Starting phenix.real_space_refine on Fri Feb 6 20:02:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ofp_70441/02_2026/9ofp_70441.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ofp_70441/02_2026/9ofp_70441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ofp_70441/02_2026/9ofp_70441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ofp_70441/02_2026/9ofp_70441.map" model { file = "/net/cci-nas-00/data/ceres_data/9ofp_70441/02_2026/9ofp_70441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ofp_70441/02_2026/9ofp_70441.cif" } resolution = 3.16 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= 0.002 sd= 0.036 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 126 5.16 5 C 17130 2.51 5 N 4391 2.21 5 O 5516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27163 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 7768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 7768 Classifications: {'peptide': 1012} Link IDs: {'PTRANS': 36, 'TRANS': 975} Chain: "B" Number of atoms: 7768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 7768 Classifications: {'peptide': 1012} Link IDs: {'PTRANS': 36, 'TRANS': 975} Chain: "C" Number of atoms: 6694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 873, 6694 Classifications: {'peptide': 873} Link IDs: {'PTRANS': 28, 'TRANS': 844} Chain breaks: 1 Chain: "H" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 944 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "M" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 944 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "N" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 6.87, per 1000 atoms: 0.25 Number of scatterers: 27163 At special positions: 0 Unit cell: (129.6, 145.8, 190.08, 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 126 16.00 O 5516 8.00 N 4391 7.00 C 17130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 32 " - pdb=" SG CYS A 229 " distance=2.03 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 263 " distance=2.03 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 319 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 384 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 444 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 541 " - pdb=" SG CYS A 554 " distance=2.03 Simple disulfide: pdb=" SG CYS A 606 " - pdb=" SG CYS A 628 " distance=2.03 Simple disulfide: pdb=" SG CYS A 611 " - pdb=" SG CYS A 617 " distance=2.03 Simple disulfide: pdb=" SG CYS A 713 " - pdb=" SG CYS A 724 " distance=2.03 Simple disulfide: pdb=" SG CYS A 915 " - pdb=" SG CYS A 926 " distance=2.03 Simple disulfide: pdb=" SG CYS A 965 " - pdb=" SG CYS A1012 " distance=2.03 Simple disulfide: pdb=" SG CYS B 32 " - pdb=" SG CYS B 229 " distance=2.03 Simple disulfide: pdb=" SG CYS B 81 " - pdb=" SG CYS B 105 " distance=2.03 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 263 " distance=2.03 Simple disulfide: pdb=" SG CYS B 316 " - pdb=" SG CYS B 319 " distance=2.04 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 384 " distance=2.04 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 444 " - pdb=" SG CYS B 495 " distance=2.04 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 554 " distance=2.02 Simple disulfide: pdb=" SG CYS B 606 " - pdb=" SG CYS B 628 " distance=2.03 Simple disulfide: pdb=" SG CYS B 611 " - pdb=" SG CYS B 617 " distance=2.03 Simple disulfide: pdb=" SG CYS B 713 " - pdb=" SG CYS B 724 " distance=2.03 Simple disulfide: pdb=" SG CYS B 915 " - pdb=" SG CYS B 926 " distance=2.04 Simple disulfide: pdb=" SG CYS B 965 " - pdb=" SG CYS B1012 " distance=2.03 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 229 " distance=2.02 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 105 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 254 " - pdb=" SG CYS C 263 " distance=2.03 Simple disulfide: pdb=" SG CYS C 444 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 541 " - pdb=" SG CYS C 554 " distance=2.03 Simple disulfide: pdb=" SG CYS C 606 " - pdb=" SG CYS C 628 " distance=2.03 Simple disulfide: pdb=" SG CYS C 611 " - pdb=" SG CYS C 617 " distance=2.03 Simple disulfide: pdb=" SG CYS C 713 " - pdb=" SG CYS C 724 " distance=2.03 Simple disulfide: pdb=" SG CYS C 915 " - pdb=" SG CYS C 926 " distance=2.03 Simple disulfide: pdb=" SG CYS C 965 " - pdb=" SG CYS C1012 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " 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 D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG A1201 " - " ASN A 111 " " NAG A1202 " - " ASN A 147 " " NAG A1203 " - " ASN A 171 " " NAG A1204 " - " ASN A 220 " " NAG A1205 " - " ASN A 332 " " NAG A1206 " - " ASN A 438 " " NAG A1207 " - " ASN A 462 " " NAG A1208 " - " ASN A 486 " " NAG A1209 " - " ASN A 516 " " NAG A1210 " - " ASN A 536 " " NAG A1211 " - " ASN A 540 " " NAG A1212 " - " ASN A 566 " " NAG A1213 " - " ASN A 579 " " NAG A1214 " - " ASN A 585 " " NAG A1215 " - " ASN A 661 " " NAG A1216 " - " ASN A1035 " " NAG B1201 " - " ASN B 111 " " NAG B1202 " - " ASN B 147 " " NAG B1203 " - " ASN B 220 " " NAG B1204 " - " ASN B 438 " " NAG B1205 " - " ASN B 462 " " NAG B1206 " - " ASN B 486 " " NAG B1207 " - " ASN B 516 " " NAG B1208 " - " ASN B 536 " " NAG B1209 " - " ASN B 540 " " NAG B1210 " - " ASN B 566 " " NAG B1211 " - " ASN B 579 " " NAG B1212 " - " ASN B 585 " " NAG B1213 " - " ASN B 661 " " NAG B1214 " - " ASN B1035 " " NAG C1201 " - " ASN C 111 " " NAG C1202 " - " ASN C 147 " " NAG C1203 " - " ASN C 171 " " NAG C1204 " - " ASN C 220 " " NAG C1205 " - " ASN C 438 " " NAG C1206 " - " ASN C 462 " " NAG C1207 " - " ASN C 486 " " NAG C1208 " - " ASN C 516 " " NAG C1209 " - " ASN C 536 " " NAG C1210 " - " ASN C 540 " " NAG C1211 " - " ASN C 566 " " NAG C1212 " - " ASN C 579 " " NAG C1213 " - " ASN C 585 " " NAG C1214 " - " ASN C 661 " " NAG C1215 " - " ASN C1035 " " NAG D 1 " - " ASN A 62 " " NAG E 1 " - " ASN A 98 " " NAG F 1 " - " ASN A 242 " " NAG G 1 " - " ASN A 325 " " NAG I 1 " - " ASN A 669 " " NAG J 1 " - " ASN A 928 " " NAG K 1 " - " ASN A1013 " " NAG O 1 " - " ASN A1018 " " NAG P 1 " - " ASN B 62 " " NAG Q 1 " - " ASN B 98 " " NAG R 1 " - " ASN B 171 " " NAG S 1 " - " ASN B 242 " " NAG T 1 " - " ASN B 325 " " NAG U 1 " - " ASN B 669 " " NAG V 1 " - " ASN B 928 " " NAG W 1 " - " ASN B1013 " " NAG X 1 " - " ASN B1018 " " NAG Y 1 " - " ASN C 62 " " NAG Z 1 " - " ASN C 98 " " NAG a 1 " - " ASN C 242 " " NAG b 1 " - " ASN C 669 " " NAG c 1 " - " ASN C 928 " " NAG d 1 " - " ASN C1013 " " NAG e 1 " - " ASN C1018 " Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.2 seconds 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6228 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 47 sheets defined 24.5% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 148 through 153 removed outlier: 3.505A pdb=" N SER A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 518 through 522 removed outlier: 4.138A pdb=" N GLY A 521 " --> pdb=" O THR A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 612 removed outlier: 3.757A pdb=" N VAL A 610 " --> pdb=" O CYS A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 622 removed outlier: 3.664A pdb=" N VAL A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 650 removed outlier: 3.523A pdb=" N LEU A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 647 " --> pdb=" O SER A 643 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET A 649 " --> pdb=" O ASP A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 659 removed outlier: 4.080A pdb=" N LEU A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 666 removed outlier: 3.532A pdb=" N PHE A 665 " --> pdb=" O VAL A 662 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY A 666 " --> pdb=" O SER A 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 662 through 666' Processing helix chain 'A' and resid 669 through 673 removed outlier: 4.383A pdb=" N SER A 672 " --> pdb=" O ASN A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 696 Processing helix chain 'A' and resid 709 through 716 removed outlier: 3.657A pdb=" N THR A 714 " --> pdb=" O TYR A 710 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 739 through 754 removed outlier: 3.823A pdb=" N ILE A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 763 removed outlier: 4.156A pdb=" N ALA A 763 " --> pdb=" O THR A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 777 removed outlier: 3.505A pdb=" N ALA A 770 " --> pdb=" O PRO A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 809 removed outlier: 3.698A pdb=" N LEU A 792 " --> pdb=" O ASN A 788 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 804 " --> pdb=" O MET A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 818 through 838 removed outlier: 3.849A pdb=" N VAL A 824 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN A 838 " --> pdb=" O VAL A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 848 removed outlier: 3.749A pdb=" N ASN A 843 " --> pdb=" O GLY A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 851 No H-bonds generated for 'chain 'A' and resid 849 through 851' Processing helix chain 'A' and resid 859 through 864 Processing helix chain 'A' and resid 868 through 915 removed outlier: 3.742A pdb=" N GLN A 874 " --> pdb=" O PRO A 870 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG A 878 " --> pdb=" O GLN A 874 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 879 " --> pdb=" O GLN A 875 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1004 No H-bonds generated for 'chain 'A' and resid 1002 through 1004' Processing helix chain 'A' and resid 1020 through 1027 removed outlier: 3.647A pdb=" N LEU A1024 " --> pdb=" O ARG A1021 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLN A1025 " --> pdb=" O SER A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1041 removed outlier: 3.560A pdb=" N GLU A1040 " --> pdb=" O LYS A1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 266 Processing helix chain 'B' and resid 371 through 376 removed outlier: 3.879A pdb=" N VAL B 374 " --> pdb=" O PHE B 371 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN B 375 " --> pdb=" O GLY B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 612 removed outlier: 3.540A pdb=" N VAL B 610 " --> pdb=" O CYS B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 622 removed outlier: 3.593A pdb=" N GLU B 619 " --> pdb=" O VAL B 615 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 620 " --> pdb=" O ARG B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 650 removed outlier: 4.637A pdb=" N LYS B 629 " --> pdb=" O THR B 625 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 631 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 646 " --> pdb=" O GLU B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 658 Processing helix chain 'B' and resid 662 through 666 removed outlier: 3.708A pdb=" N PHE B 665 " --> pdb=" O VAL B 662 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY B 666 " --> pdb=" O SER B 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 662 through 666' Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 709 through 716 removed outlier: 3.821A pdb=" N THR B 714 " --> pdb=" O TYR B 710 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS B 715 " --> pdb=" O LYS B 711 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY B 716 " --> pdb=" O LYS B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 728 removed outlier: 3.681A pdb=" N GLN B 726 " --> pdb=" O LEU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 753 removed outlier: 3.563A pdb=" N SER B 749 " --> pdb=" O MET B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 756 No H-bonds generated for 'chain 'B' and resid 754 through 756' Processing helix chain 'B' and resid 759 through 763 Processing helix chain 'B' and resid 766 through 777 removed outlier: 3.704A pdb=" N ALA B 770 " --> pdb=" O PRO B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 809 Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.636A pdb=" N THR B 815 " --> pdb=" O ASP B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 838 removed outlier: 3.515A pdb=" N THR B 823 " --> pdb=" O GLN B 819 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL B 824 " --> pdb=" O ALA B 820 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP B 833 " --> pdb=" O ASN B 829 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN B 838 " --> pdb=" O VAL B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 848 Processing helix chain 'B' and resid 849 through 851 No H-bonds generated for 'chain 'B' and resid 849 through 851' Processing helix chain 'B' and resid 860 through 867 removed outlier: 3.725A pdb=" N ARG B 866 " --> pdb=" O ALA B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 916 removed outlier: 4.259A pdb=" N GLN B 874 " --> pdb=" O PRO B 870 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN B 875 " --> pdb=" O GLN B 871 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ARG B 878 " --> pdb=" O GLN B 874 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU B 879 " --> pdb=" O GLN B 875 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 900 " --> pdb=" O THR B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1004 No H-bonds generated for 'chain 'B' and resid 1002 through 1004' Processing helix chain 'B' and resid 1020 through 1027 removed outlier: 4.498A pdb=" N GLN B1025 " --> pdb=" O SER B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1042 removed outlier: 3.619A pdb=" N GLN B1039 " --> pdb=" O ASN B1035 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 152 removed outlier: 3.656A pdb=" N VAL C 151 " --> pdb=" O ASN C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 266 Processing helix chain 'C' and resid 518 through 522 removed outlier: 3.801A pdb=" N GLY C 521 " --> pdb=" O THR C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 612 Processing helix chain 'C' and resid 614 through 622 removed outlier: 3.573A pdb=" N GLU C 619 " --> pdb=" O VAL C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 648 removed outlier: 3.998A pdb=" N CYS C 628 " --> pdb=" O TYR C 624 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS C 629 " --> pdb=" O THR C 625 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 638 " --> pdb=" O ALA C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 659 removed outlier: 3.663A pdb=" N LEU C 659 " --> pdb=" O LYS C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 666 removed outlier: 6.234A pdb=" N SER C 663 " --> pdb=" O ALA C 660 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE C 665 " --> pdb=" O VAL C 662 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY C 666 " --> pdb=" O SER C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 673 removed outlier: 4.568A pdb=" N SER C 672 " --> pdb=" O ASN C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 694 removed outlier: 3.681A pdb=" N ILE C 693 " --> pdb=" O ALA C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 714 removed outlier: 3.614A pdb=" N THR C 714 " --> pdb=" O TYR C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 729 removed outlier: 3.736A pdb=" N ASN C 729 " --> pdb=" O ALA C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 753 removed outlier: 3.694A pdb=" N MET C 743 " --> pdb=" O ASP C 739 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA C 744 " --> pdb=" O ALA C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 756 No H-bonds generated for 'chain 'C' and resid 754 through 756' Processing helix chain 'C' and resid 759 through 763 removed outlier: 3.634A pdb=" N ALA C 763 " --> pdb=" O THR C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 776 removed outlier: 3.685A pdb=" N ALA C 770 " --> pdb=" O PRO C 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 809 removed outlier: 3.641A pdb=" N LEU C 792 " --> pdb=" O ASN C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 817 removed outlier: 3.593A pdb=" N ILE C 814 " --> pdb=" O ASN C 811 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLN C 816 " --> pdb=" O ALA C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 838 removed outlier: 3.707A pdb=" N VAL C 824 " --> pdb=" O ALA C 820 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN C 838 " --> pdb=" O VAL C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 839 through 848 removed outlier: 3.539A pdb=" N ASN C 843 " --> pdb=" O GLY C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 851 No H-bonds generated for 'chain 'C' and resid 849 through 851' Processing helix chain 'C' and resid 859 through 867 removed outlier: 3.591A pdb=" N TYR C 864 " --> pdb=" O ILE C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 915 removed outlier: 4.694A pdb=" N GLN C 874 " --> pdb=" O PRO C 870 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN C 875 " --> pdb=" O GLN C 871 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG C 878 " --> pdb=" O GLN C 874 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU C 879 " --> pdb=" O GLN C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 1002 through 1004 No H-bonds generated for 'chain 'C' and resid 1002 through 1004' Processing helix chain 'C' and resid 1021 through 1027 removed outlier: 4.310A pdb=" N GLN C1025 " --> pdb=" O SER C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1042 removed outlier: 3.689A pdb=" N GLN C1039 " --> pdb=" O ASN C1035 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.599A pdb=" N ASP H 86 " --> pdb=" O ARG H 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 30 No H-bonds generated for 'chain 'M' and resid 28 through 30' Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 83 removed outlier: 5.322A pdb=" N VAL A 70 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL A 243 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ARG A 72 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL A 241 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N PHE A 74 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL A 239 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA A 237 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 233 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU A 82 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 231 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N HIS A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N PHE A 201 " --> pdb=" O TYR A 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 83 removed outlier: 5.322A pdb=" N VAL A 70 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL A 243 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ARG A 72 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL A 241 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N PHE A 74 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL A 239 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA A 237 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 233 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU A 82 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 231 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN A 250 " --> pdb=" O ASN A 242 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N SER A 244 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 95 through 96 removed outlier: 4.056A pdb=" N ALA A 216 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY A 130 " --> pdb=" O CYS A 145 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N CYS A 145 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 184 " --> pdb=" O CYS A 168 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL A 170 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N PHE A 182 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR A 172 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N SER A 180 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE A 174 " --> pdb=" O THR A 178 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 273 through 277 removed outlier: 6.615A pdb=" N GLN A 500 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA A 511 " --> pdb=" O GLN A 500 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 502 " --> pdb=" O VAL A 509 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 437 through 438 removed outlier: 5.372A pdb=" N LEU A 479 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TYR A 471 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 327 removed outlier: 6.236A pdb=" N THR A 299 " --> pdb=" O THR A 346 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N GLN A 348 " --> pdb=" O THR A 299 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE A 301 " --> pdb=" O GLN A 348 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL A 350 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU A 303 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N TYR A 414 " --> pdb=" O PHE A 385 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE A 385 " --> pdb=" O TYR A 414 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER A 416 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL A 383 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N SER A 418 " --> pdb=" O GLY A 381 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY A 420 " --> pdb=" O LYS A 379 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LYS A 379 " --> pdb=" O GLY A 420 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 327 removed outlier: 6.236A pdb=" N THR A 299 " --> pdb=" O THR A 346 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N GLN A 348 " --> pdb=" O THR A 299 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE A 301 " --> pdb=" O GLN A 348 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL A 350 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU A 303 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N SER A 407 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU A 402 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ASN A 409 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA A 400 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY A 411 " --> pdb=" O ILE A 398 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 544 through 548 removed outlier: 6.821A pdb=" N VAL A 553 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N THR A 547 " --> pdb=" O PHE A 551 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N PHE A 551 " --> pdb=" O THR A 547 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 566 removed outlier: 5.855A pdb=" N ARG A 565 " --> pdb=" O PHE B 652 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 579 through 596 removed outlier: 6.701A pdb=" N ASN A 579 " --> pdb=" O GLU A 959 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU A 959 " --> pdb=" O ASN A 579 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N SER A 581 " --> pdb=" O ASP A 957 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP A 957 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TYR A 955 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN A 585 " --> pdb=" O THR A 953 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 933 " --> pdb=" O THR A 948 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU A 950 " --> pdb=" O HIS A 931 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N HIS A 931 " --> pdb=" O LEU A 950 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 579 through 596 removed outlier: 6.701A pdb=" N ASN A 579 " --> pdb=" O GLU A 959 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU A 959 " --> pdb=" O ASN A 579 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N SER A 581 " --> pdb=" O ASP A 957 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP A 957 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TYR A 955 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN A 585 " --> pdb=" O THR A 953 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU A 959 " --> pdb=" O LYS A 983 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU A 981 " --> pdb=" O TRP A 961 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 987 " --> pdb=" O GLU A 984 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 602 through 604 Processing sheet with id=AB4, first strand: chain 'A' and resid 651 through 652 Processing sheet with id=AB5, first strand: chain 'A' and resid 1006 through 1009 removed outlier: 3.661A pdb=" N GLY A 971 " --> pdb=" O ILE A1009 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 68 through 84 removed outlier: 5.332A pdb=" N VAL B 70 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL B 243 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ARG B 72 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL B 241 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N PHE B 74 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL B 239 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA B 237 " --> pdb=" O PRO B 76 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU B 233 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU B 82 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL B 231 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N SER B 84 " --> pdb=" O CYS B 229 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N CYS B 229 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 230 " --> pdb=" O ASN B 120 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N HIS B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE B 201 " --> pdb=" O TYR B 208 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 68 through 84 removed outlier: 5.332A pdb=" N VAL B 70 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL B 243 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ARG B 72 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL B 241 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N PHE B 74 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL B 239 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA B 237 " --> pdb=" O PRO B 76 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU B 233 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU B 82 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL B 231 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N SER B 84 " --> pdb=" O CYS B 229 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N CYS B 229 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N SER B 244 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ILE B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 94 through 96 removed outlier: 3.972A pdb=" N ALA B 216 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 140 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N CYS B 168 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 183 " --> pdb=" O CYS B 168 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.670A pdb=" N GLN B 500 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA B 511 " --> pdb=" O GLN B 500 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 502 " --> pdb=" O VAL B 509 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 437 through 438 removed outlier: 6.737A pdb=" N SER B 288 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LEU B 479 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 323 through 327 removed outlier: 3.601A pdb=" N ASN B 325 " --> pdb=" O ASN B 306 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN B 306 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 299 " --> pdb=" O HIS B 344 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 338 through 339 removed outlier: 3.984A pdb=" N GLY B 420 " --> pdb=" O PHE B 380 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N SER M 100D" --> pdb=" O THR B 347 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N PHE B 349 " --> pdb=" O SER M 100D" (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 358 through 362 removed outlier: 6.724A pdb=" N ILE B 398 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 546 through 548 removed outlier: 3.691A pdb=" N LEU B 546 " --> pdb=" O VAL B 553 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 565 through 566 removed outlier: 5.960A pdb=" N ARG B 565 " --> pdb=" O PHE C 652 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 579 through 596 removed outlier: 6.603A pdb=" N ASN B 579 " --> pdb=" O GLU B 959 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLU B 959 " --> pdb=" O ASN B 579 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N SER B 581 " --> pdb=" O ASP B 957 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASP B 957 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR B 955 " --> pdb=" O PRO B 583 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN B 585 " --> pdb=" O THR B 953 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU B 950 " --> pdb=" O HIS B 931 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N HIS B 931 " --> pdb=" O LEU B 950 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 579 through 596 removed outlier: 6.603A pdb=" N ASN B 579 " --> pdb=" O GLU B 959 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLU B 959 " --> pdb=" O ASN B 579 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N SER B 581 " --> pdb=" O ASP B 957 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASP B 957 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR B 955 " --> pdb=" O PRO B 583 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN B 585 " --> pdb=" O THR B 953 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU B 959 " --> pdb=" O LYS B 983 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU B 981 " --> pdb=" O TRP B 961 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 602 through 604 Processing sheet with id=AD1, first strand: chain 'B' and resid 1006 through 1009 removed outlier: 3.638A pdb=" N GLY B 971 " --> pdb=" O ILE B1009 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N CYS B 965 " --> pdb=" O ILE B1019 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 69 through 84 removed outlier: 3.637A pdb=" N LEU C 77 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER C 235 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU C 79 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU C 233 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N CYS C 81 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N VAL C 231 " --> pdb=" O CYS C 81 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N TRP C 83 " --> pdb=" O CYS C 229 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N CYS C 229 " --> pdb=" O TRP C 83 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR C 230 " --> pdb=" O ASN C 120 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N HIS C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N PHE C 201 " --> pdb=" O TYR C 208 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 69 through 84 removed outlier: 3.637A pdb=" N LEU C 77 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER C 235 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU C 79 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU C 233 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N CYS C 81 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N VAL C 231 " --> pdb=" O CYS C 81 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N TRP C 83 " --> pdb=" O CYS C 229 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N CYS C 229 " --> pdb=" O TRP C 83 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASP C 238 " --> pdb=" O TYR C 253 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TYR C 253 " --> pdb=" O ASP C 238 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU C 240 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE C 251 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASN C 242 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 95 through 96 removed outlier: 5.799A pdb=" N GLY C 130 " --> pdb=" O CYS C 145 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N CYS C 145 " --> pdb=" O GLY C 130 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA C 140 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY C 184 " --> pdb=" O CYS C 168 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL C 170 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N PHE C 182 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR C 172 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N SER C 180 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 273 through 277 removed outlier: 6.403A pdb=" N GLN C 500 " --> pdb=" O ALA C 511 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA C 511 " --> pdb=" O GLN C 500 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C 502 " --> pdb=" O VAL C 509 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 437 through 438 removed outlier: 6.754A pdb=" N SER C 288 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LEU C 479 " --> pdb=" O ILE C 492 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR C 471 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 546 through 548 removed outlier: 3.827A pdb=" N LEU C 546 " --> pdb=" O VAL C 553 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 579 through 583 removed outlier: 4.409A pdb=" N GLU C 959 " --> pdb=" O LYS C 983 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU C 981 " --> pdb=" O TRP C 961 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 586 through 596 removed outlier: 6.055A pdb=" N LEU C 950 " --> pdb=" O HIS C 931 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N HIS C 931 " --> pdb=" O LEU C 950 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 602 through 604 Processing sheet with id=AE2, first strand: chain 'C' and resid 1006 through 1009 removed outlier: 3.619A pdb=" N GLY C 971 " --> pdb=" O ILE C1009 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE4, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.584A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA H 50 " --> pdb=" O TYR H 58 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 11 removed outlier: 4.250A pdb=" N TYR H 102 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AE7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.889A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.565A pdb=" N SER M 70 " --> pdb=" O TYR M 79 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 57 through 59 removed outlier: 5.629A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ALA M 33 " --> pdb=" O ASP M 95 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.935A pdb=" N SER N 7 " --> pdb=" O THR N 22 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR N 22 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 11 through 12 removed outlier: 5.282A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) 1013 hydrogen bonds defined for protein. 2715 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: 6.83 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7554 1.33 - 1.46: 7528 1.46 - 1.59: 12445 1.59 - 1.71: 0 1.71 - 1.84: 166 Bond restraints: 27693 Sorted by residual: bond pdb=" CA SER B 461 " pdb=" CB SER B 461 " ideal model delta sigma weight residual 1.534 1.479 0.055 1.49e-02 4.50e+03 1.35e+01 bond pdb=" CD GLN N 90 " pdb=" NE2 GLN N 90 " ideal model delta sigma weight residual 1.328 1.258 0.070 2.10e-02 2.27e+03 1.10e+01 bond pdb=" N PHE C 40 " pdb=" CA PHE C 40 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.27e-02 6.20e+03 8.47e+00 bond pdb=" C2 NAG A1208 " pdb=" C3 NAG A1208 " ideal model delta sigma weight residual 1.526 1.472 0.054 2.00e-02 2.50e+03 7.28e+00 bond pdb=" N VAL A 484 " pdb=" CA VAL A 484 " ideal model delta sigma weight residual 1.460 1.491 -0.032 1.21e-02 6.83e+03 6.79e+00 ... (remaining 27688 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 37191 3.23 - 6.47: 469 6.47 - 9.70: 55 9.70 - 12.94: 6 12.94 - 16.17: 2 Bond angle restraints: 37723 Sorted by residual: angle pdb=" N ASN C 38 " pdb=" CA ASN C 38 " pdb=" C ASN C 38 " ideal model delta sigma weight residual 112.38 100.97 11.41 1.22e+00 6.72e-01 8.75e+01 angle pdb=" N SER C 36 " pdb=" CA SER C 36 " pdb=" C SER C 36 " ideal model delta sigma weight residual 113.38 105.49 7.89 1.17e+00 7.31e-01 4.55e+01 angle pdb=" N ASN A 98 " pdb=" CA ASN A 98 " pdb=" C ASN A 98 " ideal model delta sigma weight residual 113.02 105.83 7.19 1.20e+00 6.94e-01 3.59e+01 angle pdb=" N GLU C 37 " pdb=" CA GLU C 37 " pdb=" C GLU C 37 " ideal model delta sigma weight residual 113.43 105.89 7.54 1.26e+00 6.30e-01 3.59e+01 angle pdb=" C ILE N 29 " pdb=" N THR N 30 " pdb=" CA THR N 30 " ideal model delta sigma weight residual 121.54 132.24 -10.70 1.91e+00 2.74e-01 3.14e+01 ... (remaining 37718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.81: 16398 20.81 - 41.62: 1020 41.62 - 62.43: 188 62.43 - 83.24: 101 83.24 - 104.05: 64 Dihedral angle restraints: 17771 sinusoidal: 8030 harmonic: 9741 Sorted by residual: dihedral pdb=" CB CYS A 316 " pdb=" SG CYS A 316 " pdb=" SG CYS A 319 " pdb=" CB CYS A 319 " ideal model delta sinusoidal sigma weight residual -86.00 -171.54 85.54 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS B 316 " pdb=" SG CYS B 316 " pdb=" SG CYS B 319 " pdb=" CB CYS B 319 " ideal model delta sinusoidal sigma weight residual -86.00 -144.82 58.82 1 1.00e+01 1.00e-02 4.63e+01 dihedral pdb=" CB CYS B 444 " pdb=" SG CYS B 444 " pdb=" SG CYS B 495 " pdb=" CB CYS B 495 " ideal model delta sinusoidal sigma weight residual -86.00 -29.60 -56.40 1 1.00e+01 1.00e-02 4.29e+01 ... (remaining 17768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.628: 4682 0.628 - 1.257: 0 1.257 - 1.885: 1 1.885 - 2.513: 0 2.513 - 3.141: 1 Chirality restraints: 4684 Sorted by residual: chirality pdb=" C1 NAG B1206 " pdb=" ND2 ASN B 486 " pdb=" C2 NAG B1206 " pdb=" O5 NAG B1206 " both_signs ideal model delta sigma weight residual False -2.40 0.74 -3.14 2.00e-01 2.50e+01 2.47e+02 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A1013 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-01 2.50e+01 6.20e+01 chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.07e+01 ... (remaining 4681 not shown) Planarity restraints: 4773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 486 " -0.015 2.00e-02 2.50e+03 1.29e-01 2.08e+02 pdb=" CG ASN B 486 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN B 486 " -0.110 2.00e-02 2.50e+03 pdb=" ND2 ASN B 486 " 0.228 2.00e-02 2.50e+03 pdb=" C1 NAG B1206 " -0.134 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 71 " 0.591 9.50e-02 1.11e+02 2.67e-01 5.80e+01 pdb=" NE ARG M 71 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG M 71 " 0.060 2.00e-02 2.50e+03 pdb=" NH1 ARG M 71 " -0.025 2.00e-02 2.50e+03 pdb=" NH2 ARG M 71 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 262 " 0.559 9.50e-02 1.11e+02 2.52e-01 4.81e+01 pdb=" NE ARG B 262 " -0.052 2.00e-02 2.50e+03 pdb=" CZ ARG B 262 " 0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG B 262 " -0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG B 262 " 0.001 2.00e-02 2.50e+03 ... (remaining 4770 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.12: 3 2.12 - 2.82: 7929 2.82 - 3.51: 36297 3.51 - 4.21: 63415 4.21 - 4.90: 107383 Nonbonded interactions: 215027 Sorted by model distance: nonbonded pdb=" CD1 LEU A 127 " pdb=" CG1 VAL A 221 " model vdw 1.428 3.880 nonbonded pdb=" CD1 LEU B 698 " pdb=" OE1 GLN B 832 " model vdw 1.576 3.460 nonbonded pdb=" NE2 GLN H 39 " pdb=" NE2 GLN L 38 " model vdw 1.982 3.200 nonbonded pdb=" OE2 GLU A1010 " pdb=" NE ARG B 989 " model vdw 2.175 3.120 nonbonded pdb=" OG1 THR A 100 " pdb=" C7 NAG E 1 " model vdw 2.190 3.270 ... (remaining 215022 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 294 or resid 434 through 1214)) selection = (chain 'B' and (resid 32 through 294 or resid 434 through 1214)) selection = (chain 'C' and resid 32 through 1214) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'a' selection = chain 'c' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'O' selection = chain 'S' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'e' } ncs_group { reference = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.500 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: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 28.830 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: 0.010 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.290 27840 Z= 0.198 Angle : 1.042 28.807 38121 Z= 0.483 Chirality : 0.077 3.141 4684 Planarity : 0.014 0.267 4704 Dihedral : 16.166 104.045 11414 Min Nonbonded Distance : 1.428 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.73 % Favored : 95.09 % Rotamer: Outliers : 0.56 % Allowed : 12.81 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -1.79 (0.14), residues: 3341 helix: -1.30 (0.18), residues: 685 sheet: -0.74 (0.17), residues: 838 loop : -1.32 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.067 0.007 ARG M 71 TYR 0.038 0.007 TYR H 59 PHE 0.036 0.002 PHE C 108 TRP 0.055 0.003 TRP H 36 HIS 0.010 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00345 (27693) covalent geometry : angle 0.89460 (37723) SS BOND : bond 0.00380 ( 43) SS BOND : angle 1.38564 ( 86) hydrogen bonds : bond 0.22634 ( 967) hydrogen bonds : angle 9.10829 ( 2715) link_BETA1-4 : bond 0.01624 ( 35) link_BETA1-4 : angle 3.70557 ( 105) link_NAG-ASN : bond 0.03620 ( 69) link_NAG-ASN : angle 6.79650 ( 207) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 490 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 GLU cc_start: 0.7099 (mp0) cc_final: 0.6680 (pm20) REVERT: A 295 TYR cc_start: 0.6755 (t80) cc_final: 0.6542 (t80) REVERT: A 386 SER cc_start: 0.7625 (t) cc_final: 0.6610 (p) REVERT: A 401 ASN cc_start: 0.5328 (p0) cc_final: 0.5059 (p0) REVERT: A 452 VAL cc_start: 0.8576 (t) cc_final: 0.8298 (p) REVERT: A 607 SER cc_start: 0.8460 (t) cc_final: 0.8141 (m) REVERT: A 711 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.6725 (ptpp) REVERT: A 743 MET cc_start: 0.8441 (mmt) cc_final: 0.7916 (mmt) REVERT: A 790 ARG cc_start: 0.7747 (mmm-85) cc_final: 0.7490 (ttm-80) REVERT: A 822 GLN cc_start: 0.8665 (tp40) cc_final: 0.8417 (tp40) REVERT: A 850 ARG cc_start: 0.8446 (mtp85) cc_final: 0.8204 (mtm-85) REVERT: A 851 GLN cc_start: 0.8348 (mm-40) cc_final: 0.7818 (mt0) REVERT: A 902 ARG cc_start: 0.8702 (ttm-80) cc_final: 0.8388 (ttm-80) REVERT: A 941 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7436 (mm-30) REVERT: B 58 PHE cc_start: 0.8644 (m-80) cc_final: 0.8288 (m-80) REVERT: B 109 TYR cc_start: 0.8404 (p90) cc_final: 0.7851 (p90) REVERT: B 122 ASN cc_start: 0.7559 (p0) cc_final: 0.7231 (p0) REVERT: B 207 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8094 (ttp-170) REVERT: B 260 ARG cc_start: 0.8474 (ttm110) cc_final: 0.8124 (ttm110) REVERT: B 264 ASP cc_start: 0.8107 (m-30) cc_final: 0.7833 (m-30) REVERT: B 309 HIS cc_start: 0.4616 (t-170) cc_final: 0.4392 (t-170) REVERT: B 443 LYS cc_start: 0.8531 (mtpp) cc_final: 0.8240 (mttp) REVERT: B 626 SER cc_start: 0.8869 (p) cc_final: 0.8662 (m) REVERT: B 642 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7796 (tm-30) REVERT: B 687 ARG cc_start: 0.8065 (mpp80) cc_final: 0.7725 (mtt180) REVERT: B 734 LEU cc_start: 0.8759 (mt) cc_final: 0.8441 (mp) REVERT: B 805 ASP cc_start: 0.7654 (m-30) cc_final: 0.7039 (t0) REVERT: B 851 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8277 (mm-40) REVERT: B 866 ARG cc_start: 0.8087 (ttm-80) cc_final: 0.7824 (ttm-80) REVERT: B 906 GLN cc_start: 0.8555 (tp40) cc_final: 0.8156 (mm-40) REVERT: B 941 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7696 (mm-30) REVERT: C 183 VAL cc_start: 0.8037 (m) cc_final: 0.7664 (p) REVERT: C 218 ASN cc_start: 0.7635 (OUTLIER) cc_final: 0.7338 (p0) REVERT: C 264 ASP cc_start: 0.7893 (m-30) cc_final: 0.7669 (m-30) REVERT: C 642 GLU cc_start: 0.7707 (tp30) cc_final: 0.7403 (tp30) REVERT: C 647 SER cc_start: 0.8670 (t) cc_final: 0.8392 (p) REVERT: C 743 MET cc_start: 0.8551 (tpp) cc_final: 0.8281 (mmt) REVERT: C 805 ASP cc_start: 0.8261 (m-30) cc_final: 0.7961 (m-30) REVERT: C 822 GLN cc_start: 0.8120 (tp40) cc_final: 0.7827 (tp40) REVERT: H 21 SER cc_start: 0.5998 (t) cc_final: 0.5439 (p) REVERT: H 71 ARG cc_start: 0.6472 (ttm110) cc_final: 0.6064 (ttm170) REVERT: H 73 ASN cc_start: 0.7135 (p0) cc_final: 0.6694 (t0) REVERT: H 76 ASN cc_start: 0.7160 (m-40) cc_final: 0.6284 (t0) REVERT: H 82 MET cc_start: 0.6101 (mmt) cc_final: 0.5666 (mtt) REVERT: H 102 TYR cc_start: 0.7001 (m-80) cc_final: 0.6735 (m-80) REVERT: M 19 ARG cc_start: 0.5907 (mmm160) cc_final: 0.5283 (mmm-85) REVERT: M 25 SER cc_start: 0.7407 (t) cc_final: 0.6625 (p) REVERT: M 29 PHE cc_start: 0.7897 (t80) cc_final: 0.7580 (t80) REVERT: N 34 ASN cc_start: 0.7381 (p0) cc_final: 0.6831 (p0) REVERT: N 35 TRP cc_start: 0.5258 (m100) cc_final: 0.4200 (m100) REVERT: N 98 PHE cc_start: 0.5497 (m-80) cc_final: 0.5181 (m-10) outliers start: 16 outliers final: 9 residues processed: 502 average time/residue: 0.2167 time to fit residues: 164.0705 Evaluate side-chains 446 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 434 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain M residue 86 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.0980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 309 HIS A 344 HIS A 937 ASN B 156 HIS B 811 ASN C 906 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.109931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.091322 restraints weight = 59182.423| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.77 r_work: 0.3248 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27840 Z= 0.195 Angle : 0.839 19.886 38121 Z= 0.403 Chirality : 0.051 0.637 4684 Planarity : 0.005 0.058 4704 Dihedral : 10.949 70.478 5825 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.21 % Favored : 94.64 % Rotamer: Outliers : 2.95 % Allowed : 12.64 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.39 (0.14), residues: 3341 helix: -0.05 (0.19), residues: 663 sheet: -0.62 (0.17), residues: 828 loop : -1.39 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 71 TYR 0.025 0.002 TYR A 295 PHE 0.023 0.002 PHE C 52 TRP 0.023 0.002 TRP H 36 HIS 0.011 0.002 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00443 (27693) covalent geometry : angle 0.76918 (37723) SS BOND : bond 0.00570 ( 43) SS BOND : angle 1.48338 ( 86) hydrogen bonds : bond 0.05907 ( 967) hydrogen bonds : angle 6.05960 ( 2715) link_BETA1-4 : bond 0.01211 ( 35) link_BETA1-4 : angle 3.14240 ( 105) link_NAG-ASN : bond 0.00670 ( 69) link_NAG-ASN : angle 4.00137 ( 207) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 475 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7006 (ppp80) REVERT: A 215 GLU cc_start: 0.6904 (mp0) cc_final: 0.6565 (pm20) REVERT: A 297 LYS cc_start: 0.6713 (mmmt) cc_final: 0.6419 (mmmm) REVERT: A 332 ASN cc_start: 0.4875 (OUTLIER) cc_final: 0.4245 (t0) REVERT: A 386 SER cc_start: 0.7688 (t) cc_final: 0.6800 (p) REVERT: A 401 ASN cc_start: 0.5485 (p0) cc_final: 0.5135 (p0) REVERT: A 607 SER cc_start: 0.8671 (t) cc_final: 0.8361 (m) REVERT: A 711 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.6725 (ttpp) REVERT: A 822 GLN cc_start: 0.8653 (tp40) cc_final: 0.8445 (tp40) REVERT: A 851 GLN cc_start: 0.8369 (mm-40) cc_final: 0.7933 (mt0) REVERT: A 941 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7603 (mt-10) REVERT: B 58 PHE cc_start: 0.8702 (m-80) cc_final: 0.8474 (m-10) REVERT: B 109 TYR cc_start: 0.8432 (p90) cc_final: 0.7907 (p90) REVERT: B 264 ASP cc_start: 0.8096 (m-30) cc_final: 0.7716 (m-30) REVERT: B 451 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8170 (m-30) REVERT: B 484 VAL cc_start: 0.8939 (m) cc_final: 0.8703 (p) REVERT: B 524 ASN cc_start: 0.7555 (t0) cc_final: 0.7276 (t0) REVERT: B 626 SER cc_start: 0.8755 (p) cc_final: 0.8369 (m) REVERT: B 642 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7959 (tm-30) REVERT: B 687 ARG cc_start: 0.8117 (mpp80) cc_final: 0.7740 (mtt180) REVERT: B 712 LYS cc_start: 0.8067 (tppp) cc_final: 0.7715 (mtpt) REVERT: B 805 ASP cc_start: 0.7736 (m-30) cc_final: 0.7029 (t0) REVERT: B 851 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8309 (mm-40) REVERT: B 865 ASP cc_start: 0.6717 (m-30) cc_final: 0.6410 (m-30) REVERT: B 866 ARG cc_start: 0.8190 (ttm-80) cc_final: 0.7779 (ttm-80) REVERT: B 906 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8305 (mm-40) REVERT: C 40 PHE cc_start: 0.7031 (p90) cc_final: 0.6221 (p90) REVERT: C 94 PHE cc_start: 0.5469 (OUTLIER) cc_final: 0.4732 (m-80) REVERT: C 183 VAL cc_start: 0.8019 (m) cc_final: 0.7655 (p) REVERT: C 218 ASN cc_start: 0.7524 (OUTLIER) cc_final: 0.6873 (p0) REVERT: C 264 ASP cc_start: 0.8017 (m-30) cc_final: 0.7789 (m-30) REVERT: C 642 GLU cc_start: 0.7590 (tp30) cc_final: 0.7324 (tp30) REVERT: C 743 MET cc_start: 0.8422 (tpp) cc_final: 0.8088 (mmt) REVERT: C 790 ARG cc_start: 0.7571 (ttm170) cc_final: 0.7313 (mtp85) REVERT: C 805 ASP cc_start: 0.8238 (m-30) cc_final: 0.8037 (m-30) REVERT: C 822 GLN cc_start: 0.8106 (tp40) cc_final: 0.7676 (tp40) REVERT: C 874 GLN cc_start: 0.8650 (mp10) cc_final: 0.8436 (mp10) REVERT: H 76 ASN cc_start: 0.7575 (m-40) cc_final: 0.6601 (t0) REVERT: H 82 MET cc_start: 0.6126 (mmt) cc_final: 0.5840 (mtt) REVERT: H 102 TYR cc_start: 0.7170 (m-80) cc_final: 0.6718 (m-80) REVERT: L 36 TYR cc_start: 0.5896 (m-80) cc_final: 0.5462 (m-80) REVERT: M 19 ARG cc_start: 0.5972 (mmm160) cc_final: 0.5627 (mmm160) REVERT: M 25 SER cc_start: 0.7307 (t) cc_final: 0.6588 (p) REVERT: M 29 PHE cc_start: 0.8181 (t80) cc_final: 0.7977 (t80) REVERT: N 45 LYS cc_start: 0.8249 (mmtp) cc_final: 0.7949 (mmtt) outliers start: 85 outliers final: 51 residues processed: 522 average time/residue: 0.2152 time to fit residues: 170.1250 Evaluate side-chains 497 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 439 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 928 ASN Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 654 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 906 GLN Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain C residue 81 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 1034 VAL Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 284 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 254 optimal weight: 3.9990 chunk 317 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 330 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 HIS A 888 ASN ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 HIS ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 ASN C 970 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.106641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.088401 restraints weight = 59226.936| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.80 r_work: 0.3185 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 27840 Z= 0.308 Angle : 0.913 20.386 38121 Z= 0.441 Chirality : 0.054 0.519 4684 Planarity : 0.005 0.049 4704 Dihedral : 10.333 71.809 5814 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.93 % Favored : 93.92 % Rotamer: Outliers : 4.20 % Allowed : 14.20 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.59 (0.14), residues: 3341 helix: 0.09 (0.20), residues: 664 sheet: -0.68 (0.18), residues: 801 loop : -1.69 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 38 TYR 0.021 0.003 TYR C 746 PHE 0.023 0.003 PHE C 52 TRP 0.022 0.003 TRP M 100F HIS 0.009 0.002 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00725 (27693) covalent geometry : angle 0.84563 (37723) SS BOND : bond 0.00695 ( 43) SS BOND : angle 1.71476 ( 86) hydrogen bonds : bond 0.06194 ( 967) hydrogen bonds : angle 5.95499 ( 2715) link_BETA1-4 : bond 0.01230 ( 35) link_BETA1-4 : angle 3.31310 ( 105) link_NAG-ASN : bond 0.00667 ( 69) link_NAG-ASN : angle 4.04822 ( 207) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 459 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LYS cc_start: 0.7133 (mttm) cc_final: 0.6424 (mmmt) REVERT: A 197 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.6930 (ppp80) REVERT: A 332 ASN cc_start: 0.4918 (OUTLIER) cc_final: 0.4273 (t0) REVERT: A 390 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7283 (tp) REVERT: A 401 ASN cc_start: 0.5267 (p0) cc_final: 0.4985 (p0) REVERT: A 428 LYS cc_start: 0.6615 (OUTLIER) cc_final: 0.6003 (tptp) REVERT: A 551 PHE cc_start: 0.7641 (m-80) cc_final: 0.7312 (m-80) REVERT: A 607 SER cc_start: 0.8855 (t) cc_final: 0.8469 (m) REVERT: A 711 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7380 (ttpp) REVERT: A 848 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8257 (mm-40) REVERT: A 851 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8125 (mt0) REVERT: A 941 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7734 (mt-10) REVERT: B 260 ARG cc_start: 0.8836 (ttm110) cc_final: 0.8486 (ttm110) REVERT: B 264 ASP cc_start: 0.8186 (m-30) cc_final: 0.7753 (m-30) REVERT: B 317 TYR cc_start: 0.6335 (t80) cc_final: 0.6118 (t80) REVERT: B 366 ASN cc_start: 0.7751 (p0) cc_final: 0.7512 (p0) REVERT: B 443 LYS cc_start: 0.8718 (mtpp) cc_final: 0.8508 (mttp) REVERT: B 626 SER cc_start: 0.8794 (p) cc_final: 0.8456 (m) REVERT: B 687 ARG cc_start: 0.8131 (mpp80) cc_final: 0.7723 (mtt180) REVERT: B 688 SER cc_start: 0.8467 (p) cc_final: 0.8197 (t) REVERT: B 712 LYS cc_start: 0.8305 (tppp) cc_final: 0.8037 (mtpt) REVERT: B 805 ASP cc_start: 0.7661 (m-30) cc_final: 0.7092 (t0) REVERT: B 851 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8398 (mt0) REVERT: B 906 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8208 (mm-40) REVERT: B 1039 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7182 (mm110) REVERT: C 108 PHE cc_start: 0.8100 (t80) cc_final: 0.7824 (t80) REVERT: C 114 SER cc_start: 0.8492 (m) cc_final: 0.8149 (p) REVERT: C 183 VAL cc_start: 0.8135 (m) cc_final: 0.7801 (p) REVERT: C 188 LYS cc_start: 0.8508 (tptm) cc_final: 0.8247 (tptp) REVERT: C 218 ASN cc_start: 0.7632 (OUTLIER) cc_final: 0.7376 (p0) REVERT: C 264 ASP cc_start: 0.8117 (m-30) cc_final: 0.7888 (m-30) REVERT: C 269 ASP cc_start: 0.8424 (p0) cc_final: 0.8164 (p0) REVERT: C 446 LYS cc_start: 0.8472 (ttmm) cc_final: 0.8147 (ttpp) REVERT: C 642 GLU cc_start: 0.7706 (tp30) cc_final: 0.7406 (tp30) REVERT: C 709 ASP cc_start: 0.7511 (t0) cc_final: 0.7118 (t0) REVERT: C 712 LYS cc_start: 0.8541 (mtpt) cc_final: 0.8145 (mtpp) REVERT: C 743 MET cc_start: 0.8496 (tpp) cc_final: 0.8180 (mmt) REVERT: C 822 GLN cc_start: 0.8080 (tp40) cc_final: 0.7628 (tp40) REVERT: C 874 GLN cc_start: 0.8707 (mp10) cc_final: 0.8454 (mp10) REVERT: H 29 PHE cc_start: 0.6732 (t80) cc_final: 0.6007 (t80) REVERT: H 59 TYR cc_start: 0.6502 (m-80) cc_final: 0.6117 (m-10) REVERT: H 73 ASN cc_start: 0.7808 (p0) cc_final: 0.6626 (t0) REVERT: H 76 ASN cc_start: 0.7473 (m-40) cc_final: 0.6547 (t0) REVERT: H 82 MET cc_start: 0.6012 (mmt) cc_final: 0.5792 (mtt) REVERT: M 25 SER cc_start: 0.7435 (t) cc_final: 0.6766 (p) REVERT: M 43 LYS cc_start: 0.7366 (ptpp) cc_final: 0.6900 (mtpp) REVERT: M 82 MET cc_start: 0.6329 (mtp) cc_final: 0.5833 (mmm) REVERT: M 101 ASP cc_start: 0.7748 (m-30) cc_final: 0.7518 (m-30) REVERT: N 35 TRP cc_start: 0.5441 (m100) cc_final: 0.4514 (m100) REVERT: N 45 LYS cc_start: 0.8265 (mmtp) cc_final: 0.7963 (mmtt) outliers start: 121 outliers final: 90 residues processed: 542 average time/residue: 0.2014 time to fit residues: 168.4610 Evaluate side-chains 534 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 436 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 928 ASN Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 906 GLN Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1039 GLN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 81 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 1034 VAL Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 19 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 chunk 202 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 292 optimal weight: 2.9990 chunk 254 optimal weight: 0.1980 chunk 127 optimal weight: 0.6980 chunk 249 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 729 ASN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 ASN N 89 GLN N 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.108813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.090298 restraints weight = 58892.553| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.78 r_work: 0.3231 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27840 Z= 0.160 Angle : 0.757 18.966 38121 Z= 0.363 Chirality : 0.049 0.510 4684 Planarity : 0.004 0.044 4704 Dihedral : 8.738 59.265 5814 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.34 % Favored : 95.51 % Rotamer: Outliers : 3.16 % Allowed : 16.63 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.30 (0.14), residues: 3341 helix: 0.46 (0.20), residues: 670 sheet: -0.56 (0.18), residues: 820 loop : -1.54 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 850 TYR 0.020 0.002 TYR H 90 PHE 0.018 0.002 PHE B 97 TRP 0.021 0.002 TRP M 100F HIS 0.005 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00361 (27693) covalent geometry : angle 0.69212 (37723) SS BOND : bond 0.00338 ( 43) SS BOND : angle 1.26011 ( 86) hydrogen bonds : bond 0.04761 ( 967) hydrogen bonds : angle 5.47556 ( 2715) link_BETA1-4 : bond 0.01153 ( 35) link_BETA1-4 : angle 3.04998 ( 105) link_NAG-ASN : bond 0.00556 ( 69) link_NAG-ASN : angle 3.57239 ( 207) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 460 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LYS cc_start: 0.7006 (mttm) cc_final: 0.6476 (mmmt) REVERT: A 197 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.6964 (ppp80) REVERT: A 270 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8389 (m) REVERT: A 401 ASN cc_start: 0.5382 (p0) cc_final: 0.4972 (p0) REVERT: A 423 ILE cc_start: 0.8191 (tp) cc_final: 0.7720 (tt) REVERT: A 551 PHE cc_start: 0.7646 (m-80) cc_final: 0.7364 (m-80) REVERT: A 607 SER cc_start: 0.8811 (t) cc_final: 0.8441 (m) REVERT: A 711 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.6946 (ttpp) REVERT: A 851 GLN cc_start: 0.8340 (mm-40) cc_final: 0.7994 (mt0) REVERT: A 941 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7726 (mt-10) REVERT: B 109 TYR cc_start: 0.8431 (p90) cc_final: 0.7995 (p90) REVERT: B 260 ARG cc_start: 0.8831 (ttm110) cc_final: 0.8271 (ttm110) REVERT: B 264 ASP cc_start: 0.8139 (m-30) cc_final: 0.7681 (m-30) REVERT: B 366 ASN cc_start: 0.7714 (p0) cc_final: 0.7450 (p0) REVERT: B 524 ASN cc_start: 0.7719 (t0) cc_final: 0.7472 (t0) REVERT: B 626 SER cc_start: 0.8683 (p) cc_final: 0.8348 (m) REVERT: B 631 ILE cc_start: 0.8273 (mm) cc_final: 0.8037 (mt) REVERT: B 687 ARG cc_start: 0.8163 (mpp80) cc_final: 0.7737 (mtt180) REVERT: B 688 SER cc_start: 0.8391 (p) cc_final: 0.8127 (t) REVERT: B 712 LYS cc_start: 0.8311 (tppp) cc_final: 0.8030 (mtpt) REVERT: B 805 ASP cc_start: 0.7638 (m-30) cc_final: 0.6954 (t0) REVERT: B 851 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8385 (mt0) REVERT: B 865 ASP cc_start: 0.6914 (m-30) cc_final: 0.6702 (m-30) REVERT: B 906 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8285 (mm110) REVERT: B 1039 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7263 (mp10) REVERT: C 40 PHE cc_start: 0.7185 (p90) cc_final: 0.6311 (p90) REVERT: C 108 PHE cc_start: 0.8081 (t80) cc_final: 0.7830 (t80) REVERT: C 114 SER cc_start: 0.8526 (m) cc_final: 0.8116 (p) REVERT: C 218 ASN cc_start: 0.7551 (OUTLIER) cc_final: 0.7234 (p0) REVERT: C 260 ARG cc_start: 0.8286 (mtm180) cc_final: 0.7842 (mtp-110) REVERT: C 264 ASP cc_start: 0.8099 (m-30) cc_final: 0.7881 (m-30) REVERT: C 269 ASP cc_start: 0.8385 (p0) cc_final: 0.8108 (p0) REVERT: C 446 LYS cc_start: 0.8462 (ttmm) cc_final: 0.8142 (ttpp) REVERT: C 642 GLU cc_start: 0.7681 (tp30) cc_final: 0.7348 (tp30) REVERT: C 709 ASP cc_start: 0.7446 (t0) cc_final: 0.7015 (t70) REVERT: C 712 LYS cc_start: 0.8541 (mtpt) cc_final: 0.8112 (mtpt) REVERT: C 743 MET cc_start: 0.8266 (tpp) cc_final: 0.7862 (mmt) REVERT: C 822 GLN cc_start: 0.8055 (tp40) cc_final: 0.7611 (tp40) REVERT: C 874 GLN cc_start: 0.8676 (mp10) cc_final: 0.8416 (mp10) REVERT: H 29 PHE cc_start: 0.6747 (t80) cc_final: 0.6152 (t80) REVERT: H 76 ASN cc_start: 0.7365 (m-40) cc_final: 0.6568 (t0) REVERT: H 82 MET cc_start: 0.5990 (mmt) cc_final: 0.5774 (mtt) REVERT: L 36 TYR cc_start: 0.5638 (m-80) cc_final: 0.5374 (m-80) REVERT: M 19 ARG cc_start: 0.5868 (mmm160) cc_final: 0.5468 (mmm160) REVERT: M 25 SER cc_start: 0.7440 (t) cc_final: 0.6775 (p) REVERT: M 43 LYS cc_start: 0.7408 (ptpp) cc_final: 0.6830 (mtpp) REVERT: N 35 TRP cc_start: 0.5312 (m100) cc_final: 0.4498 (m100) REVERT: N 45 LYS cc_start: 0.8260 (mmtp) cc_final: 0.7965 (mmtt) outliers start: 91 outliers final: 60 residues processed: 523 average time/residue: 0.1925 time to fit residues: 155.4163 Evaluate side-chains 510 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 444 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 906 GLN Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain B residue 1039 GLN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 81 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 1034 VAL Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 92 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 263 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 chunk 326 optimal weight: 2.9990 chunk 312 optimal weight: 4.9990 chunk 262 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 HIS ** 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 = 0.3654 r_free = 0.3654 target = 0.108389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.090023 restraints weight = 58649.661| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.74 r_work: 0.3228 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27840 Z= 0.178 Angle : 0.757 19.009 38121 Z= 0.364 Chirality : 0.049 0.480 4684 Planarity : 0.004 0.040 4704 Dihedral : 8.331 59.720 5812 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.51 % Favored : 94.34 % Rotamer: Outliers : 3.92 % Allowed : 16.63 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.25 (0.14), residues: 3341 helix: 0.57 (0.20), residues: 669 sheet: -0.47 (0.18), residues: 801 loop : -1.56 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 18 TYR 0.028 0.002 TYR L 32 PHE 0.019 0.002 PHE B 665 TRP 0.022 0.002 TRP M 100F HIS 0.009 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00409 (27693) covalent geometry : angle 0.69714 (37723) SS BOND : bond 0.00384 ( 43) SS BOND : angle 1.31572 ( 86) hydrogen bonds : bond 0.04788 ( 967) hydrogen bonds : angle 5.38952 ( 2715) link_BETA1-4 : bond 0.01095 ( 35) link_BETA1-4 : angle 2.99103 ( 105) link_NAG-ASN : bond 0.00526 ( 69) link_NAG-ASN : angle 3.43809 ( 207) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 448 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.7943 (m-80) cc_final: 0.7463 (m-80) REVERT: A 135 LYS cc_start: 0.7056 (mttm) cc_final: 0.6543 (mmmt) REVERT: A 191 ARG cc_start: 0.8168 (mmt90) cc_final: 0.7562 (mmt-90) REVERT: A 197 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.6965 (ppp80) REVERT: A 270 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.8398 (m) REVERT: A 401 ASN cc_start: 0.5404 (p0) cc_final: 0.5004 (p0) REVERT: A 423 ILE cc_start: 0.8230 (tp) cc_final: 0.7756 (tt) REVERT: A 428 LYS cc_start: 0.6365 (OUTLIER) cc_final: 0.5612 (tptp) REVERT: A 444 CYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6989 (p) REVERT: A 551 PHE cc_start: 0.7686 (m-80) cc_final: 0.7410 (m-80) REVERT: A 607 SER cc_start: 0.8777 (t) cc_final: 0.8407 (m) REVERT: A 711 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7053 (ttpp) REVERT: A 833 ASP cc_start: 0.8099 (m-30) cc_final: 0.7840 (t70) REVERT: A 851 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8050 (mt0) REVERT: A 941 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7738 (mt-10) REVERT: B 109 TYR cc_start: 0.8516 (p90) cc_final: 0.8017 (p90) REVERT: B 264 ASP cc_start: 0.8149 (m-30) cc_final: 0.7948 (m-30) REVERT: B 366 ASN cc_start: 0.7696 (p0) cc_final: 0.7441 (p0) REVERT: B 626 SER cc_start: 0.8685 (p) cc_final: 0.8344 (m) REVERT: B 631 ILE cc_start: 0.8285 (mm) cc_final: 0.8034 (mt) REVERT: B 805 ASP cc_start: 0.7590 (m-30) cc_final: 0.6967 (t0) REVERT: B 851 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8391 (mt0) REVERT: B 1039 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7365 (mp10) REVERT: C 40 PHE cc_start: 0.7233 (p90) cc_final: 0.6362 (p90) REVERT: C 94 PHE cc_start: 0.5398 (OUTLIER) cc_final: 0.4593 (m-80) REVERT: C 108 PHE cc_start: 0.8093 (t80) cc_final: 0.7827 (t80) REVERT: C 114 SER cc_start: 0.8529 (m) cc_final: 0.8137 (p) REVERT: C 134 PHE cc_start: 0.6434 (m-10) cc_final: 0.6141 (m-80) REVERT: C 218 ASN cc_start: 0.7548 (OUTLIER) cc_final: 0.6947 (p0) REVERT: C 260 ARG cc_start: 0.8265 (mtm180) cc_final: 0.7819 (mtp-110) REVERT: C 264 ASP cc_start: 0.8065 (m-30) cc_final: 0.7865 (m-30) REVERT: C 269 ASP cc_start: 0.8352 (p0) cc_final: 0.8062 (p0) REVERT: C 642 GLU cc_start: 0.7757 (tp30) cc_final: 0.7503 (tp30) REVERT: C 709 ASP cc_start: 0.7516 (t0) cc_final: 0.7098 (t70) REVERT: C 712 LYS cc_start: 0.8513 (mtpt) cc_final: 0.8137 (mtpt) REVERT: C 822 GLN cc_start: 0.8039 (tp40) cc_final: 0.7604 (tp40) REVERT: C 874 GLN cc_start: 0.8657 (mp10) cc_final: 0.8405 (mp10) REVERT: C 941 GLU cc_start: 0.8410 (mp0) cc_final: 0.7983 (mp0) REVERT: H 29 PHE cc_start: 0.6849 (t80) cc_final: 0.6145 (t80) REVERT: H 76 ASN cc_start: 0.7299 (m-40) cc_final: 0.6541 (t0) REVERT: H 82 MET cc_start: 0.6162 (mmt) cc_final: 0.5937 (mtt) REVERT: L 61 ARG cc_start: 0.5936 (ptm160) cc_final: 0.5699 (ptm160) REVERT: M 25 SER cc_start: 0.7439 (t) cc_final: 0.6781 (p) REVERT: M 43 LYS cc_start: 0.7226 (ptpp) cc_final: 0.6746 (mtpp) REVERT: N 35 TRP cc_start: 0.5359 (m100) cc_final: 0.4552 (m100) REVERT: N 45 LYS cc_start: 0.8178 (mmtp) cc_final: 0.7937 (mptt) outliers start: 113 outliers final: 84 residues processed: 530 average time/residue: 0.1921 time to fit residues: 157.7954 Evaluate side-chains 521 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 429 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 807 PHE Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 928 ASN Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain B residue 1039 GLN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 81 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 1034 VAL Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain M residue 94 LYS Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 24 optimal weight: 0.6980 chunk 54 optimal weight: 0.2980 chunk 327 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 302 optimal weight: 1.9990 chunk 203 optimal weight: 0.1980 chunk 190 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 220 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.109945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.092111 restraints weight = 58617.648| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.69 r_work: 0.3249 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27840 Z= 0.135 Angle : 0.709 18.741 38121 Z= 0.340 Chirality : 0.047 0.469 4684 Planarity : 0.004 0.040 4704 Dihedral : 7.829 59.778 5812 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.19 % Favored : 95.66 % Rotamer: Outliers : 3.72 % Allowed : 17.67 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 3341 helix: 0.81 (0.21), residues: 664 sheet: -0.33 (0.18), residues: 796 loop : -1.42 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 18 TYR 0.022 0.001 TYR C 109 PHE 0.019 0.001 PHE M 29 TRP 0.021 0.001 TRP M 100F HIS 0.012 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00300 (27693) covalent geometry : angle 0.65160 (37723) SS BOND : bond 0.00366 ( 43) SS BOND : angle 1.14498 ( 86) hydrogen bonds : bond 0.04294 ( 967) hydrogen bonds : angle 5.19763 ( 2715) link_BETA1-4 : bond 0.01125 ( 35) link_BETA1-4 : angle 2.86195 ( 105) link_NAG-ASN : bond 0.00502 ( 69) link_NAG-ASN : angle 3.22281 ( 207) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 453 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.7916 (m-80) cc_final: 0.7556 (m-80) REVERT: A 135 LYS cc_start: 0.6936 (mttm) cc_final: 0.6502 (mmmt) REVERT: A 191 ARG cc_start: 0.8164 (mmt90) cc_final: 0.7586 (mmt-90) REVERT: A 197 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6949 (ppp80) REVERT: A 259 ASN cc_start: 0.8460 (m-40) cc_final: 0.8221 (m-40) REVERT: A 401 ASN cc_start: 0.5399 (p0) cc_final: 0.5014 (p0) REVERT: A 423 ILE cc_start: 0.8243 (tp) cc_final: 0.7779 (tt) REVERT: A 428 LYS cc_start: 0.6221 (OUTLIER) cc_final: 0.5452 (tptp) REVERT: A 504 TYR cc_start: 0.8253 (t80) cc_final: 0.8016 (t80) REVERT: A 551 PHE cc_start: 0.7682 (m-80) cc_final: 0.7421 (m-80) REVERT: A 607 SER cc_start: 0.8773 (t) cc_final: 0.8416 (m) REVERT: A 687 ARG cc_start: 0.8563 (mtt180) cc_final: 0.8193 (mmm-85) REVERT: A 711 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.6819 (ttpp) REVERT: A 851 GLN cc_start: 0.8332 (mm-40) cc_final: 0.8011 (mt0) REVERT: A 941 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7743 (mt-10) REVERT: B 109 TYR cc_start: 0.8480 (p90) cc_final: 0.7993 (p90) REVERT: B 122 ASN cc_start: 0.7551 (OUTLIER) cc_final: 0.7338 (p0) REVERT: B 357 ARG cc_start: 0.7366 (ttm110) cc_final: 0.7118 (ttm110) REVERT: B 366 ASN cc_start: 0.7668 (p0) cc_final: 0.7408 (p0) REVERT: B 528 MET cc_start: 0.8224 (mmm) cc_final: 0.7685 (mmm) REVERT: B 626 SER cc_start: 0.8645 (p) cc_final: 0.8299 (m) REVERT: B 631 ILE cc_start: 0.8224 (mm) cc_final: 0.8018 (mt) REVERT: B 800 MET cc_start: 0.8738 (mmt) cc_final: 0.8382 (tpt) REVERT: B 805 ASP cc_start: 0.7537 (m-30) cc_final: 0.6849 (t0) REVERT: B 906 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8211 (mm110) REVERT: B 1039 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7264 (mp10) REVERT: C 40 PHE cc_start: 0.7230 (p90) cc_final: 0.6433 (p90) REVERT: C 94 PHE cc_start: 0.5410 (OUTLIER) cc_final: 0.4661 (m-80) REVERT: C 218 ASN cc_start: 0.7581 (OUTLIER) cc_final: 0.6898 (p0) REVERT: C 260 ARG cc_start: 0.8263 (mtm180) cc_final: 0.7828 (mtp-110) REVERT: C 269 ASP cc_start: 0.8353 (p0) cc_final: 0.8151 (p0) REVERT: C 437 MET cc_start: 0.7463 (tpp) cc_final: 0.7214 (ttt) REVERT: C 709 ASP cc_start: 0.7481 (t0) cc_final: 0.7263 (t70) REVERT: C 822 GLN cc_start: 0.8044 (tp40) cc_final: 0.7628 (tp40) REVERT: C 874 GLN cc_start: 0.8542 (mp10) cc_final: 0.8266 (mp10) REVERT: C 941 GLU cc_start: 0.8375 (mp0) cc_final: 0.7944 (mp0) REVERT: H 6 GLU cc_start: 0.5081 (OUTLIER) cc_final: 0.4599 (mp0) REVERT: H 19 ARG cc_start: 0.5328 (OUTLIER) cc_final: 0.3853 (tmm-80) REVERT: H 29 PHE cc_start: 0.6788 (t80) cc_final: 0.6213 (t80) REVERT: H 76 ASN cc_start: 0.7301 (m-40) cc_final: 0.6633 (t0) REVERT: H 82 MET cc_start: 0.6153 (mmt) cc_final: 0.5921 (mtt) REVERT: H 111 VAL cc_start: 0.3577 (p) cc_final: 0.3338 (m) REVERT: L 61 ARG cc_start: 0.6161 (ptm160) cc_final: 0.5917 (ptm160) REVERT: M 25 SER cc_start: 0.7434 (t) cc_final: 0.6774 (p) REVERT: M 43 LYS cc_start: 0.7161 (ptpp) cc_final: 0.6675 (mtpp) REVERT: N 35 TRP cc_start: 0.5300 (m100) cc_final: 0.4535 (m100) REVERT: N 45 LYS cc_start: 0.8181 (mmtp) cc_final: 0.7943 (mptt) outliers start: 107 outliers final: 75 residues processed: 531 average time/residue: 0.1757 time to fit residues: 143.9857 Evaluate side-chains 512 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 427 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 928 ASN Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 307 PHE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 906 GLN Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain B residue 1039 GLN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 81 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 715 LYS Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 1034 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain M residue 94 LYS Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 54 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 322 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 102 optimal weight: 0.0370 chunk 31 optimal weight: 0.7980 chunk 90 optimal weight: 0.0770 chunk 119 optimal weight: 0.0970 chunk 320 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 overall best weight: 0.3014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 ASN B 250 ASN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 GLN B 851 GLN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 843 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.110880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.092753 restraints weight = 58428.507| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.73 r_work: 0.3268 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27840 Z= 0.119 Angle : 0.687 18.134 38121 Z= 0.330 Chirality : 0.046 0.446 4684 Planarity : 0.004 0.040 4704 Dihedral : 7.457 58.704 5812 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.46 % Favored : 95.39 % Rotamer: Outliers : 3.26 % Allowed : 18.30 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.14), residues: 3341 helix: 1.05 (0.21), residues: 664 sheet: -0.33 (0.18), residues: 805 loop : -1.28 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 128 TYR 0.022 0.001 TYR C 109 PHE 0.033 0.001 PHE C 108 TRP 0.030 0.001 TRP H 36 HIS 0.010 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00252 (27693) covalent geometry : angle 0.63426 (37723) SS BOND : bond 0.00883 ( 43) SS BOND : angle 1.08698 ( 86) hydrogen bonds : bond 0.03963 ( 967) hydrogen bonds : angle 5.03525 ( 2715) link_BETA1-4 : bond 0.01085 ( 35) link_BETA1-4 : angle 2.73735 ( 105) link_NAG-ASN : bond 0.00488 ( 69) link_NAG-ASN : angle 3.05961 ( 207) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 453 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.7118 (mmm-85) cc_final: 0.6873 (mmm-85) REVERT: A 134 PHE cc_start: 0.7919 (m-80) cc_final: 0.7601 (m-80) REVERT: A 135 LYS cc_start: 0.6776 (mttm) cc_final: 0.6382 (mmmt) REVERT: A 191 ARG cc_start: 0.8145 (mmt90) cc_final: 0.7621 (mmt-90) REVERT: A 197 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.6994 (ppp80) REVERT: A 259 ASN cc_start: 0.8471 (m-40) cc_final: 0.8247 (m-40) REVERT: A 401 ASN cc_start: 0.5500 (p0) cc_final: 0.5124 (p0) REVERT: A 423 ILE cc_start: 0.8244 (tp) cc_final: 0.7771 (tt) REVERT: A 428 LYS cc_start: 0.6116 (OUTLIER) cc_final: 0.5279 (tptp) REVERT: A 504 TYR cc_start: 0.8246 (t80) cc_final: 0.7942 (t80) REVERT: A 551 PHE cc_start: 0.7657 (m-80) cc_final: 0.7410 (m-80) REVERT: A 607 SER cc_start: 0.8777 (t) cc_final: 0.8437 (m) REVERT: A 687 ARG cc_start: 0.8526 (mtt180) cc_final: 0.8218 (mmm-85) REVERT: A 711 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.6608 (ttpp) REVERT: A 851 GLN cc_start: 0.8326 (mm-40) cc_final: 0.7937 (mt0) REVERT: A 941 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7718 (mt-10) REVERT: B 109 TYR cc_start: 0.8459 (p90) cc_final: 0.7987 (p90) REVERT: B 122 ASN cc_start: 0.7529 (OUTLIER) cc_final: 0.7306 (p0) REVERT: B 357 ARG cc_start: 0.7339 (ttm110) cc_final: 0.7098 (ttm110) REVERT: B 366 ASN cc_start: 0.7647 (p0) cc_final: 0.7388 (p0) REVERT: B 443 LYS cc_start: 0.8739 (mttm) cc_final: 0.8521 (mttp) REVERT: B 528 MET cc_start: 0.8182 (mmm) cc_final: 0.7752 (mmm) REVERT: B 631 ILE cc_start: 0.8178 (mm) cc_final: 0.7966 (mt) REVERT: B 648 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7968 (tm-30) REVERT: B 800 MET cc_start: 0.8737 (mmt) cc_final: 0.8382 (tpt) REVERT: B 805 ASP cc_start: 0.7399 (m-30) cc_final: 0.6860 (t0) REVERT: C 40 PHE cc_start: 0.7149 (p90) cc_final: 0.6356 (p90) REVERT: C 94 PHE cc_start: 0.5101 (OUTLIER) cc_final: 0.4395 (m-80) REVERT: C 138 TYR cc_start: 0.5627 (m-80) cc_final: 0.5332 (m-10) REVERT: C 191 ARG cc_start: 0.8675 (mtp85) cc_final: 0.8406 (mtp85) REVERT: C 218 ASN cc_start: 0.7537 (OUTLIER) cc_final: 0.6872 (p0) REVERT: C 260 ARG cc_start: 0.8220 (mtm180) cc_final: 0.7891 (ttp80) REVERT: C 269 ASP cc_start: 0.8264 (p0) cc_final: 0.8050 (p0) REVERT: C 437 MET cc_start: 0.7466 (tpp) cc_final: 0.7236 (ttt) REVERT: C 709 ASP cc_start: 0.7510 (t0) cc_final: 0.7270 (t70) REVERT: C 822 GLN cc_start: 0.8055 (tp40) cc_final: 0.7643 (tp40) REVERT: C 874 GLN cc_start: 0.8406 (mp10) cc_final: 0.8153 (mp10) REVERT: C 941 GLU cc_start: 0.8388 (mp0) cc_final: 0.7952 (mp0) REVERT: H 6 GLU cc_start: 0.5249 (OUTLIER) cc_final: 0.4725 (mp0) REVERT: H 19 ARG cc_start: 0.5311 (OUTLIER) cc_final: 0.3873 (tmm-80) REVERT: H 29 PHE cc_start: 0.6898 (t80) cc_final: 0.6223 (t80) REVERT: H 76 ASN cc_start: 0.7240 (m-40) cc_final: 0.6710 (t0) REVERT: H 82 MET cc_start: 0.6140 (mmt) cc_final: 0.5871 (mtt) REVERT: H 111 VAL cc_start: 0.3502 (p) cc_final: 0.3266 (m) REVERT: M 25 SER cc_start: 0.7446 (t) cc_final: 0.6791 (p) REVERT: M 43 LYS cc_start: 0.7092 (ptpp) cc_final: 0.6637 (mtpp) REVERT: M 82 LEU cc_start: 0.5842 (OUTLIER) cc_final: 0.5548 (mt) REVERT: N 35 TRP cc_start: 0.5195 (m100) cc_final: 0.4526 (m100) REVERT: N 45 LYS cc_start: 0.8176 (mmtp) cc_final: 0.7955 (mptt) outliers start: 94 outliers final: 74 residues processed: 523 average time/residue: 0.1837 time to fit residues: 147.5171 Evaluate side-chains 508 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 425 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 928 ASN Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 906 GLN Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 81 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 715 LYS Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 1034 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 54 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 34 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 276 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 290 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 156 optimal weight: 0.0060 chunk 87 optimal weight: 0.6980 chunk 324 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 811 ASN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 843 ASN L 89 GLN L 90 GLN ** M 39 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 = 0.3678 r_free = 0.3678 target = 0.109839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.091398 restraints weight = 58900.553| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.75 r_work: 0.3251 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27840 Z= 0.150 Angle : 0.711 18.668 38121 Z= 0.343 Chirality : 0.047 0.453 4684 Planarity : 0.004 0.039 4704 Dihedral : 7.485 59.191 5810 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.15 % Favored : 94.70 % Rotamer: Outliers : 3.47 % Allowed : 18.54 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.14), residues: 3341 helix: 1.10 (0.21), residues: 664 sheet: -0.29 (0.18), residues: 796 loop : -1.28 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 128 TYR 0.022 0.002 TYR C 109 PHE 0.034 0.002 PHE H 29 TRP 0.020 0.002 TRP H 36 HIS 0.013 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00342 (27693) covalent geometry : angle 0.65815 (37723) SS BOND : bond 0.00381 ( 43) SS BOND : angle 1.27093 ( 86) hydrogen bonds : bond 0.04216 ( 967) hydrogen bonds : angle 5.05786 ( 2715) link_BETA1-4 : bond 0.01105 ( 35) link_BETA1-4 : angle 2.81094 ( 105) link_NAG-ASN : bond 0.00475 ( 69) link_NAG-ASN : angle 3.07040 ( 207) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 441 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.7109 (mmm-85) cc_final: 0.6829 (mmm-85) REVERT: A 134 PHE cc_start: 0.7920 (m-80) cc_final: 0.7597 (m-80) REVERT: A 135 LYS cc_start: 0.6834 (mttm) cc_final: 0.6401 (mmmt) REVERT: A 191 ARG cc_start: 0.8138 (mmt90) cc_final: 0.7624 (mmt-90) REVERT: A 197 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.6968 (ppp80) REVERT: A 259 ASN cc_start: 0.8480 (m-40) cc_final: 0.8245 (m-40) REVERT: A 401 ASN cc_start: 0.5516 (p0) cc_final: 0.5145 (p0) REVERT: A 423 ILE cc_start: 0.8240 (tp) cc_final: 0.7744 (tt) REVERT: A 428 LYS cc_start: 0.6205 (OUTLIER) cc_final: 0.5360 (tptp) REVERT: A 504 TYR cc_start: 0.8295 (t80) cc_final: 0.7933 (t80) REVERT: A 551 PHE cc_start: 0.7650 (m-80) cc_final: 0.7398 (m-80) REVERT: A 607 SER cc_start: 0.8791 (t) cc_final: 0.8446 (m) REVERT: A 687 ARG cc_start: 0.8546 (mtt180) cc_final: 0.8333 (mmm-85) REVERT: A 711 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.6860 (ttpp) REVERT: A 851 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7945 (mt0) REVERT: A 941 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7752 (mt-10) REVERT: B 109 TYR cc_start: 0.8429 (p90) cc_final: 0.8007 (p90) REVERT: B 122 ASN cc_start: 0.7529 (OUTLIER) cc_final: 0.7296 (p0) REVERT: B 357 ARG cc_start: 0.7352 (ttm110) cc_final: 0.7102 (ttm110) REVERT: B 366 ASN cc_start: 0.7693 (p0) cc_final: 0.7421 (p0) REVERT: B 379 LYS cc_start: 0.8501 (mmtt) cc_final: 0.8293 (mmtt) REVERT: B 443 LYS cc_start: 0.8757 (mttm) cc_final: 0.8543 (mttp) REVERT: B 528 MET cc_start: 0.8167 (mmm) cc_final: 0.7694 (mmm) REVERT: B 631 ILE cc_start: 0.8209 (mm) cc_final: 0.7998 (mt) REVERT: B 805 ASP cc_start: 0.7574 (m-30) cc_final: 0.6979 (t0) REVERT: C 40 PHE cc_start: 0.7243 (p90) cc_final: 0.6451 (p90) REVERT: C 94 PHE cc_start: 0.5114 (OUTLIER) cc_final: 0.4450 (m-80) REVERT: C 138 TYR cc_start: 0.5620 (m-80) cc_final: 0.5342 (m-10) REVERT: C 218 ASN cc_start: 0.7567 (OUTLIER) cc_final: 0.6883 (p0) REVERT: C 260 ARG cc_start: 0.8218 (mtm180) cc_final: 0.7966 (ttp80) REVERT: C 437 MET cc_start: 0.7352 (tpp) cc_final: 0.7101 (ttt) REVERT: C 709 ASP cc_start: 0.7543 (t0) cc_final: 0.7309 (t70) REVERT: C 822 GLN cc_start: 0.8064 (tp40) cc_final: 0.7642 (tp40) REVERT: C 874 GLN cc_start: 0.8399 (mp10) cc_final: 0.8133 (mp-120) REVERT: C 941 GLU cc_start: 0.8396 (mp0) cc_final: 0.7960 (mp0) REVERT: C 1023 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7750 (mm-30) REVERT: H 19 ARG cc_start: 0.5338 (OUTLIER) cc_final: 0.3830 (tmm-80) REVERT: H 76 ASN cc_start: 0.7235 (m-40) cc_final: 0.6542 (t0) REVERT: H 111 VAL cc_start: 0.3552 (p) cc_final: 0.3309 (m) REVERT: L 79 GLN cc_start: 0.5381 (mp10) cc_final: 0.5166 (mp10) REVERT: M 25 SER cc_start: 0.7448 (t) cc_final: 0.6799 (p) REVERT: M 43 LYS cc_start: 0.7063 (ptpp) cc_final: 0.6636 (mtpp) REVERT: N 35 TRP cc_start: 0.5298 (m100) cc_final: 0.4479 (m100) REVERT: N 45 LYS cc_start: 0.8175 (mmtp) cc_final: 0.7953 (mptt) outliers start: 100 outliers final: 79 residues processed: 516 average time/residue: 0.1938 time to fit residues: 153.3478 Evaluate side-chains 521 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 435 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 807 PHE Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 928 ASN Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 807 PHE Chi-restraints excluded: chain B residue 906 GLN Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 81 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 715 LYS Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 1034 VAL Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 54 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 213 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 300 optimal weight: 0.8980 chunk 221 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 241 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 GLN C 843 ASN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.109215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.090809 restraints weight = 58894.480| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.75 r_work: 0.3243 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27840 Z= 0.169 Angle : 0.729 18.456 38121 Z= 0.352 Chirality : 0.048 0.456 4684 Planarity : 0.004 0.037 4704 Dihedral : 7.603 59.586 5808 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.39 % Favored : 94.46 % Rotamer: Outliers : 3.61 % Allowed : 18.47 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.83 (0.14), residues: 3341 helix: 1.06 (0.21), residues: 664 sheet: -0.27 (0.18), residues: 788 loop : -1.29 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 905 TYR 0.026 0.002 TYR M 79 PHE 0.033 0.002 PHE C 108 TRP 0.022 0.002 TRP M 100F HIS 0.009 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00390 (27693) covalent geometry : angle 0.67707 (37723) SS BOND : bond 0.00379 ( 43) SS BOND : angle 1.25915 ( 86) hydrogen bonds : bond 0.04361 ( 967) hydrogen bonds : angle 5.10728 ( 2715) link_BETA1-4 : bond 0.01120 ( 35) link_BETA1-4 : angle 2.82574 ( 105) link_NAG-ASN : bond 0.00476 ( 69) link_NAG-ASN : angle 3.09198 ( 207) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 443 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.7958 (m-80) cc_final: 0.7623 (m-80) REVERT: A 135 LYS cc_start: 0.6863 (mttm) cc_final: 0.6435 (mmmt) REVERT: A 197 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6977 (ppp80) REVERT: A 259 ASN cc_start: 0.8483 (m-40) cc_final: 0.8248 (m-40) REVERT: A 401 ASN cc_start: 0.5445 (p0) cc_final: 0.5069 (p0) REVERT: A 423 ILE cc_start: 0.8244 (tp) cc_final: 0.7735 (tt) REVERT: A 428 LYS cc_start: 0.6271 (OUTLIER) cc_final: 0.5349 (tptp) REVERT: A 504 TYR cc_start: 0.8355 (t80) cc_final: 0.7997 (t80) REVERT: A 551 PHE cc_start: 0.7547 (m-80) cc_final: 0.7303 (m-80) REVERT: A 607 SER cc_start: 0.8781 (t) cc_final: 0.8420 (m) REVERT: A 687 ARG cc_start: 0.8562 (mtt180) cc_final: 0.8357 (mmm-85) REVERT: A 711 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.6943 (ttpp) REVERT: A 851 GLN cc_start: 0.8347 (mm-40) cc_final: 0.7993 (mt0) REVERT: A 941 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7753 (mt-10) REVERT: B 109 TYR cc_start: 0.8433 (p90) cc_final: 0.8017 (p90) REVERT: B 122 ASN cc_start: 0.7530 (OUTLIER) cc_final: 0.7296 (p0) REVERT: B 165 ASN cc_start: 0.6785 (p0) cc_final: 0.6580 (p0) REVERT: B 379 LYS cc_start: 0.8491 (mmtt) cc_final: 0.8272 (mmtt) REVERT: B 528 MET cc_start: 0.8184 (mmm) cc_final: 0.7723 (mmm) REVERT: B 616 ARG cc_start: 0.8327 (mmm160) cc_final: 0.8034 (mmm-85) REVERT: B 631 ILE cc_start: 0.8225 (mm) cc_final: 0.8009 (mt) REVERT: B 805 ASP cc_start: 0.7630 (m-30) cc_final: 0.7057 (t0) REVERT: B 1039 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7286 (mp10) REVERT: C 40 PHE cc_start: 0.7290 (p90) cc_final: 0.6552 (p90) REVERT: C 94 PHE cc_start: 0.5158 (OUTLIER) cc_final: 0.4459 (m-80) REVERT: C 218 ASN cc_start: 0.7533 (OUTLIER) cc_final: 0.6856 (p0) REVERT: C 260 ARG cc_start: 0.8174 (mtm180) cc_final: 0.7950 (ttp80) REVERT: C 437 MET cc_start: 0.7366 (tpp) cc_final: 0.7117 (ttt) REVERT: C 822 GLN cc_start: 0.8080 (tp40) cc_final: 0.7722 (tp40) REVERT: C 874 GLN cc_start: 0.8416 (mp10) cc_final: 0.8149 (mp-120) REVERT: C 941 GLU cc_start: 0.8410 (mp0) cc_final: 0.7969 (mp0) REVERT: H 6 GLU cc_start: 0.5178 (OUTLIER) cc_final: 0.4822 (mp0) REVERT: H 19 ARG cc_start: 0.5206 (OUTLIER) cc_final: 0.3916 (tmm-80) REVERT: H 76 ASN cc_start: 0.7258 (m-40) cc_final: 0.6545 (t0) REVERT: H 100 PHE cc_start: 0.6478 (m-80) cc_final: 0.6259 (m-80) REVERT: L 79 GLN cc_start: 0.5415 (mp10) cc_final: 0.5204 (mp10) REVERT: M 25 SER cc_start: 0.7460 (t) cc_final: 0.6810 (p) REVERT: M 43 LYS cc_start: 0.7077 (ptpp) cc_final: 0.6710 (mtpp) REVERT: N 35 TRP cc_start: 0.5363 (m100) cc_final: 0.4544 (m100) REVERT: N 45 LYS cc_start: 0.8176 (mmtp) cc_final: 0.7956 (mptt) outliers start: 104 outliers final: 86 residues processed: 522 average time/residue: 0.2074 time to fit residues: 166.4027 Evaluate side-chains 528 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 433 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 807 PHE Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 928 ASN Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 807 PHE Chi-restraints excluded: chain B residue 906 GLN Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain B residue 1039 GLN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 81 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 715 LYS Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain C residue 1034 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 54 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 285 optimal weight: 0.9980 chunk 250 optimal weight: 0.6980 chunk 141 optimal weight: 0.9990 chunk 312 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 295 optimal weight: 0.3980 chunk 303 optimal weight: 4.9990 chunk 154 optimal weight: 0.1980 chunk 112 optimal weight: 0.7980 chunk 37 optimal weight: 0.0060 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 GLN C 843 ASN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN M 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.110894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.092975 restraints weight = 59016.683| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.72 r_work: 0.3268 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27840 Z= 0.124 Angle : 0.697 18.453 38121 Z= 0.335 Chirality : 0.046 0.431 4684 Planarity : 0.004 0.039 4704 Dihedral : 7.334 58.042 5808 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.46 % Favored : 95.39 % Rotamer: Outliers : 3.16 % Allowed : 18.92 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.70 (0.14), residues: 3341 helix: 1.18 (0.21), residues: 666 sheet: -0.20 (0.19), residues: 772 loop : -1.21 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 905 TYR 0.027 0.001 TYR C 109 PHE 0.032 0.001 PHE C 108 TRP 0.021 0.001 TRP M 100F HIS 0.004 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00273 (27693) covalent geometry : angle 0.64726 (37723) SS BOND : bond 0.00341 ( 43) SS BOND : angle 1.08156 ( 86) hydrogen bonds : bond 0.03932 ( 967) hydrogen bonds : angle 4.96566 ( 2715) link_BETA1-4 : bond 0.01081 ( 35) link_BETA1-4 : angle 2.73529 ( 105) link_NAG-ASN : bond 0.00475 ( 69) link_NAG-ASN : angle 2.95497 ( 207) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6682 Ramachandran restraints generated. 3341 Oldfield, 0 Emsley, 3341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 447 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.7924 (m-80) cc_final: 0.7585 (m-80) REVERT: A 135 LYS cc_start: 0.6761 (mttm) cc_final: 0.6550 (mmmt) REVERT: A 193 PHE cc_start: 0.7607 (t80) cc_final: 0.7270 (t80) REVERT: A 197 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7016 (ppp80) REVERT: A 357 ARG cc_start: 0.6160 (mmp80) cc_final: 0.5815 (mmp80) REVERT: A 396 MET cc_start: 0.8229 (mtt) cc_final: 0.7877 (mtt) REVERT: A 401 ASN cc_start: 0.5457 (p0) cc_final: 0.5091 (p0) REVERT: A 423 ILE cc_start: 0.8263 (tp) cc_final: 0.7751 (tt) REVERT: A 428 LYS cc_start: 0.6055 (OUTLIER) cc_final: 0.5059 (tptp) REVERT: A 504 TYR cc_start: 0.8323 (t80) cc_final: 0.7936 (t80) REVERT: A 551 PHE cc_start: 0.7650 (m-80) cc_final: 0.7405 (m-80) REVERT: A 607 SER cc_start: 0.8806 (t) cc_final: 0.8452 (m) REVERT: A 687 ARG cc_start: 0.8528 (mtt180) cc_final: 0.8314 (mmm-85) REVERT: A 711 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.6659 (ttpp) REVERT: A 851 GLN cc_start: 0.8310 (mm-40) cc_final: 0.7941 (mt0) REVERT: A 941 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7718 (mt-10) REVERT: B 109 TYR cc_start: 0.8402 (p90) cc_final: 0.8010 (p90) REVERT: B 122 ASN cc_start: 0.7541 (OUTLIER) cc_final: 0.7309 (p0) REVERT: B 616 ARG cc_start: 0.8265 (mmm160) cc_final: 0.7998 (mmm-85) REVERT: B 687 ARG cc_start: 0.8133 (mtt90) cc_final: 0.7833 (mtt180) REVERT: B 805 ASP cc_start: 0.7561 (m-30) cc_final: 0.6973 (t0) REVERT: B 1039 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7263 (mp10) REVERT: C 40 PHE cc_start: 0.7214 (p90) cc_final: 0.6473 (p90) REVERT: C 94 PHE cc_start: 0.5097 (OUTLIER) cc_final: 0.4449 (m-80) REVERT: C 218 ASN cc_start: 0.7514 (OUTLIER) cc_final: 0.6851 (p0) REVERT: C 822 GLN cc_start: 0.8034 (tp40) cc_final: 0.7696 (tp40) REVERT: C 874 GLN cc_start: 0.8317 (mp10) cc_final: 0.8064 (mp-120) REVERT: C 941 GLU cc_start: 0.8392 (mp0) cc_final: 0.7953 (mp0) REVERT: H 6 GLU cc_start: 0.5021 (OUTLIER) cc_final: 0.4700 (mp0) REVERT: H 19 ARG cc_start: 0.4984 (OUTLIER) cc_final: 0.3505 (tmm-80) REVERT: H 76 ASN cc_start: 0.7145 (m-40) cc_final: 0.6473 (t0) REVERT: H 111 VAL cc_start: 0.3524 (p) cc_final: 0.3314 (m) REVERT: L 79 GLN cc_start: 0.5363 (mp10) cc_final: 0.5123 (mp10) REVERT: M 25 SER cc_start: 0.7433 (t) cc_final: 0.6812 (p) REVERT: M 43 LYS cc_start: 0.7152 (ptpp) cc_final: 0.6718 (mtpp) REVERT: N 35 TRP cc_start: 0.5205 (m100) cc_final: 0.4528 (m100) REVERT: N 45 LYS cc_start: 0.8168 (mmtp) cc_final: 0.7951 (mptt) outliers start: 91 outliers final: 76 residues processed: 512 average time/residue: 0.1986 time to fit residues: 157.1638 Evaluate side-chains 514 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 429 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 711 LYS Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 928 ASN Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1037 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 807 PHE Chi-restraints excluded: chain B residue 906 GLN Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain B residue 1039 GLN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 81 CYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 229 CYS Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 562 VAL Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 715 LYS Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 865 ASP Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 54 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 235 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 chunk 264 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 274 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 258 optimal weight: 3.9990 chunk 234 optimal weight: 0.4980 chunk 132 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 GLN C 843 ASN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.110806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.092985 restraints weight = 58240.605| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.69 r_work: 0.3268 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27840 Z= 0.130 Angle : 0.709 19.122 38121 Z= 0.339 Chirality : 0.047 0.423 4684 Planarity : 0.004 0.040 4704 Dihedral : 7.260 58.023 5808 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.76 % Favored : 95.09 % Rotamer: Outliers : 3.19 % Allowed : 19.17 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.14), residues: 3341 helix: 1.22 (0.21), residues: 666 sheet: -0.19 (0.19), residues: 772 loop : -1.19 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 905 TYR 0.020 0.001 TYR N 91 PHE 0.031 0.001 PHE C 108 TRP 0.032 0.002 TRP H 36 HIS 0.003 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00288 (27693) covalent geometry : angle 0.66093 (37723) SS BOND : bond 0.00324 ( 43) SS BOND : angle 1.12245 ( 86) hydrogen bonds : bond 0.03955 ( 967) hydrogen bonds : angle 4.91894 ( 2715) link_BETA1-4 : bond 0.01044 ( 35) link_BETA1-4 : angle 2.72456 ( 105) link_NAG-ASN : bond 0.00464 ( 69) link_NAG-ASN : angle 2.93597 ( 207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5831.38 seconds wall clock time: 101 minutes 15.53 seconds (6075.53 seconds total)