Starting phenix.real_space_refine on Sat Jun 29 09:34:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dan_27271/06_2024/8dan_27271.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dan_27271/06_2024/8dan_27271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dan_27271/06_2024/8dan_27271.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dan_27271/06_2024/8dan_27271.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dan_27271/06_2024/8dan_27271.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dan_27271/06_2024/8dan_27271.pdb" } resolution = 4.74 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= 0.004 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: 5 Type Number sf(0) Gaussians S 216 5.16 5 C 22136 2.51 5 N 6060 2.21 5 O 6588 1.98 5 H 33968 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 97": "OD1" <-> "OD2" Residue "A ASP 117": "OD1" <-> "OD2" Residue "A ASP 145": "OD1" <-> "OD2" Residue "A TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 209": "OD1" <-> "OD2" Residue "B PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 91": "OD1" <-> "OD2" Residue "C TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 97": "OD1" <-> "OD2" Residue "D ASP 117": "OD1" <-> "OD2" Residue "D ASP 145": "OD1" <-> "OD2" Residue "D TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 209": "OD1" <-> "OD2" Residue "E PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "E TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 91": "OD1" <-> "OD2" Residue "F TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 97": "OD1" <-> "OD2" Residue "G ASP 117": "OD1" <-> "OD2" Residue "G ASP 145": "OD1" <-> "OD2" Residue "G TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 209": "OD1" <-> "OD2" Residue "H PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 163": "OE1" <-> "OE2" Residue "H TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 91": "OD1" <-> "OD2" Residue "I TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 97": "OD1" <-> "OD2" Residue "J ASP 117": "OD1" <-> "OD2" Residue "J ASP 145": "OD1" <-> "OD2" Residue "J TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 209": "OD1" <-> "OD2" Residue "K PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 163": "OE1" <-> "OE2" Residue "K TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 91": "OD1" <-> "OD2" Residue "L TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 68968 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 6568 Classifications: {'peptide': 438} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 410} Chain: "B" Number of atoms: 6429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 6429 Classifications: {'peptide': 415} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 386} Chain: "C" Number of atoms: 4203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4203 Classifications: {'peptide': 265} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 256} Chain: "D" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 6568 Classifications: {'peptide': 438} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 410} Chain: "E" Number of atoms: 6429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 6429 Classifications: {'peptide': 415} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 386} Chain: "F" Number of atoms: 4203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4203 Classifications: {'peptide': 265} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 256} Chain: "G" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 6568 Classifications: {'peptide': 438} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 410} Chain: "H" Number of atoms: 6429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 6429 Classifications: {'peptide': 415} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 386} Chain: "I" Number of atoms: 4203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4203 Classifications: {'peptide': 265} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 256} Chain: "J" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 6568 Classifications: {'peptide': 438} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 410} Chain: "K" Number of atoms: 6429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 6429 Classifications: {'peptide': 415} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 386} Chain: "L" Number of atoms: 4203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4203 Classifications: {'peptide': 265} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 256} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 21.75, per 1000 atoms: 0.32 Number of scatterers: 68968 At special positions: 0 Unit cell: (196.8, 166.8, 180, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 216 16.00 O 6588 8.00 N 6060 7.00 C 22136 6.00 H 33968 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=68, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.02 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.05 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.04 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 28 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 204 " - pdb=" SG CYS B 229 " distance=2.03 Simple disulfide: pdb=" SG CYS B 206 " - pdb=" SG CYS B 223 " distance=2.04 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 273 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 280 " distance=2.03 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 94 " distance=2.02 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 96 " distance=2.05 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 78 " distance=2.03 Simple disulfide: pdb=" SG CYS D 259 " - pdb=" SG CYS D 271 " distance=2.03 Simple disulfide: pdb=" SG CYS D 301 " - pdb=" SG CYS D 376 " distance=2.03 Simple disulfide: pdb=" SG CYS D 306 " - pdb=" SG CYS D 380 " distance=2.03 Simple disulfide: pdb=" SG CYS D 328 " - pdb=" SG CYS D 370 " distance=2.04 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 127 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 28 " distance=2.03 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS E 155 " - pdb=" SG CYS E 269 " distance=2.03 Simple disulfide: pdb=" SG CYS E 204 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS E 206 " - pdb=" SG CYS E 223 " distance=2.04 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 273 " distance=2.03 Simple disulfide: pdb=" SG CYS F 138 " - pdb=" SG CYS F 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 145 " - pdb=" SG CYS F 280 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.02 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.05 Simple disulfide: pdb=" SG CYS G 68 " - pdb=" SG CYS G 78 " distance=2.03 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.03 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.04 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 127 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 28 " distance=2.03 Simple disulfide: pdb=" SG CYS H 94 " - pdb=" SG CYS H 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 269 " distance=2.03 Simple disulfide: pdb=" SG CYS H 204 " - pdb=" SG CYS H 229 " distance=2.03 Simple disulfide: pdb=" SG CYS H 206 " - pdb=" SG CYS H 223 " distance=2.04 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 273 " distance=2.03 Simple disulfide: pdb=" SG CYS I 138 " - pdb=" SG CYS I 187 " distance=2.03 Simple disulfide: pdb=" SG CYS I 145 " - pdb=" SG CYS I 280 " distance=2.03 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 94 " distance=2.02 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.05 Simple disulfide: pdb=" SG CYS J 68 " - pdb=" SG CYS J 78 " distance=2.03 Simple disulfide: pdb=" SG CYS J 259 " - pdb=" SG CYS J 271 " distance=2.03 Simple disulfide: pdb=" SG CYS J 301 " - pdb=" SG CYS J 376 " distance=2.03 Simple disulfide: pdb=" SG CYS J 306 " - pdb=" SG CYS J 380 " distance=2.03 Simple disulfide: pdb=" SG CYS J 328 " - pdb=" SG CYS J 370 " distance=2.04 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 127 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 28 " distance=2.03 Simple disulfide: pdb=" SG CYS K 94 " - pdb=" SG CYS K 108 " distance=2.03 Simple disulfide: pdb=" SG CYS K 155 " - pdb=" SG CYS K 269 " distance=2.03 Simple disulfide: pdb=" SG CYS K 204 " - pdb=" SG CYS K 229 " distance=2.03 Simple disulfide: pdb=" SG CYS K 206 " - pdb=" SG CYS K 223 " distance=2.04 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 273 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 187 " distance=2.03 Simple disulfide: pdb=" SG CYS L 145 " - pdb=" SG CYS L 280 " 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 NAG-ASN " NAG A 501 " - " ASN A 139 " " NAG B 501 " - " ASN B 199 " " NAG D 501 " - " ASN D 139 " " NAG E 501 " - " ASN E 199 " " NAG G 501 " - " ASN G 139 " " NAG H 501 " - " ASN H 199 " " NAG J 501 " - " ASN J 139 " " NAG K 501 " - " ASN K 199 " Time building additional restraints: 38.95 Conformation dependent library (CDL) restraints added in 5.2 seconds 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8360 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 92 sheets defined 14.1% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.23 Creating SS restraints... Processing helix chain 'A' and resid 113 through 118 Processing helix chain 'A' and resid 238 through 246 removed outlier: 3.516A pdb=" N ASN A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.685A pdb=" N CYS A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 403 through 414 Processing helix chain 'A' and resid 416 through 438 removed outlier: 3.504A pdb=" N LEU A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 358 through 365 removed outlier: 3.636A pdb=" N TYR B 362 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 399 Processing helix chain 'B' and resid 411 through 419 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 104 through 109 removed outlier: 4.200A pdb=" N ARG C 108 " --> pdb=" O TYR C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 119 Processing helix chain 'C' and resid 160 through 164 removed outlier: 3.662A pdb=" N ALA C 163 " --> pdb=" O LYS C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 244 removed outlier: 3.525A pdb=" N ARG C 241 " --> pdb=" O PRO C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 238 through 246 removed outlier: 3.516A pdb=" N ASN D 246 " --> pdb=" O MET D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 255 through 259 removed outlier: 3.686A pdb=" N CYS D 259 " --> pdb=" O PRO D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 287 Processing helix chain 'D' and resid 403 through 414 Processing helix chain 'D' and resid 416 through 438 removed outlier: 3.503A pdb=" N LEU D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG D 438 " --> pdb=" O LEU D 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 84 No H-bonds generated for 'chain 'E' and resid 82 through 84' Processing helix chain 'E' and resid 225 through 227 No H-bonds generated for 'chain 'E' and resid 225 through 227' Processing helix chain 'E' and resid 358 through 365 removed outlier: 3.636A pdb=" N TYR E 362 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 399 Processing helix chain 'E' and resid 411 through 419 Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 104 through 109 removed outlier: 4.201A pdb=" N ARG F 108 " --> pdb=" O TYR F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 119 Processing helix chain 'F' and resid 160 through 164 removed outlier: 3.661A pdb=" N ALA F 163 " --> pdb=" O LYS F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 244 removed outlier: 3.525A pdb=" N ARG F 241 " --> pdb=" O PRO F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 254 Processing helix chain 'F' and resid 264 through 268 Processing helix chain 'G' and resid 113 through 118 Processing helix chain 'G' and resid 238 through 246 removed outlier: 3.515A pdb=" N ASN G 246 " --> pdb=" O MET G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 254 Processing helix chain 'G' and resid 255 through 259 removed outlier: 3.687A pdb=" N CYS G 259 " --> pdb=" O PRO G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 287 Processing helix chain 'G' and resid 403 through 414 Processing helix chain 'G' and resid 416 through 438 removed outlier: 3.504A pdb=" N LEU G 420 " --> pdb=" O GLY G 416 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG G 438 " --> pdb=" O LEU G 434 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 84 No H-bonds generated for 'chain 'H' and resid 82 through 84' Processing helix chain 'H' and resid 225 through 227 No H-bonds generated for 'chain 'H' and resid 225 through 227' Processing helix chain 'H' and resid 358 through 365 removed outlier: 3.637A pdb=" N TYR H 362 " --> pdb=" O ILE H 358 " (cutoff:3.500A) Processing helix chain 'H' and resid 371 through 399 Processing helix chain 'H' and resid 411 through 419 Processing helix chain 'I' and resid 55 through 59 Processing helix chain 'I' and resid 104 through 109 removed outlier: 4.201A pdb=" N ARG I 108 " --> pdb=" O TYR I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 119 Processing helix chain 'I' and resid 160 through 164 removed outlier: 3.660A pdb=" N ALA I 163 " --> pdb=" O LYS I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 244 removed outlier: 3.524A pdb=" N ARG I 241 " --> pdb=" O PRO I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 254 Processing helix chain 'I' and resid 264 through 268 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 238 through 246 removed outlier: 3.515A pdb=" N ASN J 246 " --> pdb=" O MET J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 254 Processing helix chain 'J' and resid 255 through 259 removed outlier: 3.686A pdb=" N CYS J 259 " --> pdb=" O PRO J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 283 through 287 Processing helix chain 'J' and resid 403 through 414 Processing helix chain 'J' and resid 416 through 438 removed outlier: 3.504A pdb=" N LEU J 420 " --> pdb=" O GLY J 416 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG J 438 " --> pdb=" O LEU J 434 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 84 No H-bonds generated for 'chain 'K' and resid 82 through 84' Processing helix chain 'K' and resid 225 through 227 No H-bonds generated for 'chain 'K' and resid 225 through 227' Processing helix chain 'K' and resid 358 through 365 removed outlier: 3.637A pdb=" N TYR K 362 " --> pdb=" O ILE K 358 " (cutoff:3.500A) Processing helix chain 'K' and resid 371 through 399 Processing helix chain 'K' and resid 411 through 419 Processing helix chain 'L' and resid 55 through 59 Processing helix chain 'L' and resid 104 through 109 removed outlier: 4.200A pdb=" N ARG L 108 " --> pdb=" O TYR L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 119 Processing helix chain 'L' and resid 160 through 164 removed outlier: 3.661A pdb=" N ALA L 163 " --> pdb=" O LYS L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 244 removed outlier: 3.525A pdb=" N ARG L 241 " --> pdb=" O PRO L 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 249 through 254 Processing helix chain 'L' and resid 264 through 268 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.546A pdb=" N ILE A 162 " --> pdb=" O SER A 279 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 21 removed outlier: 3.698A pdb=" N VAL A 19 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 27 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ARG A 21 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ALA A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER A 35 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 132 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N THR A 126 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN A 43 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU A 45 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 47 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 120 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 147 removed outlier: 6.741A pdb=" N VAL A 120 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 47 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU A 45 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN A 43 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N THR A 126 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 132 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER A 35 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.678A pdb=" N TYR A 107 " --> pdb=" O VAL A 54 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.678A pdb=" N TYR A 107 " --> pdb=" O VAL A 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 203 through 204 removed outlier: 3.725A pdb=" N GLN A 204 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 214 " --> pdb=" O GLN A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA8, first strand: chain 'A' and resid 296 through 302 removed outlier: 4.326A pdb=" N VAL A 299 " --> pdb=" O GLN A 319 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN A 319 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N CYS A 301 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR A 317 " --> pdb=" O CYS A 301 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 343 through 346 removed outlier: 3.675A pdb=" N GLY A 326 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=AB2, first strand: chain 'B' and resid 34 through 38 removed outlier: 4.589A pdb=" N ASN B 36 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN B 107 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ARG B 96 " --> pdb=" O GLN B 107 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.602A pdb=" N GLN B 53 " --> pdb=" O SER B 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 86 through 89 removed outlier: 4.246A pdb=" N ASP B 112 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 151 through 158 Processing sheet with id=AB6, first strand: chain 'B' and resid 169 through 171 Processing sheet with id=AB7, first strand: chain 'B' and resid 183 through 184 Processing sheet with id=AB8, first strand: chain 'B' and resid 210 through 215 Processing sheet with id=AB9, first strand: chain 'B' and resid 278 through 279 removed outlier: 4.031A pdb=" N THR B 278 " --> pdb=" O HIS B 289 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS B 289 " --> pdb=" O THR B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 310 through 314 Processing sheet with id=AC2, first strand: chain 'C' and resid 34 through 41 removed outlier: 7.785A pdb=" N ILE C 287 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL C 38 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLN C 289 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASN C 40 " --> pdb=" O GLN C 289 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG C 210 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ARG C 222 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 49 through 51 Processing sheet with id=AC4, first strand: chain 'C' and resid 99 through 100 removed outlier: 4.213A pdb=" N ARG C 99 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP C 91 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TRP C 74 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP C 91 " --> pdb=" O VAL C 72 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL C 72 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TYR C 93 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG C 70 " --> pdb=" O TYR C 93 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA C 173 " --> pdb=" O LYS C 152 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 123 through 125 Processing sheet with id=AC6, first strand: chain 'D' and resid 2 through 8 removed outlier: 3.545A pdb=" N ILE D 162 " --> pdb=" O SER D 279 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 15 through 21 removed outlier: 3.698A pdb=" N VAL D 19 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU D 27 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG D 21 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ILE D 31 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL D 136 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL D 33 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG D 134 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER D 35 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY D 132 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER D 41 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR D 126 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN D 43 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL D 124 " --> pdb=" O ASN D 43 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU D 45 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU D 122 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL D 47 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL D 120 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 140 through 147 removed outlier: 6.741A pdb=" N VAL D 120 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL D 47 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU D 122 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU D 45 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL D 124 " --> pdb=" O ASN D 43 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN D 43 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR D 126 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER D 41 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY D 132 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER D 35 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG D 134 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL D 33 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL D 136 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ILE D 31 " --> pdb=" O VAL D 136 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.678A pdb=" N TYR D 107 " --> pdb=" O VAL D 54 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.678A pdb=" N TYR D 107 " --> pdb=" O VAL D 54 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 203 through 204 removed outlier: 3.724A pdb=" N GLN D 204 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL D 214 " --> pdb=" O GLN D 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 220 through 221 Processing sheet with id=AD4, first strand: chain 'D' and resid 296 through 302 removed outlier: 4.326A pdb=" N VAL D 299 " --> pdb=" O GLN D 319 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN D 319 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N CYS D 301 " --> pdb=" O THR D 317 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR D 317 " --> pdb=" O CYS D 301 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 343 through 346 removed outlier: 3.674A pdb=" N GLY D 326 " --> pdb=" O VAL D 346 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 17 through 19 Processing sheet with id=AD7, first strand: chain 'E' and resid 34 through 38 removed outlier: 4.588A pdb=" N ASN E 36 " --> pdb=" O GLN E 49 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN E 107 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ARG E 96 " --> pdb=" O GLN E 107 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.603A pdb=" N GLN E 53 " --> pdb=" O SER E 71 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 86 through 89 removed outlier: 4.245A pdb=" N ASP E 112 " --> pdb=" O LYS E 131 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 151 through 158 Processing sheet with id=AE2, first strand: chain 'E' and resid 169 through 171 Processing sheet with id=AE3, first strand: chain 'E' and resid 183 through 184 Processing sheet with id=AE4, first strand: chain 'E' and resid 210 through 215 Processing sheet with id=AE5, first strand: chain 'E' and resid 278 through 279 removed outlier: 4.030A pdb=" N THR E 278 " --> pdb=" O HIS E 289 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS E 289 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 310 through 314 Processing sheet with id=AE7, first strand: chain 'F' and resid 34 through 41 removed outlier: 7.785A pdb=" N ILE F 287 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL F 38 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLN F 289 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASN F 40 " --> pdb=" O GLN F 289 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG F 210 " --> pdb=" O ARG F 222 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ARG F 222 " --> pdb=" O ARG F 210 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 49 through 51 Processing sheet with id=AE9, first strand: chain 'F' and resid 99 through 100 removed outlier: 4.212A pdb=" N ARG F 99 " --> pdb=" O ASP F 91 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP F 91 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TRP F 74 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP F 91 " --> pdb=" O VAL F 72 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL F 72 " --> pdb=" O ASP F 91 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TYR F 93 " --> pdb=" O ARG F 70 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG F 70 " --> pdb=" O TYR F 93 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA F 173 " --> pdb=" O LYS F 152 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 123 through 125 Processing sheet with id=AF2, first strand: chain 'G' and resid 2 through 8 removed outlier: 3.546A pdb=" N ILE G 162 " --> pdb=" O SER G 279 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 15 through 21 removed outlier: 3.698A pdb=" N VAL G 19 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU G 27 " --> pdb=" O VAL G 19 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ARG G 21 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ALA G 25 " --> pdb=" O ARG G 21 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE G 31 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL G 136 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL G 33 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG G 134 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER G 35 " --> pdb=" O GLY G 132 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY G 132 " --> pdb=" O SER G 35 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER G 41 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR G 126 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASN G 43 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLU G 45 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL G 47 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL G 120 " --> pdb=" O VAL G 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 140 through 147 removed outlier: 6.741A pdb=" N VAL G 120 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL G 47 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLU G 45 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASN G 43 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR G 126 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER G 41 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY G 132 " --> pdb=" O SER G 35 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER G 35 " --> pdb=" O GLY G 132 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG G 134 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL G 33 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL G 136 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE G 31 " --> pdb=" O VAL G 136 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.678A pdb=" N TYR G 107 " --> pdb=" O VAL G 54 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.678A pdb=" N TYR G 107 " --> pdb=" O VAL G 54 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 203 through 204 removed outlier: 3.724A pdb=" N GLN G 204 " --> pdb=" O VAL G 214 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL G 214 " --> pdb=" O GLN G 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AF9, first strand: chain 'G' and resid 296 through 302 removed outlier: 4.327A pdb=" N VAL G 299 " --> pdb=" O GLN G 319 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN G 319 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N CYS G 301 " --> pdb=" O THR G 317 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR G 317 " --> pdb=" O CYS G 301 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 343 through 346 removed outlier: 3.674A pdb=" N GLY G 326 " --> pdb=" O VAL G 346 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AG3, first strand: chain 'H' and resid 17 through 19 Processing sheet with id=AG4, first strand: chain 'H' and resid 34 through 38 removed outlier: 4.589A pdb=" N ASN H 36 " --> pdb=" O GLN H 49 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN H 107 " --> pdb=" O ARG H 96 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ARG H 96 " --> pdb=" O GLN H 107 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.603A pdb=" N GLN H 53 " --> pdb=" O SER H 71 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 86 through 89 removed outlier: 4.245A pdb=" N ASP H 112 " --> pdb=" O LYS H 131 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 151 through 158 Processing sheet with id=AG8, first strand: chain 'H' and resid 169 through 171 Processing sheet with id=AG9, first strand: chain 'H' and resid 183 through 184 Processing sheet with id=AH1, first strand: chain 'H' and resid 210 through 215 Processing sheet with id=AH2, first strand: chain 'H' and resid 278 through 279 removed outlier: 4.030A pdb=" N THR H 278 " --> pdb=" O HIS H 289 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS H 289 " --> pdb=" O THR H 278 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 34 through 41 removed outlier: 7.786A pdb=" N ILE I 287 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL I 38 " --> pdb=" O ILE I 287 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLN I 289 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASN I 40 " --> pdb=" O GLN I 289 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG I 210 " --> pdb=" O ARG I 222 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ARG I 222 " --> pdb=" O ARG I 210 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 49 through 51 Processing sheet with id=AH5, first strand: chain 'I' and resid 99 through 100 removed outlier: 4.213A pdb=" N ARG I 99 " --> pdb=" O ASP I 91 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP I 91 " --> pdb=" O ARG I 99 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TRP I 74 " --> pdb=" O LEU I 89 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP I 91 " --> pdb=" O VAL I 72 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL I 72 " --> pdb=" O ASP I 91 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TYR I 93 " --> pdb=" O ARG I 70 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG I 70 " --> pdb=" O TYR I 93 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA I 173 " --> pdb=" O LYS I 152 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 123 through 125 Processing sheet with id=AH7, first strand: chain 'J' and resid 2 through 8 removed outlier: 3.546A pdb=" N ILE J 162 " --> pdb=" O SER J 279 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 15 through 21 removed outlier: 3.698A pdb=" N VAL J 19 " --> pdb=" O LEU J 27 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU J 27 " --> pdb=" O VAL J 19 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ARG J 21 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA J 25 " --> pdb=" O ARG J 21 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE J 31 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL J 33 " --> pdb=" O ARG J 134 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ARG J 134 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER J 35 " --> pdb=" O GLY J 132 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY J 132 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER J 41 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N THR J 126 " --> pdb=" O SER J 41 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASN J 43 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL J 124 " --> pdb=" O ASN J 43 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLU J 45 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU J 122 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL J 47 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL J 120 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 140 through 147 removed outlier: 6.742A pdb=" N VAL J 120 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL J 47 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU J 122 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLU J 45 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL J 124 " --> pdb=" O ASN J 43 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASN J 43 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N THR J 126 " --> pdb=" O SER J 41 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER J 41 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY J 132 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER J 35 " --> pdb=" O GLY J 132 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ARG J 134 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL J 33 " --> pdb=" O ARG J 134 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE J 31 " --> pdb=" O VAL J 136 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 51 through 54 removed outlier: 3.677A pdb=" N TYR J 107 " --> pdb=" O VAL J 54 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 51 through 54 removed outlier: 3.677A pdb=" N TYR J 107 " --> pdb=" O VAL J 54 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 203 through 204 removed outlier: 3.723A pdb=" N GLN J 204 " --> pdb=" O VAL J 214 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL J 214 " --> pdb=" O GLN J 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'J' and resid 220 through 221 Processing sheet with id=AI5, first strand: chain 'J' and resid 296 through 302 removed outlier: 4.326A pdb=" N VAL J 299 " --> pdb=" O GLN J 319 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN J 319 " --> pdb=" O VAL J 299 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N CYS J 301 " --> pdb=" O THR J 317 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR J 317 " --> pdb=" O CYS J 301 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 343 through 346 removed outlier: 3.674A pdb=" N GLY J 326 " --> pdb=" O VAL J 346 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'J' and resid 387 through 388 Processing sheet with id=AI8, first strand: chain 'K' and resid 17 through 19 Processing sheet with id=AI9, first strand: chain 'K' and resid 34 through 38 removed outlier: 4.589A pdb=" N ASN K 36 " --> pdb=" O GLN K 49 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLN K 107 " --> pdb=" O ARG K 96 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ARG K 96 " --> pdb=" O GLN K 107 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.603A pdb=" N GLN K 53 " --> pdb=" O SER K 71 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'K' and resid 86 through 89 removed outlier: 4.246A pdb=" N ASP K 112 " --> pdb=" O LYS K 131 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'K' and resid 151 through 158 Processing sheet with id=AJ4, first strand: chain 'K' and resid 169 through 171 Processing sheet with id=AJ5, first strand: chain 'K' and resid 183 through 184 Processing sheet with id=AJ6, first strand: chain 'K' and resid 210 through 215 Processing sheet with id=AJ7, first strand: chain 'K' and resid 278 through 279 removed outlier: 4.030A pdb=" N THR K 278 " --> pdb=" O HIS K 289 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS K 289 " --> pdb=" O THR K 278 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'L' and resid 34 through 41 removed outlier: 7.784A pdb=" N ILE L 287 " --> pdb=" O VAL L 36 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL L 38 " --> pdb=" O ILE L 287 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLN L 289 " --> pdb=" O VAL L 38 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASN L 40 " --> pdb=" O GLN L 289 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG L 210 " --> pdb=" O ARG L 222 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ARG L 222 " --> pdb=" O ARG L 210 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'L' and resid 49 through 51 Processing sheet with id=AK1, first strand: chain 'L' and resid 99 through 100 removed outlier: 4.212A pdb=" N ARG L 99 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP L 91 " --> pdb=" O ARG L 99 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TRP L 74 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP L 91 " --> pdb=" O VAL L 72 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL L 72 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TYR L 93 " --> pdb=" O ARG L 70 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG L 70 " --> pdb=" O TYR L 93 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA L 173 " --> pdb=" O LYS L 152 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'L' and resid 123 through 125 1188 hydrogen bonds defined for protein. 2976 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: 25.28 Time building geometry restraints manager: 41.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 33964 1.04 - 1.24: 4652 1.24 - 1.44: 11024 1.44 - 1.64: 19964 1.64 - 1.84: 272 Bond restraints: 69876 Sorted by residual: bond pdb=" N PHE D 1 " pdb=" H3 PHE D 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" N ASN F 32 " pdb=" H3 ASN F 32 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N PHE J 1 " pdb=" H2 PHE J 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N ILE E 5 " pdb=" H3 ILE E 5 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N ASN C 32 " pdb=" H2 ASN C 32 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 69871 not shown) Histogram of bond angle deviations from ideal: 11.76 - 36.71: 4 36.71 - 61.67: 4 61.67 - 86.62: 12 86.62 - 111.57: 78778 111.57 - 136.52: 47318 Bond angle restraints: 126116 Sorted by residual: angle pdb=" H1 ILE E 5 " pdb=" N ILE E 5 " pdb=" H2 ILE E 5 " ideal model delta sigma weight residual 109.47 11.76 97.71 3.00e+00 1.11e-01 1.06e+03 angle pdb=" H1 ILE K 5 " pdb=" N ILE K 5 " pdb=" H2 ILE K 5 " ideal model delta sigma weight residual 109.47 11.77 97.70 3.00e+00 1.11e-01 1.06e+03 angle pdb=" H1 ILE H 5 " pdb=" N ILE H 5 " pdb=" H2 ILE H 5 " ideal model delta sigma weight residual 109.47 11.80 97.67 3.00e+00 1.11e-01 1.06e+03 angle pdb=" H1 ILE B 5 " pdb=" N ILE B 5 " pdb=" H2 ILE B 5 " ideal model delta sigma weight residual 109.47 11.82 97.65 3.00e+00 1.11e-01 1.06e+03 angle pdb=" H1 PHE J 1 " pdb=" N PHE J 1 " pdb=" H2 PHE J 1 " ideal model delta sigma weight residual 109.47 56.67 52.80 3.00e+00 1.11e-01 3.10e+02 ... (remaining 126111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 30234 17.83 - 35.67: 2425 35.67 - 53.50: 772 53.50 - 71.33: 149 71.33 - 89.16: 44 Dihedral angle restraints: 33624 sinusoidal: 18092 harmonic: 15532 Sorted by residual: dihedral pdb=" CB CYS G 63 " pdb=" SG CYS G 63 " pdb=" SG CYS G 96 " pdb=" CB CYS G 96 " ideal model delta sinusoidal sigma weight residual 93.00 14.62 78.38 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" CB CYS D 63 " pdb=" SG CYS D 63 " pdb=" SG CYS D 96 " pdb=" CB CYS D 96 " ideal model delta sinusoidal sigma weight residual 93.00 14.63 78.37 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" CB CYS A 63 " pdb=" SG CYS A 63 " pdb=" SG CYS A 96 " pdb=" CB CYS A 96 " ideal model delta sinusoidal sigma weight residual 93.00 14.66 78.34 1 1.00e+01 1.00e-02 7.66e+01 ... (remaining 33621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 4911 0.072 - 0.145: 577 0.145 - 0.217: 4 0.217 - 0.290: 0 0.290 - 0.362: 4 Chirality restraints: 5496 Sorted by residual: chirality pdb=" CA LEU K 405 " pdb=" N LEU K 405 " pdb=" C LEU K 405 " pdb=" CB LEU K 405 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA LEU E 405 " pdb=" N LEU E 405 " pdb=" C LEU E 405 " pdb=" CB LEU E 405 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA LEU B 405 " pdb=" N LEU B 405 " pdb=" C LEU B 405 " pdb=" CB LEU B 405 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 5493 not shown) Planarity restraints: 10480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 401 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO B 402 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 402 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 402 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR K 401 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO K 402 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO K 402 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO K 402 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR H 401 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO H 402 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO H 402 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 402 " -0.021 5.00e-02 4.00e+02 ... (remaining 10477 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 2667 2.15 - 2.76: 131108 2.76 - 3.37: 190046 3.37 - 3.99: 237727 3.99 - 4.60: 356985 Nonbonded interactions: 918533 Sorted by model distance: nonbonded pdb=" O THR K 164 " pdb=" HE ARG L 64 " model vdw 1.532 1.850 nonbonded pdb=" H SER G 57 " pdb=" OD1 ASN H 242 " model vdw 1.592 1.850 nonbonded pdb=" H VAL A 330 " pdb=" O ALA A 342 " model vdw 1.600 1.850 nonbonded pdb=" H VAL G 330 " pdb=" O ALA G 342 " model vdw 1.600 1.850 nonbonded pdb=" H VAL D 330 " pdb=" O ALA D 342 " model vdw 1.600 1.850 ... (remaining 918528 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 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } Set up NCS constraints Number of NCS constrained groups: 3 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } Set refine NCS operators NCS operators will be refined. 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: 1.770 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: 0.780 Extract box with map and model: 5.850 Check model and map are aligned: 0.380 Set scattering table: 0.480 Process input model: 158.730 Find NCS groups from input model: 2.670 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 173.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 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 : 0.003 0.045 35908 Z= 0.169 Angle : 0.526 6.045 48900 Z= 0.279 Chirality : 0.044 0.362 5496 Planarity : 0.003 0.038 6264 Dihedral : 13.829 89.165 13120 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.75 (0.13), residues: 4448 helix: 0.96 (0.27), residues: 428 sheet: -0.63 (0.14), residues: 1532 loop : -0.59 (0.13), residues: 2488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 407 HIS 0.005 0.001 HIS D 275 PHE 0.010 0.001 PHE D 398 TYR 0.012 0.001 TYR K 403 ARG 0.005 0.000 ARG E 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 SER cc_start: 0.5512 (t) cc_final: 0.5023 (m) REVERT: A 117 ASP cc_start: 0.6717 (t0) cc_final: 0.6306 (t0) REVERT: A 120 VAL cc_start: 0.6472 (t) cc_final: 0.6189 (t) REVERT: A 203 ILE cc_start: 0.8081 (mm) cc_final: 0.7765 (mm) REVERT: A 246 ASN cc_start: 0.7748 (m-40) cc_final: 0.6819 (t0) REVERT: A 375 THR cc_start: 0.6769 (m) cc_final: 0.6409 (m) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2892 time to fit residues: 50.8343 Evaluate side-chains 101 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.375 Evaluate side-chains 145 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ILE cc_start: 0.8559 (pt) cc_final: 0.8342 (pt) REVERT: B 114 VAL cc_start: 0.9001 (p) cc_final: 0.8746 (m) REVERT: B 152 LEU cc_start: 0.8458 (mm) cc_final: 0.7731 (mp) REVERT: B 288 LEU cc_start: 0.8056 (mm) cc_final: 0.7824 (mm) REVERT: B 312 GLU cc_start: 0.5523 (tt0) cc_final: 0.5289 (tt0) REVERT: B 331 TYR cc_start: 0.6288 (t80) cc_final: 0.5865 (t80) REVERT: B 358 ILE cc_start: 0.6934 (mm) cc_final: 0.6577 (mp) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.3056 time to fit residues: 51.7502 Evaluate side-chains 105 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.370 Evaluate side-chains 73 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 189 ASN cc_start: 0.6979 (p0) cc_final: 0.6765 (p0) REVERT: C 193 ILE cc_start: 0.7751 (tt) cc_final: 0.7386 (tp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3080 time to fit residues: 25.2217 Evaluate side-chains 53 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 371 optimal weight: 3.9990 chunk 333 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 224 optimal weight: 0.0980 chunk 178 optimal weight: 3.9990 chunk 344 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 256 optimal weight: 4.9990 chunk 399 optimal weight: 1.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 52 HIS ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 HIS ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 GLN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 HIS E 289 HIS E 321 ASN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 ASN ** L 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 GLN L 245 ASN L 289 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 35908 Z= 0.347 Angle : 0.613 8.554 48900 Z= 0.329 Chirality : 0.043 0.368 5496 Planarity : 0.006 0.089 6264 Dihedral : 5.624 54.781 5136 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.21 % Allowed : 3.65 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.15 (0.13), residues: 4448 helix: 1.33 (0.28), residues: 400 sheet: -1.15 (0.13), residues: 1616 loop : -0.74 (0.13), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 74 HIS 0.011 0.002 HIS H 252 PHE 0.032 0.002 PHE D 257 TYR 0.025 0.002 TYR L 104 ARG 0.009 0.001 ARG H 396 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8024 Ramachandran restraints generated. 4012 Oldfield, 0 Emsley, 4012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8024 Ramachandran restraints generated. 4012 Oldfield, 0 Emsley, 4012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 2 GLU cc_start: 0.7730 (tp30) cc_final: 0.7160 (tp30) REVERT: D 16 LYS cc_start: 0.7635 (mttt) cc_final: 0.7327 (mttt) REVERT: D 136 VAL cc_start: 0.8239 (t) cc_final: 0.7590 (t) REVERT: D 330 VAL cc_start: 0.8902 (m) cc_final: 0.8695 (m) outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 0.2415 time to fit residues: 35.9358 Evaluate side-chains 100 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.375 Evaluate side-chains 114 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 136 LYS cc_start: 0.7840 (pttp) cc_final: 0.7567 (ptpp) outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.3005 time to fit residues: 40.6839 Evaluate side-chains 86 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.379 Evaluate side-chains 67 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 114 ASN cc_start: 0.8623 (p0) cc_final: 0.8125 (t0) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.3400 time to fit residues: 25.3946 Evaluate side-chains 57 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 222 optimal weight: 0.5980 chunk 124 optimal weight: 0.1980 chunk 332 optimal weight: 0.8980 chunk 272 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 400 optimal weight: 0.1980 chunk 432 optimal weight: 5.9990 chunk 356 optimal weight: 0.5980 chunk 396 optimal weight: 0.0170 chunk 136 optimal weight: 6.9990 chunk 321 optimal weight: 10.0000 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 49 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 35908 Z= 0.254 Angle : 0.683 10.560 48900 Z= 0.354 Chirality : 0.049 0.401 5496 Planarity : 0.007 0.151 6264 Dihedral : 5.692 51.790 5136 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.31 % Allowed : 3.34 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.47 (0.13), residues: 4448 helix: 0.91 (0.27), residues: 408 sheet: -1.25 (0.13), residues: 1588 loop : -1.04 (0.12), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 89 HIS 0.029 0.002 HIS A 52 PHE 0.015 0.002 PHE D 414 TYR 0.019 0.002 TYR G 107 ARG 0.081 0.002 ARG G 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8024 Ramachandran restraints generated. 4012 Oldfield, 0 Emsley, 4012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8024 Ramachandran restraints generated. 4012 Oldfield, 0 Emsley, 4012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 2 GLU cc_start: 0.7627 (tp30) cc_final: 0.7321 (tp30) REVERT: D 117 ASP cc_start: 0.6963 (t0) cc_final: 0.6579 (t0) REVERT: D 136 VAL cc_start: 0.8208 (t) cc_final: 0.7675 (t) REVERT: D 270 ASN cc_start: 0.5794 (t0) cc_final: 0.5566 (t0) REVERT: D 278 ILE cc_start: 0.7582 (mp) cc_final: 0.7255 (pt) REVERT: D 339 LEU cc_start: 0.8298 (mm) cc_final: 0.8012 (mm) REVERT: D 362 GLN cc_start: 0.7604 (tp40) cc_final: 0.7030 (tp-100) REVERT: D 364 ASN cc_start: 0.7509 (p0) cc_final: 0.6033 (p0) outliers start: 3 outliers final: 0 residues processed: 120 average time/residue: 0.1933 time to fit residues: 29.5393 Evaluate side-chains 97 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.380 Evaluate side-chains 107 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 9 PHE cc_start: 0.6420 (t80) cc_final: 0.6038 (t80) REVERT: E 136 LYS cc_start: 0.7742 (pttp) cc_final: 0.7344 (ptpp) REVERT: E 152 LEU cc_start: 0.7492 (mm) cc_final: 0.7025 (mt) REVERT: E 251 ASP cc_start: 0.8289 (p0) cc_final: 0.7831 (p0) REVERT: E 335 ASN cc_start: 0.7884 (m-40) cc_final: 0.7543 (m-40) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2475 time to fit residues: 31.9494 Evaluate side-chains 96 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.366 Evaluate side-chains 64 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 114 ASN cc_start: 0.8625 (p0) cc_final: 0.7990 (t0) REVERT: L 144 TYR cc_start: 0.5355 (t80) cc_final: 0.4865 (t80) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.2841 time to fit residues: 20.5166 Evaluate side-chains 50 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 395 optimal weight: 0.0980 chunk 300 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 44 optimal weight: 0.0040 chunk 191 optimal weight: 0.4980 chunk 268 optimal weight: 0.9990 chunk 401 optimal weight: 0.0980 chunk 425 optimal weight: 6.9990 chunk 209 optimal weight: 4.9990 chunk 380 optimal weight: 0.0270 chunk 114 optimal weight: 0.9980 overall best weight: 0.1450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 HIS ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 HIS Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 177 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6261 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 35908 Z= 0.281 Angle : 0.689 15.855 48900 Z= 0.354 Chirality : 0.047 0.365 5496 Planarity : 0.008 0.148 6264 Dihedral : 5.629 51.276 5136 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.10 % Allowed : 1.67 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.49 (0.13), residues: 4448 helix: 0.98 (0.28), residues: 408 sheet: -1.26 (0.13), residues: 1596 loop : -1.08 (0.12), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 89 HIS 0.063 0.003 HIS D 52 PHE 0.016 0.002 PHE D 189 TYR 0.132 0.003 TYR D 137 ARG 0.047 0.002 ARG J 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8024 Ramachandran restraints generated. 4012 Oldfield, 0 Emsley, 4012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8024 Ramachandran restraints generated. 4012 Oldfield, 0 Emsley, 4012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 2 GLU cc_start: 0.7553 (tp30) cc_final: 0.7347 (tp30) REVERT: D 117 ASP cc_start: 0.7132 (t0) cc_final: 0.6816 (t0) REVERT: D 136 VAL cc_start: 0.8268 (t) cc_final: 0.7709 (t) REVERT: D 270 ASN cc_start: 0.5786 (t0) cc_final: 0.5507 (t0) REVERT: D 278 ILE cc_start: 0.7660 (mp) cc_final: 0.7443 (pt) REVERT: D 339 LEU cc_start: 0.8257 (mm) cc_final: 0.7971 (mm) REVERT: D 362 GLN cc_start: 0.7575 (tp40) cc_final: 0.7038 (tp-100) REVERT: D 364 ASN cc_start: 0.7531 (p0) cc_final: 0.6057 (p0) outliers start: 1 outliers final: 0 residues processed: 116 average time/residue: 0.1936 time to fit residues: 28.5342 Evaluate side-chains 105 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.375 Evaluate side-chains 104 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 9 PHE cc_start: 0.6468 (t80) cc_final: 0.6063 (t80) REVERT: E 65 THR cc_start: 0.6634 (p) cc_final: 0.6414 (p) REVERT: E 136 LYS cc_start: 0.7720 (pttp) cc_final: 0.7367 (ptpp) REVERT: E 251 ASP cc_start: 0.8285 (p0) cc_final: 0.7800 (p0) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2526 time to fit residues: 31.5445 Evaluate side-chains 92 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.384 Evaluate side-chains 61 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 114 ASN cc_start: 0.8620 (p0) cc_final: 0.7944 (t0) REVERT: L 144 TYR cc_start: 0.5367 (t80) cc_final: 0.4891 (t80) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2598 time to fit residues: 18.1346 Evaluate side-chains 50 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 354 optimal weight: 0.0270 chunk 241 optimal weight: 5.9990 chunk 6 optimal weight: 0.2980 chunk 316 optimal weight: 0.5980 chunk 175 optimal weight: 4.9990 chunk 362 optimal weight: 0.0470 chunk 293 optimal weight: 0.0370 chunk 0 optimal weight: 2.9990 chunk 217 optimal weight: 0.8980 chunk 381 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 177 HIS ** E 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6262 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 35908 Z= 0.260 Angle : 0.664 7.316 48900 Z= 0.349 Chirality : 0.048 0.363 5496 Planarity : 0.007 0.117 6264 Dihedral : 5.604 51.003 5136 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.56 (0.12), residues: 4448 helix: 0.85 (0.27), residues: 408 sheet: -1.25 (0.13), residues: 1592 loop : -1.15 (0.12), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP G 89 HIS 0.060 0.003 HIS D 52 PHE 0.023 0.002 PHE G 51 TYR 0.068 0.002 TYR J 137 ARG 0.007 0.001 ARG K 365 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8024 Ramachandran restraints generated. 4012 Oldfield, 0 Emsley, 4012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8024 Ramachandran restraints generated. 4012 Oldfield, 0 Emsley, 4012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 117 ASP cc_start: 0.7178 (t0) cc_final: 0.6837 (t0) REVERT: D 135 ILE cc_start: 0.6359 (pt) cc_final: 0.6029 (pt) REVERT: D 136 VAL cc_start: 0.8255 (t) cc_final: 0.7764 (t) REVERT: D 270 ASN cc_start: 0.5792 (t0) cc_final: 0.5500 (t0) REVERT: D 276 ILE cc_start: 0.5989 (mm) cc_final: 0.5769 (mm) REVERT: D 278 ILE cc_start: 0.7660 (mp) cc_final: 0.7447 (pt) REVERT: D 362 GLN cc_start: 0.7567 (tp40) cc_final: 0.7036 (tp-100) REVERT: D 364 ASN cc_start: 0.7498 (p0) cc_final: 0.5981 (p0) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1875 time to fit residues: 28.5271 Evaluate side-chains 101 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.373 Evaluate side-chains 103 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 9 PHE cc_start: 0.6475 (t80) cc_final: 0.6076 (t80) REVERT: E 136 LYS cc_start: 0.7698 (pttp) cc_final: 0.7366 (ptpp) REVERT: E 251 ASP cc_start: 0.8283 (p0) cc_final: 0.7801 (p0) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2161 time to fit residues: 27.5212 Evaluate side-chains 91 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.370 Evaluate side-chains 61 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 114 ASN cc_start: 0.8542 (p0) cc_final: 0.7869 (t0) REVERT: L 144 TYR cc_start: 0.5360 (t80) cc_final: 0.5033 (t80) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2739 time to fit residues: 18.9688 Evaluate side-chains 52 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 143 optimal weight: 0.3980 chunk 383 optimal weight: 0.0370 chunk 84 optimal weight: 0.0470 chunk 249 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 425 optimal weight: 9.9990 chunk 353 optimal weight: 0.7980 chunk 197 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 223 optimal weight: 3.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 HIS ** D 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 177 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6253 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 35908 Z= 0.260 Angle : 0.664 7.316 48900 Z= 0.349 Chirality : 0.048 0.363 5496 Planarity : 0.007 0.117 6264 Dihedral : 5.604 51.003 5136 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.10 % Allowed : 0.10 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.56 (0.12), residues: 4448 helix: 0.85 (0.27), residues: 408 sheet: -1.25 (0.13), residues: 1592 loop : -1.15 (0.12), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP G 89 HIS 0.060 0.003 HIS G 52 PHE 0.023 0.002 PHE G 51 TYR 0.068 0.002 TYR J 137 ARG 0.007 0.001 ARG K 365 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8024 Ramachandran restraints generated. 4012 Oldfield, 0 Emsley, 4012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8024 Ramachandran restraints generated. 4012 Oldfield, 0 Emsley, 4012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 135 ILE cc_start: 0.6345 (pt) cc_final: 0.6054 (pt) REVERT: D 136 VAL cc_start: 0.8252 (t) cc_final: 0.7808 (t) REVERT: D 270 ASN cc_start: 0.5857 (t0) cc_final: 0.5508 (t0) REVERT: D 278 ILE cc_start: 0.7677 (mp) cc_final: 0.7389 (pt) REVERT: D 339 LEU cc_start: 0.8255 (mm) cc_final: 0.7956 (mm) REVERT: D 362 GLN cc_start: 0.7587 (tp40) cc_final: 0.7041 (tp-100) REVERT: D 364 ASN cc_start: 0.7531 (p0) cc_final: 0.5992 (p0) outliers start: 1 outliers final: 1 residues processed: 112 average time/residue: 0.2114 time to fit residues: 29.5492 Evaluate side-chains 98 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.379 Evaluate side-chains 103 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 9 PHE cc_start: 0.6476 (t80) cc_final: 0.6080 (t80) REVERT: E 136 LYS cc_start: 0.7694 (pttp) cc_final: 0.7365 (ptpp) REVERT: E 251 ASP cc_start: 0.8282 (p0) cc_final: 0.7802 (p0) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2202 time to fit residues: 27.9409 Evaluate side-chains 91 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.371 Evaluate side-chains 59 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 114 ASN cc_start: 0.8514 (p0) cc_final: 0.7864 (t0) REVERT: L 144 TYR cc_start: 0.5464 (t80) cc_final: 0.4987 (t80) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2987 time to fit residues: 19.8024 Evaluate side-chains 50 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 798, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.8355 > 50: distance: 3 - 4: 14.831 distance: 3 - 8: 13.816 distance: 4 - 5: 20.261 distance: 4 - 7: 13.144 distance: 4 - 9: 9.049 distance: 5 - 6: 15.679 distance: 5 - 13: 19.393 distance: 7 - 10: 26.357 distance: 7 - 11: 33.113 distance: 7 - 12: 26.725 distance: 13 - 14: 22.415 distance: 13 - 25: 9.228 distance: 14 - 15: 13.832 distance: 14 - 17: 18.949 distance: 14 - 26: 23.575 distance: 15 - 16: 18.523 distance: 15 - 34: 12.665 distance: 17 - 18: 14.736 distance: 17 - 27: 14.444 distance: 17 - 28: 14.104 distance: 18 - 19: 16.509 distance: 18 - 20: 16.440 distance: 19 - 21: 9.391 distance: 19 - 29: 18.416 distance: 20 - 22: 9.901 distance: 20 - 30: 8.397 distance: 21 - 23: 37.322 distance: 21 - 31: 26.929 distance: 22 - 23: 40.403 distance: 22 - 32: 10.668 distance: 23 - 24: 48.544 distance: 24 - 33: 30.882 distance: 34 - 35: 23.950 distance: 34 - 41: 24.432 distance: 35 - 36: 8.835 distance: 35 - 38: 10.497 distance: 35 - 42: 10.093 distance: 36 - 37: 14.716 distance: 36 - 50: 18.571 distance: 38 - 39: 14.708 distance: 38 - 40: 35.254 distance: 38 - 43: 11.687 distance: 39 - 44: 12.640 distance: 39 - 45: 12.423 distance: 39 - 46: 17.169 distance: 40 - 47: 20.603 distance: 40 - 48: 17.226 distance: 40 - 49: 35.877 distance: 50 - 51: 14.666 distance: 50 - 59: 13.190 distance: 51 - 54: 20.935 distance: 51 - 60: 10.977 distance: 52 - 53: 23.073 distance: 52 - 65: 17.782 distance: 54 - 55: 13.991 distance: 54 - 61: 26.005 distance: 54 - 62: 25.160 distance: 55 - 56: 33.087 distance: 55 - 63: 24.415 distance: 55 - 64: 12.951 distance: 56 - 57: 14.853 distance: 56 - 58: 8.576 distance: 65 - 66: 8.717 distance: 65 - 76: 12.792 distance: 66 - 67: 5.838 distance: 66 - 69: 6.318 distance: 66 - 77: 11.977 distance: 67 - 68: 18.029 distance: 67 - 85: 14.565 distance: 69 - 70: 7.861 distance: 69 - 78: 22.352 distance: 69 - 79: 29.280 distance: 70 - 71: 6.208 distance: 70 - 72: 7.446 distance: 71 - 73: 12.828 distance: 71 - 80: 16.800 distance: 72 - 74: 3.817 distance: 72 - 81: 14.602 distance: 73 - 75: 6.152 distance: 73 - 82: 17.800 distance: 74 - 75: 6.207 distance: 74 - 83: 9.736 distance: 75 - 84: 5.014 distance: 85 - 86: 6.043 distance: 85 - 90: 18.059 distance: 86 - 87: 13.847 distance: 86 - 89: 19.567 distance: 86 - 91: 14.213 distance: 87 - 88: 29.569 distance: 87 - 95: 16.389 distance: 89 - 92: 13.879 distance: 89 - 93: 14.230 distance: 89 - 94: 17.055 distance: 95 - 96: 4.819 distance: 95 - 101: 11.896 distance: 96 - 97: 8.949 distance: 96 - 99: 17.433 distance: 96 - 102: 17.089 distance: 97 - 98: 8.981 distance: 97 - 109: 6.336 distance: 99 - 100: 16.428 distance: 99 - 103: 23.194 distance: 99 - 104: 20.675 distance: 100 - 101: 17.726 distance: 100 - 105: 10.575 distance: 100 - 106: 5.530 distance: 101 - 107: 15.524 distance: 101 - 108: 22.120 distance: 109 - 110: 4.316 distance: 109 - 117: 12.348 distance: 110 - 111: 7.303 distance: 110 - 113: 5.738 distance: 110 - 118: 3.415 distance: 111 - 112: 14.739 distance: 113 - 114: 3.676 distance: 113 - 119: 10.969 distance: 113 - 120: 11.262 distance: 114 - 115: 14.781 distance: 114 - 116: 8.249 distance: 121 - 127: 5.022 distance: 122 - 123: 4.951 distance: 122 - 125: 4.165 distance: 123 - 124: 16.243 distance: 125 - 126: 9.659 distance: 125 - 129: 5.438 distance: 125 - 130: 4.108