Starting phenix.real_space_refine on Sun Jul 5 21:29:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dlw_27518/07_2026/8dlw_27518.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlw_27518/07_2026/8dlw_27518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8dlw_27518/07_2026/8dlw_27518.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dlw_27518/07_2026/8dlw_27518.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dlw_27518/07_2026/8dlw_27518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlw_27518/07_2026/8dlw_27518.map" model { file = "/net/cci-nas-00/data/ceres_data/8dlw_27518/07_2026/8dlw_27518.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlw_27518/07_2026/8dlw_27518.cif" } resolution = 2.16 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= -0.001 sd= 0.047 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 19254 2.51 5 N 4947 2.21 5 O 5919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30267 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 7978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 7978 Classifications: {'peptide': 1029} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 56, 'TRANS': 972} Chain breaks: 7 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 7978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 7978 Classifications: {'peptide': 1029} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 56, 'TRANS': 972} Chain breaks: 7 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 39 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: 7978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 7978 Classifications: {'peptide': 1029} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 56, 'TRANS': 972} Chain breaks: 7 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 39 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: "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: "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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 10 Time building chain proxies: 6.06, per 1000 atoms: 0.20 Number of scatterers: 30267 At special positions: 0 Unit cell: (136, 141, 187, 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 5919 8.00 N 4947 7.00 C 19254 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=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.04 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG 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 61 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 165 " " 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 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 165 " " 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 61 " " NAG E1302 " - " ASN E 234 " " NAG E1303 " - " ASN E 165 " " 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: 2.12 Conformation dependent library (CDL) restraints added in 1.3 seconds 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7008 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 66 sheets defined 23.4% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.647A 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: 4.238A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 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: 4.010A 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 945 through 965 removed outlier: 3.699A 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: 4.696A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.644A 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: 4.227A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 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: 4.020A 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 945 through 965 removed outlier: 3.706A 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: 4.697A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.686A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.612A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 111 removed outlier: 3.925A 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 removed outlier: 3.526A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.662A 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: 4.230A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 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: 4.015A 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 945 through 965 removed outlier: 3.690A 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: 4.697A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.677A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.608A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (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 removed outlier: 3.545A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.636A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.608A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 111 removed outlier: 3.928A 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 removed outlier: 3.538A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.886A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.108A 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: 6.214A pdb=" N PHE A 43 " --> pdb=" O ARG E 567 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 4.322A 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: 3.925A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.542A 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: 4.288A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.318A 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: 6.719A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.954A 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: 4.325A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.161A 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: 6.671A 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: 6.511A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.609A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.939A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.658A 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: 5.940A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.588A 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: 4.554A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.790A pdb=" N LYS A 790 " --> pdb=" O ASN E 703 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.678A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.870A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.105A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.925A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.537A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 132 through 141 removed outlier: 4.289A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.710A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.348A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.157A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.673A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.505A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.760A pdb=" N LYS E 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.949A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.947A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.552A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.655A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AD9, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.667A pdb=" N MET C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 10 through 11 removed outlier: 3.916A