Starting phenix.real_space_refine on Sun Apr 14 04:21:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7web_32445/04_2024/7web_32445.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7web_32445/04_2024/7web_32445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7web_32445/04_2024/7web_32445.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7web_32445/04_2024/7web_32445.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7web_32445/04_2024/7web_32445.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7web_32445/04_2024/7web_32445.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.067 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 133 5.16 5 C 19345 2.51 5 N 4984 2.21 5 O 5951 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ASP 112": "OD1" <-> "OD2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1014": "OE1" <-> "OE2" Residue "C TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 193": "OD1" <-> "OD2" Residue "C PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 30413 Number of models: 1 Model: "" Number of chains: 30 Chain: "G" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 941 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 941 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "C" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "D" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1041} Chain breaks: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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: "M" 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: "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: 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: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 15.81, per 1000 atoms: 0.52 Number of scatterers: 30413 At special positions: 0 Unit cell: (145.52, 143.38, 254.66, 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 133 16.00 O 5951 8.00 N 4984 7.00 C 19345 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 97 " distance=2.04 Simple disulfide: pdb=" SG CYS G 102 " - pdb=" SG CYS G 107 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 102 " - pdb=" SG CYS H 107 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 161 " distance=2.04 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.04 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.04 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.02 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 134 " 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=2.04 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 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 D1029 " - pdb=" SG CYS D1040 " distance=2.03 Simple disulfide: pdb=" SG CYS D1079 " - pdb=" SG CYS D1123 " 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=7, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 1 " - " ASN B 328 " " NAG B1301 " - " ASN B1155 " " NAG B1302 " - " ASN B 123 " " NAG B1303 " - " ASN B 143 " " NAG B1304 " - " ASN B 17 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 600 " " NAG B1307 " - " ASN B 654 " " NAG B1308 " - " ASN B 613 " " NAG B1309 " - " ASN B 706 " " NAG C1303 " - " ASN C1155 " " NAG C1304 " - " ASN C 123 " " NAG C1305 " - " ASN C 143 " " NAG C1306 " - " ASN C 17 " " NAG C1307 " - " ASN C 61 " " NAG C1308 " - " ASN C 600 " " NAG C1309 " - " ASN C 654 " " NAG C1310 " - " ASN C 613 " " NAG C1311 " - " ASN C 706 " " NAG D1302 " - " ASN D1155 " " NAG D1303 " - " ASN D 143 " " NAG D1304 " - " ASN D 17 " " NAG D1305 " - " ASN D 61 " " NAG D1306 " - " ASN D 600 " " NAG D1307 " - " ASN D 654 " " NAG D1308 " - " ASN D 613 " " NAG D1309 " - " ASN D 706 " " NAG E 1 " - " ASN B 714 " " NAG J 1 " - " ASN B 798 " " NAG K 1 " - " ASN B1095 " " NAG M 1 " - " ASN B1131 " " NAG N 1 " - " ASN C 231 " " NAG P 1 " - " ASN C 714 " " NAG R 1 " - " ASN C 798 " " NAG S 1 " - " ASN C1095 " " NAG T 1 " - " ASN C1131 " " NAG U 1 " - " ASN D 231 " " NAG W 1 " - " ASN D 714 " " NAG X 1 " - " ASN D1071 " " NAG Y 1 " - " ASN D 798 " " NAG Z 1 " - " ASN D1095 " " NAG a 1 " - " ASN D1131 " Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.38 Conformation dependent library (CDL) restraints added in 5.7 seconds 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7042 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 61 sheets defined 21.2% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'G' and resid 88 through 92 removed outlier: 3.613A pdb=" N THR G 92 " --> pdb=" O SER G 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.539A pdb=" N THR H 92 " --> pdb=" O SER H 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.910A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 362 through 367 removed outlier: 3.824A pdb=" N TYR B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 408 removed outlier: 4.547A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 543 Processing helix chain 'B' and