Starting phenix.real_space_refine on Fri Mar 6 10:49:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k43_22659/03_2026/7k43_22659.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k43_22659/03_2026/7k43_22659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k43_22659/03_2026/7k43_22659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k43_22659/03_2026/7k43_22659.map" model { file = "/net/cci-nas-00/data/ceres_data/7k43_22659/03_2026/7k43_22659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k43_22659/03_2026/7k43_22659.cif" } resolution = 2.6 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= 0.005 sd= 0.138 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 147 5.16 5 C 19341 2.51 5 N 4956 2.21 5 O 5946 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 219 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30390 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 8019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8019 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 52, 'TRANS': 981} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "H" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 962 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 792 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} 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 Chain: "B" Number of atoms: 8019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8019 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 52, 'TRANS': 981} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 962 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "D" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 792 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} 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 Chain: "E" Number of atoms: 8019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8019 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 52, 'TRANS': 981} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "F" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 962 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "G" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 792 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} 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 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: 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: "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: 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: "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: 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: "a" 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: "b" 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: "c" 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 7.62, per 1000 atoms: 0.25 Number of scatterers: 30390 At special positions: 0 Unit cell: (144.9, 138.6, 185.85, 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 147 16.00 O 5946 8.00 N 4956 7.00 C 19341 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.08 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=1.83 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.15 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.06 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.17 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.08 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=1.83 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.15 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.06 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.17 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.08 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=1.83 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.02 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.15 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.05 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.02 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.04 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.04 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.06 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.04 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.01 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.02 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.17 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " 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 Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " BETA1-6 " NAG K 1 " - " FUC K 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 4 " " NAG Z 1 " - " FUC Z 4 " NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 61 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 165 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG E1301 " - " ASN E 165 " " NAG E1302 " - " ASN E 234 " " NAG E1303 " - " ASN E 61 " " NAG E1304 " - " ASN E 282 " " NAG E1305 " - " ASN E 331 " " NAG E1306 " - " ASN E 603 " " NAG E1307 " - " ASN E 616 " " NAG E1308 " - " ASN E 657 " " NAG E1309 " - " ASN E 709 " " NAG E1310 " - " ASN E1074 " " NAG I 1 " - " ASN A 17 " " NAG J 1 " - " ASN A 122 " " NAG K 1 " - " ASN A 343 " " NAG M 1 " - " ASN A 717 " " NAG N 1 " - " ASN A 801 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 17 " " NAG R 1 " - " ASN B 122 " " NAG S 1 " - " ASN B 343 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN E 17 " " NAG Y 1 " - " ASN E 122 " " NAG Z 1 " - " ASN E 343 " " NAG a 1 " - " ASN E 717 " " NAG b 1 " - " ASN E 801 " " NAG c 1 " - " ASN E1098 " " NAG d 1 " - " ASN E1134 " Time building additional restraints: 3.31 Conformation dependent library (CDL) restraints added in 1.3 seconds 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7044 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 66 sheets defined 23.9% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.773A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.193A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.977A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.828A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.861A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 107 through 111 removed outlier: 3.888A pdb=" N TYR H 111 " --> pdb=" O GLY H 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.773A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.194A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.977A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.828A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.861A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 107 through 111 removed outlier: 3.887A pdb=" N TYR C 111 " --> pdb=" O GLY C 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.772A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 386 through 389 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.194A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'E' and resid 737 through 744 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 850 through 855 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 886 through 890 Processing helix chain 'E' and resid 897 through 909 Processing helix chain 'E' and resid 912 through 919 removed outlier: 3.978A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.828A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.861A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 107 through 111 removed outlier: 3.888A pdb=" N TYR F 111 " --> pdb=" O GLY F 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'G' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.877A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.728A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.510A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 5.387A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 141 removed outlier: 4.142A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.291A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.225A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.776A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.581A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.599A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.823A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.984A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.503A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.039A pdb=" N ILE A 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.731A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.668A pdb=" N GLU H 10 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.668A pdb=" N GLU H 10 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR H 114 