pdb=" N TYR C 114 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AE3, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.498A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.498A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 27 through 30 removed outlier: 7.890A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N HIS E 207 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N ALA E 222 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 47 through 55 removed outlier: 3.922A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 84 through 85 removed outlier: 5.473A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 132 through 141 removed outlier: 4.271A pdb=" N SER E 162 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N CYS E 136 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TYR E 160 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP E 138 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ARG E 158 " --> pdb=" O ASP E 138 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 311 through 319 removed outlier: 6.717A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASN E 317 " --> pdb=" O GLY E 593 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLY E 593 " --> pdb=" O ASN E 317 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.167A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.682A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AF5, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.509A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 711 through 713 removed outlier: 3.931A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 718 through 728 removed outlier: 5.928A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.545A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.661A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AG2, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.657A pdb=" N MET F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TRP F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.895A pdb=" N TYR F 114 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AG5, first strand: chain 'G' and resid 54 through 55 removed outlier: 6.534A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 54 through 55 removed outlier: 6.534A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AG8, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.610A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 10 through 11 removed outlier: 4.125A pdb=" N TYR H 114 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AH2, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.486A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.486A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) 1365 hydrogen bonds defined for protein. 3603 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: 8.44 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9335 1.34 - 1.46: 8087 1.46 - 1.59: 13355 1.59 - 1.71: 0 1.71 - 1.83: 192 Bond restraints: 30969 Sorted by residual: bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 8.91e+00 bond pdb=" C1 NAG Z 2 " pdb=" O5 NAG Z 2 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.67e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.61e+00 bond pdb=" CG LEU B 916 " pdb=" CD2 LEU B 916 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 7.90e+00 bond pdb=" C1 NAG a 2 " pdb=" O5 NAG a 2 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.54e+00 ... (remaining 30964 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 40688 2.56 - 5.12: 1305 5.12 - 7.67: 138 7.67 - 10.23: 16 10.23 - 12.79: 9 Bond angle restraints: 42156 Sorted by residual: angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 117.50 -6.80 1.22e+00 6.72e-01 3.11e+01 angle pdb=" N PRO E 986 " pdb=" CA PRO E 986 " pdb=" C PRO E 986 " ideal model delta sigma weight residual 110.70 117.47 -6.77 1.22e+00 6.72e-01 3.08e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 117.33 -6.63 1.22e+00 6.72e-01 2.96e+01 angle pdb=" CA TYR H 103 " pdb=" CB TYR H 103 " pdb=" CG TYR H 103 " ideal model delta sigma weight residual 113.90 122.95 -9.05 1.80e+00 3.09e-01 2.53e+01 angle pdb=" C GLY G 51 " pdb=" N ALA G 52 " pdb=" CA ALA G 52 " ideal model delta sigma weight residual 121.54 130.83 -9.29 1.91e+00 2.74e-01 2.37e+01 ... (remaining 42151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 16927 17.91 - 35.81: 623 35.81 - 53.72: 108 53.72 - 71.63: 54 71.63 - 89.53: 33 Dihedral angle restraints: 17745 sinusoidal: 6816 harmonic: 10929 Sorted by residual: dihedral pdb=" CD1 TYR E 449 " pdb=" CE1 TYR E 449 " pdb=" CZ TYR E 449 " pdb=" OH TYR E 449 " ideal model delta harmonic sigma weight residual -180.00 -158.03 -21.97 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CD1 TYR B 449 " pdb=" CE1 TYR B 449 " pdb=" CZ TYR B 449 " pdb=" OH TYR B 449 " ideal model delta harmonic sigma weight residual 180.00 -158.09 -21.91 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" SG CYS A 131 " pdb=" CB CYS A 166 " pdb=" SG CYS A 166 " pdb=" CA CYS A 166 " ideal model delta sinusoidal sigma weight residual 79.00 9.23 69.77 1 2.00e+01 2.50e-03 1.57e+01 ... (remaining 17742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 4365 0.094 - 0.189: 547 0.189 - 0.283: 36 0.283 - 0.377: 5 0.377 - 0.472: 3 Chirality restraints: 4956 Sorted by residual: chirality pdb=" CG LEU E 916 " pdb=" CB LEU E 916 " pdb=" CD1 LEU E 916 " pdb=" CD2 LEU E 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.12 -0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" CG LEU B 916 " pdb=" CB LEU B 916 " pdb=" CD1 LEU B 916 " pdb=" CD2 LEU B 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" CG LEU A 916 " pdb=" CB LEU A 916 " pdb=" CD1 LEU A 916 " pdb=" CD2 LEU A 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.05e+00 ... (remaining 4953 not shown) Planarity restraints: 5391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 449 " 0.007 2.00e-02 2.50e+03 7.73e-02 1.20e+02 pdb=" CG TYR E 449 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR E 449 " 0.107 2.00e-02 2.50e+03 pdb=" CD2 TYR E 449 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR E 449 " -0.108 2.00e-02 2.50e+03 pdb=" CE2 TYR E 449 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR E 449 " -0.110 2.00e-02 2.50e+03 pdb=" OH TYR E 449 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 449 " -0.007 2.00e-02 2.50e+03 7.72e-02 1.19e+02 pdb=" CG TYR B 449 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR B 449 " -0.108 2.00e-02 2.50e+03 pdb=" CD2 TYR B 449 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 449 " 0.108 2.00e-02 2.50e+03 pdb=" CE2 TYR B 449 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 449 " 0.109 2.00e-02 2.50e+03 pdb=" OH TYR B 449 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 356 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C LYS E 356 " 0.059 2.00e-02 2.50e+03 pdb=" O LYS E 356 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG E 357 " -0.020 2.00e-02 2.50e+03 ... (remaining 5388 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 8035 2.81 - 3.33: 25392 3.33 - 3.86: 51390 3.86 - 4.38: 59345 4.38 - 4.90: 103153 Nonbonded interactions: 247315 Sorted by model distance: nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR E 37 " pdb=" O LEU E 54 " model vdw 2.292 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR A 369 " pdb=" OD2 ASP E 420 " model vdw 2.342 3.040 nonbonded pdb=" NE2 GLN B 493 " pdb=" OH TYR C 103 " model vdw 2.349 3.120 ... (remaining 247310 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: 0.08 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: 4.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 28.740 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 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 : 0.007 0.093 31095 Z= 0.311 Angle : 1.066 12.789 42486 Z= 0.599 Chirality : 0.063 0.472 4956 Planarity : 0.008 0.077 5340 Dihedral : 11.118 89.535 10593 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.29 % Favored : 97.65 % Rotamer: Outliers : 0.19 % Allowed : 2.10 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 0.82 (0.13), residues: 3708 helix: 1.46 (0.18), residues: 669 sheet: 0.94 (0.15), residues: 1020 loop : 0.10 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 98 TYR 0.112 0.004 TYR E 449 PHE 0.039 0.003 PHE A 329 TRP 0.033 0.003 TRP F 106 HIS 0.014 0.002 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00665 / 0.31 (30969) covalent geometry : angle 1.05337 / 0.60 (42156) SS BOND : bond 0.00635 / 0.44 ( 48) SS BOND : angle 1.99911 / 1.46 ( 96) hydrogen bonds : bond 0.12045 / 7.85 ( 1314) hydrogen bonds : angle 7.69618 / 5.33 ( 3603) link_BETA1-4 : bond 0.01005 / 0.61 ( 24) link_BETA1-4 : angle 1.86206 / 1.20 ( 72) link_BETA1-6 : bond 0.00227 / 0.12 ( 3) link_BETA1-6 : angle 1.05996 / 0.62 ( 9) link_NAG-ASN : bond 0.00362 / 0.27 ( 51) link_NAG-ASN : angle 2.32511 / 1.59 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 419 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 11 VAL cc_start: 0.8725 (t) cc_final: 0.8159 (m) REVERT: C 12 LYS cc_start: 0.8947 (mmtt) cc_final: 0.8371 (ttmm) REVERT: E 869 MET cc_start: 0.9311 (mtt) cc_final: 0.9051 (mtm) REVERT: F 12 LYS cc_start: 0.8217 (mmtt) cc_final: 0.8009 (ttmm) REVERT: F 46 GLU cc_start: 0.7868 (tt0) cc_final: 0.7537 (tt0) REVERT: F 67 ARG cc_start: 0.6421 (mtp180) cc_final: 0.6103 (ttp80) REVERT: G 38 GLN cc_start: 0.7495 (tt0) cc_final: 0.7120 (tm130) REVERT: L 38 GLN cc_start: 0.7805 (tt0) cc_final: 0.7522 (tm130) REVERT: L 83 ASP cc_start: 0.7673 (m-30) cc_final: 0.7053 (m-30) outliers start: 6 outliers final: 0 residues processed: 425 average time/residue: 0.7235 time to fit residues: 357.3259 Evaluate side-chains 230 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN A 185 ASN A 901 GLN A 907 ASN A 913 GLN A 955 ASN A1010 GLN B 137 ASN B 185 ASN B 901 GLN B1010 GLN E 185 ASN E 658 ASN E 901 GLN E 913 GLN E1010 GLN ** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.087035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.056579 restraints weight = 73320.638| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.97 r_work: 0.2864 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 31095 Z= 0.223 Angle : 0.661 10.013 42486 Z= 0.340 Chirality : 0.045 0.242 4956 Planarity : 0.005 0.071 5340 Dihedral : 4.514 21.233 4062 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.35 % Allowed : 6.32 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 0.99 (0.13), residues: 3708 helix: 2.06 (0.20), residues: 690 sheet: 0.99 (0.15), residues: 1002 loop : 0.04 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 237 TYR 0.024 0.002 TYR B1067 PHE 0.021 0.002 PHE E 86 TRP 0.027 0.002 TRP F 106 HIS 0.005 0.001 HIS E1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 (30969) covalent geometry : angle 0.64994 / 0.34 (42156) SS BOND : bond 0.00398 / 0.25 ( 48) SS BOND : angle 0.85627 / 0.59 ( 96) hydrogen bonds : bond 0.04922 / 3.21 ( 1314) hydrogen bonds : angle 6.21195 / 4.30 ( 3603) link_BETA1-4 : bond 0.00551 / 0.38 ( 24) link_BETA1-4 : angle 1.17160 / 0.82 ( 72) link_BETA1-6 : bond 0.00044 / 0.02 ( 3) link_BETA1-6 : angle 1.35012 / 0.82 ( 9) link_NAG-ASN : bond 0.00191 / 0.13 ( 51) link_NAG-ASN : angle 1.95637 / 1.31 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 258 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.8455 (ttm110) cc_final: 0.8218 (mtp-110) REVERT: A 516 GLU cc_start: 0.8488 (tt0) cc_final: 0.8263 (tt0) REVERT: B 227 VAL cc_start: 0.9388 (p) cc_final: 0.9173 (m) REVERT: B 319 ARG cc_start: 0.8589 (ttm110) cc_final: 0.7998 (ttm-80) REVERT: B 900 MET cc_start: 0.9484 (mtp) cc_final: 0.9225 (ttm) REVERT: C 10 GLU cc_start: 0.7407 (tm-30) cc_final: 0.6752 (tm-30) REVERT: C 12 LYS cc_start: 0.9084 (mmtt) cc_final: 0.8790 (ttmm) REVERT: C 41 PRO cc_start: 0.8455 (Cg_exo) cc_final: 0.8203 (Cg_endo) REVERT: C 46 GLU cc_start: 0.8433 (tt0) cc_final: 0.7774 (pt0) REVERT: C 70 MET cc_start: 0.8847 (mtt) cc_final: 0.8518 (mtm) REVERT: D 78 ARG cc_start: 0.8058 (tmm-80) cc_final: 0.7796 (ptm-80) REVERT: E 227 VAL cc_start: 0.9359 (p) cc_final: 0.9140 (m) REVERT: F 10 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7409 (tm-30) REVERT: F 19 LYS cc_start: 0.8998 (ttmm) cc_final: 0.8727 (ttmm) REVERT: F 46 GLU cc_start: 0.8573 (tt0) cc_final: 0.7992 (tt0) REVERT: F 85 ARG cc_start: 0.7175 (ttp80) cc_final: 0.6934 (ttp80) REVERT: G 27 GLN cc_start: 0.8457 (mp10) cc_final: 0.8156 (mp10) REVERT: G 38 GLN cc_start: 0.7653 (tt0) cc_final: 0.7404 (pp30) REVERT: G 48 LEU cc_start: 0.8652 (mm) cc_final: 0.8387 (mm) REVERT: G 55 ARG cc_start: 0.8434 (ttm110) cc_final: 0.8064 (ttm110) REVERT: G 88 TYR cc_start: 0.8685 (m-80) cc_final: 0.8247 (m-80) REVERT: H 11 VAL cc_start: 0.8798 (t) cc_final: 0.8429 (m) REVERT: H 12 LYS cc_start: 0.8832 (ttmm) cc_final: 0.7956 (ttmm) REVERT: H 87 ARG cc_start: 0.8749 (mtm-85) cc_final: 0.8499 (mtm-85) REVERT: L 24 ARG cc_start: 0.7416 (mpp80) cc_final: 0.7215 (mpp80) REVERT: L 48 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8596 (mm) REVERT: L 62 ARG cc_start: 0.8135 (ttm170) cc_final: 0.7803 (ttm170) REVERT: L 70 THR cc_start: 0.9185 (p) cc_final: 0.8919 (t) outliers start: 75 outliers final: 20 residues processed: 296 average time/residue: 0.7568 time to fit residues: 260.2558 Evaluate side-chains 238 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 217 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 786 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 342 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 292 optimal weight: 0.8980 chunk 205 optimal weight: 5.9990 chunk 199 optimal weight: 0.9990 chunk 269 optimal weight: 4.9990 chunk 308 optimal weight: 1.9990 chunk 268 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN B 115 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN E 115 GLN E 137 ASN ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 GLN H 43 GLN L 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.085319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.054590 restraints weight = 73729.325| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.01 r_work: 0.2814 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 31095 Z= 0.240 Angle : 0.654 9.593 42486 Z= 0.330 Chirality : 0.046 0.211 4956 Planarity : 0.005 0.071 5340 Dihedral : 4.551 20.581 4062 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.16 % Allowed : 7.29 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 0.97 (0.13), residues: 3708 helix: 2.35 (0.20), residues: 663 sheet: 0.73 (0.15), residues: 1032 loop : 0.08 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.026 0.002 TYR E1067 PHE 0.024 0.002 PHE A 133 TRP 0.026 0.002 TRP F 106 HIS 0.006 0.001 HIS E1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.24 (30969) covalent geometry : angle 0.64165 / 0.33 (42156) SS BOND : bond 0.00372 / 0.24 ( 48) SS BOND : angle 0.74898 / 0.52 ( 96) hydrogen bonds : bond 0.04881 / 3.17 ( 1314) hydrogen bonds : angle 5.90999 / 4.08 ( 3603) link_BETA1-4 : bond 0.00494 / 0.33 ( 24) link_BETA1-4 : angle 1.02033 / 0.71 ( 72) link_BETA1-6 : bond 0.00092 / 0.05 ( 3) link_BETA1-6 : angle 1.37920 / 0.84 ( 9) link_NAG-ASN : bond 0.00181 / 0.13 ( 51) link_NAG-ASN : angle 2.04863 / 1.39 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 242 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.9615 (mtt) cc_final: 0.9410 (mtm) REVERT: B 237 ARG cc_start: 0.8889 (ttm170) cc_final: 0.8438 (mtp85) REVERT: C 10 GLU cc_start: 0.7454 (tm-30) cc_final: 0.7247 (tm-30) REVERT: C 41 PRO cc_start: 0.8652 (Cg_exo) cc_final: 0.8439 (Cg_endo) REVERT: C 46 GLU cc_start: 0.8491 (tt0) cc_final: 0.7821 (pt0) REVERT: C 48 MET cc_start: 0.8779 (mtp) cc_final: 0.8486 (mtp) REVERT: C 70 MET cc_start: 0.8755 (mtt) cc_final: 0.8489 (mtm) REVERT: D 46 ARG cc_start: 0.8688 (ttp-170) cc_final: 0.8459 (ptt90) REVERT: D 62 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8072 (ttm170) REVERT: D 105 VAL cc_start: 0.7790 (OUTLIER) cc_final: 0.7567 (t) REVERT: E 242 LEU cc_start: 0.8833 (mp) cc_final: 0.8083 (tp) REVERT: E 790 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.9086 (mmmt) REVERT: F 19 LYS cc_start: 0.9094 (ttmm) cc_final: 0.8826 (ttmm) REVERT: F 46 GLU cc_start: 0.8681 (tt0) cc_final: 0.8138 (tt0) REVERT: F 82 GLU cc_start: 0.8927 (tp30) cc_final: 0.8680 (tp30) REVERT: F 98 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7785 (ttt180) REVERT: G 5 MET cc_start: 0.8400 (pmm) cc_final: 0.8129 (pmm) REVERT: G 27 GLN cc_start: 0.8280 (mp10) cc_final: 0.8018 (mp10) REVERT: G 88 TYR cc_start: 0.8583 (m-80) cc_final: 0.8162 (m-80) REVERT: G 104 LYS cc_start: 0.8692 (tptt) cc_final: 0.7915 (tmmt) REVERT: H 10 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6835 (tm-30) REVERT: H 12 LYS cc_start: 0.8680 (ttmm) cc_final: 0.8230 (mtpp) REVERT: H 23 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8418 (tptp) REVERT: H 87 ARG cc_start: 0.8694 (mtm-85) cc_final: 0.8478 (mtm-85) REVERT: L 5 MET cc_start: 0.8448 (pmm) cc_final: 0.8220 (pmm) REVERT: L 48 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8531 (mm) REVERT: L 71 ASP cc_start: 0.8781 (t70) cc_final: 0.8505 (p0) outliers start: 69 outliers final: 28 residues processed: 277 average time/residue: 0.7765 time to fit residues: 249.7682 Evaluate side-chains 253 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 786 LYS Chi-restraints excluded: chain E residue 790 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 35 optimal weight: 1.9990 chunk 314 optimal weight: 0.6980 chunk 226 optimal weight: 50.0000 chunk 211 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 275 optimal weight: 7.9990 chunk 259 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 289 optimal weight: 2.9990 chunk 278 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN D 27 GLN E 762 GLN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.085909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.055494 restraints weight = 73216.822| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.99 r_work: 0.2840 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31095 Z= 0.152 Angle : 0.588 9.919 42486 Z= 0.296 Chirality : 0.043 0.163 4956 Planarity : 0.004 0.059 5340 Dihedral : 4.368 19.218 4062 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.13 % Allowed : 7.69 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 0.98 (0.13), residues: 3708 helix: 2.51 (0.19), residues: 660 sheet: 0.81 (0.15), residues: 1011 loop : -0.01 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 87 TYR 0.019 0.001 TYR B1067 PHE 0.022 0.001 PHE B 133 TRP 0.019 0.001 TRP F 106 HIS 0.002 0.001 HIS E1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (30969) covalent geometry : angle 0.57791 / 0.29 (42156) SS BOND : bond 0.00424 / 0.30 ( 48) SS BOND : angle 0.71021 / 0.47 ( 96) hydrogen bonds : bond 0.04284 / 2.79 ( 1314) hydrogen bonds : angle 5.68446 / 3.92 ( 3603) link_BETA1-4 : bond 0.00509 / 0.33 ( 24) link_BETA1-4 : angle 0.97337 / 0.67 ( 72) link_BETA1-6 : bond 0.00030 / 0.01 ( 3) link_BETA1-6 : angle 1.31725 / 0.80 ( 9) link_NAG-ASN : bond 0.00190 / 0.14 ( 51) link_NAG-ASN : angle 1.80247 / 1.21 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 243 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.9604 (mtt) cc_final: 0.9403 (mtm) REVERT: A 940 SER cc_start: 0.8485 (OUTLIER) cc_final: 0.8100 (m) REVERT: B 237 ARG cc_start: 0.8853 (ttm170) cc_final: 0.8448 (mtp85) REVERT: B 900 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.9021 (mtm) REVERT: C 10 GLU cc_start: 0.7389 (tm-30) cc_final: 0.6673 (tm-30) REVERT: C 46 GLU cc_start: 0.8487 (tt0) cc_final: 0.8266 (tt0) REVERT: C 48 MET cc_start: 0.8748 (mtp) cc_final: 0.8521 (mtp) REVERT: D 46 ARG cc_start: 0.8706 (ttp-170) cc_final: 0.8306 (ttp-170) REVERT: D 78 ARG cc_start: 0.7840 (ptm-80) cc_final: 0.7636 (ptm-80) REVERT: E 227 VAL cc_start: 0.9427 (p) cc_final: 0.9216 (m) REVERT: E 242 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8165 (tp) REVERT: F 10 GLU cc_start: 0.7010 (tm-30) cc_final: 0.6692 (tm-30) REVERT: F 19 LYS cc_start: 0.9098 (ttmm) cc_final: 0.8837 (ttmm) REVERT: F 46 GLU cc_start: 0.8663 (tt0) cc_final: 0.8084 (tt0) REVERT: F 82 GLU cc_start: 0.8790 (tp30) cc_final: 0.8538 (tp30) REVERT: F 85 ARG cc_start: 0.6883 (ttp80) cc_final: 0.6638 (ttp80) REVERT: F 89 ASP cc_start: 0.8652 (p0) cc_final: 0.8235 (p0) REVERT: F 98 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8089 (ttt180) REVERT: G 27 GLN cc_start: 0.8453 (mp10) cc_final: 0.8016 (mp10) REVERT: G 38 GLN cc_start: 0.7212 (pp30) cc_final: 0.6770 (pp30) REVERT: G 46 ARG cc_start: 0.8724 (ttp-170) cc_final: 0.8304 (ttp-170) REVERT: G 48 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8804 (mm) REVERT: G 55 ARG cc_start: 0.8568 (ttm110) cc_final: 0.8160 (ttm110) REVERT: G 62 ARG cc_start: 0.8129 (ttm170) cc_final: 0.7802 (ttm170) REVERT: G 78 ARG cc_start: 0.8344 (mtm110) cc_final: 0.7767 (ptp90) REVERT: G 80 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7054 (mp0) REVERT: G 88 TYR cc_start: 0.8509 (m-80) cc_final: 0.8087 (m-80) REVERT: G 104 LYS cc_start: 0.8652 (tptt) cc_final: 0.7850 (tmmt) REVERT: H 10 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6647 (tm-30) REVERT: H 12 LYS cc_start: 0.8627 (ttmm) cc_final: 0.8378 (mtpp) REVERT: H 13 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7830 (mmtt) REVERT: H 23 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8439 (tptp) REVERT: H 81 MET cc_start: 0.8247 (tpp) cc_final: 0.6614 (tpp) REVERT: H 82 GLU cc_start: 0.8713 (tp30) cc_final: 0.8377 (tp30) REVERT: H 87 ARG cc_start: 0.8693 (mtm-85) cc_final: 0.8455 (mtm-85) REVERT: L 48 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8584 (mm) REVERT: L 62 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7804 (ttm170) REVERT: L 71 ASP cc_start: 0.8792 (t70) cc_final: 0.8504 (p0) REVERT: L 78 ARG cc_start: 0.8119 (pmm-80) cc_final: 0.7568 (pmm-80) outliers start: 68 outliers final: 26 residues processed: 279 average time/residue: 0.7905 time to fit residues: 255.4015 Evaluate side-chains 255 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 221 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 786 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 105 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 263 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 262 optimal weight: 0.5980 chunk 330 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.084095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.053517 restraints weight = 73674.794| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.98 r_work: 0.2787 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 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 : 0.006 0.081 31095 Z= 0.272 Angle : 0.653 8.345 42486 Z= 0.330 Chirality : 0.045 0.206 4956 Planarity : 0.005 0.073 5340 Dihedral : 4.637 21.530 4062 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.10 % Allowed : 8.44 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 0.82 (0.13), residues: 3708 helix: 2.35 (0.20), residues: 666 sheet: 0.62 (0.16), residues: 987 loop : -0.05 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 85 TYR 0.026 0.002 TYR E1067 PHE 0.021 0.002 PHE B 329 TRP 0.023 0.002 TRP F 106 HIS 0.005 0.001 HIS E1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.27 (30969) covalent geometry : angle 0.64264 / 0.33 (42156) SS BOND : bond 0.00373 / 0.24 ( 48) SS BOND : angle 0.73593 / 0.51 ( 96) hydrogen bonds : bond 0.04943 / 3.21 ( 1314) hydrogen bonds : angle 5.78618 / 4.00 ( 3603) link_BETA1-4 : bond 0.00419 / 0.28 ( 24) link_BETA1-4 : angle 1.02355 / 0.72 ( 72) link_BETA1-6 : bond 0.00260 / 0.13 ( 3) link_BETA1-6 : angle 1.45676 / 0.88 ( 9) link_NAG-ASN : bond 0.00299 / 0.21 ( 51) link_NAG-ASN : angle 1.88324 / 1.25 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 219 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: A 869 MET cc_start: 0.9661 (mtt) cc_final: 0.9441 (mtm) REVERT: B 237 ARG cc_start: 0.8884 (ttm170) cc_final: 0.8525 (mtp85) REVERT: C 10 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7020 (tm-30) REVERT: C 19 LYS cc_start: 0.9185 (ttmm) cc_final: 0.8906 (ttmm) REVERT: C 48 MET cc_start: 0.8770 (mtp) cc_final: 0.8539 (mtp) REVERT: D 46 ARG cc_start: 0.8720 (ttp-170) cc_final: 0.8429 (ttp-170) REVERT: D 62 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8026 (ttm170) REVERT: D 71 ASP cc_start: 0.8700 (m-30) cc_final: 0.8467 (p0) REVERT: D 78 ARG cc_start: 0.7930 (ptm-80) cc_final: 0.7673 (ptm-80) REVERT: E 242 LEU cc_start: 0.8792 (mp) cc_final: 0.8106 (tp) REVERT: E 452 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.8905 (mtt180) REVERT: F 10 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7287 (tm-30) REVERT: F 19 LYS cc_start: 0.9088 (ttmm) cc_final: 0.8772 (ttmm) REVERT: F 82 GLU cc_start: 0.8799 (tp30) cc_final: 0.8517 (tp30) REVERT: F 98 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7818 (ttt180) REVERT: G 4 MET cc_start: 0.8577 (mmm) cc_final: 0.7893 (mmm) REVERT: G 27 GLN cc_start: 0.8483 (mp10) cc_final: 0.8057 (mp10) REVERT: G 38 GLN cc_start: 0.7297 (pp30) cc_final: 0.6759 (pp30) REVERT: G 43 GLN cc_start: 0.8898 (pt0) cc_final: 0.8532 (pm20) REVERT: G 46 ARG cc_start: 0.8689 (ttp-170) cc_final: 0.8229 (ttp-170) REVERT: G 48 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8764 (mm) REVERT: G 55 ARG cc_start: 0.8610 (ttm110) cc_final: 0.8295 (ttm110) REVERT: G 78 ARG cc_start: 0.8374 (mtm110) cc_final: 0.7830 (ptp90) REVERT: G 80 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7321 (mp0) REVERT: G 88 TYR cc_start: 0.8517 (m-80) cc_final: 0.8109 (m-80) REVERT: H 10 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6617 (tm-30) REVERT: H 12 LYS cc_start: 0.8596 (ttmm) cc_final: 0.8312 (mtpp) REVERT: H 13 LYS cc_start: 0.7977 (mmtt) cc_final: 0.7745 (mmtt) REVERT: H 82 GLU cc_start: 0.8752 (tp30) cc_final: 0.8543 (tp30) REVERT: L 27 GLN cc_start: 0.9175 (mt0) cc_final: 0.8960 (mp10) REVERT: L 43 GLN cc_start: 0.9076 (pt0) cc_final: 0.8730 (pm20) REVERT: L 48 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8582 (mm) REVERT: L 55 ARG cc_start: 0.8706 (ttm110) cc_final: 0.8420 (ttm-80) REVERT: L 71 ASP cc_start: 0.8784 (t70) cc_final: 0.8491 (p0) outliers start: 67 outliers final: 27 residues processed: 259 average time/residue: 0.8104 time to fit residues: 242.9214 Evaluate side-chains 238 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 452 ARG Chi-restraints excluded: chain E residue 786 LYS Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 57 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 194 optimal weight: 0.9980 chunk 249 optimal weight: 0.9980 chunk 343 optimal weight: 2.9990 chunk 297 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 356 optimal weight: 0.7980 chunk 162 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 190 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 658 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.085758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.055596 restraints weight = 73045.385| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.97 r_work: 0.2842 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31095 Z= 0.122 Angle : 0.568 8.836 42486 Z= 0.286 Chirality : 0.043 0.163 4956 Planarity : 0.004 0.054 5340 Dihedral : 4.278 18.160 4062 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.88 % Allowed : 9.07 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 0.96 (0.13), residues: 3708 helix: 2.61 (0.19), residues: 666 sheet: 0.56 (0.15), residues: 1020 loop : 0.06 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 87 TYR 0.018 0.001 TYR A1067 PHE 0.016 0.001 PHE B 133 TRP 0.015 0.001 TRP F 106 HIS 0.002 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (30969) covalent geometry : angle 0.55927 / 0.28 (42156) SS BOND : bond 0.00218 / 0.14 ( 48) SS BOND : angle 0.65605 / 0.44 ( 96) hydrogen bonds : bond 0.04008 / 2.62 ( 1314) hydrogen bonds : angle 5.51926 / 3.81 ( 3603) link_BETA1-4 : bond 0.00526 / 0.35 ( 24) link_BETA1-4 : angle 0.91946 / 0.62 ( 72) link_BETA1-6 : bond 0.00085 / 0.04 ( 3) link_BETA1-6 : angle 1.22607 / 0.75 ( 9) link_NAG-ASN : bond 0.00221 / 0.15 ( 51) link_NAG-ASN : angle 1.63425 / 1.09 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 231 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.7959 (tp) REVERT: A 869 MET cc_start: 0.9629 (mtt) cc_final: 0.9397 (mtm) REVERT: A 940 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.8168 (m) REVERT: A 1094 VAL cc_start: 0.9428 (OUTLIER) cc_final: 0.9209 (p) REVERT: B 237 ARG cc_start: 0.8857 (ttm170) cc_final: 0.8644 (mtp85) REVERT: B 242 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8163 (tp) REVERT: C 10 GLU cc_start: 0.7361 (tm-30) cc_final: 0.7084 (tm-30) REVERT: C 19 LYS cc_start: 0.9115 (ttmm) cc_final: 0.8866 (ttmm) REVERT: C 48 MET cc_start: 0.8680 (mtp) cc_final: 0.8453 (mtp) REVERT: D 27 GLN cc_start: 0.9067 (pm20) cc_final: 0.8701 (pm20) REVERT: D 46 ARG cc_start: 0.8733 (ttp-170) cc_final: 0.8428 (ttp-170) REVERT: D 62 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.8118 (ttp80) REVERT: D 71 ASP cc_start: 0.8762 (m-30) cc_final: 0.8453 (p0) REVERT: D 78 ARG cc_start: 0.7938 (ptm-80) cc_final: 0.7372 (ptm-80) REVERT: E 227 VAL cc_start: 0.9417 (p) cc_final: 0.9210 (m) REVERT: E 242 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8179 (tp) REVERT: E 646 ARG cc_start: 0.8274 (tpt90) cc_final: 0.8061 (tpm170) REVERT: E 935 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: F 10 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7300 (tm-30) REVERT: F 19 LYS cc_start: 0.9017 (ttmm) cc_final: 0.8773 (ttmm) REVERT: F 82 GLU cc_start: 0.8820 (tp30) cc_final: 0.8573 (tp30) REVERT: F 120 LEU cc_start: 0.8881 (tp) cc_final: 0.8668 (tm) REVERT: G 4 MET cc_start: 0.8611 (mmm) cc_final: 0.7673 (mmm) REVERT: G 27 GLN cc_start: 0.8530 (mp10) cc_final: 0.8114 (mp10) REVERT: G 38 GLN cc_start: 0.7368 (pp30) cc_final: 0.6992 (pp30) REVERT: G 46 ARG cc_start: 0.8766 (ttp-170) cc_final: 0.8232 (ttp80) REVERT: G 48 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8807 (mm) REVERT: G 62 ARG cc_start: 0.8236 (ttm170) cc_final: 0.7858 (ttm170) REVERT: G 78 ARG cc_start: 0.8436 (mtm110) cc_final: 0.7993 (ptp90) REVERT: G 80 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7179 (mp0) REVERT: G 88 TYR cc_start: 0.8415 (m-80) cc_final: 0.7971 (m-80) REVERT: G 104 LYS cc_start: 0.8645 (tptt) cc_final: 0.7904 (tmmt) REVERT: H 10 GLU cc_start: 0.7220 (tm-30) cc_final: 0.6648 (tm-30) REVERT: H 12 LYS cc_start: 0.8659 (ttmm) cc_final: 0.8433 (mtpp) REVERT: H 13 LYS cc_start: 0.7931 (mmtt) cc_final: 0.7728 (mmtt) REVERT: H 23 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8642 (tptm) REVERT: H 38 ARG cc_start: 0.7606 (ptm160) cc_final: 0.7173 (ptm160) REVERT: H 46 GLU cc_start: 0.8696 (tt0) cc_final: 0.7847 (tt0) REVERT: H 82 GLU cc_start: 0.8687 (tp30) cc_final: 0.8437 (tp30) REVERT: H 85 ARG cc_start: 0.8538 (ttp80) cc_final: 0.8057 (ttp80) REVERT: L 48 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8517 (mm) REVERT: L 71 ASP cc_start: 0.8799 (t70) cc_final: 0.8504 (p0) REVERT: L 78 ARG cc_start: 0.8494 (pmm-80) cc_final: 0.8070 (pmm150) outliers start: 60 outliers final: 25 residues processed: 265 average time/residue: 0.7766 time to fit residues: 237.4507 Evaluate side-chains 251 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 786 LYS Chi-restraints excluded: chain E residue 900 MET Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 935 GLN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 5 optimal weight: 5.9990 chunk 26 optimal weight: 0.0870 chunk 318 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 344 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 187 optimal weight: 0.0270 chunk 308 optimal weight: 3.9990 chunk 305 optimal weight: 0.9980 chunk 292 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 65 GLN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.085446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.055233 restraints weight = 72983.203| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.97 r_work: 0.2833 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31095 Z= 0.143 Angle : 0.577 7.809 42486 Z= 0.291 Chirality : 0.043 0.161 4956 Planarity : 0.004 0.056 5340 Dihedral : 4.217 18.402 4062 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.66 % Allowed : 9.35 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 0.97 (0.13), residues: 3708 helix: 2.67 (0.19), residues: 666 sheet: 0.61 (0.15), residues: 1005 loop : 0.03 (0.14), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 18 TYR 0.020 0.001 TYR B 28 PHE 0.014 0.001 PHE E 898 TRP 0.016 0.001 TRP F 106 HIS 0.003 0.001 HIS E1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (30969) covalent geometry : angle 0.56803 / 0.29 (42156) SS BOND : bond 0.00227 / 0.14 ( 48) SS BOND : angle 0.64764 / 0.44 ( 96) hydrogen bonds : bond 0.04058 / 2.65 ( 1314) hydrogen bonds : angle 5.45467 / 3.77 ( 3603) link_BETA1-4 : bond 0.00484 / 0.32 ( 24) link_BETA1-4 : angle 0.92841 / 0.64 ( 72) link_BETA1-6 : bond 0.00034 / 0.02 ( 3) link_BETA1-6 : angle 1.26448 / 0.77 ( 9) link_NAG-ASN : bond 0.00197 / 0.14 ( 51) link_NAG-ASN : angle 1.64967 / 1.10 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 223 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.7935 (tp) REVERT: A 869 MET cc_start: 0.9594 (mtt) cc_final: 0.9381 (mtm) REVERT: A 1094 VAL cc_start: 0.9421 (OUTLIER) cc_final: 0.9205 (p) REVERT: B 237 ARG cc_start: 0.8840 (ttm170) cc_final: 0.8597 (mtp85) REVERT: B 242 LEU cc_start: 0.8684 (mp) cc_final: 0.8109 (tp) REVERT: C 19 LYS cc_start: 0.9114 (ttmm) cc_final: 0.8857 (ttmm) REVERT: C 48 MET cc_start: 0.8680 (mtp) cc_final: 0.8468 (mtp) REVERT: D 27 GLN cc_start: 0.9059 (pm20) cc_final: 0.8757 (pm20) REVERT: D 46 ARG cc_start: 0.8760 (ttp-170) cc_final: 0.8510 (ttp-110) REVERT: D 62 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.8106 (ttp80) REVERT: D 71 ASP cc_start: 0.8789 (m-30) cc_final: 0.8549 (p0) REVERT: D 78 ARG cc_start: 0.7932 (ptm-80) cc_final: 0.7370 (ptm-80) REVERT: E 227 VAL cc_start: 0.9413 (p) cc_final: 0.9212 (m) REVERT: E 242 LEU cc_start: 0.8765 (mp) cc_final: 0.8230 (tp) REVERT: E 646 ARG cc_start: 0.8260 (tpt90) cc_final: 0.8051 (tpm170) REVERT: E 935 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8298 (tt0) REVERT: F 10 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7282 (tm-30) REVERT: F 87 ARG cc_start: 0.8777 (mtm-85) cc_final: 0.8492 (mtm-85) REVERT: F 98 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8097 (ttt180) REVERT: F 120 LEU cc_start: 0.8884 (tp) cc_final: 0.8672 (tm) REVERT: G 2 ILE cc_start: 0.8550 (tt) cc_final: 0.8137 (tt) REVERT: G 4 MET cc_start: 0.8603 (mmm) cc_final: 0.7688 (mmm) REVERT: G 27 GLN cc_start: 0.8533 (mp10) cc_final: 0.7980 (mp10) REVERT: G 38 GLN cc_start: 0.7478 (pp30) cc_final: 0.6712 (pp30) REVERT: G 43 GLN cc_start: 0.8888 (pt0) cc_final: 0.8562 (pm20) REVERT: G 46 ARG cc_start: 0.8729 (ttp-170) cc_final: 0.8142 (ttp80) REVERT: G 48 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8811 (mm) REVERT: G 78 ARG cc_start: 0.8397 (mtm110) cc_final: 0.7970 (ptp90) REVERT: G 88 TYR cc_start: 0.8405 (m-80) cc_final: 0.7987 (m-80) REVERT: G 104 LYS cc_start: 0.8614 (tptt) cc_final: 0.7920 (tmmt) REVERT: H 10 GLU cc_start: 0.7252 (tm-30) cc_final: 0.6674 (tm-30) REVERT: H 12 LYS cc_start: 0.8665 (ttmm) cc_final: 0.8440 (mtpp) REVERT: H 13 LYS cc_start: 0.7958 (mmtt) cc_final: 0.7720 (mmtt) REVERT: H 23 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8543 (tptm) REVERT: H 46 GLU cc_start: 0.8699 (tt0) cc_final: 0.7998 (tt0) REVERT: H 82 GLU cc_start: 0.8664 (tp30) cc_final: 0.8424 (tp30) REVERT: H 85 ARG cc_start: 0.8537 (ttp80) cc_final: 0.8075 (ttp80) REVERT: L 5 MET cc_start: 0.8529 (pmm) cc_final: 0.8308 (pmm) REVERT: L 43 GLN cc_start: 0.8954 (pm20) cc_final: 0.8291 (pm20) REVERT: L 48 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8597 (mm) REVERT: L 71 ASP cc_start: 0.8823 (t70) cc_final: 0.8490 (p0) REVERT: L 78 ARG cc_start: 0.8594 (pmm-80) cc_final: 0.8066 (pmm150) REVERT: L 80 GLU cc_start: 0.7151 (mp0) cc_final: 0.6837 (mp0) outliers start: 53 outliers final: 29 residues processed: 254 average time/residue: 0.8056 time to fit residues: 235.8659 Evaluate side-chains 253 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 786 LYS Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 935 GLN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 130 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 206 optimal weight: 8.9990 chunk 306 optimal weight: 0.9980 chunk 256 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 293 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 241 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.084429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.053992 restraints weight = 73596.171| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.98 r_work: 0.2801 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 31095 Z= 0.220 Angle : 0.613 8.555 42486 Z= 0.309 Chirality : 0.044 0.189 4956 Planarity : 0.004 0.060 5340 Dihedral : 4.370 20.125 4062 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.88 % Allowed : 9.54 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 0.94 (0.14), residues: 3708 helix: 2.71 (0.20), residues: 648 sheet: 0.52 (0.15), residues: 1017 loop : 0.06 (0.14), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 18 TYR 0.023 0.001 TYR E1067 PHE 0.017 0.001 PHE E 898 TRP 0.018 0.001 TRP F 106 HIS 0.004 0.001 HIS E1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 (30969) covalent geometry : angle 0.60452 / 0.31 (42156) SS BOND : bond 0.00296 / 0.19 ( 48) SS BOND : angle 0.68812 / 0.48 ( 96) hydrogen bonds : bond 0.04465 / 2.90 ( 1314) hydrogen bonds : angle 5.54501 / 3.83 ( 3603) link_BETA1-4 : bond 0.00435 / 0.29 ( 24) link_BETA1-4 : angle 0.93951 / 0.66 ( 72) link_BETA1-6 : bond 0.00162 / 0.08 ( 3) link_BETA1-6 : angle 1.39628 / 0.85 ( 9) link_NAG-ASN : bond 0.00230 / 0.16 ( 51) link_NAG-ASN : angle 1.70445 / 1.12 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 213 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.7943 (tp) REVERT: A 869 MET cc_start: 0.9639 (mtt) cc_final: 0.9414 (mtm) REVERT: A 1094 VAL cc_start: 0.9479 (OUTLIER) cc_final: 0.9245 (p) REVERT: B 237 ARG cc_start: 0.8872 (ttm170) cc_final: 0.8600 (mtp85) REVERT: B 242 LEU cc_start: 0.8666 (mp) cc_final: 0.8102 (tp) REVERT: C 10 GLU cc_start: 0.6689 (tm-30) cc_final: 0.6416 (tm-30) REVERT: C 19 LYS cc_start: 0.9117 (ttmm) cc_final: 0.8830 (ttmm) REVERT: C 23 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8613 (tptm) REVERT: C 48 MET cc_start: 0.8716 (mtp) cc_final: 0.8499 (mtp) REVERT: D 27 GLN cc_start: 0.9063 (pm20) cc_final: 0.8856 (pm20) REVERT: D 46 ARG cc_start: 0.8771 (ttp-170) cc_final: 0.8508 (ttp-110) REVERT: D 62 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7966 (ttp80) REVERT: D 71 ASP cc_start: 0.8818 (m-30) cc_final: 0.8597 (p0) REVERT: D 78 ARG cc_start: 0.7917 (ptm-80) cc_final: 0.7684 (ptm-80) REVERT: E 227 VAL cc_start: 0.9416 (p) cc_final: 0.9214 (m) REVERT: E 242 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8202 (tp) REVERT: E 319 ARG cc_start: 0.8573 (ttm110) cc_final: 0.8305 (mtp-110) REVERT: E 452 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8866 (mtt180) REVERT: E 646 ARG cc_start: 0.8295 (tpt90) cc_final: 0.8071 (tpm170) REVERT: F 10 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7256 (tm-30) REVERT: F 81 MET cc_start: 0.8561 (tmm) cc_final: 0.8334 (tmm) REVERT: F 98 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7811 (ttt180) REVERT: F 120 LEU cc_start: 0.8882 (tp) cc_final: 0.8678 (tm) REVERT: G 2 ILE cc_start: 0.8615 (tt) cc_final: 0.8190 (tt) REVERT: G 4 MET cc_start: 0.8597 (mmm) cc_final: 0.7724 (mmm) REVERT: G 27 GLN cc_start: 0.8523 (mp10) cc_final: 0.7947 (mp10) REVERT: G 38 GLN cc_start: 0.7612 (pp30) cc_final: 0.6837 (pp30) REVERT: G 46 ARG cc_start: 0.8736 (ttp-170) cc_final: 0.8097 (ttp-170) REVERT: G 48 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8833 (mm) REVERT: G 78 ARG cc_start: 0.8367 (mtm110) cc_final: 0.8057 (ptp90) REVERT: G 88 TYR cc_start: 0.8479 (m-80) cc_final: 0.8054 (m-80) REVERT: G 104 LYS cc_start: 0.8695 (tptt) cc_final: 0.8100 (tmmt) REVERT: H 10 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6595 (tm-30) REVERT: H 13 LYS cc_start: 0.7956 (mmtt) cc_final: 0.7702 (mmtt) REVERT: H 23 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8446 (tptm) REVERT: H 46 GLU cc_start: 0.8709 (tt0) cc_final: 0.7952 (tt0) REVERT: H 82 GLU cc_start: 0.8683 (tp30) cc_final: 0.8434 (tp30) REVERT: H 85 ARG cc_start: 0.8562 (ttp80) cc_final: 0.8100 (ttp80) REVERT: L 43 GLN cc_start: 0.8940 (pm20) cc_final: 0.8285 (pm20) REVERT: L 48 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8586 (mm) REVERT: L 71 ASP cc_start: 0.8821 (t70) cc_final: 0.8559 (p0) REVERT: L 78 ARG cc_start: 0.8631 (pmm-80) cc_final: 0.8295 (pmm150) outliers start: 60 outliers final: 27 residues processed: 249 average time/residue: 0.8393 time to fit residues: 240.6343 Evaluate side-chains 244 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 452 ARG Chi-restraints excluded: chain E residue 786 LYS Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 143 optimal weight: 0.8980 chunk 270 optimal weight: 0.0670 chunk 119 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 245 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 294 optimal weight: 0.9990 chunk 241 optimal weight: 0.0670 chunk 172 optimal weight: 0.9990 chunk 302 optimal weight: 0.8980 chunk 159 optimal weight: 0.0170 overall best weight: 0.3894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 955 ASN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.086004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.055964 restraints weight = 73127.716| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.97 r_work: 0.2855 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 31095 Z= 0.108 Angle : 0.574 9.656 42486 Z= 0.287 Chirality : 0.042 0.167 4956 Planarity : 0.004 0.061 5340 Dihedral : 4.142 17.325 4062 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.38 % Allowed : 10.01 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 1.03 (0.14), residues: 3708 helix: 2.74 (0.19), residues: 666 sheet: 0.60 (0.15), residues: 1023 loop : 0.09 (0.14), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 18 TYR 0.021 0.001 TYR A 28 PHE 0.014 0.001 PHE A 133 TRP 0.013 0.001 TRP H 106 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (30969) covalent geometry : angle 0.56649 / 0.29 (42156) SS BOND : bond 0.00192 / 0.12 ( 48) SS BOND : angle 0.65828 / 0.44 ( 96) hydrogen bonds : bond 0.03776 / 2.47 ( 1314) hydrogen bonds : angle 5.35546 / 3.70 ( 3603) link_BETA1-4 : bond 0.00522 / 0.35 ( 24) link_BETA1-4 : angle 0.89662 / 0.61 ( 72) link_BETA1-6 : bond 0.00114 / 0.06 ( 3) link_BETA1-6 : angle 1.17490 / 0.72 ( 9) link_NAG-ASN : bond 0.00225 / 0.15 ( 51) link_NAG-ASN : angle 1.54969 / 1.03 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 0.975 Fit side-chains REVERT: A 242 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8017 (tp) REVERT: A 869 MET cc_start: 0.9625 (mtt) cc_final: 0.9421 (mtm) REVERT: A 940 SER cc_start: 0.8553 (OUTLIER) cc_final: 0.8142 (m) REVERT: A 1094 VAL cc_start: 0.9353 (OUTLIER) cc_final: 0.9140 (p) REVERT: B 237 ARG cc_start: 0.8849 (ttm170) cc_final: 0.8598 (mtp85) REVERT: B 242 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8094 (tp) REVERT: C 10 GLU cc_start: 0.6769 (tm-30) cc_final: 0.6384 (tm-30) REVERT: C 19 LYS cc_start: 0.9063 (ttmm) cc_final: 0.8744 (ttmm) REVERT: C 81 MET cc_start: 0.8528 (tmm) cc_final: 0.8151 (tpt) REVERT: D 43 GLN cc_start: 0.8862 (mt0) cc_final: 0.8634 (mt0) REVERT: D 46 ARG cc_start: 0.8749 (ttp-170) cc_final: 0.8495 (ttp-110) REVERT: D 62 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7807 (ttp80) REVERT: D 71 ASP cc_start: 0.8804 (m-30) cc_final: 0.8571 (p0) REVERT: D 78 ARG cc_start: 0.7878 (ptm-80) cc_final: 0.7632 (ptm-80) REVERT: D 88 TYR cc_start: 0.8429 (m-80) cc_final: 0.8141 (m-80) REVERT: E 242 LEU cc_start: 0.8702 (mp) cc_final: 0.8253 (tp) REVERT: E 646 ARG cc_start: 0.8251 (tpt90) cc_final: 0.8014 (tpm170) REVERT: E 1094 VAL cc_start: 0.9343 (m) cc_final: 0.9064 (p) REVERT: F 10 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7374 (tm-30) REVERT: F 46 GLU cc_start: 0.8731 (tt0) cc_final: 0.8211 (tt0) REVERT: F 81 MET cc_start: 0.8475 (tmm) cc_final: 0.8229 (tmm) REVERT: F 87 ARG cc_start: 0.8817 (mtm-85) cc_final: 0.8569 (mtm-85) REVERT: F 98 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8146 (ttt180) REVERT: G 2 ILE cc_start: 0.8557 (tt) cc_final: 0.8105 (tt) REVERT: G 4 MET cc_start: 0.8590 (mmm) cc_final: 0.7700 (mmm) REVERT: G 27 GLN cc_start: 0.8569 (mp10) cc_final: 0.8022 (mp10) REVERT: G 38 GLN cc_start: 0.7685 (pp30) cc_final: 0.7108 (pp30) REVERT: G 46 ARG cc_start: 0.8753 (ttp-170) cc_final: 0.8310 (ttp80) REVERT: G 48 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8834 (mm) REVERT: G 88 TYR cc_start: 0.8409 (m-80) cc_final: 0.8004 (m-80) REVERT: G 104 LYS cc_start: 0.8641 (tptt) cc_final: 0.8012 (tmmt) REVERT: H 10 GLU cc_start: 0.7350 (tm-30) cc_final: 0.6936 (tm-30) REVERT: H 12 LYS cc_start: 0.8706 (ttmm) cc_final: 0.8483 (mtpp) REVERT: H 13 LYS cc_start: 0.7941 (mmtt) cc_final: 0.7585 (mmtt) REVERT: H 23 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8515 (tptm) REVERT: H 46 GLU cc_start: 0.8741 (tt0) cc_final: 0.8093 (tt0) REVERT: H 82 GLU cc_start: 0.8610 (tp30) cc_final: 0.8264 (tp30) REVERT: H 85 ARG cc_start: 0.8564 (ttp80) cc_final: 0.8299 (ptp90) REVERT: L 43 GLN cc_start: 0.8919 (pm20) cc_final: 0.8666 (pm20) REVERT: L 48 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8582 (mm) REVERT: L 71 ASP cc_start: 0.8843 (t70) cc_final: 0.8541 (p0) REVERT: L 78 ARG cc_start: 0.8617 (pmm-80) cc_final: 0.8190 (pmm150) REVERT: L 98 THR cc_start: 0.9005 (m) cc_final: 0.8622 (p) outliers start: 44 outliers final: 23 residues processed: 256 average time/residue: 0.7824 time to fit residues: 231.3111 Evaluate side-chains 249 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 786 LYS Chi-restraints excluded: chain E residue 900 MET Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 278 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 325 optimal weight: 4.9990 chunk 158 optimal weight: 0.0870 chunk 141 optimal weight: 5.9990 chunk 199 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 317 optimal weight: 2.9990 chunk 238 optimal weight: 6.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.084521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.054276 restraints weight = 73163.050| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.95 r_work: 0.2811 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 31095 Z= 0.205 Angle : 0.618 9.284 42486 Z= 0.310 Chirality : 0.044 0.196 4956 Planarity : 0.005 0.073 5340 Dihedral : 4.317 19.853 4062 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.22 % Allowed : 10.60 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 0.93 (0.14), residues: 3708 helix: 2.48 (0.19), residues: 690 sheet: 0.57 (0.15), residues: 1011 loop : 0.04 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 85 TYR 0.028 0.001 TYR E 28 PHE 0.040 0.001 PHE E 168 TRP 0.017 0.001 TRP F 106 HIS 0.004 0.001 HIS E1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (30969) covalent geometry : angle 0.61031 / 0.31 (42156) SS BOND : bond 0.00255 / 0.17 ( 48) SS BOND : angle 0.67337 / 0.46 ( 96) hydrogen bonds : bond 0.04335 / 2.81 ( 1314) hydrogen bonds : angle 5.45630 / 3.77 ( 3603) link_BETA1-4 : bond 0.00446 / 0.30 ( 24) link_BETA1-4 : angle 0.92772 / 0.65 ( 72) link_BETA1-6 : bond 0.00097 / 0.05 ( 3) link_BETA1-6 : angle 1.35041 / 0.82 ( 9) link_NAG-ASN : bond 0.00222 / 0.16 ( 51) link_NAG-ASN : angle 1.66002 / 1.09 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 1.183 Fit side-chains REVERT: A 242 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.7999 (tp) REVERT: A 869 MET cc_start: 0.9637 (mtt) cc_final: 0.9415 (mtm) REVERT: A 940 SER cc_start: 0.8583 (OUTLIER) cc_final: 0.8173 (m) REVERT: A 1094 VAL cc_start: 0.9443 (OUTLIER) cc_final: 0.9221 (p) REVERT: B 237 ARG cc_start: 0.8868 (ttm170) cc_final: 0.8594 (mtp85) REVERT: B 242 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8086 (tp) REVERT: C 10 GLU cc_start: 0.6945 (tm-30) cc_final: 0.6630 (tm-30) REVERT: C 19 LYS cc_start: 0.9056 (ttmm) cc_final: 0.8721 (ttmm) REVERT: C 46 GLU cc_start: 0.8326 (tt0) cc_final: 0.7851 (pt0) REVERT: C 85 ARG cc_start: 0.8437 (mtm110) cc_final: 0.7973 (ptp-110) REVERT: D 46 ARG cc_start: 0.8729 (ttp-170) cc_final: 0.8479 (ttp-110) REVERT: D 62 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7804 (ttp80) REVERT: D 71 ASP cc_start: 0.8834 (m-30) cc_final: 0.8602 (p0) REVERT: D 78 ARG cc_start: 0.7842 (ptm-80) cc_final: 0.7581 (ptm-80) REVERT: E 242 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8256 (tp) REVERT: E 646 ARG cc_start: 0.8311 (tpt90) cc_final: 0.8044 (tpm170) REVERT: F 10 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7343 (tm-30) REVERT: F 46 GLU cc_start: 0.8739 (tt0) cc_final: 0.8222 (tt0) REVERT: F 87 ARG cc_start: 0.8870 (mtm-85) cc_final: 0.8640 (mtm-85) REVERT: F 98 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8134 (ttt180) REVERT: G 2 ILE cc_start: 0.8635 (tt) cc_final: 0.8179 (tt) REVERT: G 4 MET cc_start: 0.8592 (mmm) cc_final: 0.7752 (mmm) REVERT: G 27 GLN cc_start: 0.8561 (mp10) cc_final: 0.8019 (mp10) REVERT: G 38 GLN cc_start: 0.7757 (pp30) cc_final: 0.7033 (pp30) REVERT: G 46 ARG cc_start: 0.8727 (ttp-170) cc_final: 0.8223 (ttp-170) REVERT: G 48 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8856 (mm) REVERT: G 80 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7057 (mp0) REVERT: G 88 TYR cc_start: 0.8451 (m-80) cc_final: 0.8059 (m-80) REVERT: H 12 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8369 (ttpp) REVERT: H 13 LYS cc_start: 0.7918 (mmtt) cc_final: 0.7582 (mmtt) REVERT: H 23 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8454 (tptm) REVERT: H 46 GLU cc_start: 0.8722 (tt0) cc_final: 0.7958 (tt0) REVERT: H 82 GLU cc_start: 0.8626 (tp30) cc_final: 0.8323 (tp30) REVERT: H 85 ARG cc_start: 0.8594 (ttp80) cc_final: 0.8313 (ptp90) REVERT: L 43 GLN cc_start: 0.8931 (pm20) cc_final: 0.8281 (pm20) REVERT: L 48 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8597 (mm) REVERT: L 71 ASP cc_start: 0.8810 (t70) cc_final: 0.8468 (p0) REVERT: L 78 ARG cc_start: 0.8645 (pmm-80) cc_final: 0.8236 (pmm150) outliers start: 39 outliers final: 22 residues processed: 237 average time/residue: 0.7398 time to fit residues: 202.0191 Evaluate side-chains 235 residues out of total 3261 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 786 LYS Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 95 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 313 optimal weight: 0.9980 chunk 339 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 288 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 955 ASN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.085098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.055040 restraints weight = 73370.818| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.96 r_work: 0.2835 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31095 Z= 0.141 Angle : 0.591 9.405 42486 Z= 0.298 Chirality : 0.043 0.172 4956 Planarity : 0.004 0.073 5340 Dihedral : 4.258 19.509 4062 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.19 % Allowed : 10.79 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 0.98 (0.14), residues: 3708 helix: 2.52 (0.19), residues: 690 sheet: 0.62 (0.15), residues: 1017 loop : 0.06 (0.14), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG L 18 TYR 0.020 0.001 TYR A 28 PHE 0.038 0.001 PHE E 168 TRP 0.015 0.001 TRP F 106 HIS 0.002 0.001 HIS E1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (30969) covalent geometry : angle 0.58347 / 0.30 (42156) SS BOND : bond 0.00217 / 0.14 ( 48) SS BOND : angle 0.64118 / 0.43 ( 96) hydrogen bonds : bond 0.04020 / 2.61 ( 1314) hydrogen bonds : angle 5.38919 / 3.73 ( 3603) link_BETA1-4 : bond 0.00484 / 0.32 ( 24) link_BETA1-4 : angle 0.90571 / 0.62 ( 72) link_BETA1-6 : bond 0.00027 / 0.01 ( 3) link_BETA1-6 : angle 1.26988 / 0.77 ( 9) link_NAG-ASN : bond 0.00193 / 0.14 ( 51) link_NAG-ASN : angle 1.57690 / 1.04 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17402.87 seconds wall clock time: 295 minutes 37.83 seconds (17737.83 seconds total)