resid 616 through 621 Processing helix chain 'B' and resid 630 through 634 removed outlier: 3.684A pdb=" N TYR B 633 " --> pdb=" O TRP B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 751 removed outlier: 3.582A pdb=" N SER B 747 " --> pdb=" O SER B 743 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 749 " --> pdb=" O GLU B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 755 through 780 removed outlier: 3.638A pdb=" N GLN B 759 " --> pdb=" O SER B 755 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 760 " --> pdb=" O PHE B 756 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 773 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 removed outlier: 3.824A pdb=" N LEU B 818 " --> pdb=" O PHE B 814 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 819 " --> pdb=" O ILE B 815 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 823 " --> pdb=" O LEU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 851 Processing helix chain 'B' and resid 863 through 879 removed outlier: 3.596A pdb=" N ALA B 868 " --> pdb=" O ASP B 864 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN B 869 " --> pdb=" O GLU B 865 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR B 870 " --> pdb=" O MET B 866 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 872 " --> pdb=" O ALA B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 887 removed outlier: 4.113A pdb=" N GLY B 886 " --> pdb=" O TRP B 883 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B 887 " --> pdb=" O THR B 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 883 through 887' Processing helix chain 'B' and resid 894 through 907 removed outlier: 4.150A pdb=" N ALA B 900 " --> pdb=" O ALA B 896 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR B 901 " --> pdb=" O MET B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 915 removed outlier: 3.750A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 915 " --> pdb=" O ASN B 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 910 through 915' Processing helix chain 'B' and resid 916 through 938 removed outlier: 3.716A pdb=" N SER B 926 " --> pdb=" O ASN B 922 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA B 927 " --> pdb=" O GLN B 923 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 929 " --> pdb=" O ASN B 925 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 931 " --> pdb=" O ALA B 927 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR B 938 " --> pdb=" O SER B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 961 removed outlier: 4.081A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN B 952 " --> pdb=" O VAL B 948 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN B 957 " --> pdb=" O ALA B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 965 Processing helix chain 'B' and resid 973 through 981 removed outlier: 4.172A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE B 978 " --> pdb=" O LEU B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1029 removed outlier: 3.596A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 993 " --> pdb=" O GLN B 989 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY B 996 " --> pdb=" O ARG B 992 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B1000 " --> pdb=" O GLY B 996 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B1002 " --> pdb=" O LEU B 998 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU B1021 " --> pdb=" O ALA B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1115 No H-bonds generated for 'chain 'B' and resid 1113 through 1115' Processing helix chain 'B' and resid 1137 through 1158 removed outlier: 3.628A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE B1145 " --> pdb=" O GLU B1141 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU B1147 " --> pdb=" O ASP B1143 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU B1148 " --> pdb=" O SER B1144 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER B1158 " --> pdb=" O LYS B1154 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.736A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 380 through 384 removed outlier: 3.738A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.510A pdb=" N ILE C 407 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 419 removed outlier: 3.514A pdb=" N TYR C 418 " --> pdb=" O ASN C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 621 Processing helix chain 'C' and resid 736 through 741 Processing helix chain 'C' and resid 743 through 751 removed outlier: 3.636A pdb=" N SER C 747 " --> pdb=" O SER C 743 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU C 749 " --> pdb=" O GLU C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 755 through 779 removed outlier: 3.850A pdb=" N LEU C 760 " --> pdb=" O PHE C 756 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS C 773 " --> pdb=" O VAL C 769 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 822 removed outlier: 3.637A pdb=" N ASP C 817 " --> pdb=" O SER C 813 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 819 " --> pdb=" O ILE C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 879 removed outlier: 3.863A pdb=" N GLN C 869 " --> pdb=" O GLU C 865 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA C 876 " --> pdb=" O SER C 872 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 879 " --> pdb=" O LEU C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 907 removed outlier: 3.720A pdb=" N ASN C 904 " --> pdb=" O ALA C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.985A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 removed outlier: 3.720A pdb=" N ALA C 927 " --> pdb=" O GLN C 923 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C 930 " --> pdb=" O SER C 926 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE C 931 " --> pdb=" O ALA C 927 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP C 933 " --> pdb=" O GLY C 929 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR C 938 " --> pdb=" O SER C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 963 removed outlier: 3.919A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN C 950 " --> pdb=" O GLN C 946 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN C 952 " --> pdb=" O VAL C 948 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 960 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 975 through 979 Processing helix chain 'C' and resid 982 through 1030 removed outlier: 3.875A pdb=" N GLU C 987 " --> pdb=" O LYS C 983 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL C 988 " --> pdb=" O VAL C 984 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 993 " --> pdb=" O GLN C 989 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C1003 " --> pdb=" O GLN C 999 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR C1004 " --> pdb=" O SER C1000 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA C1013 " --> pdb=" O LEU C1009 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU C1014 " --> pdb=" O ILE C1010 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C1021 " --> pdb=" O ALA C1017 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER C1027 " --> pdb=" O ALA C1023 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C1030 " --> pdb=" O MET C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1113 through 1115 No H-bonds generated for 'chain 'C' and resid 1113 through 1115' Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 3.751A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1145 through 1158 removed outlier: 3.767A pdb=" N HIS C1156 " --> pdb=" O TYR C1152 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER C1158 " --> pdb=" O LYS C1154 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 301 Processing helix chain 'D' and resid 334 through 340 removed outlier: 4.227A pdb=" N VAL D 338 " --> pdb=" O PRO D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 350 removed outlier: 3.578A pdb=" N TRP D 350 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 368 removed outlier: 3.584A pdb=" N LEU D 368 " --> pdb=" O VAL D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 387 removed outlier: 3.698A pdb=" N LEU D 384 " --> pdb=" O PRO D 381 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASN D 385 " --> pdb=" O THR D 382 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP D 386 " --> pdb=" O LYS D 383 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU D 387 " --> pdb=" O LEU D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 408 removed outlier: 3.841A pdb=" N VAL D 404 " --> pdb=" O GLY D 401 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG D 405 " --> pdb=" O ASP D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 634 Processing helix chain 'D' and resid 734 through 741 removed outlier: 3.812A pdb=" N CYS D 740 " --> pdb=" O THR D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 752 removed outlier: 4.090A pdb=" N SER D 747 " --> pdb=" O SER D 743 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASN D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU D 749 " --> pdb=" O GLU D 745 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN D 752 " --> pdb=" O ASN D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 762 Processing helix chain 'D' and resid 763 through 779 removed outlier: 3.615A pdb=" N ILE D 767 " --> pdb=" O ALA D 763 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA D 768 " --> pdb=" O LEU D 764 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP D 772 " --> pdb=" O ALA D 768 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR D 775 " --> pdb=" O GLN D 771 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN D 776 " --> pdb=" O ASP D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 822 removed outlier: 3.963A pdb=" N LEU D 818 " --> pdb=" O PHE