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.558A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.558A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.877A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.510A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.387A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 132 through 141 removed outlier: 4.141A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.291A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.225A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE B 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.776A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.581A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.599A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.823A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.985A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.503A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.732A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.669A pdb=" N GLU C 10 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TRP C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.669A pdb=" N GLU C 10 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR C 114 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AE9, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.558A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.558A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 27 through 30 removed outlier: 7.877A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N HIS E 207 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N ALA E 222 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 47 through 55 removed outlier: 3.509A pdb=" N VAL E 47 " --> pdb=" O TYR E 279 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 83 through 85 removed outlier: 5.387A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 132 through 141 removed outlier: 4.141A pdb=" N SER E 162 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N CYS E 136 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TYR E 160 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP E 138 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ARG E 158 " --> pdb=" O ASP E 138 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.291A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.776A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.581A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AG1, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AG2, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.599A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 711 through 713 removed outlier: 3.824A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 718 through 728 removed outlier: 5.984A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.503A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.731A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AG8, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.669A pdb=" N GLU F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TRP F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.669A pdb=" N GLU F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR F 114 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AH2, first strand: chain 'G' and resid 54 through 55 removed outlier: 6.558A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 54 through 55 removed outlier: 6.558A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) 1341 hydrogen bonds defined for protein. 3528 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: 8.77 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5502 1.32 - 1.45: 10265 1.45 - 1.59: 15106 1.59 - 1.73: 30 1.73 - 1.86: 186 Bond restraints: 31089 Sorted by residual: bond pdb=" C CYS A 662 " pdb=" O CYS A 662 " ideal model delta sigma weight residual 1.234 1.348 -0.113 1.20e-02 6.94e+03 8.90e+01 bond pdb=" C CYS E 662 " pdb=" O CYS E 662 " ideal model delta sigma weight residual 1.234 1.348 -0.113 1.20e-02 6.94e+03 8.87e+01 bond pdb=" C CYS B 662 " pdb=" O CYS B 662 " ideal model delta sigma weight residual 1.234 1.347 -0.113 1.20e-02 6.94e+03 8.85e+01 bond pdb=" C ASN B 61 " pdb=" O ASN B 61 " ideal model delta sigma weight residual 1.233 1.336 -0.103 1.28e-02 6.10e+03 6.43e+01 bond pdb=" C ASN E 61 " pdb=" O ASN E 61 " ideal model delta sigma weight residual 1.233 1.336 -0.103 1.28e-02 6.10e+03 6.43e+01 ... (remaining 31084 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.44: 41628 4.44 - 8.89: 666 8.89 - 13.33: 12 13.33 - 17.78: 6 17.78 - 22.22: 3 Bond angle restraints: 42315 Sorted by residual: angle pdb=" CD1 LEU L 34 " pdb=" CG LEU L 34 " pdb=" CD2 LEU L 34 " ideal model delta sigma weight residual 110.80 133.02 -22.22 2.20e+00 2.07e-01 1.02e+02 angle pdb=" CD1 LEU D 34 " pdb=" CG LEU D 34 " pdb=" CD2 LEU D 34 " ideal model delta sigma weight residual 110.80 133.01 -22.21 2.20e+00 2.07e-01 1.02e+02 angle pdb=" CD1 LEU G 34 " pdb=" CG LEU G 34 " pdb=" CD2 LEU G 34 " ideal model delta sigma weight residual 110.80 133.01 -22.21 2.20e+00 2.07e-01 1.02e+02 angle pdb=" N ASN A 165 " pdb=" CA ASN A 165 " pdb=" CB ASN A 165 " ideal model delta sigma weight residual 112.46 128.16 -15.70 1.57e+00 4.06e-01 1.00e+02 angle pdb=" N ASN E 165 " pdb=" CA ASN E 165 " pdb=" CB ASN E 165 " ideal model delta sigma weight residual 112.46 128.15 -15.69 1.57e+00 4.06e-01 9.98e+01 ... (remaining 42310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.94: 18765 21.94 - 43.88: 471 43.88 - 65.81: 96 65.81 - 87.75: 57 87.75 - 109.69: 18 Dihedral angle restraints: 19407 sinusoidal: 8427 harmonic: 10980 Sorted by residual: dihedral pdb=" N ASN E 165 " pdb=" C ASN E 165 " pdb=" CA ASN E 165 " pdb=" CB ASN E 165 " ideal model delta harmonic sigma weight residual 122.80 154.52 -31.72 0 2.50e+00 1.60e-01 1.61e+02 dihedral pdb=" N ASN A 165 " pdb=" C ASN A 165 " pdb=" CA ASN A 165 " pdb=" CB ASN A 165 " ideal model delta harmonic sigma weight residual 122.80 154.51 -31.71 0 2.50e+00 1.60e-01 1.61e+02 dihedral pdb=" N ASN B 165 " pdb=" C ASN B 165 " pdb=" CA ASN B 165 " pdb=" CB ASN B 165 " ideal model delta harmonic sigma weight residual 122.80 154.48 -31.68 0 2.50e+00 1.60e-01 1.61e+02 ... (remaining 19404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.248: 4775 0.248 - 0.496: 193 0.496 - 0.744: 9 0.744 - 0.992: 0 0.992 - 1.240: 3 Chirality restraints: 4980 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.53e+01 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.49e+01 chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.45e+01 ... (remaining 4977 not shown) Planarity restraints: 5403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 106 " 0.038 2.00e-02 2.50e+03 2.21e-02 1.22e+01 pdb=" CG TRP C 106 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP C 106 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 106 " -0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP C 106 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP C 106 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 106 " -0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 106 " 0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 106 " -0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP C 106 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 106 " -0.039 2.00e-02 2.50e+03 2.20e-02 1.22e+01 pdb=" CG TRP F 106 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP F 106 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP F 106 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP F 106 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP F 106 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 106 " 0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 106 " -0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 106 " 0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP F 106 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 106 " -0.038 2.00e-02 2.50e+03 2.20e-02 1.21e+01 pdb=" CG TRP H 106 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP H 106 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP H 106 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP H 106 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP H 106 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP H 106 " 0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 106 " -0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 106 " 0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP H 106 " -0.022 2.00e-02 2.50e+03 ... (remaining 5400 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.94: 14379 2.94 - 3.43: 27078 3.43 - 3.92: 52505 3.92 - 4.41: 60955 4.41 - 4.90: 98482 Nonbonded interactions: 253399 Sorted by model distance: nonbonded pdb=" NZ LYS A1028 " pdb=" O PHE A1042 " model vdw 2.456 3.120 nonbonded pdb=" NZ LYS E1028 " pdb=" O PHE E1042 " model vdw 2.456 3.120 nonbonded pdb=" NZ LYS B1028 " pdb=" O PHE B1042 " model vdw 2.456 3.120 nonbonded pdb=" N PRO B 600 " pdb=" O PRO B 600 " model vdw 2.466 2.496 nonbonded pdb=" N PRO E 600 " pdb=" O PRO E 600 " model vdw 2.466 2.496 ... (remaining 253394 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'K' selection = chain 'S' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.540 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 32.750 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.110 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:7.