H 10 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7070 (mm-30) REVERT: H 32 TYR cc_start: 0.8596 (m-80) cc_final: 0.8082 (m-80) REVERT: H 80 TYR cc_start: 0.8794 (m-80) cc_final: 0.8237 (m-10) REVERT: F 4 MET cc_start: 0.8124 (mmm) cc_final: 0.7506 (mmm) REVERT: F 36 TRP cc_start: 0.8258 (m100) cc_final: 0.7853 (m100) REVERT: F 98 MET cc_start: 0.8884 (mmm) cc_final: 0.8545 (mtt) REVERT: E 48 MET cc_start: 0.8489 (mtp) cc_final: 0.7812 (mtp) REVERT: K 97 ARG cc_start: 0.8595 (mmt180) cc_final: 0.8387 (mmp-170) REVERT: J 10 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7853 (mm-30) REVERT: J 19 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8665 (tptp) REVERT: J 48 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7899 (mmt) REVERT: J 107 MET cc_start: 0.8318 (mtt) cc_final: 0.7962 (mtt) outliers start: 54 outliers final: 39 residues processed: 253 average time/residue: 0.2436 time to fit residues: 95.0989 Evaluate side-chains 232 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 483 PHE Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain H residue 202 ASN Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 98 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 301 optimal weight: 20.0000 chunk 131 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 279 optimal weight: 3.9990 chunk 357 optimal weight: 9.9990 chunk 350 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 241 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 952 ASN H 65 GLN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.112060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.068230 restraints weight = 108261.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.066963 restraints weight = 69467.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.066790 restraints weight = 57814.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.067214 restraints weight = 55365.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.067383 restraints weight = 46113.558| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 35158 Z= 0.290 Angle : 0.620 9.618 47999 Z= 0.315 Chirality : 0.045 0.265 5610 Planarity : 0.004 0.053 6065 Dihedral : 5.271 54.401 5963 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.74 % Allowed : 10.25 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.13), residues: 4252 helix: 1.19 (0.19), residues: 747 sheet: 0.31 (0.15), residues: 1300 loop : -0.60 (0.14), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 67 TYR 0.044 0.002 TYR L 99 PHE 0.032 0.002 PHE L 29 TRP 0.012 0.001 TRP H 102 HIS 0.007 0.001 HIS A 652 Details of bonding type rmsd covalent geometry : bond 0.00687 (35040) covalent geometry : angle 0.61239 (47699) SS BOND : bond 0.00323 ( 54) SS BOND : angle 0.92272 ( 108) hydrogen bonds : bond 0.04145 ( 1387) hydrogen bonds : angle 5.49901 ( 3846) link_BETA1-4 : bond 0.00268 ( 19) link_BETA1-4 : angle 1.36836 ( 57) link_BETA1-6 : bond 0.00167 ( 3) link_BETA1-6 : angle 1.62607 ( 9) link_NAG-ASN : bond 0.00372 ( 42) link_NAG-ASN : angle 1.61045 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 193 time to evaluate : 1.254 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: A 92 PHE cc_start: 0.7780 (t80) cc_final: 0.7325 (t80) REVERT: A 118 LEU cc_start: 0.9674 (tp) cc_final: 0.9355 (mp) REVERT: A 461 PHE cc_start: 0.8580 (m-80) cc_final: 0.8227 (t80) REVERT: A 486 TYR cc_start: 0.8672 (m-80) cc_final: 0.8088 (m-80) REVERT: B 133 PHE cc_start: 0.7286 (OUTLIER) cc_final: 0.6738 (m-80) REVERT: B 210 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.7957 (tp) REVERT: B 422 LEU cc_start: 0.9329 (tp) cc_final: 0.9088 (tp) REVERT: B 897 MET cc_start: 0.9007 (mtp) cc_final: 0.8654 (mtp) REVERT: B 899 MET cc_start: 0.9084 (mmm) cc_final: 0.8621 (tpt) REVERT: C 229 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8081 (tp) REVERT: C 350 TRP cc_start: 0.8574 (p-90) cc_final: 0.8057 (p-90) REVERT: C 399 ILE cc_start: 0.8368 (pt) cc_final: 0.8079 (pt) REVERT: C 502 TYR cc_start: 0.8964 (m-80) cc_final: 0.8651 (m-10) REVERT: C 728 MET cc_start: 0.8598 (ptp) cc_final: 0.8355 (ptp) REVERT: C 737 MET cc_start: 0.8174 (tpp) cc_final: 0.7941 (tpt) REVERT: H 10 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6951 (mm-30) REVERT: H 32 TYR cc_start: 0.8636 (m-80) cc_final: 0.8143 (m-80) REVERT: H 80 TYR cc_start: 0.8774 (m-80) cc_final: 0.8239 (m-10) REVERT: F 4 MET cc_start: 0.8156 (mmm) cc_final: 0.7467 (mmm) REVERT: F 36 TRP cc_start: 0.8320 (m100) cc_final: 0.7825 (m100) REVERT: E 23 LYS cc_start: 0.9198 (mttt) cc_final: 0.8983 (mppt) REVERT: E 48 MET cc_start: 0.8512 (mtp) cc_final: 0.7617 (mtp) REVERT: E 94 TYR cc_start: 0.8492 (m-80) cc_final: 0.8286 (m-80) REVERT: K 97 ARG cc_start: 0.8533 (mmt180) cc_final: 0.8248 (mmp-170) REVERT: J 10 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7702 (mm-30) REVERT: J 48 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7981 (mmt) REVERT: J 94 TYR cc_start: 0.8335 (m-10) cc_final: 0.8120 (m-10) REVERT: J 107 MET cc_start: 0.8352 (mtt) cc_final: 0.8009 (mtt) outliers start: 65 outliers final: 47 residues processed: 245 average time/residue: 0.2409 time to fit residues: 91.7238 Evaluate side-chains 234 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 183 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 870 TYR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 483 PHE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 866 MET Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain H residue 202 ASN Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain J residue 98 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 268 optimal weight: 1.9990 chunk 380 optimal weight: 0.0370 chunk 396 optimal weight: 50.0000 chunk 411 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 chunk 235 optimal weight: 6.9990 chunk 305 optimal weight: 0.0370 chunk 1 optimal weight: 2.9990 chunk 421 optimal weight: 20.0000 chunk 326 optimal weight: 30.0000 overall best weight: 1.1940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 GLN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 ASN ** F 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.119474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 127)---------------| | r_work = 0.3505 r_free = 0.3505 target = 0.077503 restraints weight = 116237.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.078699 restraints weight = 75834.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.077953 restraints weight = 56466.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.078152 restraints weight = 59842.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.078150 restraints weight = 54786.604| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35158 Z= 0.122 Angle : 0.536 12.111 47999 Z= 0.271 Chirality : 0.043 0.216 5610 Planarity : 0.004 0.086 6065 Dihedral : 4.995 52.352 5963 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.39 % Allowed : 10.87 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.13), residues: 4252 helix: 1.54 (0.20), residues: 746 sheet: 0.35 (0.15), residues: 1293 loop : -0.49 (0.14), residues: 2213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 97 TYR 0.039 0.001 TYR L 99 PHE 0.029 0.001 PHE L 29 TRP 0.013 0.001 TRP E 102 HIS 0.003 0.001 HIS C1045 