D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 863 through 879 removed outlier: 3.542A pdb=" N ALA D 868 " --> pdb=" O ASP D 864 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN D 869 " --> pdb=" O GLU D 865 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR D 870 " --> pdb=" O MET D 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 887 removed outlier: 3.555A pdb=" N GLY D 886 " --> pdb=" O TRP D 883 " (cutoff:3.500A) Processing helix chain 'D' and resid 894 through 907 removed outlier: 4.448A pdb=" N ALA D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR D 901 " --> pdb=" O MET D 897 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 915 removed outlier: 3.923A pdb=" N TYR D 914 " --> pdb=" O GLN D 910 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU D 915 " --> pdb=" O ASN D 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 910 through 915' Processing helix chain 'D' and resid 916 through 938 removed outlier: 3.820A pdb=" N LYS D 930 " --> pdb=" O SER D 926 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE D 931 " --> pdb=" O ALA D 927 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN D 932 " --> pdb=" O ILE D 928 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP D 933 " --> pdb=" O GLY D 929 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER D 936 " --> pdb=" O GLN D 932 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR D 938 " --> pdb=" O SER D 934 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 963 removed outlier: 4.119A pdb=" N VAL D 948 " --> pdb=" O LYS D 944 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL D 949 " --> pdb=" O LEU D 945 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN D 952 " --> pdb=" O VAL D 948 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 963 " --> pdb=" O LEU D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1029 removed outlier: 4.006A pdb=" N GLN D 989 " --> pdb=" O GLU D 985 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY D 996 " --> pdb=" O ARG D 992 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER D1027 " --> pdb=" O ALA D1023 " (cutoff:3.500A) Processing helix chain 'D' and resid 1139 through 1158 removed outlier: 5.127A pdb=" N PHE D1145 " --> pdb=" O GLU D1141 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS D1151 " --> pdb=" O GLU D1147 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.787A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.203A pdb=" N GLU G 10 " --> pdb=" O THR G 121 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU G 35 " --> pdb=" O TRP G 51 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TRP G 51 " --> pdb=" O LEU G 35 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TRP G 37 " --> pdb=" O ILE G 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.203A pdb=" N GLU G 10 " --> pdb=" O THR G 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 18 through 20 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.517A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N CYS H 22 " --> pdb=" O ALA H 80 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ALA H 80 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.683A pdb=" N GLY H 50 " --> pdb=" O TRP H 37 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG H 39 " --> pdb=" O TRP H 48 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N TRP H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.698A pdb=" N LEU I 11 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN I 38 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEU I 47 " --> pdb=" O GLN I 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.628A pdb=" N SER L 54 " --> pdb=" O SER L 50 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU L 34 " --> pdb=" O SER L 50 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN L 39 " --> pdb=" O VAL L 86 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLN L 91 " --> pdb=" O THR L 98 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.628A pdb=" N SER L 54 " --> pdb=" O SER L 50 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU L 34 " --> pdb=" O SER L 50 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN L 39 " --> pdb=" O VAL L 86 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AB5, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.630A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.021A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 99 through 103 Processing sheet with id=AB8, first strand: chain 'B' and resid 113 through 118 removed outlier: 3.523A pdb=" N VAL B 128 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE B 163 " --> pdb=" O VAL B 128 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 308 through 315 removed outlier: 5.462A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N SER B 313 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B 592 