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 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 : 0.018 0.203 31215 Z= 0.964 Angle : 1.517 22.220 42645 Z= 0.988 Chirality : 0.109 1.240 4980 Planarity : 0.006 0.053 5352 Dihedral : 11.436 109.691 12219 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.07 % Favored : 97.85 % Rotamer: Outliers : 0.09 % Allowed : 1.69 % Favored : 98.22 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 1.61 % 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: 0.34 (0.12), residues: 3723 helix: -0.24 (0.17), residues: 717 sheet: 0.80 (0.14), residues: 1104 loop : 0.21 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E1000 TYR 0.040 0.005 TYR B 495 PHE 0.023 0.004 PHE B 718 TRP 0.039 0.007 TRP F 106 HIS 0.006 0.002 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.01769 (31089) covalent geometry : angle 1.49822 (42315) SS BOND : bond 0.06954 ( 48) SS BOND : angle 3.46562 ( 96) hydrogen bonds : bond 0.15765 ( 1296) hydrogen bonds : angle 8.01886 ( 3528) link_BETA1-4 : bond 0.07611 ( 24) link_BETA1-4 : angle 3.76189 ( 72) link_BETA1-6 : bond 0.04843 ( 3) link_BETA1-6 : angle 3.21265 ( 9) link_NAG-ASN : bond 0.06887 ( 51) link_NAG-ASN : angle 2.42260 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 627 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 755 GLN cc_start: 0.8104 (mt0) cc_final: 0.7838 (mt0) REVERT: A 1041 ASP cc_start: 0.7616 (m-30) cc_final: 0.7357 (m-30) REVERT: H 81 MET cc_start: 0.7215 (tpp) cc_final: 0.6660 (tmm) REVERT: L 73 THR cc_start: 0.8297 (p) cc_final: 0.8091 (t) REVERT: B 535 LYS cc_start: 0.7856 (mtmt) cc_final: 0.7644 (mtmm) REVERT: B 755 GLN cc_start: 0.8226 (mt0) cc_final: 0.7770 (mt0) REVERT: B 1041 ASP cc_start: 0.7665 (m-30) cc_final: 0.7415 (m-30) REVERT: E 535 LYS cc_start: 0.7787 (mtmt) cc_final: 0.7562 (mtmm) REVERT: E 821 LEU cc_start: 0.8833 (mt) cc_final: 0.8521 (mt) REVERT: E 904 TYR cc_start: 0.7372 (m-10) cc_final: 0.7010 (m-10) REVERT: E 1041 ASP cc_start: 0.7703 (m-30) cc_final: 0.7412 (m-30) REVERT: E 1058 HIS cc_start: 0.8310 (m-70) cc_final: 0.8109 (m-70) outliers start: 3 outliers final: 4 residues processed: 627 average time/residue: 0.7073 time to fit residues: 516.2174 Evaluate side-chains 396 residues out of total 3270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 392 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain E residue 1135 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 498 GLN A 779 GLN A 907 ASN A1058 HIS A1071 GLN B 30 ASN B 271 GLN B 498 GLN B 580 GLN B 613 GLN B 779 GLN B 907 ASN B1071 GLN E 30 ASN ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN E 613 GLN E 907 ASN E1071 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.181191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.150041 restraints weight = 31231.390| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.26 r_work: 0.3405 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 31215 Z= 0.167 Angle : 0.664 11.823 42645 Z= 0.344 Chirality : 0.046 0.292 4980 Planarity : 0.005 0.067 5352 Dihedral : 6.910 70.096 5702 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.62 % Allowed : 8.37 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.78 (0.13), residues: 3723 helix: 1.63 (0.20), residues: 663 sheet: 0.86 (0.15), residues: 1059 loop : 0.01 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 319 TYR 0.022 0.002 TYR B 28 PHE 0.020 0.002 PHE C 29 TRP 0.016 0.002 TRP H 106 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00377 (31089) covalent geometry : angle 0.64047 (42315) SS BOND : bond 0.00323 ( 48) SS BOND : angle 0.98177 ( 96) hydrogen bonds : bond 0.05060 ( 1296) hydrogen bonds : angle 6.39496 ( 3528) link_BETA1-4 : bond 0.00685 ( 24) link_BETA1-4 : angle 2.26839 ( 72) link_BETA1-6 : bond 0.00549 ( 3) link_BETA1-6 : angle 1.29833 ( 9) link_NAG-ASN : bond 0.00602 ( 51) link_NAG-ASN : angle 2.48633 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 440 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7953 (mmtp) cc_final: 0.7665 (mptp) REVERT: A 177 MET cc_start: 0.6993 (ttm) cc_final: 0.6479 (ttm) REVERT: A 205 SER cc_start: 0.8600 (p) cc_final: 0.8396 (t) REVERT: A 278 LYS cc_start: 0.8842 (tttt) cc_final: 0.8504 (ttmt) REVERT: A 462 LYS cc_start: 0.8790 (mmtt) cc_final: 0.8512 (mmtp) REVERT: A 471 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7780 (mt-10) REVERT: A 619 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: A 776 LYS cc_start: 0.8717 (tttt) cc_final: 0.8403 (ttpp) REVERT: A 817 PHE cc_start: 0.8322 (t80) cc_final: 0.8016 (t80) REVERT: A 904 TYR cc_start: 0.8252 (m-10) cc_final: 0.8008 (m-10) REVERT: A 921 LYS cc_start: 0.8667 (tmtt) cc_final: 0.7842 (mppt) REVERT: A 995 ARG cc_start: 0.8326 (mtp180) cc_final: 0.7932 (ttp-170) REVERT: A 1041 ASP cc_start: 0.8502 (m-30) cc_final: 0.8240 (m-30) REVERT: A 1123 SER cc_start: 0.8191 (m) cc_final: 0.7860 (m) REVERT: H 113 ASP cc_start: 0.7959 (p0) cc_final: 0.7747 (p0) REVERT: L 73 THR cc_start: 0.8118 (p) cc_final: 0.7905 (t) REVERT: B 40 ASP cc_start: 0.8287 (p0) cc_final: 0.8087 (p0) REVERT: B 205 SER cc_start: 0.8535 (p) cc_final: 0.8256 (t) REVERT: B 556 ASN cc_start: 0.7505 (OUTLIER) cc_final: 0.7175 (m110) REVERT: B 580 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7906 (mp10) REVERT: B 817 PHE cc_start: 0.8253 (t80) cc_final: 0.8034 (t80) REVERT: B 894 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8427 (mt) REVERT: B 936 ASP cc_start: 0.6573 (m-30) cc_final: 0.6366 (t70) REVERT: B 1041 ASP cc_start: 0.8499 (m-30) cc_final: 0.8232 (m-30) REVERT: B 1073 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6925 (mppt) REVERT: C 3 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.6847 (mp10) REVERT: C 10 GLU cc_start: 0.6698 (mm-30) cc_final: 0.6183 (tp30) REVERT: C 81 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7330 (tmm) REVERT: E 168 PHE cc_start: 0.7418 (t80) cc_final: 0.7151 (t80) REVERT: E 427 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7417 (m-30) REVERT: E 702 GLU cc_start: 0.7777 (tt0) cc_final: 0.7427 (tm-30) REVERT: E 780 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7822 (pt0) REVERT: E 791 THR cc_start: 0.7543 (OUTLIER) cc_final: 0.7117 (m) REVERT: E 821 LEU cc_start: 0.8779 (mt) cc_final: 0.8530 (mt) REVERT: E 921 LYS cc_start: 0.8727 (tmtt) cc_final: 0.7895 (mppt) REVERT: E 936 ASP cc_start: 0.6995 (m-30) cc_final: 0.6468 (t70) REVERT: E 1041 ASP cc_start: 0.8602 (m-30) cc_final: 0.8355 (m-30) REVERT: E 1058 HIS cc_start: 0.8765 (m-70) cc_final: 0.8551 (m-70) REVERT: F 81 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.7204 (tmm) REVERT: F 113 ASP cc_start: 0.8064 (p0) cc_final: 0.7792 (p0) REVERT: G 73 THR cc_start: 0.7944 (p) cc_final: 0.7718 (t) outliers start: 84 outliers final: 30 residues processed: 484 average time/residue: 0.6624 time to fit residues: 376.2773 Evaluate side-chains 406 residues out of total 3270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 364 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 477 SER Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 7 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 111 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 351 optimal weight: 0.7980 chunk 358 optimal weight: 0.0670 chunk 324 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 285 optimal weight: 1.9990 chunk 233 optimal weight: 0.9990 chunk 313 optimal weight: 0.6980 chunk 165 optimal weight: 0.3980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 271 GLN A 779 GLN A 935 GLN A1058 HIS B 52 GLN B 115 GLN B 271 GLN B 779 GLN B 804 GLN B 901 GLN E 52 GLN E 81 ASN E 901 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.180858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.148404 restraints weight = 31171.810| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.25 r_work: 0.3398 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31215 Z= 0.142 Angle : 0.584 9.146 42645 Z= 0.302 Chirality : 0.044 0.212 4980 Planarity : 0.004 0.051 5352 Dihedral : 5.424 54.709 5696 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.78 % Allowed : 10.47 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.81 (0.13), residues: 3723 helix: 1.57 (0.19), residues: 723 sheet: 1.00 (0.15), residues: 1083 loop : -0.08 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 78 TYR 0.028 0.001 TYR E 28 PHE 0.016 0.002 PHE C 29 TRP 0.016 0.002 TRP F 106 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00319 (31089) covalent geometry : angle 0.56711 (42315) SS BOND : bond 0.00287 ( 48) SS BOND : angle 1.19197 ( 96) hydrogen bonds : bond 0.04531 ( 1296) hydrogen bonds : angle 5.89155 ( 3528) link_BETA1-4 : bond 0.00711 ( 24) link_BETA1-4 : angle 1.71429 ( 72) link_BETA1-6 : bond 0.00319 ( 3) link_BETA1-6 : angle 1.30997 ( 9) link_NAG-ASN : bond 0.00398 ( 51) link_NAG-ASN : angle 1.93112 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 413 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8234 (mtt-85) cc_final: 0.8032 (mtt-85) REVERT: A 41 LYS cc_start: 0.8104 (mmtp) cc_final: 0.7776 (mmmt) REVERT: A 177 MET cc_start: 0.6971 (ttm) cc_final: 0.6588 (ttm) REVERT: A 191 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7853 (mt-10) REVERT: A 278 LYS cc_start: 0.8787 (tttt) cc_final: 0.8461 (ttmt) REVERT: A 462 LYS cc_start: 0.8794 (mmtt) cc_final: 0.8522 (mmtp) REVERT: A 466 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7446 (mtp180) REVERT: A 471 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: A 619 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: A 725 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7916 (tm-30) REVERT: A 776 LYS cc_start: 0.8693 (tttt) cc_final: 0.8320 (ttpp) REVERT: A 817 PHE cc_start: 0.8348 (t80) cc_final: 0.8066 (t80) REVERT: A 921 LYS cc_start: 0.8625 (tmtt) cc_final: 0.7862 (mppt) REVERT: A 935 GLN cc_start: 0.7848 (tt0) cc_final: 0.7558 (tt0) REVERT: A 995 ARG cc_start: 0.8394 (mtp180) cc_final: 0.7978 (ttp-170) REVERT: A 1041 ASP cc_start: 0.8546 (m-30) cc_final: 0.8318 (m-30) REVERT: A 1058 HIS cc_start: 0.8746 (m-70) cc_final: 0.8529 (m170) REVERT: A 1113 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.8066 (mt0) REVERT: A 1123 SER cc_start: 0.8074 (m) cc_final: 0.7747 (m) REVERT: H 98 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.7769 (ttt180) REVERT: L 104 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7338 (tptt) REVERT: B 478 THR cc_start: 0.8053 (m) cc_final: 0.7781 (t) REVERT: B 556 ASN cc_start: 0.7563 (OUTLIER) cc_final: 0.7223 (m110) REVERT: B 580 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7772 (mp10) REVERT: B 646 ARG cc_start: 0.7788 (tmt170) cc_final: 0.7425 (tmt170) REVERT: B 755 GLN cc_start: 0.8322 (mt0) cc_final: 0.7991 (mt0) REVERT: B 814 LYS cc_start: 0.5837 (mmtm) cc_final: 0.5346 (mtpm) REVERT: B 1041 ASP cc_start: 0.8523 (m-30) cc_final: 0.8269 (m-30) REVERT: B 1073 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7251 (mppt) REVERT: C 3 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.6824 (mp10) REVERT: C 10 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6215 (tp30) REVERT: C 81 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7393 (tmm) REVERT: D 27 GLN cc_start: 0.7256 (mt0) cc_final: 0.6853 (pt0) REVERT: E 177 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6811 (ttm) REVERT: E 427 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7423 (m-30) REVERT: E 591 SER cc_start: 0.7849 (m) cc_final: 0.7509 (p) REVERT: E 702 GLU cc_start: 0.7687 (tt0) cc_final: 0.7359 (tm-30) REVERT: E 776 LYS cc_start: 0.8694 (tttt) cc_final: 0.8403 (ttpp) REVERT: E 780 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7882 (pt0) REVERT: E 821 LEU cc_start: 0.8787 (mt) cc_final: 0.8566 (mt) REVERT: E 921 LYS cc_start: 0.8702 (tmtt) cc_final: 0.7901 (mppt) REVERT: E 936 ASP cc_start: 0.7043 (m-30) cc_final: 0.6605 (t70) REVERT: E 1041 ASP cc_start: 0.8687 (m-30) cc_final: 0.8448 (m-30) REVERT: E 1058 HIS cc_start: 0.8810 (m-70) cc_final: 0.8578 (m-70) REVERT: F 70 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7482 (mtt) REVERT: F 81 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7412 (tmm) REVERT: F 113 ASP cc_start: 0.7979 (p0) cc_final: 0.7758 (p0) REVERT: G 27 GLN cc_start: 0.7209 (mt0) cc_final: 0.6947 (pt0) REVERT: G 78 ARG cc_start: 0.6853 (mtp85) cc_final: 0.6274 (ppt-90) outliers start: 89 outliers final: 31 residues processed: 466 average time/residue: 0.6702 time to fit residues: 366.7941 Evaluate side-chains 417 residues out of total 3270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 369 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 477 SER Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 586 ASP Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 865 LEU Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 7 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 242 optimal weight: 3.9990 chunk 331 optimal weight: 0.6980 chunk 212 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 294 optimal weight: 0.0570 chunk 315 optimal weight: 0.8980 chunk 325 optimal weight: 0.6980 chunk 240 optimal weight: 1.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 314 GLN A 779 GLN A 901 GLN B 81 ASN B 188 ASN B 271 GLN B 501 ASN B 779 GLN B 955 ASN E 804 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.173121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.147697 restraints weight = 30883.496| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.62 r_work: 0.3281 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31215 Z= 0.135 Angle : 0.548 7.143 42645 Z= 0.282 Chirality : 0.043 0.212 4980 Planarity : 0.004 0.045 5352 Dihedral : 4.726 50.864 5694 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.09 % Allowed : 10.87 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.84 (0.13), residues: 3723 helix: 1.89 (0.20), residues: 690 sheet: 0.97 (0.15), residues: 1059 loop : -0.11 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 346 TYR 0.021 0.001 TYR E 28 PHE 0.014 0.001 PHE C 29 TRP 0.015 0.002 TRP C 106 HIS 0.003 0.001 HIS E1083 Details of bonding type rmsd covalent geometry : bond 0.00307 (31089) covalent geometry : angle 0.53287 (42315) SS BOND : bond 0.00263 ( 48) SS BOND : angle 0.92320 ( 96) hydrogen bonds : bond 0.04284 ( 1296) hydrogen bonds : angle 5.68583 ( 3528) link_BETA1-4 : bond 0.00564 ( 24) link_BETA1-4 : angle 1.62514 ( 72) link_BETA1-6 : bond 0.00255 ( 3) link_BETA1-6 : angle 1.30497 ( 9) link_NAG-ASN : bond 0.00291 ( 51) link_NAG-ASN : angle 1.83372 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 396 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7042 (ttm) cc_final: 0.6661 (ttm) REVERT: A 466 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7092 (mtp180) REVERT: A 619 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: A 725 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: A 776 LYS cc_start: 0.8743 (tttt) cc_final: 0.8541 (ttpp) REVERT: A 817 PHE cc_start: 0.8444 (t80) cc_final: 0.8235 (t80) REVERT: A 921 LYS cc_start: 0.8720 (tmtt) cc_final: 0.8162 (mppt) REVERT: A 995 ARG cc_start: 0.8523 (mtp180) cc_final: 0.8210 (ttp-170) REVERT: A 1041 ASP cc_start: 0.8443 (m-30) cc_final: 0.8217 (m-30) REVERT: A 1113 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8127 (mt0) REVERT: A 1123 SER cc_start: 0.8073 (m) cc_final: 0.7807 (m) REVERT: H 98 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.7776 (ttt180) REVERT: L 34 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8481 (tm) REVERT: L 64 SER cc_start: 0.7727 (p) cc_final: 0.7357 (t) REVERT: L 104 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7557 (tptt) REVERT: B 121 ASN cc_start: 0.7972 (t0) cc_final: 0.7722 (t0) REVERT: B 177 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6654 (tmm) REVERT: B 556 ASN cc_start: 0.7717 (OUTLIER) cc_final: 0.7383 (m110) REVERT: B 646 ARG cc_start: 0.8055 (tmt170) cc_final: 0.7739 (tmt170) REVERT: B 755 GLN cc_start: 0.8402 (mt0) cc_final: 0.8058 (mt0) REVERT: B 817 PHE cc_start: 0.8378 (t80) cc_final: 0.8067 (t80) REVERT: B 1041 ASP cc_start: 0.8313 (m-30) cc_final: 0.8071 (m-30) REVERT: B 1091 ARG cc_start: 0.8034 (mtt180) cc_final: 0.7826 (mtt90) REVERT: C 3 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.6935 (mp10) REVERT: C 10 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6486 (tp30) REVERT: C 81 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7433 (tmm) REVERT: D 27 GLN cc_start: 0.7404 (mt0) cc_final: 0.7114 (pt0) REVERT: E 168 PHE cc_start: 0.7563 (t80) cc_final: 0.7230 (t80) REVERT: E 177 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6952 (ttm) REVERT: E 428 ASP cc_start: 0.8000 (p0) cc_final: 0.7767 (p0) REVERT: E 591 SER cc_start: 0.7985 (m) cc_final: 0.7755 (p) REVERT: E 702 GLU cc_start: 0.7769 (tt0) cc_final: 0.7312 (tm-30) REVERT: E 780 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8058 (pt0) REVERT: E 821 LEU cc_start: 0.9001 (mt) cc_final: 0.8780 (mt) REVERT: E 921 LYS cc_start: 0.8788 (tmtt) cc_final: 0.8180 (mppt) REVERT: E 936 ASP cc_start: 0.7350 (m-30) cc_final: 0.6979 (t70) REVERT: E 1041 ASP cc_start: 0.8572 (m-30) cc_final: 0.8339 (m-30) REVERT: F 70 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7407 (mtt) REVERT: F 81 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7382 (tmm) REVERT: F 113 ASP cc_start: 0.7828 (p0) cc_final: 0.7621 (p0) REVERT: G 27 GLN cc_start: 0.7347 (mt0) cc_final: 0.7069 (pt0) REVERT: G 34 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8466 (tm) REVERT: G 78 ARG cc_start: 0.6848 (mtp85) cc_final: 0.6267 (ttp80) outliers start: 99 outliers final: 49 residues processed: 459 average time/residue: 0.6602 time to fit residues: 356.5573 Evaluate side-chains 424 residues out of total 3270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 359 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 477 SER Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 586 ASP Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 865 LEU Chi-restraints excluded: chain E residue 918 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 86 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 105 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 142 optimal weight: 0.4980 chunk 360 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 346 optimal weight: 2.9990 chunk 229 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 271 GLN A 314 GLN A 907 ASN A1058 HIS B 271 GLN B 501 ASN B 779 GLN B 804 GLN ** E 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1058 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.172244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.140953 restraints weight = 30728.668| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.86 r_work: 0.3280 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31215 Z= 0.148 Angle : 0.554 7.049 42645 Z= 0.284 Chirality : 0.043 0.217 4980 Planarity : 0.004 0.049 5352 Dihedral : 4.600 43.892 5694 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.28 % Allowed : 11.59 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.78 (0.13), residues: 3723 helix: 1.96 (0.20), residues: 690 sheet: 0.92 (0.15), residues: 1056 loop : -0.19 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 346 TYR 0.022 0.001 TYR E 28 PHE 0.022 0.001 PHE A 592 TRP 0.016 0.002 TRP C 106 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00344 (31089) covalent geometry : angle 0.53961 (42315) SS BOND : bond 0.00269 ( 48) SS BOND : angle 0.82041 ( 96) hydrogen bonds : bond 0.04315 ( 1296) hydrogen bonds : angle 5.64100 ( 3528) link_BETA1-4 : bond 0.00581 ( 24) link_BETA1-4 : angle 1.50740 ( 72) link_BETA1-6 : bond 0.00248 ( 3) link_BETA1-6 : angle 1.28923 ( 9) link_NAG-ASN : bond 0.00278 ( 51) link_NAG-ASN : angle 1.82174 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 378 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7005 (ttm) cc_final: 0.6764 (tpp) REVERT: A 466 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7269 (mtp180) REVERT: A 619 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: A 725 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7836 (tm-30) REVERT: A 776 LYS cc_start: 0.8720 (tttt) cc_final: 0.8479 (ttpp) REVERT: A 921 LYS cc_start: 0.8663 (tmtt) cc_final: 0.8098 (mppt) REVERT: A 995 ARG cc_start: 0.8432 (mtp180) cc_final: 0.8152 (ttp-170) REVERT: A 1038 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7753 (mmtt) REVERT: A 1041 ASP cc_start: 0.8379 (m-30) cc_final: 0.8158 (m-30) REVERT: A 1113 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8119 (mt0) REVERT: A 1123 SER cc_start: 0.8087 (m) cc_final: 0.7788 (m) REVERT: H 10 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6526 (mm-30) REVERT: H 82 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7685 (tp30) REVERT: L 34 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8404 (tm) REVERT: L 64 SER cc_start: 0.7686 (p) cc_final: 0.7289 (t) REVERT: L 78 ARG cc_start: 0.7093 (ppt170) cc_final: 0.6630 (pmt-80) REVERT: B 556 ASN cc_start: 0.7663 (OUTLIER) cc_final: 0.7331 (m110) REVERT: B 568 ASP cc_start: 0.6774 (OUTLIER) cc_final: 0.6562 (p0) REVERT: B 646 ARG cc_start: 0.7960 (tmt170) cc_final: 0.7612 (tmt170) REVERT: B 755 GLN cc_start: 0.8400 (mt0) cc_final: 0.8061 (mt0) REVERT: B 1041 ASP cc_start: 0.8238 (m-30) cc_final: 0.8000 (m-30) REVERT: C 3 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.6968 (mp10) REVERT: C 10 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6382 (tp30) REVERT: C 81 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7436 (tmm) REVERT: D 27 GLN cc_start: 0.7324 (mt0) cc_final: 0.7003 (pt0) REVERT: E 177 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.7080 (ttm) REVERT: E 537 LYS cc_start: 0.7679 (ttmt) cc_final: 0.6897 (mmtm) REVERT: E 603 ASN cc_start: 0.7608 (OUTLIER) cc_final: 0.7380 (t0) REVERT: E 646 ARG cc_start: 0.7710 (tmt170) cc_final: 0.7474 (tpt-90) REVERT: E 702 GLU cc_start: 0.7725 (tt0) cc_final: 0.7356 (tm-30) REVERT: E 780 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8034 (pt0) REVERT: E 821 LEU cc_start: 0.8918 (mt) cc_final: 0.8710 (mt) REVERT: E 921 LYS cc_start: 0.8736 (tmtt) cc_final: 0.8114 (mppt) REVERT: E 936 ASP cc_start: 0.7167 (m-30) cc_final: 0.6789 (t70) REVERT: E 1041 ASP cc_start: 0.8569 (m-30) cc_final: 0.8336 (m-30) REVERT: F 70 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7431 (mtt) REVERT: F 81 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7418 (tmm) REVERT: G 27 GLN cc_start: 0.7293 (mt0) cc_final: 0.7002 (pt0) REVERT: G 34 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8457 (tm) REVERT: G 78 ARG cc_start: 0.6816 (mtp85) cc_final: 0.6549 (ppt170) outliers start: 105 outliers final: 56 residues processed: 447 average time/residue: 0.6850 time to fit residues: 364.1518 Evaluate side-chains 428 residues out of total 3270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 355 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 477 SER Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 556 ASN Chi-restraints excluded: chain E residue 586 ASP Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 865 LEU Chi-restraints excluded: chain E residue 918 GLU Chi-restraints excluded: chain E residue 967 SER Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 86 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 171 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 357 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 178 optimal weight: 0.8980 chunk 239 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 chunk 264 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 314 GLN A 804 GLN A1058 HIS B 271 GLN B 501 ASN B 779 GLN B 804 GLN E 81 ASN E1058 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.171681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.145452 restraints weight = 30833.416| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.73 r_work: 0.3259 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 31215 Z= 0.156 Angle : 0.561 11.217 42645 Z= 0.287 Chirality : 0.043 0.220 4980 Planarity : 0.004 0.053 5352 Dihedral : 4.582 36.318 5694 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.56 % Allowed : 11.72 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.68 (0.13), residues: 3723 helix: 1.91 (0.20), residues: 690 sheet: 0.86 (0.15), residues: 1038 loop : -0.26 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 319 TYR 0.025 0.001 TYR A 28 PHE 0.024 0.001 PHE B 592 TRP 0.017 0.002 TRP C 106 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00363 (31089) covalent geometry : angle 0.54506 (42315) SS BOND : bond 0.00284 ( 48) SS BOND : angle 1.44316 ( 96) hydrogen bonds : bond 0.04352 ( 1296) hydrogen bonds : angle 5.64651 ( 3528) link_BETA1-4 : bond 0.00548 ( 24) link_BETA1-4 : angle 1.47809 ( 72) link_BETA1-6 : bond 0.00224 ( 3) link_BETA1-6 : angle 1.27686 ( 9) link_NAG-ASN : bond 0.00315 ( 51) link_NAG-ASN : angle 1.78467 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 368 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7022 (ttm) cc_final: 0.6792 (tpp) REVERT: A 466 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7286 (mtp180) REVERT: A 580 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.6186 (mp10) REVERT: A 619 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: A 725 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: A 776 LYS cc_start: 0.8771 (tttt) cc_final: 0.8548 (ttpp) REVERT: A 921 LYS cc_start: 0.8714 (tmtt) cc_final: 0.8160 (mppt) REVERT: A 995 ARG cc_start: 0.8478 (mtp180) cc_final: 0.8193 (ttp-170) REVERT: A 1038 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7761 (mmtt) REVERT: A 1041 ASP cc_start: 0.8419 (m-30) cc_final: 0.8208 (m-30) REVERT: A 1113 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8156 (mm-40) REVERT: A 1123 SER cc_start: 0.8093 (m) cc_final: 0.7814 (m) REVERT: H 10 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6593 (mm-30) REVERT: H 82 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7743 (tp30) REVERT: L 4 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6454 (ttm) REVERT: L 64 SER cc_start: 0.7697 (p) cc_final: 0.7335 (t) REVERT: B 129 LYS cc_start: 0.8061 (mtpp) cc_final: 0.7796 (ttpp) REVERT: B 556 ASN cc_start: 0.7683 (OUTLIER) cc_final: 0.7354 (m110) REVERT: B 646 ARG cc_start: 0.8016 (tmt170) cc_final: 0.7665 (tmt170) REVERT: B 755 GLN cc_start: 0.8415 (mt0) cc_final: 0.8083 (mt0) REVERT: B 1041 ASP cc_start: 0.8250 (m-30) cc_final: 0.7942 (m-30) REVERT: C 3 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7014 (mp10) REVERT: C 10 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6454 (tp30) REVERT: C 81 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7442 (tmm) REVERT: D 27 GLN cc_start: 0.7453 (mt0) cc_final: 0.7175 (pt0) REVERT: E 157 PHE cc_start: 0.6671 (t80) cc_final: 0.6396 (t80) REVERT: E 177 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.7159 (ttm) REVERT: E 466 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7976 (mtp-110) REVERT: E 537 LYS cc_start: 0.7798 (ttmt) cc_final: 0.7064 (mmtm) REVERT: E 603 ASN cc_start: 0.7605 (OUTLIER) cc_final: 0.7389 (t0) REVERT: E 702 GLU cc_start: 0.7829 (tt0) cc_final: 0.7350 (tm-30) REVERT: E 780 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8078 (pt0) REVERT: E 821 LEU cc_start: 0.8967 (mt) cc_final: 0.8764 (mt) REVERT: E 921 LYS cc_start: 0.8773 (tmtt) cc_final: 0.8187 (mppt) REVERT: E 936 ASP cc_start: 0.7314 (m-30) cc_final: 0.6916 (t70) REVERT: E 990 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7469 (tt0) REVERT: E 1041 ASP cc_start: 0.8563 (m-30) cc_final: 0.8346 (m-30) REVERT: F 70 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7474 (mtt) REVERT: F 81 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7446 (tmm) REVERT: G 27 GLN cc_start: 0.7364 (mt0) cc_final: 0.7085 (pt0) REVERT: G 34 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8489 (tm) REVERT: G 78 ARG cc_start: 0.7059 (mtp85) cc_final: 0.6735 (ttp80) outliers start: 114 outliers final: 66 residues processed: 447 average time/residue: 0.6424 time to fit residues: 340.2493 Evaluate side-chains 439 residues out of total 3270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 355 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 466 ARG Chi-restraints excluded: chain E residue 477 SER Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 556 ASN Chi-restraints excluded: chain E residue 586 ASP Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 658 ASN Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 750 SER Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 918 GLU Chi-restraints excluded: chain E residue 967 SER Chi-restraints excluded: chain E residue 1123 SER Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 86 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 49 optimal weight: 2.9990 chunk 241 optimal weight: 6.9990 chunk 309 optimal weight: 0.0470 chunk 170 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 237 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 340 optimal weight: 0.5980 chunk 305 optimal weight: 0.0970 chunk 31 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 188 ASN A 314 GLN B 115 GLN B 271 GLN B 501 ASN ** E 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.173043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.141895 restraints weight = 30947.577| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.88 r_work: 0.3295 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31215 Z= 0.117 Angle : 0.532 6.616 42645 Z= 0.271 Chirality : 0.042 0.211 4980 Planarity : 0.004 0.051 5352 Dihedral : 4.337 28.556 5694 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.75 % Allowed : 12.90 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.72 (0.13), residues: 3723 helix: 2.01 (0.20), residues: 708 sheet: 0.87 (0.16), residues: 1005 loop : -0.26 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 346 TYR 0.025 0.001 TYR A 28 PHE 0.027 0.001 PHE A 592 TRP 0.016 0.001 TRP F 106 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00267 (31089) covalent geometry : angle 0.51804 (42315) SS BOND : bond 0.00226 ( 48) SS BOND : angle 0.78224 ( 96) hydrogen bonds : bond 0.04005 ( 1296) hydrogen bonds : angle 5.51179 ( 3528) link_BETA1-4 : bond 0.00568 ( 24) link_BETA1-4 : angle 1.42796 ( 72) link_BETA1-6 : bond 0.00242 ( 3) link_BETA1-6 : angle 1.30455 ( 9) link_NAG-ASN : bond 0.00276 ( 51) link_NAG-ASN : angle 1.76328 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 385 time to evaluate : 1.049 Fit side-chains REVERT: A 177 MET cc_start: 0.6896 (ttm) cc_final: 0.6663 (tpp) REVERT: A 466 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7290 (mtp180) REVERT: A 580 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8052 (mp10) REVERT: A 646 ARG cc_start: 0.7880 (tmt170) cc_final: 0.7515 (mtt180) REVERT: A 725 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7848 (tm-30) REVERT: A 776 LYS cc_start: 0.8687 (tttt) cc_final: 0.8453 (ttpp) REVERT: A 921 LYS cc_start: 0.8680 (tmtt) cc_final: 0.8126 (mppt) REVERT: A 995 ARG cc_start: 0.8414 (mtp180) cc_final: 0.8133 (ttp-170) REVERT: A 1038 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7862 (mmtt) REVERT: A 1041 ASP cc_start: 0.8375 (m-30) cc_final: 0.8154 (m-30) REVERT: A 1113 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8174 (mt0) REVERT: A 1123 SER cc_start: 0.8074 (m) cc_final: 0.7805 (m) REVERT: H 10 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6522 (mm-30) REVERT: L 4 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6410 (ttm) REVERT: L 27 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7216 (pm20) REVERT: L 78 ARG cc_start: 0.7024 (ppt170) cc_final: 0.6267 (ttp-110) REVERT: B 129 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7833 (ttpp) REVERT: B 556 ASN cc_start: 0.7682 (OUTLIER) cc_final: 0.7357 (m110) REVERT: B 603 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7617 (t160) REVERT: B 646 ARG cc_start: 0.7934 (tmt170) cc_final: 0.7579 (tmt170) REVERT: B 755 GLN cc_start: 0.8323 (mt0) cc_final: 0.8030 (mt0) REVERT: B 817 PHE cc_start: 0.8266 (t80) cc_final: 0.7952 (t80) REVERT: B 1041 ASP cc_start: 0.8224 (m-30) cc_final: 0.7923 (m-30) REVERT: C 3 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.6921 (mp10) REVERT: C 10 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6342 (tp30) REVERT: C 81 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7443 (tmm) REVERT: D 27 GLN cc_start: 0.7448 (mt0) cc_final: 0.7099 (pt0) REVERT: D 62 ARG cc_start: 0.7183 (ptp90) cc_final: 0.6778 (ttp80) REVERT: E 177 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.7101 (ttm) REVERT: E 191 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7850 (mm-30) REVERT: E 466 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.8005 (mtp180) REVERT: E 702 GLU cc_start: 0.7807 (tt0) cc_final: 0.7314 (tm-30) REVERT: E 780 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7996 (pt0) REVERT: E 921 LYS cc_start: 0.8714 (tmtt) cc_final: 0.8099 (mppt) REVERT: E 936 ASP cc_start: 0.7191 (m-30) cc_final: 0.6790 (t70) REVERT: E 990 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7418 (tt0) REVERT: E 1041 ASP cc_start: 0.8548 (m-30) cc_final: 0.8314 (m-30) REVERT: E 1091 ARG cc_start: 0.8114 (mtm-85) cc_final: 0.7898 (mtm-85) REVERT: E 1123 SER cc_start: 0.8148 (m) cc_final: 0.7899 (m) REVERT: F 70 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7432 (mtt) REVERT: F 81 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7272 (tmm) REVERT: G 27 GLN cc_start: 0.7301 (mt0) cc_final: 0.6961 (pt0) REVERT: G 34 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8465 (tm) REVERT: G 78 ARG cc_start: 0.6992 (mtp85) cc_final: 0.6679 (ttp80) outliers start: 88 outliers final: 54 residues processed: 446 average time/residue: 0.6233 time to fit residues: 329.2670 Evaluate side-chains 422 residues out of total 3270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 351 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 466 ARG Chi-restraints excluded: chain E residue 477 SER Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 556 ASN Chi-restraints excluded: chain E residue 586 ASP Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 750 SER Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 967 SER Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 86 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 95 optimal weight: 0.9990 chunk 349 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 205 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 314 GLN A1058 HIS B 271 GLN B 501 ASN B 804 GLN E 81 ASN E 188 ASN E 271 GLN E 501 ASN ** E 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1058 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.171833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.146074 restraints weight = 30836.142| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.68 r_work: 0.3263 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31215 Z= 0.155 Angle : 0.558 6.573 42645 Z= 0.285 Chirality : 0.043 0.261 4980 Planarity : 0.004 0.064 5352 Dihedral : 4.394 29.673 5694 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.94 % Allowed : 13.25 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.13), residues: 3723 helix: 2.01 (0.20), residues: 690 sheet: 0.88 (0.16), residues: 1005 loop : -0.30 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 319 TYR 0.016 0.001 TYR L 92 PHE 0.026 0.001 PHE B 592 TRP 0.016 0.002 TRP H 106 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00363 (31089) covalent geometry : angle 0.54424 (42315) SS BOND : bond 0.00265 ( 48) SS BOND : angle 0.80389 ( 96) hydrogen bonds : bond 0.04295 ( 1296) hydrogen bonds : angle 5.57753 ( 3528) link_BETA1-4 : bond 0.00556 ( 24) link_BETA1-4 : angle 1.42396 ( 72) link_BETA1-6 : bond 0.00241 ( 3) link_BETA1-6 : angle 1.29206 ( 9) link_NAG-ASN : bond 0.00279 ( 51) link_NAG-ASN : angle 1.83623 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 363 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 177 MET cc_start: 0.6937 (ttm) cc_final: 0.6696 (tpp) REVERT: A 466 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7242 (mtp180) REVERT: A 580 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8119 (mp10) REVERT: A 646 ARG cc_start: 0.7983 (tmt170) cc_final: 0.7616 (mtt180) REVERT: A 725 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7906 (tm-30) REVERT: A 776 LYS cc_start: 0.8783 (tttt) cc_final: 0.8562 (ttpp) REVERT: A 921 LYS cc_start: 0.8737 (tmtt) cc_final: 0.8205 (mppt) REVERT: A 995 ARG cc_start: 0.8475 (mtp180) cc_final: 0.8193 (ttp-170) REVERT: A 1038 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7881 (mmtt) REVERT: A 1041 ASP cc_start: 0.8411 (m-30) cc_final: 0.8202 (m-30) REVERT: A 1113 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8153 (mm-40) REVERT: A 1123 SER cc_start: 0.8091 (m) cc_final: 0.7810 (m) REVERT: H 10 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6623 (mm-30) REVERT: L 27 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.7182 (pm20) REVERT: B 556 ASN cc_start: 0.7748 (OUTLIER) cc_final: 0.7416 (m110) REVERT: B 603 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7715 (t160) REVERT: B 646 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7673 (tmt170) REVERT: B 755 GLN cc_start: 0.8408 (mt0) cc_final: 0.8081 (mt0) REVERT: B 1041 ASP cc_start: 0.8235 (m-30) cc_final: 0.7936 (m-30) REVERT: C 3 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7024 (mp10) REVERT: C 10 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6475 (tp30) REVERT: C 81 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7524 (tmm) REVERT: D 27 GLN cc_start: 0.7482 (mt0) cc_final: 0.7125 (pt0) REVERT: E 157 PHE cc_start: 0.6706 (t80) cc_final: 0.6383 (t80) REVERT: E 466 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.8006 (mtp180) REVERT: E 537 LYS cc_start: 0.7763 (ttmt) cc_final: 0.7033 (mmtm) REVERT: E 702 GLU cc_start: 0.7834 (tt0) cc_final: 0.7345 (tm-30) REVERT: E 780 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8063 (pt0) REVERT: E 918 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: E 921 LYS cc_start: 0.8767 (tmtt) cc_final: 0.8184 (mppt) REVERT: E 936 ASP cc_start: 0.7255 (m-30) cc_final: 0.6860 (t70) REVERT: E 990 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7391 (tt0) REVERT: F 70 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7487 (mtt) REVERT: F 81 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7453 (tmm) REVERT: G 27 GLN cc_start: 0.7302 (mt0) cc_final: 0.6999 (pt0) REVERT: G 34 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8507 (tm) outliers start: 94 outliers final: 60 residues processed: 428 average time/residue: 0.5991 time to fit residues: 304.7422 Evaluate side-chains 424 residues out of total 3270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 347 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 466 ARG Chi-restraints excluded: chain E residue 477 SER Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 556 ASN Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 750 SER Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 918 GLU Chi-restraints excluded: chain E residue 967 SER Chi-restraints excluded: chain E residue 1123 SER Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 86 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 5.9990 chunk 112 optimal weight: 0.0670 chunk 120 optimal weight: 3.9990 chunk 297 optimal weight: 0.0000 chunk 178 optimal weight: 0.8980 chunk 201 optimal weight: 1.9990 chunk 360 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 333 optimal weight: 5.9990 chunk 213 optimal weight: 0.6980 overall best weight: 0.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 314 GLN A1071 GLN B 271 GLN B 501 ASN E 501 ASN ** E 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.172781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.141799 restraints weight = 30867.331| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.91 r_work: 0.3291 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31215 Z= 0.124 Angle : 0.536 6.882 42645 Z= 0.274 Chirality : 0.043 0.294 4980 Planarity : 0.004 0.061 5352 Dihedral : 4.264 28.853 5694 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.87 % Allowed : 13.50 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.69 (0.13), residues: 3723 helix: 1.99 (0.20), residues: 711 sheet: 0.85 (0.16), residues: 1005 loop : -0.28 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 319 TYR 0.016 0.001 TYR A1067 PHE 0.030 0.001 PHE A 592 TRP 0.019 0.001 TRP E 64 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00284 (31089) covalent geometry : angle 0.52294 (42315) SS BOND : bond 0.00226 ( 48) SS BOND : angle 0.74625 ( 96) hydrogen bonds : bond 0.04024 ( 1296) hydrogen bonds : angle 5.48133 ( 3528) link_BETA1-4 : bond 0.00561 ( 24) link_BETA1-4 : angle 1.37647 ( 72) link_BETA1-6 : bond 0.00241 ( 3) link_BETA1-6 : angle 1.30528 ( 9) link_NAG-ASN : bond 0.00251 ( 51) link_NAG-ASN : angle 1.77382 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 356 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 177 MET cc_start: 0.6890 (ttm) cc_final: 0.6639 (tpp) REVERT: A 466 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7318 (mtp180) REVERT: A 580 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8068 (mp10) REVERT: A 646 ARG cc_start: 0.8021 (tmt170) cc_final: 0.7534 (mtt180) REVERT: A 725 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7862 (tm-30) REVERT: A 776 LYS cc_start: 0.8695 (tttt) cc_final: 0.8461 (ttpp) REVERT: A 921 LYS cc_start: 0.8681 (tmtt) cc_final: 0.8131 (mppt) REVERT: A 995 ARG cc_start: 0.8411 (mtp180) cc_final: 0.8121 (ttp-170) REVERT: A 1038 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7863 (mmtt) REVERT: A 1041 ASP cc_start: 0.8362 (m-30) cc_final: 0.8155 (m-30) REVERT: A 1113 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8160 (mm-40) REVERT: A 1123 SER cc_start: 0.8087 (m) cc_final: 0.7802 (m) REVERT: H 10 GLU cc_start: 0.6846 (mm-30) cc_final: 0.6531 (mm-30) REVERT: L 4 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6544 (ttm) REVERT: L 27 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.7170 (pm20) REVERT: B 556 ASN cc_start: 0.7705 (OUTLIER) cc_final: 0.7374 (m110) REVERT: B 603 ASN cc_start: 0.7856 (OUTLIER) cc_final: 0.7578 (t160) REVERT: B 646 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7593 (tmt170) REVERT: B 755 GLN cc_start: 0.8393 (mt0) cc_final: 0.8061 (mt0) REVERT: B 817 PHE cc_start: 0.8211 (t80) cc_final: 0.7948 (t80) REVERT: B 1041 ASP cc_start: 0.8202 (m-30) cc_final: 0.7902 (m-30) REVERT: C 3 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.6940 (mp10) REVERT: C 10 GLU cc_start: 0.6963 (mm-30) cc_final: 0.6370 (tp30) REVERT: C 70 MET cc_start: 0.8329 (mtm) cc_final: 0.7902 (mtm) REVERT: C 81 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7452 (tmm) REVERT: D 27 GLN cc_start: 0.7450 (mt0) cc_final: 0.7082 (pt0) REVERT: D 78 ARG cc_start: 0.6453 (ppt170) cc_final: 0.6249 (ppt90) REVERT: E 157 PHE cc_start: 0.6665 (t80) cc_final: 0.6321 (t80) REVERT: E 466 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.8022 (mtp180) REVERT: E 702 GLU cc_start: 0.7803 (tt0) cc_final: 0.7314 (tm-30) REVERT: E 780 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7994 (pt0) REVERT: E 918 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7385 (mt-10) REVERT: E 921 LYS cc_start: 0.8715 (tmtt) cc_final: 0.8108 (mppt) REVERT: E 936 ASP cc_start: 0.7126 (m-30) cc_final: 0.6767 (t70) REVERT: E 983 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7607 (ttm170) REVERT: E 1123 SER cc_start: 0.8128 (OUTLIER) cc_final: 0.7877 (m) REVERT: F 70 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7442 (mtt) REVERT: F 81 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7328 (tmm) REVERT: G 27 GLN cc_start: 0.7255 (mt0) cc_final: 0.6956 (pt0) REVERT: G 34 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8494 (tm) REVERT: G 78 ARG cc_start: 0.6813 (ttp-110) cc_final: 0.6599 (ppt-90) outliers start: 92 outliers final: 59 residues processed: 419 average time/residue: 0.6213 time to fit residues: 309.8822 Evaluate side-chains 429 residues out of total 3270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 350 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 466 ARG Chi-restraints excluded: chain E residue 477 SER Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 556 ASN Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 750 SER Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 918 GLU Chi-restraints excluded: chain E residue 967 SER Chi-restraints excluded: chain E residue 983 ARG Chi-restraints excluded: chain E residue 1123 SER Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 326 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 302 optimal weight: 2.9990 chunk 319 optimal weight: 0.8980 chunk 372 optimal weight: 5.9990 chunk 247 optimal weight: 0.0870 chunk 173 optimal weight: 8.9990 chunk 188 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A1058 HIS B 271 GLN B 501 ASN E 81 ASN E 501 ASN ** E 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1058 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.172186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.141274 restraints weight = 30723.471| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.83 r_work: 0.3283 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31215 Z= 0.140 Angle : 0.551 8.352 42645 Z= 0.281 Chirality : 0.043 0.209 4980 Planarity : 0.004 0.070 5352 Dihedral : 4.294 29.202 5694 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.75 % Allowed : 13.65 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.13), residues: 3723 helix: 1.85 (0.19), residues: 726 sheet: 0.84 (0.16), residues: 1005 loop : -0.29 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 319 TYR 0.016 0.001 TYR A1067 PHE 0.029 0.001 PHE B 592 TRP 0.019 0.002 TRP E 64 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00325 (31089) covalent geometry : angle 0.53842 (42315) SS BOND : bond 0.00245 ( 48) SS BOND : angle 0.78549 ( 96) hydrogen bonds : bond 0.04146 ( 1296) hydrogen bonds : angle 5.50825 ( 3528) link_BETA1-4 : bond 0.00536 ( 24) link_BETA1-4 : angle 1.35520 ( 72) link_BETA1-6 : bond 0.00233 ( 3) link_BETA1-6 : angle 1.30543 ( 9) link_NAG-ASN : bond 0.00274 ( 51) link_NAG-ASN : angle 1.74329 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7446 Ramachandran restraints generated. 3723 Oldfield, 0 Emsley, 3723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 359 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6892 (ttm) cc_final: 0.6641 (tpp) REVERT: A 466 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7374 (mtp180) REVERT: A 580 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8079 (mp10) REVERT: A 646 ARG cc_start: 0.8023 (tmt170) cc_final: 0.7591 (mtt180) REVERT: A 725 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7863 (tm-30) REVERT: A 776 LYS cc_start: 0.8758 (tttt) cc_final: 0.8529 (ttpp) REVERT: A 921 LYS cc_start: 0.8688 (tmtt) cc_final: 0.8157 (mppt) REVERT: A 995 ARG cc_start: 0.8417 (mtp180) cc_final: 0.8127 (ttp-170) REVERT: A 1038 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7874 (mmtt) REVERT: A 1041 ASP cc_start: 0.8368 (m-30) cc_final: 0.8162 (m-30) REVERT: A 1113 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8161 (mm-40) REVERT: A 1123 SER cc_start: 0.8117 (m) cc_final: 0.7855 (m) REVERT: H 10 GLU cc_start: 0.6845 (mm-30) cc_final: 0.6542 (mm-30) REVERT: L 27 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.7302 (pm20) REVERT: B 556 ASN cc_start: 0.7706 (OUTLIER) cc_final: 0.7365 (m110) REVERT: B 646 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7605 (tmt170) REVERT: B 755 GLN cc_start: 0.8401 (mt0) cc_final: 0.8074 (mt0) REVERT: B 817 PHE cc_start: 0.8262 (t80) cc_final: 0.7991 (t80) REVERT: B 1041 ASP cc_start: 0.8192 (m-30) cc_final: 0.7891 (m-30) REVERT: C 3 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.6947 (mp10) REVERT: C 70 MET cc_start: 0.8305 (mtm) cc_final: 0.7850 (mtm) REVERT: D 27 GLN cc_start: 0.7448 (mt0) cc_final: 0.7070 (pt0) REVERT: E 157 PHE cc_start: 0.6672 (t80) cc_final: 0.6355 (t80) REVERT: E 346 ARG cc_start: 0.7724 (mmm160) cc_final: 0.7520 (mmm160) REVERT: E 428 ASP cc_start: 0.7746 (p0) cc_final: 0.7296 (p0) REVERT: E 466 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.8014 (mtp180) REVERT: E 537 LYS cc_start: 0.7679 (ttmt) cc_final: 0.6925 (mmtm) REVERT: E 702 GLU cc_start: 0.7792 (tt0) cc_final: 0.7312 (tm-30) REVERT: E 780 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8001 (pt0) REVERT: E 918 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7398 (mt-10) REVERT: E 921 LYS cc_start: 0.8712 (tmtt) cc_final: 0.8123 (mppt) REVERT: E 936 ASP cc_start: 0.7182 (m-30) cc_final: 0.6807 (t70) REVERT: E 983 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7611 (ttm170) REVERT: E 990 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7347 (tt0) REVERT: F 70 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7487 (mtt) REVERT: F 81 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7404 (tmm) REVERT: G 27 GLN cc_start: 0.7272 (mt0) cc_final: 0.6966 (pt0) REVERT: G 34 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8515 (tm) outliers start: 88 outliers final: 63 residues processed: 418 average time/residue: 0.6212 time to fit residues: 309.0128 Evaluate side-chains 427 residues out of total 3270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 348 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 466 ARG Chi-restraints excluded: chain E residue 477 SER Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 556 ASN Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 780 GLU Chi-restraints excluded: chain E residue 791 THR Chi-restraints excluded: chain E residue 918 GLU Chi-restraints excluded: chain E residue 967 SER Chi-restraints excluded: chain E residue 983 ARG Chi-restraints excluded: chain E residue 1123 SER Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 233 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 304 optimal weight: 2.9990 chunk 356 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 358 optimal weight: 0.0370 chunk 113 optimal weight: 0.9990 chunk 374 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 314 GLN A1058 HIS B 271 GLN B 501 ASN B 804 GLN B1135 ASN E 81 ASN E 501 ASN ** E 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1058 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.171679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.144666 restraints weight = 30849.102| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.77 r_work: 0.3265 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31215 Z= 0.151 Angle : 0.559 7.853 42645 Z= 0.286 Chirality : 0.043 0.206 4980 Planarity : 0.004 0.072 5352 Dihedral : 4.356 29.886 5694 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.84 % Allowed : 13.53 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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: 0.62 (0.13), residues: 3723 helix: 1.88 (0.20), residues: 705 sheet: 0.77 (0.16), residues: 1035 loop : -0.29 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 319 TYR 0.016 0.001 TYR A1067 PHE 0.026 0.001 PHE E 592 TRP 0.016 0.002 TRP C 106 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00354 (31089) covalent geometry : angle 0.54695 (42315) SS BOND : bond 0.00259 ( 48) SS BOND : angle 0.78908 ( 96) hydrogen bonds : bond 0.04252 ( 1296) hydrogen bonds : angle 5.55082 ( 3528) link_BETA1-4 : bond 0.00530 ( 24) link_BETA1-4 : angle 1.34670 ( 72) link_BETA1-6 : bond 0.00226 ( 3) link_BETA1-6 : angle 1.31749 ( 9) link_NAG-ASN : bond 0.00254 ( 51) link_NAG-ASN : angle 1.73749 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12853.27 seconds wall clock time: 219 minutes 2.55 seconds (13142.55 seconds total)