Details of bonding type rmsd covalent geometry : bond 0.00279 (35040) covalent geometry : angle 0.53050 (47699) SS BOND : bond 0.00249 ( 54) SS BOND : angle 0.69313 ( 108) hydrogen bonds : bond 0.03545 ( 1387) hydrogen bonds : angle 5.23417 ( 3846) link_BETA1-4 : bond 0.00269 ( 19) link_BETA1-4 : angle 1.12905 ( 57) link_BETA1-6 : bond 0.00125 ( 3) link_BETA1-6 : angle 1.56851 ( 9) link_NAG-ASN : bond 0.00191 ( 42) link_NAG-ASN : angle 1.35227 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 192 time to evaluate : 1.374 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: A 92 PHE cc_start: 0.7584 (t80) cc_final: 0.7010 (t80) REVERT: A 118 LEU cc_start: 0.9752 (tp) cc_final: 0.9410 (mp) REVERT: A 486 TYR cc_start: 0.8870 (m-80) cc_final: 0.8276 (m-80) REVERT: B 133 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7197 (m-80) REVERT: B 210 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8300 (tp) REVERT: B 422 LEU cc_start: 0.9333 (tp) cc_final: 0.9061 (tp) REVERT: B 897 MET cc_start: 0.8912 (mtp) cc_final: 0.8589 (mtp) REVERT: B 1138 LEU cc_start: 0.9242 (mp) cc_final: 0.8882 (tt) REVERT: C 229 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7935 (tp) REVERT: C 350 TRP cc_start: 0.8528 (p-90) cc_final: 0.8104 (p-90) REVERT: C 399 ILE cc_start: 0.8387 (pt) cc_final: 0.8072 (pt) REVERT: C 502 TYR cc_start: 0.9224 (m-80) cc_final: 0.8880 (m-10) REVERT: C 728 MET cc_start: 0.8550 (ptp) cc_final: 0.8350 (ptp) REVERT: L 71 ASP cc_start: 0.9632 (p0) cc_final: 0.9398 (m-30) REVERT: H 10 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7183 (mm-30) REVERT: H 32 TYR cc_start: 0.8562 (m-80) cc_final: 0.8042 (m-80) REVERT: H 80 TYR cc_start: 0.8857 (m-80) cc_final: 0.8564 (m-10) REVERT: F 4 MET cc_start: 0.8269 (mmm) cc_final: 0.7552 (mmm) REVERT: F 36 TRP cc_start: 0.8419 (m100) cc_final: 0.7744 (m100) REVERT: F 98 MET cc_start: 0.8709 (mpp) cc_final: 0.8276 (ptp) REVERT: E 48 MET cc_start: 0.8610 (mtp) cc_final: 0.7721 (mtp) REVERT: E 94 TYR cc_start: 0.8722 (m-80) cc_final: 0.8452 (m-80) REVERT: K 97 ARG cc_start: 0.8628 (mmt180) cc_final: 0.8319 (mmp-170) REVERT: J 10 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8013 (mm-30) REVERT: J 48 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7964 (mmm) REVERT: J 94 TYR cc_start: 0.8485 (m-10) cc_final: 0.8225 (m-10) REVERT: J 107 MET cc_start: 0.8345 (mtt) cc_final: 0.8017 (mtt) outliers start: 52 outliers final: 41 residues processed: 234 average time/residue: 0.2355 time to fit residues: 85.6177 Evaluate side-chains 227 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 182 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 483 PHE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain H residue 202 ASN Chi-restraints excluded: chain H residue 213 ASP Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 98 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 5 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 chunk 175 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 322 optimal weight: 30.0000 chunk 346 optimal weight: 6.9990 chunk 354 optimal weight: 8.9990 chunk 407 optimal weight: 4.9990 chunk 391 optimal weight: 40.0000 chunk 66 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1103 GLN ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.112301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.067973 restraints weight = 108977.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.066358 restraints weight = 65044.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.067592 restraints weight = 55418.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.067612 restraints weight = 42353.