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR B 609 " --> pdb=" O CYS B 646 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS B 646 " --> pdb=" O TYR B 609 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 321 through 322 removed outlier: 7.857A pdb=" N GLU B 321 " --> pdb=" O ASN B 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 351 through 355 removed outlier: 4.195A pdb=" N ASN B 351 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 396 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR B 393 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 510 " --> pdb=" O CYS B 429 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL B 430 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS B 375 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B 432 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR B 373 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AC4, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC5, first strand: chain 'B' and resid 470 through 471 removed outlier: 3.601A pdb=" N TYR B 470 " --> pdb=" O TYR B 486 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR B 486 " --> pdb=" O TYR B 470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 548 through 551 removed outlier: 3.540A pdb=" N THR B 585 " --> pdb=" O VAL B 548 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 651 through 657 removed outlier: 5.476A pdb=" N THR B 693 " --> pdb=" O VAL B 653 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASN B 655 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS B 668 " --> pdb=" O TYR B 692 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 708 through 712 Processing sheet with id=AC9, first strand: chain 'B' and resid 715 through 725 removed outlier: 3.556A pdb=" N SER B 718 " --> pdb=" O THR B1063 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 715 through 725 removed outlier: 3.556A pdb=" N SER B 718 " --> pdb=" O THR B1063 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 730 through 732 removed outlier: 4.384A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 784 through 787 removed outlier: 5.302A pdb=" N ILE B 785 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1117 through 1119 Processing sheet with id=AD5, first strand: chain 'B' and resid 1091 through 1094 removed outlier: 3.613A pdb=" N THR B1102 " --> pdb=" O VAL B1091 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 31 removed outlier: 8.288A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA C 261 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE C 198 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL C 224 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N SER C 200 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.109A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 81 through 83 removed outlier: 7.561A pdb=" N ARG C 234 " --> pdb=" O PHE C 104 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N PHE C 104 " --> pdb=" O ARG C 234 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLN C 236 " --> pdb=" O TRP C 102 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N TRP C 102 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU C 238 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR C 112 " --> pdb=" O PHE C 131 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE C 131 " --> pdb=" O THR C 112 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.452A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N SER C 313 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 592 " --> pdb=" O SER C 313 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 321 through 323 removed outlier: 3.804A pdb=" N GLU C 321 " --> pdb=" O CYS C 535 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE C 540 " --> pdb=" O LEU C 543 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR C 585 " --> pdb=" O VAL C 548 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 353 through 355 removed outlier: 3.581A pdb=" N ALA C 394 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP C 433 " --> pdb=" O ARG C 506 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL C 430 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS C 375 " --> pdb=" O VAL C 430 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 388 through 389 Processing sheet with id=AE4, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE5, first strand: chain 'C' and resid 470 through 471 removed outlier: 3.723A pdb=" N TYR C 470 " --> pdb=" O TYR C 486 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 651 through 657 removed outlier: 6.187A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N VAL C 653 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER C 688 " --> pdb=" O GLN C 672 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN C 672 " --> pdb=" O SER C 688 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 708 through 712 Processing sheet with id=AE8, first strand: chain 'C' and resid 715 through 725 removed outlier: 3.771A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 732 through 733 removed outlier: 3.681A pdb=" N SER C 732 " --> pdb=" O THR C 856 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 784 through 785 removed outlier: 3.523A pdb=" N ILE C 785 " --> pdb=" O ALA D 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 1078 through 1079 removed outlier: 4.717A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id=AF4, first strand: chain 'D' and resid 27 through 31 removed outlier: 3.933A pdb=" N SER D 60 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ASN D 61 " --> pdb=" O TYR D 266 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N TYR D 266 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA D 261 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N SER D 200 " --> pdb=" O PRO D 222 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.621A pdb=" N ASP D 284 " --> pdb=" O LYS D 275 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 82 through 83 removed outlier: 4.554A pdb=" N PHE D 163 " --> pdb=" O VAL D 128 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 308 through 311 removed outlier: 3.562A pdb=" N GLY D 591 " --> pdb=" O GLN D 610 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 322 through 325 removed outlier: 7.830A pdb=" N ILE D 323 " --> pdb=" O ASN D 539 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE D 540 " --> pdb=" O LEU D 543 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR D 585 " --> pdb=" O VAL D 548 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 351 through 355 removed outlier: 3.558A pdb=" N ASN D 351 " --> pdb=" O SER D 396 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER D 511 " --> pdb=" O TYR D 393 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL D 430 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS D 375 " --> pdb=" O VAL D 430 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 449 through 451 Processing sheet with id=AG2, first strand: chain 'D' and resid 470 through 471 Processing sheet with id=AG3, first strand: chain 'D' and resid 651 through 652 removed outlier: 6.463A pdb=" N GLU D 651 " --> pdb=" O ALA D 691 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N THR D 693 " --> pdb=" O GLU D 651 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE D 667 " --> pdb=" O ILE D 663 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 708 through 712 removed outlier: 3.810A pdb=" N THR D1073 " --> pdb=" O SER D1094 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 715 through 724 removed outlier: 3.538A pdb=" N PHE D1049 " --> pdb=" O LEU D1060 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET D1047 " --> pdb=" O VAL D1062 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TYR D1064 " --> pdb=" O HIS D1045 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS D1045 " --> pdb=" O TYR D1064 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 732 through 733 removed outlier: 3.502A pdb=" N SER D 732 " --> pdb=" O THR D 856 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 1117 through 1122 removed outlier: 4.769A pdb=" N ALA D1084 " --> pdb=" O SER D1120 " (cutoff:3.500A) 991 hydrogen bonds defined for protein. 2598 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: 13.38 Time building geometry restraints manager: 14.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9529 1.34 - 1.46: 7670 1.46 - 1.59: 13740 1.59 - 1.71: 0 1.71 - 1.83: 167 Bond restraints: 31106 Sorted by residual: bond pdb=" C1 NAG X 2 " pdb=" O5 NAG X 2 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" N ILE B 323 " pdb=" CA ILE B 323 " ideal model delta sigma weight residual 1.456 1.500 -0.045 1.11e-02 8.12e+03 1.63e+01 bond pdb=" N PHE C 326 " pdb=" CA PHE C 326 " ideal model delta sigma weight residual 1.455 1.492 -0.037 9.60e-03 1.09e+04 1.49e+01 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" N VAL D 317 " pdb=" CA VAL D 317 " ideal model delta sigma weight residual 1.458 1.496 -0.039 1.14e-02 7.69e+03 1.15e+01 ... (remaining 31101 not shown) Histogram of bond angle deviations from ideal: 97.14 - 104.56: 474 104.56 - 111.98: 15529 111.98 - 119.40: 10142 119.40 - 126.81: 15803 126.81 - 134.23: 357 Bond angle restraints: 42305 Sorted by residual: angle pdb=" CA PHE C 326 " pdb=" C PHE C 326 " pdb=" N PRO C 327 " ideal model delta sigma weight residual 117.95 123.38 -5.43 7.70e-01 1.69e+00 4.97e+01 angle pdb=" C THR C 19 " pdb=" CA THR C 19 " pdb=" CB THR C 19 " ideal model delta sigma weight residual 116.54 110.43 6.11 1.15e+00 7.56e-01 2.82e+01 angle pdb=" CA PHE C 326 " pdb=" C PHE C 326 " pdb=" O PHE C 326 " ideal model delta sigma weight residual 120.34 115.85 4.49 9.20e-01 1.18e+00 2.38e+01 angle pdb=" C THR D 19 " pdb=" CA THR D 19 " pdb=" CB THR D 19 " ideal model delta sigma weight residual 115.79 110.13 5.66 1.19e+00 7.06e-01 2.26e+01 angle pdb=" CA ASN C 143 " pdb=" C ASN C 143 " pdb=" O ASN C 143 " ideal model delta sigma weight residual 122.45 116.86 5.59 1.30e+00 5.92e-01 1.85e+01 ... (remaining 42300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.95: 18309 24.95 - 49.89: 998 49.89 - 74.84: 97 74.84 - 99.79: 64 99.79 - 124.73: 42 Dihedral angle restraints: 19510 sinusoidal: 8571 harmonic: 10939 Sorted by residual: dihedral pdb=" CA ASP C 140 " pdb=" C ASP C 140 " pdb=" N HIS C 141 " pdb=" CA HIS C 141 " ideal model delta harmonic sigma weight residual 180.00 -133.47 -46.53 0 5.00e+00 4.00e-02 8.66e+01 dihedral pdb=" CA ASP D 140 " pdb=" C ASP D 140 " pdb=" N HIS D 141 " pdb=" CA HIS D 141 " ideal model delta harmonic sigma weight residual -180.00 -133.79 -46.21 0 5.00e+00 4.00e-02 8.54e+01 dihedral pdb=" CB CYS D 735 " pdb=" SG CYS D 735 " pdb=" SG CYS D 757 " pdb=" CB CYS D 757 " ideal model delta sinusoidal sigma weight residual 93.00 13.70 79.30 1 1.00e+01 1.00e-02 7.82e+01 ... (remaining 19507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4710 0.098 - 0.197: 254 0.197 - 0.295: 14 0.295 - 0.394: 1 0.394 - 0.492: 1 Chirality restraints: 4980 Sorted by residual: chirality pdb=" CA ASN C 144 " pdb=" N ASN C 144 " pdb=" C ASN C 144 " pdb=" CB ASN C 144 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN D1071 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA ASN C 143 " pdb=" N ASN C 143 " pdb=" C ASN C 143 " pdb=" CB ASN C 143 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 4977 not shown) Planarity restraints: 5395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1301 " 0.023 2.00e-02 2.50e+03 3.24e-02 1.31e+01 pdb=" C7 NAG C1301 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG C1301 " 0.032 2.00e-02 2.50e+03 pdb=" N2 NAG C1301 " -0.013 2.00e-02 2.50e+03 pdb=" O7 NAG C1301 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 321 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C GLU B 321 " 0.037 2.00e-02 2.50e+03 pdb=" O GLU B 321 " -0.014 2.00e-02 2.50e+03 pdb=" N SER B 322 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 627 " 0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO B 628 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 628 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 628 " 0.025 5.00e-02 4.00e+02 ... (remaining 5392 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 584 2.67 - 3.23: 28769 3.23 - 3.78: 44837 3.78 - 4.34: 60517 4.34 - 4.90: 98128 Nonbonded interactions: 232835 Sorted by model distance: nonbonded pdb=" CG ARG C 463 " pdb=" O7 NAG C1301 " model vdw 2.109 2.752 nonbonded pdb=" OG SER G 33 " pdb=" O CYS G 102 " model vdw 2.130 2.440 nonbonded pdb=" O PRO B 227 " pdb=" NH2 ARG C 354 " model vdw 2.143 2.520 nonbonded pdb=" O GLY C 877 " pdb=" OG SER C 881 " model vdw 2.181 2.440 nonbonded pdb=" NH2 ARG B 564 " pdb=" OD1 ASP B 565 " model vdw 2.186 2.520 ... (remaining 232830 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' selection = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' } ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 14 through 1159 or resid 1301 through 1309)) selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'S' selection = chain 'T' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.790 Check model and map are aligned: 0.420 Set scattering table: 0.280 Process input model: 81.970 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.420 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 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 0.085 31106 Z= 0.277 Angle : 0.649 11.521 42305 Z= 0.330 Chirality : 0.048 0.492 4980 Planarity : 0.004 0.052 5353 Dihedral : 15.998 124.733 12333 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.71 % Favored : 94.24 % Rotamer: Outliers : 0.15 % Allowed : 0.49 % Favored : 99.36 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.30 (0.13), residues: 3716 helix: -0.94 (0.20), residues: 675 sheet: 0.25 (0.19), residues: 776 loop : -1.27 (0.13), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 630 HIS 0.006 0.001 HIS C 141 PHE 0.015 0.001 PHE C 487 TYR 0.020 0.001 TYR G 96 ARG 0.008 0.000 ARG D 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 173 time to evaluate : 3.334 Fit side-chains REVERT: G 67 GLU cc_start: 0.7686 (pm20) cc_final: 0.7262 (pp20) REVERT: L 96 PRO cc_start: 0.5049 (Cg_exo) cc_final: 0.4845 (Cg_endo) REVERT: B 512 PHE cc_start: 0.6940 (p90) cc_final: 0.6724 (p90) REVERT: C 335 PHE cc_start: 0.7070 (m-80) cc_final: 0.6846 (m-80) outliers start: 5 outliers final: 0 residues processed: 178 average time/residue: 0.4261 time to fit residues: 126.8056 Evaluate side-chains 116 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 3.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 313 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 189 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 290 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 216 optimal weight: 2.9990 chunk 336 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 60 ASN ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN I 91 GLN L 39 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1139 GLN ** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 ASN ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 923 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 31106 Z= 0.295 Angle : 0.640 9.696 42305 Z= 0.325 Chirality : 0.047 0.407 4980 Planarity : 0.004 0.056 5353 Dihedral : 11.364 114.190 5579 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.73 % Favored : 94.24 % Rotamer: Outliers : 0.52 % Allowed : 7.97 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.29 (0.13), residues: 3716 helix: -0.69 (0.20), residues: 700 sheet: 0.21 (0.18), residues: 793 loop : -1.35 (0.13), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 64 HIS 0.006 0.001 HIS C 141 PHE 0.030 0.002 PHE D 559 TYR 0.029 0.001 TYR C 262 ARG 0.009 0.000 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 3.549 Fit side-chains revert: symmetry clash REVERT: G 3 GLN cc_start: 0.7163 (tm-30) cc_final: 0.6900 (tm-30) REVERT: G 67 GLU cc_start: 0.7732 (pm20) cc_final: 0.7407 (pm20) REVERT: L 96 PRO cc_start: 0.4808 (Cg_exo) cc_final: 0.4583 (Cg_endo) REVERT: B 512 PHE cc_start: 0.7230 (p90) cc_final: 0.6839 (p90) REVERT: B 589 PHE cc_start: 0.6843 (p90) cc_final: 0.6478 (p90) REVERT: B 622 HIS cc_start: 0.7233 (m90) cc_final: 0.6915 (m90) REVERT: C 335 PHE cc_start: 0.6984 (m-80) cc_final: 0.6642 (m-80) REVERT: C 559 PHE cc_start: 0.7072 (p90) cc_final: 0.6779 (p90) REVERT: C 1139 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8573 (tp-100) REVERT: D 148 MET cc_start: 0.6223 (tpp) cc_final: 0.5996 (tpp) REVERT: D 181 PHE cc_start: 0.6012 (m-80) cc_final: 0.5387 (m-10) outliers start: 17 outliers final: 12 residues processed: 145 average time/residue: 0.4246 time to fit residues: 104.1083 Evaluate side-chains 131 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 3.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 1139 GLN Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 983 LYS Chi-restraints excluded: chain D residue 1138 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 187 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 280 optimal weight: 5.9990 chunk 229 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 337 optimal weight: 0.2980 chunk 364 optimal weight: 4.9990 chunk 300 optimal weight: 20.0000 chunk 334 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 270 optimal weight: 8.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 90 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1139 GLN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31106 Z= 0.290 Angle : 0.612 9.995 42305 Z= 0.307 Chirality : 0.046 0.420 4980 Planarity : 0.004 0.053 5353 Dihedral : 9.674 113.819 5579 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.08 % Favored : 93.86 % Rotamer: Outliers : 0.98 % Allowed : 11.51 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % 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: -1.32 (0.13), residues: 3716 helix: -0.59 (0.20), residues: 699 sheet: 0.17 (0.18), residues: 822 loop : -1.42 (0.13), residues: 2195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 64 HIS 0.004 0.001 HIS C1085 PHE 0.022 0.001 PHE D 559 TYR 0.028 0.001 TYR C 262 ARG 0.006 0.000 ARG C 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 3.569 Fit side-chains revert: symmetry clash REVERT: G 67 GLU cc_start: 0.7826 (pm20) cc_final: 0.7588 (pm20) REVERT: B 512 PHE cc_start: 0.7295 (p90) cc_final: 0.6879 (p90) REVERT: B 589 PHE cc_start: 0.6686 (p90) cc_final: 0.6353 (p90) REVERT: C 335 PHE cc_start: 0.6881 (m-80) cc_final: 0.6457 (m-80) REVERT: C 559 PHE cc_start: 0.7075 (p90) cc_final: 0.6758 (p90) REVERT: D 148 MET cc_start: 0.6199 (tpp) cc_final: 0.5992 (tpp) REVERT: D 181 PHE cc_start: 0.6026 (m-80) cc_final: 0.5584 (m-10) REVERT: D 999 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7961 (tm-30) outliers start: 32 outliers final: 20 residues processed: 152 average time/residue: 0.4053 time to fit residues: 106.8326 Evaluate side-chains 135 residues out of total 3284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 414 ASN Chi-restraints excluded: chain D residue 983 LYS Chi-restraints excluded: chain D residue 1138 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 333 optimal weight: 2.9990 chunk 253 optimal weight: 0.9980 chunk 175 optimal weight: 20.0000 chunk 37 optimal weight: 40.0000 chunk 161 optimal weight: 9.9990 chunk 226 optimal weight: 1.9990 chunk 338 optimal weight: 0.0050 chunk 358 optimal weight: 0.5980 chunk 176 optimal weight: 3.9990 chunk 321 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: