Starting phenix.real_space_refine on Sat Mar 7 08:27:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qti_14141/03_2026/7qti_14141.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qti_14141/03_2026/7qti_14141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qti_14141/03_2026/7qti_14141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qti_14141/03_2026/7qti_14141.map" model { file = "/net/cci-nas-00/data/ceres_data/7qti_14141/03_2026/7qti_14141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qti_14141/03_2026/7qti_14141.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 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 165 5.16 5 C 25407 2.51 5 N 6639 2.21 5 O 7883 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40094 Number of models: 1 Model: "" Number of chains: 31 Chain: "G" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1729 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "H" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1729 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "C" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "E" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1645 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1637 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain: "I" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1729 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "J" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "D" Number of atoms: 8623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8623 Classifications: {'peptide': 1103} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 56, 'TRANS': 1046} Chain breaks: 4 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 8589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 8589 Classifications: {'peptide': 1096} Link IDs: {'PTRANS': 56, 'TRANS': 1039} Chain breaks: 4 Chain: "A" Number of atoms: 8609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 8609 Classifications: {'peptide': 1100} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 56, 'TRANS': 1043} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "K" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 8.80, per 1000 atoms: 0.22 Number of scatterers: 40094 At special positions: 0 Unit cell: (146.633, 199.2, 264.217, 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 165 16.00 O 7883 8.00 N 6639 7.00 C 25407 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=62, symmetry=0 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 152 " - pdb=" SG CYS G 208 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS H 214 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 106 " distance=2.03 Simple disulfide: pdb=" SG CYS F 150 " - pdb=" SG CYS F 206 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 152 " - pdb=" SG CYS I 208 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS J 214 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 134 " - pdb=" SG CYS J 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 129 " - pdb=" SG CYS D 161 " distance=2.03 Simple disulfide: pdb=" SG CYS D 288 " - pdb=" SG CYS D 298 " distance=2.03 Simple disulfide: pdb=" SG CYS D 333 " - pdb=" SG CYS D 358 " distance=2.03 Simple disulfide: pdb=" SG CYS D 376 " - pdb=" SG CYS D 429 " distance=2.03 Simple disulfide: pdb=" SG CYS D 388 " - pdb=" SG CYS D 522 " distance=2.03 Simple disulfide: pdb=" SG CYS D 477 " - pdb=" SG CYS D 485 " distance=2.03 Simple disulfide: pdb=" SG CYS D 535 " - pdb=" SG CYS D 587 " distance=2.03 Simple disulfide: pdb=" SG CYS D 614 " - pdb=" SG CYS D 646 " distance=2.03 Simple disulfide: pdb=" SG CYS D 659 " - pdb=" SG CYS D 668 " distance=2.03 Simple disulfide: pdb=" SG CYS D 735 " - pdb=" SG CYS D 757 " distance=2.03 Simple disulfide: pdb=" SG CYS D 740 " - pdb=" SG CYS D 746 " distance=2.03 Simple disulfide: pdb=" SG CYS D 837 " - pdb=" SG CYS D 848 " distance=2.03 Simple disulfide: pdb=" SG CYS D1029 " - pdb=" SG CYS D1040 " distance=2.03 Simple disulfide: pdb=" SG CYS D1079 " - pdb=" SG CYS D1123 " distance=2.03 Simple disulfide: pdb=" SG CYS K 129 " - pdb=" SG CYS K 161 " distance=2.03 Simple disulfide: pdb=" SG CYS K 288 " - pdb=" SG CYS K 298 " distance=2.03 Simple disulfide: pdb=" SG CYS K 333 " - pdb=" SG CYS K 358 " distance=2.03 Simple disulfide: pdb=" SG CYS K 376 " - pdb=" SG CYS K 429 " distance=2.03 Simple disulfide: pdb=" SG CYS K 388 " - pdb=" SG CYS K 522 " distance=2.03 Simple disulfide: pdb=" SG CYS K 477 " - pdb=" SG CYS K 485 " distance=2.03 Simple disulfide: pdb=" SG CYS K 535 " - pdb=" SG CYS K 587 " distance=2.04 Simple disulfide: pdb=" SG CYS K 614 " - pdb=" SG CYS K 646 " distance=2.03 Simple disulfide: pdb=" SG CYS K 659 " - pdb=" SG CYS K 668 " distance=2.04 Simple disulfide: pdb=" SG CYS K 735 " - pdb=" SG CYS K 757 " distance=2.03 Simple disulfide: pdb=" SG CYS K 740 " - pdb=" SG CYS K 746 " distance=2.03 Simple disulfide: pdb=" SG CYS K 837 " - pdb=" SG CYS K 848 " distance=2.03 Simple disulfide: pdb=" SG CYS K1029 " - pdb=" SG CYS K1040 " distance=2.03 Simple disulfide: pdb=" SG CYS K1079 " - pdb=" SG CYS K1123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.04 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.04 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 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 ALPHA1-3 " BMA X 3 " - " MAN X 4 " BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " 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 b 2 " - " BMA b 3 " NAG-ASN " NAG A1301 " - " ASN A 613 " " NAG A1302 " - " ASN A 654 " " NAG A1303 " - " ASN A1071 " " NAG A1304 " - " ASN A 706 " " NAG A1305 " - " ASN A 120 " " NAG A1306 " - " ASN A 159 " " NAG D1301 " - " ASN D 328 " " NAG D1302 " - " ASN D 613 " " NAG D1303 " - " ASN D 654 " " NAG D1304 " - " ASN D1071 " " NAG D1305 " - " ASN D1131 " " NAG D1306 " - " ASN D 120 " " NAG D1307 " - " ASN D 135 " " NAG D1308 " - " ASN D 159 " " NAG K1301 " - " ASN K 328 " " NAG K1302 " - " ASN K 706 " " NAG K1303 " - " ASN K 61 " " NAG K1304 " - " ASN K 340 " " NAG K1305 " - " ASN K 600 " " NAG K1306 " - " ASN K 613 " " NAG K1307 " - " ASN K 654 " " NAG K1308 " - " ASN K1071 " " NAG K1309 " - " ASN K 798 " " NAG K1310 " - " ASN K 120 " " NAG K1311 " - " ASN K 159 " " NAG K1312 " - " ASN K 231 " " NAG L 1 " - " ASN D 279 " " NAG M 1 " - " ASN D 340 " " NAG N 1 " - " ASN D 706 " " NAG O 1 " - " ASN D 714 " " NAG P 1 " - " ASN D 798 " " NAG Q 1 " - " ASN D1095 " " NAG R 1 " - " ASN K1095 " " NAG S 1 " - " ASN K 279 " " NAG T 1 " - " ASN K1131 " " NAG U 1 " - " ASN K 714 " " NAG V 1 " - " ASN A 279 " " NAG W 1 " - " ASN A 328 " " NAG X 1 " - " ASN A 340 " " NAG Y 1 " - " ASN A1095 " " NAG Z 1 " - " ASN A1131 " " NAG a 1 " - " ASN A 714 " " NAG b 1 " - " ASN A 798 " Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 1.6 seconds 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9424 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 92 sheets defined 17.8% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.568A pdb=" N LYS G 65 " --> pdb=" O GLU G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 168 through 170 No H-bonds generated for 'chain 'G' and resid 168 through 170' Processing helix chain 'G' and resid 199 through 201 No H-bonds generated for 'chain 'G' and resid 199 through 201' Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.896A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 183 through 188 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 199 through 201 No H-bonds generated for 'chain 'B' and resid 199 through 201' Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.802A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 127 Processing helix chain 'C' and resid 183 through 188 Processing helix chain 'E' and resid 122 through 128 removed outlier: 3.717A pdb=" N SER E 128 " --> pdb=" O GLU E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 28 through 31 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 137 through 139 No H-bonds generated for 'chain 'F' and resid 137 through 139' Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 139 through 141 No H-bonds generated for 'chain 'I' and resid 139 through 141' Processing helix chain 'I' and resid 168 through 170 No H-bonds generated for 'chain 'I' and resid 168 through 170' Processing helix chain 'I' and resid 199 through 201 No H-bonds generated for 'chain 'I' and resid 199 through 201' Processing helix chain 'J' and resid 121 through 127 removed outlier: 3.547A pdb=" N SER J 127 " --> pdb=" O GLU J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 188 Processing helix chain 'D' and resid 69 through 73 removed outlier: 3.805A pdb=" N ASN D 72 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 155 removed outlier: 4.131A pdb=" N VAL D 154 " --> pdb=" O GLU D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 301 Processing helix chain 'D' and resid 334 through 340 removed outlier: 3.893A pdb=" N VAL D 338 " --> pdb=" O PRO D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 369 removed outlier: 3.834A pdb=" N ALA D 369 " --> pdb=" O LEU D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 384 Processing helix chain 'D' and resid 402 through 407 removed outlier: 4.133A pdb=" N ARG D 405 " --> pdb=" O ASP D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 419 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 540 through 543 Processing helix chain 'D' and resid 734 through 740 Processing helix chain 'D' and resid 743 through 752 removed outlier: 3.695A pdb=" N GLN D 752 " --> pdb=" O ASN D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 780 Processing helix chain 'D' and resid 813 through 824 Processing helix chain 'D' and resid 863 through 882 removed outlier: 3.607A pdb=" N ILE D 867 " --> pdb=" O THR D 863 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA D 868 " --> pdb=" O ASP D 864 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN D 869 " --> pdb=" O GLU D 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 888 removed outlier: 3.524A pdb=" N GLY D 886 " --> pdb=" O TRP D 883 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY D 888 " --> pdb=" O PHE D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 894 through 905 Processing helix chain 'D' and resid 910 through 937 removed outlier: 6.837A pdb=" N LYS D 918 " --> pdb=" O TYR D 914 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU D 919 " --> pdb=" O GLU D 915 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE D 931 " --> pdb=" O ALA D 927 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN D 932 " --> pdb=" O ILE D 928 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP D 933 " --> pdb=" O GLY D 929 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 962 removed outlier: 3.757A pdb=" N VAL D 948 " --> pdb=" O LYS D 944 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL D 949 " --> pdb=" O LEU D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 963 through 965 No H-bonds generated for 'chain 'D' and resid 963 through 965' Processing helix chain 'D' and resid 973 through 981 Processing helix chain 'D' and resid 982 through 1030 removed outlier: 4.923A pdb=" N VAL D 988 " --> pdb=" O PRO D 984 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D 993 " --> pdb=" O GLN D 989 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA D1013 " --> pdb=" O LEU D1009 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU D1014 " --> pdb=" O ILE D1010 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 74 removed outlier: 3.754A pdb=" N GLY K 73 " --> pdb=" O SER K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 291 through 301 Processing helix chain 'K' and resid 362 through 368 removed outlier: 3.645A pdb=" N TYR K 366 " --> pdb=" O TYR K 362 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 384 removed outlier: 3.616A pdb=" N LEU K 384 " --> pdb=" O PRO K 381 " (cutoff:3.500A) Processing helix chain 'K' and resid 402 through 405 removed outlier: 4.208A pdb=" N ARG K 405 " --> pdb=" O ASP K 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 402 through 405' Processing helix chain 'K' and resid 413 through 419 Processing helix chain 'K' and resid 435 through 440 removed outlier: 3.821A pdb=" N SER K 440 " --> pdb=" O ASN K 436 " (cutoff:3.500A) Processing helix chain 'K' and resid 499 through 502 Processing helix chain 'K' and resid 734 through 740 Processing helix chain 'K' and resid 743 through 752 removed outlier: 4.276A pdb=" N GLN K 752 " --> pdb=" O ASN K 748 " (cutoff:3.500A) Processing helix chain 'K' and resid 756 through 780 removed outlier: 3.860A pdb=" N LEU K 760 " --> pdb=" O PHE K 756 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP K 772 " --> pdb=" O ALA K 768 " (cutoff:3.500A) Processing helix chain 'K' and resid 813 through 824 Processing helix chain 'K' and resid 825 through 827 No H-bonds generated for 'chain 'K' and resid 825 through 827' Processing helix chain 'K' and resid 863 through 882 removed outlier: 3.789A pdb=" N ILE K 867 " --> pdb=" O THR K 863 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA K 868 " --> pdb=" O ASP K 864 " (cutoff:3.500A) Processing helix chain 'K' and resid 883 through 887 Processing helix chain 'K' and resid 894 through 905 Processing helix chain 'K' and resid 910 through 937 removed outlier: 3.523A pdb=" N TYR K 914 " --> pdb=" O GLN K 910 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LYS K 918 " --> pdb=" O TYR K 914 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU K 919 " --> pdb=" O GLU K 915 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN K 932 " --> pdb=" O ILE K 928 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP K 933 " --> pdb=" O GLY K 929 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER K 937 " --> pdb=" O ASP K 933 " (cutoff:3.500A) Processing helix chain 'K' and resid 942 through 962 removed outlier: 3.703A pdb=" N VAL K 948 " --> pdb=" O LYS K 944 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL K 949 " --> pdb=" O LEU K 945 " (cutoff:3.500A) Processing helix chain 'K' and resid 963 through 965 No H-bonds generated for 'chain 'K' and resid 963 through 965' Processing helix chain 'K' and resid 973 through 980 Processing helix chain 'K' and resid 982 through 1030 removed outlier: 4.908A pdb=" N VAL K 988 " --> pdb=" O PRO K 984 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA K1013 " --> pdb=" O LEU K1009 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU K1014 " --> pdb=" O ILE K1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.553A pdb=" N ASN A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.501A pdb=" N ASN A 367 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.518A pdb=" N LYS A 383 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 380 through 384' Processing helix chain 'A' and resid 401 through 408 removed outlier: 4.135A pdb=" N ARG A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 420 Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 616 through 621 Processing helix chain 'A' and resid 734 through 740 removed outlier: 3.626A pdb=" N CYS A 740 " --> pdb=" O THR A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 757 through 780 removed outlier: 3.671A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 824 Processing helix chain 'A' and resid 846 through 852 Processing helix chain 'A' and resid 863 through 881 removed outlier: 3.625A pdb=" N ILE A 867 " --> pdb=" O THR A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 910 through 937 removed outlier: 6.969A pdb=" N LYS A 918 " --> pdb=" O TYR A 914 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 919 " --> pdb=" O GLU A 915 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.704A pdb=" N GLN A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 980 removed outlier: 3.550A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.406A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.836A pdb=" N LEU G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.520A pdb=" N LYS G 98 " --> pdb=" O ILE G 114 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE G 114 " --> pdb=" O LYS G 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 132 through 136 removed outlier: 5.872A pdb=" N TYR G 188 " --> pdb=" O ASP G 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 143 through 144 removed outlier: 3.701A pdb=" N THR G 147 " --> pdb=" O SER G 144 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TYR G 188 " --> pdb=" O ASP G 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 163 through 166 removed outlier: 4.662A pdb=" N TYR G 206 " --> pdb=" O VAL G 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.490A pdb=" N LEU H 11 " --> pdb=" O ASP H 105 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR H 85 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN H 89 " --> pdb=" O ALA H 34 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA H 34 " --> pdb=" O GLN H 89 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N TYR H 49 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 114 through 118 removed outlier: 4.772A pdb=" N SER H 131 " --> pdb=" O LEU H 181 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU H 181 " --> pdb=" O SER H 131 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL H 133 " --> pdb=" O LEU H 179 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU H 179 " --> pdb=" O VAL H 133 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU H 135 " --> pdb=" O SER H 177 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N SER H 177 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ASN H 137 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU H 175 " --> pdb=" O ASN H 137 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 153 through 155 removed outlier: 4.394A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.598A pdb=" N SER B 78 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP B 73 " --> pdb=" O SER B 78 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.225A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 132 through 136 removed outlier: 3.639A pdb=" N ASP B 156 " --> pdb=" O TYR B 188 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR B 188 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 143 through 144 removed outlier: 3.639A pdb=" N ASP B 156 " --> pdb=" O TYR B 188 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR B 188 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 163 through 166 removed outlier: 3.777A pdb=" N THR B 163 " --> pdb=" O ASN B 211 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYR B 206 " --> pdb=" O VAL B 223 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.593A pdb=" N CYS C 23 " --> pdb=" O PHE C 71 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE C 71 " --> pdb=" O CYS C 23 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.132A pdb=" N LEU C 11 " --> pdb=" O ASP C 105 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TYR C 49 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 114 through 118 removed outlier: 5.476A pdb=" N TYR C 173 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 153 through 155 removed outlier: 4.374A pdb=" N TRP C 148 " --> pdb=" O GLN C 155 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS C 207 " --> pdb=" O CYS C 194 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.665A pdb=" N ALA E 19 " --> pdb=" O ILE E 76 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP E 71 " --> pdb=" O SER E 68 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.393A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 115 through 119 removed outlier: 5.868A pdb=" N TYR E 174 " --> pdb=" O ASN E 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 154 through 156 removed outlier: 4.520A pdb=" N TRP E 149 " --> pdb=" O GLN E 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.705A pdb=" N THR F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP F 73 " --> pdb=" O THR F 78 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.706A pdb=" N VAL F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TRP F 50 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP F 50 " --> pdb=" O ASP F 59 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP F 59 " --> pdb=" O TRP F 50 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AC9, first strand: chain 'F' and resid 130 through 134 removed outlier: 6.034A pdb=" N TYR F 186 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 141 through 142 removed outlier: 6.034A pdb=" N TYR F 186 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 161 through 164 removed outlier: 3.652A pdb=" N CYS F 206 " --> pdb=" O LYS F 219 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.728A pdb=" N LEU I 81 " --> pdb=" O LEU I 20 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER I 78 " --> pdb=" O ASP I 73 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP I 73 " --> pdb=" O SER I 78 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.361A pdb=" N GLY I 10 " --> pdb=" O THR I 122 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLY I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY I 50 " --> pdb=" O GLY I 59 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY I 59 " --> pdb=" O GLY I 50 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.361A pdb=" N GLY I 10 " --> pdb=" O THR I 122 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS I 98 " --> pdb=" O ILE I 114 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE I 114 " --> pdb=" O LYS I 98 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 132 through 136 removed outlier: 6.042A pdb=" N TYR I 188 " --> pdb=" O ASP I 156 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 143 through 144 removed outlier: 6.042A pdb=" N TYR I 188 " --> pdb=" O ASP I 156 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 163 through 166 removed outlier: 4.553A pdb=" N TYR I 206 " --> pdb=" O VAL I 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 5 through 6 removed outlier: 3.708A pdb=" N LEU J 73 " --> pdb=" O VAL J 21 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N CYS J 23 " --> pdb=" O PHE J 71 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE J 71 " --> pdb=" O CYS J 23 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.314A pdb=" N LEU J 11 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N TYR J 49 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 114 through 118 Processing sheet with id=AE3, first strand: chain 'J' and resid 153 through 155 removed outlier: 4.463A pdb=" N TRP J 148 " --> pdb=" O GLN J 155 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 28 through 30 Processing sheet with id=AE5, first strand: chain 'D' and resid 36 through 37 removed outlier: 7.292A pdb=" N VAL D 36 " --> pdb=" O LEU D 220 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N SER D 200 " --> pdb=" O PRO D 222 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL D 224 " --> pdb=" O ILE D 198 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS D 190 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR D 199 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS D 201 " --> pdb=" O GLU D 186 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 50 through 55 removed outlier: 3.815A pdb=" N GLN D 268 " --> pdb=" O PHE D 55 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N THR D 271 " --> pdb=" O ASP D 287 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ASP D 287 " --> pdb=" O THR D 271 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU D 273 " --> pdb=" O ALA D 285 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA D 285 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LYS D 275 " --> pdb=" O THR D 283 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 66 through 67 Processing sheet with id=AE8, first strand: chain 'D' and resid 82 through 83 removed outlier: 3.512A pdb=" N GLY D 105 " --> pdb=" O ARG D 234 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE D 104 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU D 115 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER D 114 " --> pdb=" O CYS D 129 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE D 163 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLU D 130 " --> pdb=" O CYS D 161 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N CYS D 161 " --> pdb=" O GLU D 130 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 99 through 100 removed outlier: 3.740A pdb=" N ARG D 100 " --> pdb=" O LEU D 238 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 308 through 316 removed outlier: 3.511A pdb=" N THR D 312 " --> pdb=" O VAL D 592 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL D 592 " --> pdb=" O THR D 312 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASN D 314 " --> pdb=" O GLY D 590 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY D 590 " --> pdb=" O ASN D 314 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY D 591 " --> pdb=" O GLN D 610 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 322 through 323 removed outlier: 3.631A pdb=" N THR D 550 " --> pdb=" O ASP D 583 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASP D 571 " --> pdb=" O ILE D 584 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY D 563 " --> pdb=" O ASP D 571 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE A 43 " --> pdb=" O PHE D 562 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 351 through 355 removed outlier: 3.829A pdb=" N ASN D 351 " --> pdb=" O SER D 396 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER D 396 " --> pdb=" O ASN D 351 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL D 392 " --> pdb=" O ILE D 355 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 449 through 451 Processing sheet with id=AF5, first strand: chain 'D' and resid 470 through 471 Processing sheet with id=AF6, first strand: chain 'D' and resid 651 through 652 removed outlier: 5.951A pdb=" N GLU D 651 " --> pdb=" O ALA D 691 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR D 693 " --> pdb=" O GLU D 651 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER D 688 " --> pdb=" O GLN D 672 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE D 667 " --> pdb=" O ILE D 663 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 698 through 699 removed outlier: 6.661A pdb=" N ALA D 698 " --> pdb=" O ILE A 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'D' and resid 709 through 710 removed outlier: 3.553A pdb=" N THR D1073 " --> pdb=" O SER D1094 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA D1075 " --> pdb=" O PHE D1092 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE D1092 " --> pdb=" O ALA D1075 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 714 through 725 removed outlier: 3.653A pdb=" N MET D1047 " --> pdb=" O VAL D1062 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TYR D1064 " --> pdb=" O HIS D1045 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N HIS D1045 " --> pdb=" O TYR D1064 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 730 through 733 removed outlier: 4.696A pdb=" N LYS D 730 " --> pdb=" O LEU D 858 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 784 through 785 Processing sheet with id=AG3, first strand: chain 'D' and resid 1117 through 1122 removed outlier: 4.755A pdb=" N ALA D1084 " --> pdb=" O SER D1120 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 28 through 30 Processing sheet with id=AG5, first strand: chain 'K' and resid 36 through 37 removed outlier: 6.881A pdb=" N VAL K 36 " --> pdb=" O LEU K 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'K' and resid 48 through 55 removed outlier: 3.704A pdb=" N PHE K 55 " --> pdb=" O GLN K 268 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN K 268 " --> pdb=" O PHE K 55 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N THR K 271 " --> pdb=" O ASP K 287 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ASP K 287 " --> pdb=" O THR K 271 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU K 273 " --> pdb=" O ALA K 285 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA K 285 " --> pdb=" O LEU K 273 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LYS K 275 " --> pdb=" O THR K 283 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 66 through 67 Processing sheet with id=AG8, first strand: chain 'K' and resid 82 through 83 Processing sheet with id=AG9, first strand: chain 'K' and resid 87 through 88 removed outlier: 3.771A pdb=" N LYS K 190 " --> pdb=" O LYS K 197 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL K 224 " --> pdb=" O ILE K 198 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 126 through 133 removed outlier: 3.973A pdb=" N TYR K 165 " --> pdb=" O ILE K 126 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL K 128 " --> pdb=" O PHE K 163 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE K 163 " --> pdb=" O VAL K 128 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N GLU K 130 " --> pdb=" O CYS K 161 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N CYS K 161 " --> pdb=" O GLU K 130 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N GLN K 132 " --> pdb=" O ASN K 159 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ASN K 159 " --> pdb=" O GLN K 132 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 308 through 316 removed outlier: 7.271A pdb=" N VAL K 592 " --> pdb=" O THR K 312 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASN K 314 " --> pdb=" O GLY K 590 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY K 590 " --> pdb=" O ASN K 314 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY K 591 " --> pdb=" O GLN K 610 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 322 through 323 removed outlier: 3.890A pdb=" N PHE K 540 " --> pdb=" O LEU K 543 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 351 through 355 removed outlier: 3.914A pdb=" N ASN K 351 " --> pdb=" O SER K 396 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER K 396 " --> pdb=" O ASN K 351 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS K 353 " --> pdb=" O ALA K 394 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA K 394 " --> pdb=" O LYS K 353 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE K 355 " --> pdb=" O VAL K 392 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL K 392 " --> pdb=" O ILE K 355 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 449 through 451 removed outlier: 3.571A pdb=" N TYR K 450 " --> pdb=" O ARG K 490 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 470 through 471 Processing sheet with id=AH7, first strand: chain 'K' and resid 550 through 551 removed outlier: 3.777A pdb=" N THR K 550 " --> pdb=" O ASP K 583 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 651 through 652 removed outlier: 6.038A pdb=" N GLU K 651 " --> pdb=" O ALA K 691 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N THR K 693 " --> pdb=" O GLU K 651 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR K 692 " --> pdb=" O CYS K 668 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE K 667 " --> pdb=" O ILE K 663 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 709 through 725 removed outlier: 6.364A pdb=" N ALA K 710 " --> pdb=" O ASN K1071 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASN K1071 " --> pdb=" O ALA K 710 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLU K1069 " --> pdb=" O PRO K 712 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET K1047 " --> pdb=" O VAL K1062 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N TYR K1064 " --> pdb=" O HIS K1045 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N HIS K1045 " --> pdb=" O TYR K1064 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 709 through 725 removed outlier: 6.364A pdb=" N ALA K 710 " --> pdb=" O ASN K1071 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASN K1071 " --> pdb=" O ALA K 710 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLU K1069 " --> pdb=" O PRO K 712 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR K1073 " --> pdb=" O SER K1094 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'K' and resid 730 through 733 removed outlier: 4.478A pdb=" N LYS K 730 " --> pdb=" O LEU K 858 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'K' and resid 784 through 785 Processing sheet with id=AI4, first strand: chain 'K' and resid 1117 through 1122 removed outlier: 4.547A pdb=" N ALA K1084 " --> pdb=" O SER K1120 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AI6, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.302A pdb=" N VAL A 36 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 221 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE A 198 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP A 225 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE A 196 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 201 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 88 " --> pdb=" O PHE A 189 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.524A pdb=" N PHE A 55 " --> pdb=" O GLN A 268 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A 268 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AI9, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.613A pdb=" N GLY A 105 " --> pdb=" O ARG A 234 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'A' and resid 113 through 114 removed outlier: 3.524A pdb=" N CYS A 129 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 163 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N GLU A 130 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N CYS A 161 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 10.449A pdb=" N GLN A 132 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N ASN A 159 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'A' and resid 308 through 310 Processing sheet with id=AJ3, first strand: chain 'A' and resid 321 through 322 removed outlier: 6.544A pdb=" N GLU A 321 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N ASN A 539 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A 547 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A 585 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.712A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 396 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 392 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN A 391 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 428 " --> pdb=" O TYR A 377 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR A 377 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AJ6, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.074A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN A 672 " --> pdb=" O SER A 688 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'A' and resid 709 through 710 Processing sheet with id=AJ8, first strand: chain 'A' and resid 714 through 725 removed outlier: 3.723A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.608A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AK2, first strand: chain 'A' and resid 1091 through 1094 1382 hydrogen bonds defined for protein. 3621 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: 10.87 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7275 1.33 - 1.46: 12771 1.46 - 1.59: 20763 1.59 - 1.71: 0 1.71 - 1.84: 202 Bond restraints: 41011 Sorted by residual: bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.499 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C1 NAG Y 2 " pdb=" O5 NAG Y 2 " ideal model delta sigma weight residual 1.406 1.499 -0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" C GLU B 160 " pdb=" N PRO B 161 " ideal model delta sigma weight residual 1.333 1.370 -0.037 1.01e-02 9.80e+03 1.31e+01 bond pdb=" N VAL H 96 " pdb=" CA VAL H 96 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.14e-02 7.69e+03 1.19e+01 bond pdb=" N ASP A 140 " pdb=" CA ASP A 140 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.19e-02 7.06e+03 1.03e+01 ... (remaining 41006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 54849 2.49 - 4.98: 856 4.98 - 7.48: 65 7.48 - 9.97: 8 9.97 - 12.46: 4 Bond angle restraints: 55782 Sorted by residual: angle pdb=" N PRO C 95 " pdb=" CA PRO C 95 " pdb=" C PRO C 95 " ideal model delta sigma weight residual 112.33 101.62 10.71 1.87e+00 2.86e-01 3.28e+01 angle pdb=" N ILE F 48 " pdb=" CA ILE F 48 " pdb=" C ILE F 48 " ideal model delta sigma weight residual 113.47 108.07 5.40 1.01e+00 9.80e-01 2.86e+01 angle pdb=" N PRO I 161 " pdb=" CA PRO I 161 " pdb=" C PRO I 161 " ideal model delta sigma weight residual 112.47 122.94 -10.47 2.06e+00 2.36e-01 2.58e+01 angle pdb=" CA GLU B 160 " pdb=" C GLU B 160 " pdb=" N PRO B 161 " ideal model delta sigma weight residual 118.44 126.48 -8.04 1.59e+00 3.96e-01 2.55e+01 angle pdb=" N GLU A 151 " pdb=" CA GLU A 151 " pdb=" C GLU A 151 " ideal model delta sigma weight residual 113.43 107.12 6.31 1.26e+00 6.30e-01 2.51e+01 ... (remaining 55777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.79: 23933 24.79 - 49.57: 1100 49.57 - 74.36: 152 74.36 - 99.14: 64 99.14 - 123.93: 52 Dihedral angle restraints: 25301 sinusoidal: 10614 harmonic: 14687 Sorted by residual: dihedral pdb=" CB CYS A 837 " pdb=" SG CYS A 837 " pdb=" SG CYS A 848 " pdb=" CB CYS A 848 " ideal model delta sinusoidal sigma weight residual 93.00 177.46 -84.46 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS A 288 " pdb=" SG CYS A 288 " pdb=" SG CYS A 298 " pdb=" CB CYS A 298 " ideal model delta sinusoidal sigma weight residual 93.00 162.51 -69.51 1 1.00e+01 1.00e-02 6.24e+01 dihedral pdb=" CB CYS K1079 " pdb=" SG CYS K1079 " pdb=" SG CYS K1123 " pdb=" CB CYS K1123 " ideal model delta sinusoidal sigma weight residual -86.00 -32.53 -53.47 1 1.00e+01 1.00e-02 3.89e+01 ... (remaining 25298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 6370 0.130 - 0.260: 86 0.260 - 0.390: 13 0.390 - 0.519: 1 0.519 - 0.649: 1 Chirality restraints: 6471 Sorted by residual: chirality pdb=" CA TYR J 94 " pdb=" N TYR J 94 " pdb=" C TYR J 94 " pdb=" CB TYR J 94 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN D 340 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" C1 NAG K1310 " pdb=" ND2 ASN K 120 " pdb=" C2 NAG K1310 " pdb=" O5 NAG K1310 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 6468 not shown) Planarity restraints: 7159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K1310 " -0.252 2.00e-02 2.50e+03 2.11e-01 5.59e+02 pdb=" C7 NAG K1310 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG K1310 " -0.170 2.00e-02 2.50e+03 pdb=" N2 NAG K1310 " 0.356 2.00e-02 2.50e+03 pdb=" O7 NAG K1310 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 80 " -0.068 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO E 81 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO E 81 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO E 81 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS I 155 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C LYS I 155 " 0.056 2.00e-02 2.50e+03 pdb=" O LYS I 155 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP I 156 " -0.019 2.00e-02 2.50e+03 ... (remaining 7156 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1154 2.70 - 3.25: 38380 3.25 - 3.80: 60699 3.80 - 4.35: 77025 4.35 - 4.90: 130681 Nonbonded interactions: 307939 Sorted by model distance: nonbonded pdb=" NH2 ARG J 24 " pdb=" O PHE J 71 " model vdw 2.151 3.120 nonbonded pdb=" OH TYR D 89 " pdb=" OE1 GLU D 186 " model vdw 2.174 3.040 nonbonded pdb=" O GLN E 101 " pdb=" NH1 ARG F 44 " model vdw 2.205 3.120 nonbonded pdb=" O LEU A 290 " pdb=" OG1 THR A 629 " model vdw 2.206 3.040 nonbonded pdb=" O HIS I 101 " pdb=" ND1 HIS I 101 " model vdw 2.208 3.120 ... (remaining 307934 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 19 through 837 or resid 848 through 1306)) selection = (chain 'D' and (resid 19 through 837 or resid 848 through 1306)) selection = (chain 'K' and resid 19 through 1306) } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'a' selection = chain 'b' } 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 38.450 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.230 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:1.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 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 0.093 41137 Z= 0.235 Angle : 0.745 20.284 56098 Z= 0.415 Chirality : 0.050 0.649 6471 Planarity : 0.005 0.211 7116 Dihedral : 15.361 123.928 15691 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.50 % Favored : 94.18 % Rotamer: Outliers : 0.91 % Allowed : 0.89 % Favored : 98.19 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.12), residues: 5015 helix: 1.36 (0.21), residues: 735 sheet: 0.48 (0.15), residues: 1318 loop : -1.13 (0.11), residues: 2962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 18 TYR 0.029 0.001 TYR D 901 PHE 0.036 0.001 PHE K 163 TRP 0.023 0.001 TRP I 53 HIS 0.006 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00403 (41011) covalent geometry : angle 0.71341 (55782) SS BOND : bond 0.00285 ( 62) SS BOND : angle 0.69779 ( 124) hydrogen bonds : bond 0.23124 ( 1319) hydrogen bonds : angle 8.49211 ( 3621) link_ALPHA1-3 : bond 0.00418 ( 1) link_ALPHA1-3 : angle 1.53242 ( 3) link_BETA1-4 : bond 0.00843 ( 20) link_BETA1-4 : angle 2.79766 ( 60) link_NAG-ASN : bond 0.00674 ( 43) link_NAG-ASN : angle 4.16796 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 310 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 93 SER cc_start: 0.5995 (OUTLIER) cc_final: 0.5707 (p) REVERT: J 94 TYR cc_start: 0.7173 (OUTLIER) cc_final: 0.6573 (t80) REVERT: K 141 HIS cc_start: 0.5415 (OUTLIER) cc_final: 0.4750 (p90) REVERT: K 142 LYS cc_start: 0.4290 (OUTLIER) cc_final: 0.3776 (mmmt) REVERT: K 148 MET cc_start: 0.5914 (OUTLIER) cc_final: 0.5334 (ttp) outliers start: 40 outliers final: 10 residues processed: 346 average time/residue: 0.2229 time to fit residues: 128.0486 Evaluate side-chains 224 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain J residue 94 TYR Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 526 LYS Chi-restraints excluded: chain D residue 529 ASN Chi-restraints excluded: chain K residue 141 HIS Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 146 SER Chi-restraints excluded: chain K residue 148 MET Chi-restraints excluded: chain A residue 242 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 494 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN C 166 GLN E 101 GLN E 125 GLN I 35 HIS I 110 ASN D 85 ASN D 202 HIS D 357 ASN ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 989 GLN K 610 GLN K 801 GLN K 932 GLN A 79 ASN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.155991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.091879 restraints weight = 104337.738| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 5.02 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 41137 Z= 0.151 Angle : 0.665 19.402 56098 Z= 0.328 Chirality : 0.047 0.382 6471 Planarity : 0.004 0.064 7116 Dihedral : 10.610 113.068 6811 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.62 % Favored : 94.20 % Rotamer: Outliers : 0.94 % Allowed : 6.67 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.12), residues: 5015 helix: 1.36 (0.20), residues: 739 sheet: 0.41 (0.14), residues: 1409 loop : -1.15 (0.11), residues: 2867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 405 TYR 0.027 0.002 TYR K 165 PHE 0.031 0.002 PHE K 163 TRP 0.013 0.001 TRP F 47 HIS 0.007 0.001 HIS D 622 Details of bonding type rmsd covalent geometry : bond 0.00345 (41011) covalent geometry : angle 0.63080 (55782) SS BOND : bond 0.00328 ( 62) SS BOND : angle 0.93206 ( 124) hydrogen bonds : bond 0.04807 ( 1319) hydrogen bonds : angle 6.10853 ( 3621) link_ALPHA1-3 : bond 0.00784 ( 1) link_ALPHA1-3 : angle 2.66218 ( 3) link_BETA1-4 : bond 0.00806 ( 20) link_BETA1-4 : angle 2.87932 ( 60) link_NAG-ASN : bond 0.00586 ( 43) link_NAG-ASN : angle 3.94781 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 229 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 PHE cc_start: 0.5847 (p90) cc_final: 0.5634 (p90) REVERT: B 38 ARG cc_start: 0.6585 (ptt90) cc_final: 0.6300 (ptp-170) REVERT: C 142 ARG cc_start: 0.5281 (tpt170) cc_final: 0.4310 (mpt180) REVERT: F 2 MET cc_start: 0.6448 (mtt) cc_final: 0.6233 (mmt) REVERT: F 74 MET cc_start: 0.8156 (mmp) cc_final: 0.7359 (mpp) REVERT: I 101 HIS cc_start: 0.5895 (t-90) cc_final: 0.5429 (t-90) REVERT: D 357 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.8146 (t0) REVERT: D 756 PHE cc_start: 0.7003 (t80) cc_final: 0.6739 (t80) REVERT: D 947 ASP cc_start: 0.8516 (m-30) cc_final: 0.8304 (m-30) REVERT: D 1089 GLU cc_start: 0.8583 (pm20) cc_final: 0.8360 (pm20) REVERT: K 266 TYR cc_start: 0.7691 (m-80) cc_final: 0.6770 (m-80) REVERT: K 384 LEU cc_start: 0.8689 (mp) cc_final: 0.8459 (mp) REVERT: A 217 PHE cc_start: 0.7003 (m-80) cc_final: 0.6778 (t80) outliers start: 41 outliers final: 25 residues processed: 258 average time/residue: 0.2205 time to fit residues: 95.6000 Evaluate side-chains 225 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 166 GLN Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 357 ASN Chi-restraints excluded: chain D residue 527 SER Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 569 THR Chi-restraints excluded: chain K residue 990 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 760 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 2 optimal weight: 9.9990 chunk 320 optimal weight: 7.9990 chunk 42 optimal weight: 40.0000 chunk 185 optimal weight: 10.0000 chunk 300 optimal weight: 2.9990 chunk 217 optimal weight: 0.6980 chunk 254 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 157 optimal weight: 0.5980 chunk 265 optimal weight: 0.5980 chunk 445 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 168 GLN K1068 GLN A 79 ASN A 144 ASN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 923 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 = 0.4495 r_free = 0.4495 target = 0.155598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.099836 restraints weight = 115885.565| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 5.90 r_work: 0.3238 rms_B_bonded: 5.34 restraints_weight: 2.0000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 41137 Z= 0.118 Angle : 0.611 18.179 56098 Z= 0.298 Chirality : 0.045 0.362 6471 Planarity : 0.004 0.071 7116 Dihedral : 9.470 112.167 6787 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.44 % Favored : 94.40 % Rotamer: Outliers : 1.03 % Allowed : 8.64 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.12), residues: 5015 helix: 1.41 (0.20), residues: 745 sheet: 0.49 (0.14), residues: 1380 loop : -1.13 (0.11), residues: 2890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1104 TYR 0.019 0.001 TYR C 94 PHE 0.018 0.001 PHE D 131 TRP 0.013 0.001 TRP B 47 HIS 0.007 0.001 HIS K 141 Details of bonding type rmsd covalent geometry : bond 0.00264 (41011) covalent geometry : angle 0.57853 (55782) SS BOND : bond 0.00270 ( 62) SS BOND : angle 0.82739 ( 124) hydrogen bonds : bond 0.04273 ( 1319) hydrogen bonds : angle 5.63703 ( 3621) link_ALPHA1-3 : bond 0.00990 ( 1) link_ALPHA1-3 : angle 1.79231 ( 3) link_BETA1-4 : bond 0.00748 ( 20) link_BETA1-4 : angle 2.84011 ( 60) link_NAG-ASN : bond 0.00614 ( 43) link_NAG-ASN : angle 3.63740 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ARG cc_start: 0.6304 (ptt90) cc_final: 0.5991 (ptp-170) REVERT: B 115 TRP cc_start: 0.5669 (m-10) cc_final: 0.5399 (m-90) REVERT: C 142 ARG cc_start: 0.5301 (tpt170) cc_final: 0.4233 (mpt180) REVERT: F 2 MET cc_start: 0.6544 (mtt) cc_final: 0.6335 (mmt) REVERT: F 74 MET cc_start: 0.8302 (mmp) cc_final: 0.7708 (mpp) REVERT: I 101 HIS cc_start: 0.5309 (t-90) cc_final: 0.4772 (t-90) REVERT: D 375 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8817 (ptmm) REVERT: D 391 ASN cc_start: 0.7835 (m-40) cc_final: 0.7567 (m110) REVERT: D 630 TRP cc_start: 0.7761 (m-10) cc_final: 0.7551 (m-10) REVERT: D 756 PHE cc_start: 0.6957 (t80) cc_final: 0.6740 (t80) REVERT: D 770 GLU cc_start: 0.8501 (tp30) cc_final: 0.8087 (tp30) REVERT: K 143 ASN cc_start: 0.6912 (OUTLIER) cc_final: 0.6383 (t0) REVERT: K 266 TYR cc_start: 0.7969 (m-80) cc_final: 0.7017 (m-80) REVERT: K 372 PHE cc_start: 0.4123 (m-80) cc_final: 0.3895 (m-80) REVERT: K 379 VAL cc_start: 0.7697 (t) cc_final: 0.7438 (p) REVERT: K 658 GLU cc_start: 0.8049 (tp30) cc_final: 0.7783 (tp30) REVERT: A 217 PHE cc_start: 0.7067 (m-80) cc_final: 0.6865 (t80) REVERT: A 262 TYR cc_start: 0.8399 (p90) cc_final: 0.8181 (p90) REVERT: A 976 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8456 (m-30) REVERT: A 982 ASP cc_start: 0.7560 (t0) cc_final: 0.7016 (t0) REVERT: A 985 GLU cc_start: 0.8482 (mp0) cc_final: 0.8159 (mp0) outliers start: 45 outliers final: 28 residues processed: 258 average time/residue: 0.2177 time to fit residues: 94.1146 Evaluate side-chains 230 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 166 GLN Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 527 SER Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain K residue 40 ASP Chi-restraints excluded: chain K residue 143 ASN Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 498 TYR Chi-restraints excluded: chain K residue 866 MET Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 976 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 438 optimal weight: 0.0060 chunk 9 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 157 optimal weight: 0.1980 chunk 403 optimal weight: 10.0000 chunk 419 optimal weight: 7.9990 chunk 172 optimal weight: 0.4980 chunk 209 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 299 optimal weight: 3.9990 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 GLN ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 ASN K 952 ASN A 79 ASN ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 962 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.154823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.096026 restraints weight = 114803.513| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 5.08 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 41137 Z= 0.130 Angle : 0.608 17.243 56098 Z= 0.296 Chirality : 0.045 0.361 6471 Planarity : 0.004 0.064 7116 Dihedral : 8.581 97.967 6783 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.64 % Favored : 94.20 % Rotamer: Outliers : 1.33 % Allowed : 9.62 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.12), residues: 5015 helix: 1.46 (0.20), residues: 743 sheet: 0.47 (0.14), residues: 1398 loop : -1.11 (0.11), residues: 2874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 405 TYR 0.025 0.001 TYR K 165 PHE 0.032 0.001 PHE K 163 TRP 0.012 0.001 TRP K 350 HIS 0.007 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00300 (41011) covalent geometry : angle 0.57654 (55782) SS BOND : bond 0.00385 ( 62) SS BOND : angle 0.83071 ( 124) hydrogen bonds : bond 0.04092 ( 1319) hydrogen bonds : angle 5.32885 ( 3621) link_ALPHA1-3 : bond 0.01053 ( 1) link_ALPHA1-3 : angle 1.91788 ( 3) link_BETA1-4 : bond 0.00727 ( 20) link_BETA1-4 : angle 2.84369 ( 60) link_NAG-ASN : bond 0.00578 ( 43) link_NAG-ASN : angle 3.55596 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 201 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ARG cc_start: 0.6032 (ptt90) cc_final: 0.5760 (ptp-170) REVERT: I 101 HIS cc_start: 0.6229 (t-90) cc_final: 0.5646 (t-90) REVERT: D 226 LEU cc_start: 0.8960 (mm) cc_final: 0.8322 (tp) REVERT: D 375 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8702 (ptmm) REVERT: D 513 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7285 (pt0) REVERT: D 756 PHE cc_start: 0.6887 (t80) cc_final: 0.6618 (t80) REVERT: D 947 ASP cc_start: 0.8499 (m-30) cc_final: 0.8296 (m-30) REVERT: K 266 TYR cc_start: 0.7674 (m-80) cc_final: 0.6807 (m-80) REVERT: K 372 PHE cc_start: 0.4091 (m-80) cc_final: 0.3884 (m-80) REVERT: K 379 VAL cc_start: 0.7537 (t) cc_final: 0.7318 (p) REVERT: K 663 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.7960 (mm) REVERT: A 976 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8566 (m-30) REVERT: A 982 ASP cc_start: 0.7797 (t0) cc_final: 0.7074 (t0) REVERT: A 985 GLU cc_start: 0.8510 (mp0) cc_final: 0.8079 (mp0) outliers start: 58 outliers final: 36 residues processed: 245 average time/residue: 0.2109 time to fit residues: 88.4105 Evaluate side-chains 230 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 166 GLN Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 513 GLU Chi-restraints excluded: chain D residue 527 SER Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain K residue 40 ASP Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 498 TYR Chi-restraints excluded: chain K residue 663 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 976 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 93 optimal weight: 50.0000 chunk 15 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 273 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 482 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 123 optimal weight: 40.0000 chunk 163 optimal weight: 9.9990 chunk 362 optimal weight: 1.9990 chunk 184 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 82 GLN ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 ASN K 989 GLN A 79 ASN ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN A 923 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.160881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.095750 restraints weight = 97198.847| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 5.28 r_work: 0.3128 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 41137 Z= 0.315 Angle : 0.739 16.700 56098 Z= 0.368 Chirality : 0.049 0.387 6471 Planarity : 0.005 0.059 7116 Dihedral : 8.353 96.115 6783 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.90 % Favored : 92.96 % Rotamer: Outliers : 1.55 % Allowed : 10.88 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.12), residues: 5015 helix: 0.97 (0.20), residues: 740 sheet: 0.28 (0.14), residues: 1415 loop : -1.30 (0.11), residues: 2860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K1104 TYR 0.028 0.002 TYR K 89 PHE 0.024 0.002 PHE A 217 TRP 0.034 0.002 TRP I 36 HIS 0.013 0.002 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00743 (41011) covalent geometry : angle 0.70648 (55782) SS BOND : bond 0.00429 ( 62) SS BOND : angle 1.22862 ( 124) hydrogen bonds : bond 0.05718 ( 1319) hydrogen bonds : angle 5.62582 ( 3621) link_ALPHA1-3 : bond 0.00971 ( 1) link_ALPHA1-3 : angle 1.86755 ( 3) link_BETA1-4 : bond 0.00754 ( 20) link_BETA1-4 : angle 2.97823 ( 60) link_NAG-ASN : bond 0.00703 ( 43) link_NAG-ASN : angle 4.01463 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 201 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 38 ARG cc_start: 0.6437 (ptt90) cc_final: 0.6129 (ptp90) REVERT: F 2 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.6642 (mmm) REVERT: F 202 GLN cc_start: 0.3369 (tp40) cc_final: 0.2907 (mt0) REVERT: I 101 HIS cc_start: 0.6039 (t-90) cc_final: 0.5445 (t-90) REVERT: D 513 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7315 (pt0) REVERT: D 756 PHE cc_start: 0.7502 (t80) cc_final: 0.7205 (t80) REVERT: K 200 SER cc_start: 0.9490 (OUTLIER) cc_final: 0.9147 (m) REVERT: K 230 ILE cc_start: 0.8818 (tp) cc_final: 0.8551 (tt) REVERT: K 372 PHE cc_start: 0.4017 (m-80) cc_final: 0.3764 (m-80) REVERT: K 663 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8343 (mm) REVERT: A 42 VAL cc_start: 0.8691 (OUTLIER) cc_final: 0.8372 (m) REVERT: A 170 PHE cc_start: 0.8398 (m-10) cc_final: 0.8191 (m-10) REVERT: A 454 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.6909 (ttt180) REVERT: A 1089 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8117 (tm-30) outliers start: 68 outliers final: 41 residues processed: 256 average time/residue: 0.2178 time to fit residues: 95.1088 Evaluate side-chains 225 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 178 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain F residue 2 MET Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 166 GLN Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 513 GLU Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 988 VAL Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 40 ASP Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 498 TYR Chi-restraints excluded: chain K residue 543 LEU Chi-restraints excluded: chain K residue 569 THR Chi-restraints excluded: chain K residue 663 ILE Chi-restraints excluded: chain K residue 1133 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1078 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 60 optimal weight: 0.0050 chunk 297 optimal weight: 9.9990 chunk 263 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 chunk 346 optimal weight: 0.9990 chunk 243 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 283 optimal weight: 0.9990 chunk 333 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 ASN F 181 GLN ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.153367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.093975 restraints weight = 114363.567| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 5.10 r_work: 0.3194 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 41137 Z= 0.114 Angle : 0.614 17.790 56098 Z= 0.300 Chirality : 0.045 0.356 6471 Planarity : 0.004 0.090 7116 Dihedral : 7.702 92.895 6781 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.14 % Favored : 94.72 % Rotamer: Outliers : 1.26 % Allowed : 12.11 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.12), residues: 5015 helix: 1.39 (0.20), residues: 740 sheet: 0.27 (0.14), residues: 1437 loop : -1.14 (0.11), residues: 2838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C 24 TYR 0.017 0.001 TYR A1064 PHE 0.031 0.001 PHE K 163 TRP 0.010 0.001 TRP F 164 HIS 0.007 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00251 (41011) covalent geometry : angle 0.57875 (55782) SS BOND : bond 0.00406 ( 62) SS BOND : angle 0.88465 ( 124) hydrogen bonds : bond 0.04189 ( 1319) hydrogen bonds : angle 5.17960 ( 3621) link_ALPHA1-3 : bond 0.00984 ( 1) link_ALPHA1-3 : angle 1.92433 ( 3) link_BETA1-4 : bond 0.00720 ( 20) link_BETA1-4 : angle 3.03146 ( 60) link_NAG-ASN : bond 0.00661 ( 43) link_NAG-ASN : angle 3.74055 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 198 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ARG cc_start: 0.6059 (ptt90) cc_final: 0.5779 (ptp-170) REVERT: F 202 GLN cc_start: 0.3743 (tp40) cc_final: 0.3396 (mt0) REVERT: I 101 HIS cc_start: 0.5068 (t-90) cc_final: 0.4532 (t-90) REVERT: D 405 ARG cc_start: 0.8952 (mtm110) cc_final: 0.8688 (ptp-110) REVERT: D 756 PHE cc_start: 0.7201 (t80) cc_final: 0.6952 (t80) REVERT: D 770 GLU cc_start: 0.8410 (tp30) cc_final: 0.8179 (tp30) REVERT: K 230 ILE cc_start: 0.8826 (tp) cc_final: 0.8565 (tt) REVERT: K 266 TYR cc_start: 0.8253 (m-80) cc_final: 0.7434 (m-80) REVERT: K 372 PHE cc_start: 0.3892 (m-80) cc_final: 0.3615 (m-80) REVERT: K 663 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8296 (mm) REVERT: K 1089 GLU cc_start: 0.8590 (pm20) cc_final: 0.8384 (mp0) REVERT: A 42 VAL cc_start: 0.8593 (t) cc_final: 0.8290 (m) REVERT: A 1089 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8149 (tm-30) outliers start: 55 outliers final: 34 residues processed: 241 average time/residue: 0.2191 time to fit residues: 89.8351 Evaluate side-chains 217 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 182 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 138 ASN Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 83 MET Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 166 GLN Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain K residue 40 ASP Chi-restraints excluded: chain K residue 498 TYR Chi-restraints excluded: chain K residue 663 ILE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 981 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 474 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 365 optimal weight: 3.9990 chunk 40 optimal weight: 0.0030 chunk 46 optimal weight: 3.9990 chunk 231 optimal weight: 8.9990 chunk 222 optimal weight: 0.3980 chunk 145 optimal weight: 20.0000 chunk 464 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 75 optimal weight: 30.0000 overall best weight: 1.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 ASN ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 GLN ** K 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.152798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.092196 restraints weight = 114080.037| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 5.53 r_work: 0.3189 rms_B_bonded: 5.43 restraints_weight: 2.0000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 41137 Z= 0.136 Angle : 0.613 17.691 56098 Z= 0.298 Chirality : 0.045 0.353 6471 Planarity : 0.004 0.052 7116 Dihedral : 7.361 92.166 6780 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.72 % Favored : 94.16 % Rotamer: Outliers : 1.51 % Allowed : 12.27 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.12), residues: 5015 helix: 1.37 (0.20), residues: 742 sheet: 0.26 (0.14), residues: 1411 loop : -1.10 (0.11), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 405 TYR 0.018 0.001 TYR K 89 PHE 0.026 0.001 PHE A 389 TRP 0.019 0.001 TRP G 36 HIS 0.006 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00314 (41011) covalent geometry : angle 0.57922 (55782) SS BOND : bond 0.00295 ( 62) SS BOND : angle 0.85981 ( 124) hydrogen bonds : bond 0.04199 ( 1319) hydrogen bonds : angle 5.09061 ( 3621) link_ALPHA1-3 : bond 0.00948 ( 1) link_ALPHA1-3 : angle 1.73826 ( 3) link_BETA1-4 : bond 0.00745 ( 20) link_BETA1-4 : angle 3.20729 ( 60) link_NAG-ASN : bond 0.00640 ( 43) link_NAG-ASN : angle 3.61018 ( 129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 186 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 38 ARG cc_start: 0.5967 (ptt90) cc_final: 0.5708 (ptp-170) REVERT: F 202 GLN cc_start: 0.3812 (tp40) cc_final: 0.3519 (mt0) REVERT: I 101 HIS cc_start: 0.5192 (t-90) cc_final: 0.4746 (t-90) REVERT: D 375 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8580 (ptmm) REVERT: D 405 ARG cc_start: 0.8934 (mtm110) cc_final: 0.8623 (ptp-110) REVERT: D 756 PHE cc_start: 0.7201 (t80) cc_final: 0.6963 (t80) REVERT: K 230 ILE cc_start: 0.8880 (tp) cc_final: 0.8633 (tt) REVERT: K 266 TYR cc_start: 0.8344 (m-80) cc_final: 0.7499 (m-80) REVERT: K 372 PHE cc_start: 0.3999 (m-80) cc_final: 0.3658 (m-80) REVERT: K 663 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8326 (mm) REVERT: A 42 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8288 (m) REVERT: A 454 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.6837 (ttt180) REVERT: A 985 GLU cc_start: 0.8510 (mp0) cc_final: 0.8238 (mp0) REVERT: A 1089 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8197 (tm-30) outliers start: 66 outliers final: 42 residues processed: 242 average time/residue: 0.2081 time to fit residues: 85.7820 Evaluate side-chains 229 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 166 GLN Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 40 ASP Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 386 ASP Chi-restraints excluded: chain K residue 498 TYR Chi-restraints excluded: chain K residue 663 ILE Chi-restraints excluded: chain K residue 783 LYS Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 630 TRP Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 960 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 306 optimal weight: 2.9990 chunk 294 optimal weight: 9.9990 chunk 210 optimal weight: 3.9990 chunk 97 optimal weight: 50.0000 chunk 156 optimal weight: 0.9990 chunk 348 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 215 optimal weight: 5.9990 chunk 184 optimal weight: 20.0000 chunk 330 optimal weight: 20.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN E 161 GLN D 113 GLN ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 GLN ** K 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 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 = 0.4434 r_free = 0.4434 target = 0.162160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.096986 restraints weight = 95806.609| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 5.70 r_work: 0.3173 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 41137 Z= 0.166 Angle : 0.634 17.847 56098 Z= 0.310 Chirality : 0.046 0.353 6471 Planarity : 0.004 0.061 7116 Dihedral : 7.206 91.294 6780 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.00 % Favored : 93.86 % Rotamer: Outliers : 1.49 % Allowed : 12.77 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.12), residues: 5015 helix: 1.24 (0.20), residues: 746 sheet: 0.23 (0.14), residues: 1409 loop : -1.13 (0.11), residues: 2860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 405 TYR 0.028 0.001 TYR A 834 PHE 0.029 0.002 PHE K 235 TRP 0.013 0.001 TRP I 53 HIS 0.006 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00391 (41011) covalent geometry : angle 0.60144 (55782) SS BOND : bond 0.00323 ( 62) SS BOND : angle 0.97034 ( 124) hydrogen bonds : bond 0.04494 ( 1319) hydrogen bonds : angle 5.08299 ( 3621) link_ALPHA1-3 : bond 0.00832 ( 1) link_ALPHA1-3 : angle 1.69136 ( 3) link_BETA1-4 : bond 0.00772 ( 20) link_BETA1-4 : angle 3.16923 ( 60) link_NAG-ASN : bond 0.00609 ( 43) link_NAG-ASN : angle 3.59808 ( 129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 190 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 38 ARG cc_start: 0.6399 (ptt90) cc_final: 0.6032 (ptp-170) REVERT: F 202 GLN cc_start: 0.3448 (tp40) cc_final: 0.3001 (mt0) REVERT: I 101 HIS cc_start: 0.6042 (t-90) cc_final: 0.5423 (t-90) REVERT: D 375 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8567 (ptmm) REVERT: D 756 PHE cc_start: 0.7378 (t80) cc_final: 0.7115 (t80) REVERT: D 770 GLU cc_start: 0.8501 (tp30) cc_final: 0.8300 (tp30) REVERT: K 172 MET cc_start: 0.8722 (tpp) cc_final: 0.7876 (pmm) REVERT: K 200 SER cc_start: 0.9490 (OUTLIER) cc_final: 0.9176 (m) REVERT: K 230 ILE cc_start: 0.9029 (tp) cc_final: 0.8783 (tt) REVERT: K 266 TYR cc_start: 0.8470 (m-80) cc_final: 0.7678 (m-80) REVERT: K 372 PHE cc_start: 0.4260 (m-80) cc_final: 0.3935 (m-80) REVERT: K 658 GLU cc_start: 0.8230 (tp30) cc_final: 0.7860 (pt0) REVERT: K 663 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8344 (mm) REVERT: K 1089 GLU cc_start: 0.8624 (pm20) cc_final: 0.8379 (mp0) REVERT: A 454 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.6892 (ttt180) REVERT: A 777 GLU cc_start: 0.8924 (tp30) cc_final: 0.8573 (tt0) REVERT: A 791 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8661 (pt) REVERT: A 985 GLU cc_start: 0.8542 (mp0) cc_final: 0.8330 (mp0) REVERT: A 1089 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8225 (tm-30) outliers start: 65 outliers final: 48 residues processed: 247 average time/residue: 0.2175 time to fit residues: 91.1210 Evaluate side-chains 232 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 179 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 138 ASN Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 166 GLN Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 40 ASP Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 359 VAL Chi-restraints excluded: chain K residue 386 ASP Chi-restraints excluded: chain K residue 498 TYR Chi-restraints excluded: chain K residue 663 ILE Chi-restraints excluded: chain K residue 783 LYS Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 630 TRP Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 960 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 434 optimal weight: 9.9990 chunk 292 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 379 optimal weight: 0.7980 chunk 386 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 chunk 310 optimal weight: 3.9990 chunk 362 optimal weight: 1.9990 chunk 318 optimal weight: 7.9990 chunk 277 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 166 GLN C 138 ASN D 23 GLN ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 GLN ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.152546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.094041 restraints weight = 114303.810| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 5.18 r_work: 0.3194 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 41137 Z= 0.126 Angle : 0.612 17.669 56098 Z= 0.298 Chirality : 0.045 0.345 6471 Planarity : 0.004 0.060 7116 Dihedral : 6.999 90.089 6780 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.66 % Favored : 94.20 % Rotamer: Outliers : 1.39 % Allowed : 13.23 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.12), residues: 5015 helix: 1.34 (0.20), residues: 744 sheet: 0.25 (0.14), residues: 1419 loop : -1.09 (0.11), residues: 2852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 405 TYR 0.016 0.001 TYR K 89 PHE 0.028 0.001 PHE K 235 TRP 0.029 0.001 TRP I 53 HIS 0.006 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00291 (41011) covalent geometry : angle 0.57931 (55782) SS BOND : bond 0.00282 ( 62) SS BOND : angle 0.85494 ( 124) hydrogen bonds : bond 0.04083 ( 1319) hydrogen bonds : angle 4.96084 ( 3621) link_ALPHA1-3 : bond 0.00804 ( 1) link_ALPHA1-3 : angle 1.70372 ( 3) link_BETA1-4 : bond 0.00772 ( 20) link_BETA1-4 : angle 3.12884 ( 60) link_NAG-ASN : bond 0.00613 ( 43) link_NAG-ASN : angle 3.51618 ( 129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 187 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ARG cc_start: 0.6100 (ptt90) cc_final: 0.5647 (ptp-170) REVERT: F 202 GLN cc_start: 0.3694 (tp40) cc_final: 0.3322 (mt0) REVERT: I 101 HIS cc_start: 0.4943 (t-90) cc_final: 0.4560 (t-90) REVERT: D 23 GLN cc_start: 0.5485 (OUTLIER) cc_final: 0.4568 (tp40) REVERT: D 86 ASP cc_start: 0.8302 (m-30) cc_final: 0.7907 (t70) REVERT: D 375 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8637 (ptmm) REVERT: D 405 ARG cc_start: 0.9057 (mtm110) cc_final: 0.8749 (ptp-110) REVERT: D 756 PHE cc_start: 0.7258 (t80) cc_final: 0.7010 (t80) REVERT: K 172 MET cc_start: 0.8724 (tpp) cc_final: 0.7868 (pmm) REVERT: K 200 SER cc_start: 0.9497 (OUTLIER) cc_final: 0.9191 (m) REVERT: K 230 ILE cc_start: 0.9044 (tp) cc_final: 0.8815 (tt) REVERT: K 266 TYR cc_start: 0.8368 (m-80) cc_final: 0.7529 (m-80) REVERT: K 372 PHE cc_start: 0.3955 (m-80) cc_final: 0.3645 (m-80) REVERT: K 658 GLU cc_start: 0.8214 (tp30) cc_final: 0.7884 (pt0) REVERT: K 663 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8351 (mm) REVERT: A 42 VAL cc_start: 0.8597 (t) cc_final: 0.8315 (m) REVERT: A 286 VAL cc_start: 0.8632 (OUTLIER) cc_final: 0.8431 (m) REVERT: A 454 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7020 (ttt180) REVERT: A 777 GLU cc_start: 0.8909 (tp30) cc_final: 0.8516 (tt0) REVERT: A 791 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8707 (pt) REVERT: A 985 GLU cc_start: 0.8535 (mp0) cc_final: 0.8285 (mp0) REVERT: A 1089 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8235 (tm-30) outliers start: 61 outliers final: 45 residues processed: 243 average time/residue: 0.2201 time to fit residues: 90.4036 Evaluate side-chains 237 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 185 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 138 ASN Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 166 GLN Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 735 CYS Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 40 ASP Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 386 ASP Chi-restraints excluded: chain K residue 498 TYR Chi-restraints excluded: chain K residue 578 THR Chi-restraints excluded: chain K residue 663 ILE Chi-restraints excluded: chain K residue 783 LYS Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 630 TRP Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 976 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 133 optimal weight: 9.9990 chunk 182 optimal weight: 7.9990 chunk 89 optimal weight: 50.0000 chunk 86 optimal weight: 30.0000 chunk 242 optimal weight: 0.6980 chunk 94 optimal weight: 20.0000 chunk 265 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 212 optimal weight: 3.9990 chunk 463 optimal weight: 4.9990 chunk 452 optimal weight: 5.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN D 23 GLN ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 GLN ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.155741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.091460 restraints weight = 98505.844| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 4.85 r_work: 0.3170 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 41137 Z= 0.163 Angle : 0.630 17.698 56098 Z= 0.308 Chirality : 0.045 0.349 6471 Planarity : 0.004 0.055 7116 Dihedral : 6.969 90.138 6780 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.06 % Favored : 93.80 % Rotamer: Outliers : 1.33 % Allowed : 13.32 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.12), residues: 5015 helix: 1.26 (0.20), residues: 745 sheet: 0.22 (0.14), residues: 1419 loop : -1.11 (0.11), residues: 2851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 405 TYR 0.032 0.001 TYR A 834 PHE 0.029 0.001 PHE K 235 TRP 0.028 0.001 TRP I 53 HIS 0.006 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00383 (41011) covalent geometry : angle 0.59816 (55782) SS BOND : bond 0.00295 ( 62) SS BOND : angle 0.90121 ( 124) hydrogen bonds : bond 0.04289 ( 1319) hydrogen bonds : angle 4.98978 ( 3621) link_ALPHA1-3 : bond 0.00732 ( 1) link_ALPHA1-3 : angle 1.64237 ( 3) link_BETA1-4 : bond 0.00739 ( 20) link_BETA1-4 : angle 3.13602 ( 60) link_NAG-ASN : bond 0.00605 ( 43) link_NAG-ASN : angle 3.52920 ( 129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 189 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ARG cc_start: 0.6450 (ptt90) cc_final: 0.6099 (ptp-170) REVERT: F 202 GLN cc_start: 0.3434 (tp40) cc_final: 0.3011 (mt0) REVERT: I 101 HIS cc_start: 0.5734 (t-90) cc_final: 0.5185 (t-90) REVERT: D 23 GLN cc_start: 0.5851 (OUTLIER) cc_final: 0.4664 (tp40) REVERT: D 86 ASP cc_start: 0.8346 (m-30) cc_final: 0.7976 (t70) REVERT: D 375 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8599 (ptmm) REVERT: D 405 ARG cc_start: 0.9045 (mtm110) cc_final: 0.8722 (ptp-110) REVERT: D 756 PHE cc_start: 0.7370 (t80) cc_final: 0.7123 (t80) REVERT: K 172 MET cc_start: 0.8702 (tpp) cc_final: 0.7879 (pmm) REVERT: K 200 SER cc_start: 0.9476 (OUTLIER) cc_final: 0.9144 (m) REVERT: K 230 ILE cc_start: 0.9071 (tp) cc_final: 0.8850 (tt) REVERT: K 266 TYR cc_start: 0.8401 (m-80) cc_final: 0.7555 (m-80) REVERT: K 372 PHE cc_start: 0.3847 (m-80) cc_final: 0.3565 (m-80) REVERT: K 658 GLU cc_start: 0.8277 (tp30) cc_final: 0.7919 (pt0) REVERT: K 663 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8326 (mm) REVERT: A 42 VAL cc_start: 0.8545 (t) cc_final: 0.8267 (m) REVERT: A 286 VAL cc_start: 0.8651 (OUTLIER) cc_final: 0.8408 (m) REVERT: A 454 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.6938 (ttt180) REVERT: A 777 GLU cc_start: 0.8931 (tp30) cc_final: 0.8527 (tt0) REVERT: A 791 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8727 (pt) REVERT: A 985 GLU cc_start: 0.8541 (mp0) cc_final: 0.8300 (mp0) REVERT: A 1089 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8198 (tm-30) outliers start: 58 outliers final: 47 residues processed: 237 average time/residue: 0.2169 time to fit residues: 87.6013 Evaluate side-chains 239 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 185 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 138 ASN Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 166 GLN Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 735 CYS Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 40 ASP Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 386 ASP Chi-restraints excluded: chain K residue 498 TYR Chi-restraints excluded: chain K residue 578 THR Chi-restraints excluded: chain K residue 663 ILE Chi-restraints excluded: chain K residue 783 LYS Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 630 TRP Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 976 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 76 optimal weight: 7.9990 chunk 147 optimal weight: 0.0570 chunk 373 optimal weight: 4.9990 chunk 294 optimal weight: 20.0000 chunk 382 optimal weight: 0.4980 chunk 461 optimal weight: 0.9990 chunk 445 optimal weight: 5.9990 chunk 415 optimal weight: 4.9990 chunk 230 optimal weight: 5.9990 chunk 353 optimal weight: 0.9980 chunk 475 optimal weight: 0.6980 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.152091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.091377 restraints weight = 114039.831| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 5.77 r_work: 0.3171 rms_B_bonded: 5.59 restraints_weight: 2.0000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.248 41137 Z= 0.150 Angle : 0.733 59.178 56098 Z= 0.387 Chirality : 0.045 0.440 6471 Planarity : 0.004 0.129 7116 Dihedral : 6.964 90.133 6780 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.02 % Favored : 93.84 % Rotamer: Outliers : 1.23 % Allowed : 13.53 % Favored : 85.24 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.12), residues: 5015 helix: 1.28 (0.20), residues: 745 sheet: 0.23 (0.14), residues: 1419 loop : -1.10 (0.11), residues: 2851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 405 TYR 0.022 0.001 TYR A 834 PHE 0.025 0.001 PHE K 235 TRP 0.032 0.001 TRP G 36 HIS 0.006 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00345 (41011) covalent geometry : angle 0.70644 (55782) SS BOND : bond 0.00282 ( 62) SS BOND : angle 0.87881 ( 124) hydrogen bonds : bond 0.04217 ( 1319) hydrogen bonds : angle 4.99135 ( 3621) link_ALPHA1-3 : bond 0.00738 ( 1) link_ALPHA1-3 : angle 1.65311 ( 3) link_BETA1-4 : bond 0.00847 ( 20) link_BETA1-4 : angle 3.13527 ( 60) link_NAG-ASN : bond 0.00599 ( 43) link_NAG-ASN : angle 3.52213 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19519.48 seconds wall clock time: 331 minutes 31.02 seconds (19891.02 seconds total)