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.067831 restraints weight = 39390.668| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 35158 Z= 0.250 Angle : 0.603 12.045 47999 Z= 0.305 Chirality : 0.045 0.243 5610 Planarity : 0.004 0.055 6065 Dihedral : 5.105 51.976 5963 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.39 % Allowed : 11.11 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.13), residues: 4252 helix: 1.30 (0.19), residues: 745 sheet: 0.20 (0.14), residues: 1330 loop : -0.56 (0.14), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 87 TYR 0.035 0.001 TYR L 99 PHE 0.023 0.002 PHE C 453 TRP 0.009 0.001 TRP F 36 HIS 0.006 0.001 HIS A 652 Details of bonding type rmsd covalent geometry : bond 0.00592 (35040) covalent geometry : angle 0.59425 (47699) SS BOND : bond 0.00303 ( 54) SS BOND : angle 1.20933 ( 108) hydrogen bonds : bond 0.03943 ( 1387) hydrogen bonds : angle 5.39397 ( 3846) link_BETA1-4 : bond 0.00235 ( 19) link_BETA1-4 : angle 1.25633 ( 57) link_BETA1-6 : bond 0.00134 ( 3) link_BETA1-6 : angle 1.62082 ( 9) link_NAG-ASN : bond 0.00318 ( 42) link_NAG-ASN : angle 1.62302 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 182 time to evaluate : 1.223 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 92 PHE cc_start: 0.7690 (t80) cc_final: 0.7241 (t80) REVERT: A 118 LEU cc_start: 0.9736 (tp) cc_final: 0.9414 (mp) REVERT: A 461 PHE cc_start: 0.8612 (m-80) cc_final: 0.8256 (t80) REVERT: A 486 TYR cc_start: 0.8814 (m-80) cc_final: 0.8229 (m-80) REVERT: B 133 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.7062 (m-80) REVERT: B 210 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8145 (tp) REVERT: B 422 LEU cc_start: 0.9350 (tp) cc_final: 0.9084 (tp) REVERT: B 737 MET cc_start: 0.8264 (tpt) cc_final: 0.8024 (tpt) REVERT: B 897 MET cc_start: 0.8968 (mtp) cc_final: 0.8635 (mtp) REVERT: B 1138 LEU cc_start: 0.9187 (mp) cc_final: 0.8832 (tt) REVERT: C 229 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8086 (tp) REVERT: C 350 TRP cc_start: 0.8616 (p-90) cc_final: 0.8094 (p-90) REVERT: C 399 ILE cc_start: 0.8441 (pt) cc_final: 0.8130 (pt) REVERT: C 502 TYR cc_start: 0.9147 (m-80) cc_final: 0.8772 (m-10) REVERT: H 10 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7159 (mm-30) REVERT: H 32 TYR cc_start: 0.8586 (m-80) cc_final: 0.8121 (m-80) REVERT: H 80 TYR cc_start: 0.8900 (m-80) cc_final: 0.8624 (m-10) REVERT: F 4 MET cc_start: 0.8332 (mmm) cc_final: 0.7782 (mmm) REVERT: F 36 TRP cc_start: 0.8463 (m100) cc_final: 0.7935 (m100) REVERT: F 98 MET cc_start: 0.8639 (mpp) cc_final: 0.8134 (ptp) REVERT: E 48 MET cc_start: 0.8676 (mtp) cc_final: 0.7745 (mtp) REVERT: E 94 TYR cc_start: 0.8624 (m-80) cc_final: 0.8243 (m-80) REVERT: K 97 ARG cc_start: 0.8605 (mmt180) cc_final: 0.8291 (mmp-170) REVERT: J 10 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8007 (mm-30) REVERT: J 13 LYS cc_start: 0.9077 (tppt) cc_final: 0.8859 (tppt) REVERT: J 48 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8040 (mmt) REVERT: J 94 TYR cc_start: 0.8541 (m-10) cc_final: 0.8310 (m-10) REVERT: J 107 MET cc_start: 0.8372 (mtt) cc_final: 0.8039 (mtt) outliers start: 52 outliers final: 44 residues processed: 226 average time/residue: 0.2528 time to fit residues: 88.7047 Evaluate side-chains 225 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 483 PHE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 202 ASN Chi-restraints excluded: chain H residue 213 ASP Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 98 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 308 optimal weight: 30.0000 chunk 328 optimal weight: 8.9990 chunk 294 optimal weight: 2.9990 chunk 346 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 26 optimal weight: 20.0000 chunk 124 optimal weight: 0.7980 chunk 50 optimal weight: 0.1980 chunk 383 optimal weight: 40.0000 chunk 249 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1103 GLN ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.113535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.068050 restraints weight = 108523.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.069793 restraints weight = 64404.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.069554 restraints weight = 39499.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.069782 restraints weight = 41463.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.069922 restraints weight = 38203.410| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35158 Z= 0.132 Angle : 0.541 9.757 47999 Z= 0.274 Chirality : 0.043 0.236 5610 Planarity : 0.004 0.048 6065 Dihedral : 4.885 52.195 5963 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.42 % Allowed : 11.24 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.13), residues: 4252 helix: 1.54 (0.20), residues: 741 sheet: 0.23 (0.14), residues: 1342 loop : -0.48 (0.14), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 87 TYR 0.028 0.001 TYR L 99 PHE 0.025 0.001 PHE A 389 TRP 0.012 0.001 TRP E 102 HIS 0.003 0.001 HIS A1045 Details of bonding type rmsd covalent geometry : bond 0.00307 (35040) covalent geometry : angle 0.53419 (47699) SS BOND : bond 0.00230 ( 54) SS BOND : angle 0.95989 ( 108) hydrogen bonds : bond 0.03478 ( 1387) hydrogen bonds : angle 5.18862 ( 3846) link_BETA1-4 : bond 0.00270 ( 19) link_BETA1-4 : angle 1.10060 ( 57) link_BETA1-6 : bond 0.00145 ( 3) link_BETA1-6 : angle 1.51964 ( 9) link_NAG-ASN : bond 0.00199 ( 42) link_NAG-ASN : angle 1.41444 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 192 time to evaluate : 1.262 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: A 92 PHE cc_start: 0.7549 (t80) cc_final: 0.7049 (t80) REVERT: A 118 LEU cc_start: 0.9702 (tp) cc_final: 0.9394 (mp) REVERT: A 461 PHE cc_start: 0.8513 (m-80) cc_final: 0.8175 (t80) REVERT: A 486 TYR cc_start: 0.8711 (m-80) cc_final: 0.8013 (m-80) REVERT: B 133 PHE cc_start: 0.7341 (OUTLIER) cc_final: 0.6838 (m-80) REVERT: B 210 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8068 (tp) REVERT: B 229 LEU cc_start: 0.8594 (mt) cc_final: 0.8077 (tp) REVERT: B 422 LEU cc_start: 0.9331 (tp) cc_final: 0.9074 (tp) REVERT: B 737 MET cc_start: 0.8246 (tpt) cc_final: 0.8036 (tpt) REVERT: B 897 MET cc_start: 0.8821 (mtp) cc_final: 0.8540 (mtp) REVERT: B 1138 LEU cc_start: 0.9193 (mp) cc_final: 0.8835 (tt) REVERT: C 229 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8018 (tp) REVERT: C 350 TRP cc_start: 0.8517 (p-90) cc_final: 0.8102 (p-90) REVERT: C 399 ILE cc_start: 0.8362 (pt) cc_final: 0.8060 (pt) REVERT: C 502 TYR cc_start: 0.9030 (m-80) cc_final: 0.8689 (m-10) REVERT: L 71 ASP cc_start: 0.9570 (p0) cc_final: 0.9301 (m-30) REVERT: H 10 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7059 (mm-30) REVERT: H 32 TYR cc_start: 0.8553 (m-80) cc_final: 0.8078 (m-80) REVERT: H 80 TYR cc_start: 0.8786 (m-80) cc_final: 0.8494 (m-10) REVERT: F 4 MET cc_start: 0.8196 (mmm) cc_final: 0.7543 (mmm) REVERT: F 36 TRP cc_start: 0.8342 (m100) cc_final: 0.7886 (m100) REVERT: F 97 ARG cc_start: 0.8703 (mtp-110) cc_final: 0.8339 (mtp-110) REVERT: F 98 MET cc_start: 0.8579 (mpp) cc_final: 0.8106 (ptp) REVERT: E 48 MET cc_start: 0.8521 (mtp) cc_final: 0.7553 (mtp) REVERT: E 94 TYR cc_start: 0.8518 (m-80) cc_final: 0.8117 (m-80) REVERT: K 97 ARG cc_start: 0.8595 (mmt180) cc_final: 0.8270 (mmp-170) REVERT: K 198 GLU cc_start: 0.9584 (tt0) cc_final: 0.9198 (pt0) REVERT: J 10 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7958 (mm-30) REVERT: J 13 LYS cc_start: 0.9054 (tppt) cc_final: 0.8831 (tppt) REVERT: J 48 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7772 (mmm) REVERT: J 107 MET cc_start: 0.8378 (mtt) cc_final: 0.8045 (mtt) outliers start: 53 outliers final: 42 residues processed: 236 average time/residue: 0.2523 time to fit residues: 91.9824 Evaluate side-chains 229 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 483 PHE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 202 ASN Chi-restraints excluded: chain H residue 213 ASP Chi-restraints excluded: chain F residue 145 ARG Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 98 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 1 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 chunk 336 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 chunk 395 optimal weight: 20.0000 chunk 196 optimal weight: 1.9990 chunk 177 optimal weight: 0.5980 chunk 316 optimal weight: 20.0000 chunk 368 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 352 optimal weight: 0.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1103 GLN ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.112494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.066652 restraints weight = 109011.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.068118 restraints weight = 71077.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.067656 restraints weight = 46304.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.067891 restraints weight = 46127.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.068051 restraints weight = 40469.815| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 35158 Z= 0.231 Angle : 0.589 9.910 47999 Z= 0.298 Chirality : 0.044 0.240 5610 Planarity : 0.004 0.090 6065 Dihedral : 4.957 51.812 5963 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.20 % Allowed : 11.64 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.13), residues: 4252 helix: 1.31 (0.20), residues: 743 sheet: 0.22 (0.14), residues: 1340 loop : -0.54 (0.14), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 405 TYR 0.029 0.001 TYR L 99 PHE 0.023 0.002 PHE A 389 TRP 0.035 0.001 TRP B 104 HIS 0.005 0.001 HIS A1061 Details of bonding type rmsd covalent geometry : bond 0.00546 (35040) covalent geometry : angle 0.58203 (47699) SS BOND : bond 0.00295 ( 54) SS BOND : angle 0.96953 ( 108) hydrogen bonds : bond 0.03856 ( 1387) hydrogen bonds : angle 5.31168 ( 3846) link_BETA1-4 : bond 0.00253 ( 19) link_BETA1-4 : angle 1.21456 ( 57) link_BETA1-6 : bond 0.00175 ( 3) link_BETA1-6 : angle 1.57135 ( 9) link_NAG-ASN : bond 0.00300 ( 42) link_NAG-ASN : angle 1.52750 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 1.201 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: A 92 PHE cc_start: 0.7597 (t80) cc_final: 0.7030 (t80) REVERT: A 118 LEU cc_start: 0.9731 (tp) cc_final: 0.9423 (mt) REVERT: A 461 PHE cc_start: 0.8537 (m-80) cc_final: 0.8182 (t80) REVERT: A 486 TYR cc_start: 0.8761 (m-80) cc_final: 0.8136 (m-80) REVERT: B 133 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.7004 (m-80) REVERT: B 210 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8156 (tp) REVERT: B 422 LEU cc_start: 0.9332 (tp) cc_final: 0.9066 (tp) REVERT: B 737 MET cc_start: 0.8259 (tpt) cc_final: 0.8053 (tpt) REVERT: B 897 MET cc_start: 0.8940 (mtp) cc_final: 0.8610 (mtp) REVERT: B 1138 LEU cc_start: 0.9264 (mp) cc_final: 0.8882 (tt) REVERT: C 229 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8178 (tp) REVERT: C 350 TRP cc_start: 0.8588 (p-90) cc_final: 0.8071 (p-90) REVERT: C 399 ILE cc_start: 0.8436 (pt) cc_final: 0.8121 (pt) REVERT: C 502 TYR cc_start: 0.9118 (m-80) cc_final: 0.8732 (m-10) REVERT: L 145 ARG cc_start: 0.7543 (ptt180) cc_final: 0.6675 (ptt-90) REVERT: H 10 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7166 (mm-30) REVERT: H 32 TYR cc_start: 0.8575 (m-80) cc_final: 0.8082 (m-80) REVERT: H 80 TYR cc_start: 0.8851 (m-80) cc_final: 0.8565 (m-10) REVERT: F 4 MET cc_start: 0.8283 (mmm) cc_final: 0.7553 (mmm) REVERT: F 36 TRP cc_start: 0.8444 (m100) cc_final: 0.8044 (m100) REVERT: F 97 ARG cc_start: 0.8760 (mtp-110) cc_final: 0.8408 (mtp-110) REVERT: F 98 MET cc_start: 0.8659 (mpp) cc_final: 0.8106 (ptp) REVERT: E 48 MET cc_start: 0.8628 (mtp) cc_final: 0.7657 (mtp) REVERT: E 94 TYR cc_start: 0.8608 (m-80) cc_final: 0.8158 (m-80) REVERT: K 97 ARG cc_start: 0.8610 (mmt180) cc_final: 0.8264 (mmp-170) REVERT: K 198 GLU cc_start: 0.9589 (tt0) cc_final: 0.9216 (pt0) REVERT: J 10 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8047 (mm-30) REVERT: J 48 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.7820 (mmm) REVERT: J 67 ARG cc_start: 0.7899 (tpt90) cc_final: 0.6516 (tpt-90) REVERT: J 107 MET cc_start: 0.8405 (mtt) cc_final: 0.8079 (mtt) outliers start: 45 outliers final: 40 residues processed: 221 average time/residue: 0.2545 time to fit residues: 86.6957 Evaluate side-chains 223 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 483 PHE Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 202 ASN Chi-restraints excluded: chain H residue 213 ASP Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain J residue 98 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 10 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 234 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 349 optimal weight: 30.0000 chunk 190 optimal weight: 0.9980 chunk 340 optimal weight: 40.0000 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.113534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.069377 restraints weight = 108204.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.069755 restraints weight = 65052.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.069608 restraints weight = 44267.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.069873 restraints weight = 42849.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.070007 restraints weight = 41016.241| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35158 Z= 0.131 Angle : 0.551 10.103 47999 Z= 0.279 Chirality : 0.044 0.224 5610 Planarity : 0.004 0.083 6065 Dihedral : 4.797 51.657 5963 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.31 % Allowed : 11.70 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.13), residues: 4252 helix: 1.54 (0.20), residues: 741 sheet: 0.20 (0.14), residues: 1376 loop : -0.45 (0.14), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 145 TYR 0.028 0.001 TYR F 176 PHE 0.029 0.001 PHE F 142 TRP 0.031 0.001 TRP B 104 HIS 0.003 0.001 HIS A1045 Details of bonding type rmsd covalent geometry : bond 0.00304 (35040) covalent geometry : angle 0.54504 (47699) SS BOND : bond 0.00199 ( 54) SS BOND : angle 0.77144 ( 108) hydrogen bonds : bond 0.03485 ( 1387) hydrogen bonds : angle 5.13430 ( 3846) link_BETA1-4 : bond 0.00299 ( 19) link_BETA1-4 : angle 1.09390 ( 57) link_BETA1-6 : bond 0.00100 ( 3) link_BETA1-6 : angle 1.56533 ( 9) link_NAG-ASN : bond 0.00184 ( 42) link_NAG-ASN : angle 1.35362 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7765.58 seconds wall clock time: 134 minutes 15.06 seconds (8055.06 seconds total)