Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 10:29:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qti_14141/05_2023/7qti_14141.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qti_14141/05_2023/7qti_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qti_14141/05_2023/7qti_14141.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qti_14141/05_2023/7qti_14141.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qti_14141/05_2023/7qti_14141.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qti_14141/05_2023/7qti_14141.pdb" } 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 ------------------------------------------------------------------------------- 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 Residue "H GLU 70": "OE1" <-> "OE2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "I GLU 160": "OE1" <-> "OE2" Residue "J GLU 70": "OE1" <-> "OE2" Residue "D GLU 295": "OE1" <-> "OE2" Residue "D GLU 306": "OE1" <-> "OE2" Residue "D GLU 403": "OE1" <-> "OE2" Residue "K GLU 149": "OE1" <-> "OE2" Residue "K GLU 209": "OE1" <-> "OE2" Residue "K GLU 985": "OE1" <-> "OE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A GLU 1014": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/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 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 chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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 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 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 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 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 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 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 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 chiralities: 6 Time building chain proxies: 21.03, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 21.24 Conformation dependent library (CDL) restraints added in 6.1 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: 3.71 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: 23.11 Time building geometry restraints manager: 22.22 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: 99.75 - 106.66: 1158 106.66 - 113.57: 22637 113.57 - 120.49: 15167 120.49 - 127.40: 16462 127.40 - 134.31: 358 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 - 17.91: 21898 17.91 - 35.82: 1644 35.82 - 53.73: 318 53.73 - 71.65: 64 71.65 - 89.56: 41 Dihedral angle restraints: 23965 sinusoidal: 9278 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 23962 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 2.520 nonbonded pdb=" OH TYR D 89 " pdb=" OE1 GLU D 186 " model vdw 2.174 2.440 nonbonded pdb=" O GLN E 101 " pdb=" NH1 ARG F 44 " model vdw 2.205 2.520 nonbonded pdb=" O LEU A 290 " pdb=" OG1 THR A 629 " model vdw 2.206 2.440 nonbonded pdb=" O HIS I 101 " pdb=" ND1 HIS I 101 " model vdw 2.208 2.520 ... (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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 837 or resid 848 through 1144 or resid 1301 thr \ ough 1306)) selection = (chain 'D' and (resid 19 through 837 or resid 848 through 1144 or resid 1301 thr \ ough 1306)) selection = (chain 'K' and (resid 19 through 1144 or resid 1301 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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 9.730 Check model and map are aligned: 0.610 Set scattering table: 0.350 Process input model: 114.520 Find NCS groups from input model: 3.500 Set up NCS constraints: 0.480 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.240 ------------------------------------------------------------------------------- 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 41011 Z= 0.263 Angle : 0.713 12.462 55782 Z= 0.410 Chirality : 0.050 0.649 6471 Planarity : 0.005 0.211 7116 Dihedral : 13.453 89.557 14355 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 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 *********************** 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 fitting. rotamer outliers: 40 poor density : 310 time to evaluate : 5.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 12 residues processed: 346 average time/residue: 0.4842 time to fit residues: 276.5982 Evaluate side-chains 218 residues out of total 4385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 206 time to evaluate : 4.052 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.5077 time to fit residues: 16.0791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 423 optimal weight: 9.9990 chunk 379 optimal weight: 2.9990 chunk 210 optimal weight: 0.9980 chunk 129 optimal weight: 30.0000 chunk 256 optimal weight: 0.7980 chunk 202 optimal weight: 0.9980 chunk 392 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 292 optimal weight: 9.9990 chunk 454 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN D 85 ASN ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 ASN ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 989 GLN K 801 GLN K 932 GLN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.1143 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: