Starting phenix.real_space_refine on Tue Feb 13 14:27:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybu_33729/02_2024/7ybu_33729_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybu_33729/02_2024/7ybu_33729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybu_33729/02_2024/7ybu_33729.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybu_33729/02_2024/7ybu_33729.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybu_33729/02_2024/7ybu_33729_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ybu_33729/02_2024/7ybu_33729_neut_trim_updated.pdb" } resolution = 2.2 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= -0.000 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 312 5.16 5 C 34188 2.51 5 N 9528 2.21 5 O 10290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 60": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A GLU 271": "OE1" <-> "OE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A GLU 302": "OE1" <-> "OE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A GLU 362": "OE1" <-> "OE2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 548": "NH1" <-> "NH2" Residue "A GLU 720": "OE1" <-> "OE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B GLU 179": "OE1" <-> "OE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B GLU 203": "OE1" <-> "OE2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B GLU 237": "OE1" <-> "OE2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B GLU 287": "OE1" <-> "OE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B GLU 301": "OE1" <-> "OE2" Residue "B GLU 302": "OE1" <-> "OE2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "B GLU 349": "OE1" <-> "OE2" Residue "B GLU 357": "OE1" <-> "OE2" Residue "B GLU 362": "OE1" <-> "OE2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B GLU 422": "OE1" <-> "OE2" Residue "B GLU 461": "OE1" <-> "OE2" Residue "B GLU 487": "OE1" <-> "OE2" Residue "B PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 548": "NH1" <-> "NH2" Residue "B GLU 720": "OE1" <-> "OE2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C GLU 87": "OE1" <-> "OE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C GLU 290": "OE1" <-> "OE2" Residue "C GLU 301": "OE1" <-> "OE2" Residue "C GLU 326": "OE1" <-> "OE2" Residue "C GLU 331": "OE1" <-> "OE2" Residue "C GLU 404": "OE1" <-> "OE2" Residue "C GLU 421": "OE1" <-> "OE2" Residue "C GLU 470": "OE1" <-> "OE2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D GLU 129": "OE1" <-> "OE2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D GLU 151": "OE1" <-> "OE2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D GLU 203": "OE1" <-> "OE2" Residue "D GLU 204": "OE1" <-> "OE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D GLU 248": "OE1" <-> "OE2" Residue "D GLU 261": "OE1" <-> "OE2" Residue "D GLU 271": "OE1" <-> "OE2" Residue "D GLU 287": "OE1" <-> "OE2" Residue "D GLU 289": "OE1" <-> "OE2" Residue "D GLU 301": "OE1" <-> "OE2" Residue "D GLU 302": "OE1" <-> "OE2" Residue "D GLU 311": "OE1" <-> "OE2" Residue "D GLU 318": "OE1" <-> "OE2" Residue "D GLU 336": "OE1" <-> "OE2" Residue "D GLU 349": "OE1" <-> "OE2" Residue "D GLU 357": "OE1" <-> "OE2" Residue "D GLU 362": "OE1" <-> "OE2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "D GLU 403": "OE1" <-> "OE2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "D GLU 422": "OE1" <-> "OE2" Residue "D GLU 461": "OE1" <-> "OE2" Residue "D GLU 487": "OE1" <-> "OE2" Residue "D PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 548": "NH1" <-> "NH2" Residue "D GLU 720": "OE1" <-> "OE2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E GLU 87": "OE1" <-> "OE2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "E GLU 242": "OE1" <-> "OE2" Residue "E GLU 243": "OE1" <-> "OE2" Residue "E GLU 290": "OE1" <-> "OE2" Residue "E GLU 301": "OE1" <-> "OE2" Residue "E GLU 326": "OE1" <-> "OE2" Residue "E GLU 331": "OE1" <-> "OE2" Residue "E GLU 404": "OE1" <-> "OE2" Residue "E GLU 421": "OE1" <-> "OE2" Residue "E GLU 470": "OE1" <-> "OE2" Residue "F GLU 60": "OE1" <-> "OE2" Residue "F GLU 73": "OE1" <-> "OE2" Residue "F GLU 108": "OE1" <-> "OE2" Residue "F GLU 129": "OE1" <-> "OE2" Residue "F GLU 148": "OE1" <-> "OE2" Residue "F GLU 151": "OE1" <-> "OE2" Residue "F GLU 159": "OE1" <-> "OE2" Residue "F GLU 179": "OE1" <-> "OE2" Residue "F GLU 188": "OE1" <-> "OE2" Residue "F GLU 203": "OE1" <-> "OE2" Residue "F GLU 204": "OE1" <-> "OE2" Residue "F GLU 211": "OE1" <-> "OE2" Residue "F GLU 236": "OE1" <-> "OE2" Residue "F GLU 237": "OE1" <-> "OE2" Residue "F GLU 248": "OE1" <-> "OE2" Residue "F GLU 261": "OE1" <-> "OE2" Residue "F GLU 271": "OE1" <-> "OE2" Residue "F GLU 287": "OE1" <-> "OE2" Residue "F GLU 289": "OE1" <-> "OE2" Residue "F GLU 301": "OE1" <-> "OE2" Residue "F GLU 302": "OE1" <-> "OE2" Residue "F GLU 311": "OE1" <-> "OE2" Residue "F GLU 318": "OE1" <-> "OE2" Residue "F GLU 336": "OE1" <-> "OE2" Residue "F GLU 349": "OE1" <-> "OE2" Residue "F GLU 357": "OE1" <-> "OE2" Residue "F GLU 362": "OE1" <-> "OE2" Residue "F GLU 372": "OE1" <-> "OE2" Residue "F GLU 397": "OE1" <-> "OE2" Residue "F GLU 403": "OE1" <-> "OE2" Residue "F ARG 416": "NH1" <-> "NH2" Residue "F GLU 422": "OE1" <-> "OE2" Residue "F GLU 461": "OE1" <-> "OE2" Residue "F GLU 487": "OE1" <-> "OE2" Residue "F PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 548": "NH1" <-> "NH2" Residue "F GLU 720": "OE1" <-> "OE2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G GLU 68": "OE1" <-> "OE2" Residue "G GLU 81": "OE1" <-> "OE2" Residue "G GLU 87": "OE1" <-> "OE2" Residue "G GLU 168": "OE1" <-> "OE2" Residue "G GLU 242": "OE1" <-> "OE2" Residue "G GLU 243": "OE1" <-> "OE2" Residue "G GLU 290": "OE1" <-> "OE2" Residue "G GLU 301": "OE1" <-> "OE2" Residue "G GLU 326": "OE1" <-> "OE2" Residue "G GLU 331": "OE1" <-> "OE2" Residue "G GLU 404": "OE1" <-> "OE2" Residue "G GLU 421": "OE1" <-> "OE2" Residue "G GLU 470": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 73": "OE1" <-> "OE2" Residue "H GLU 108": "OE1" <-> "OE2" Residue "H GLU 129": "OE1" <-> "OE2" Residue "H GLU 148": "OE1" <-> "OE2" Residue "H GLU 151": "OE1" <-> "OE2" Residue "H GLU 159": "OE1" <-> "OE2" Residue "H GLU 179": "OE1" <-> "OE2" Residue "H GLU 188": "OE1" <-> "OE2" Residue "H GLU 203": "OE1" <-> "OE2" Residue "H GLU 204": "OE1" <-> "OE2" Residue "H GLU 211": "OE1" <-> "OE2" Residue "H GLU 236": "OE1" <-> "OE2" Residue "H GLU 237": "OE1" <-> "OE2" Residue "H GLU 248": "OE1" <-> "OE2" Residue "H GLU 261": "OE1" <-> "OE2" Residue "H GLU 271": "OE1" <-> "OE2" Residue "H GLU 287": "OE1" <-> "OE2" Residue "H GLU 289": "OE1" <-> "OE2" Residue "H GLU 301": "OE1" <-> "OE2" Residue "H GLU 302": "OE1" <-> "OE2" Residue "H GLU 311": "OE1" <-> "OE2" Residue "H GLU 318": "OE1" <-> "OE2" Residue "H GLU 336": "OE1" <-> "OE2" Residue "H GLU 349": "OE1" <-> "OE2" Residue "H GLU 357": "OE1" <-> "OE2" Residue "H GLU 362": "OE1" <-> "OE2" Residue "H GLU 372": "OE1" <-> "OE2" Residue "H GLU 397": "OE1" <-> "OE2" Residue "H GLU 403": "OE1" <-> "OE2" Residue "H ARG 416": "NH1" <-> "NH2" Residue "H GLU 422": "OE1" <-> "OE2" Residue "H GLU 461": "OE1" <-> "OE2" Residue "H GLU 487": "OE1" <-> "OE2" Residue "H PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 548": "NH1" <-> "NH2" Residue "H GLU 720": "OE1" <-> "OE2" Residue "I ARG 53": "NH1" <-> "NH2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "I GLU 87": "OE1" <-> "OE2" Residue "I GLU 168": "OE1" <-> "OE2" Residue "I GLU 242": "OE1" <-> "OE2" Residue "I GLU 243": "OE1" <-> "OE2" Residue "I PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 290": "OE1" <-> "OE2" Residue "I GLU 301": "OE1" <-> "OE2" Residue "I GLU 326": "OE1" <-> "OE2" Residue "I GLU 331": "OE1" <-> "OE2" Residue "I GLU 404": "OE1" <-> "OE2" Residue "I GLU 421": "OE1" <-> "OE2" Residue "I GLU 470": "OE1" <-> "OE2" Residue "J GLU 60": "OE1" <-> "OE2" Residue "J GLU 73": "OE1" <-> "OE2" Residue "J GLU 108": "OE1" <-> "OE2" Residue "J GLU 129": "OE1" <-> "OE2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J GLU 151": "OE1" <-> "OE2" Residue "J GLU 159": "OE1" <-> "OE2" Residue "J GLU 179": "OE1" <-> "OE2" Residue "J GLU 188": "OE1" <-> "OE2" Residue "J GLU 203": "OE1" <-> "OE2" Residue "J GLU 204": "OE1" <-> "OE2" Residue "J GLU 211": "OE1" <-> "OE2" Residue "J GLU 236": "OE1" <-> "OE2" Residue "J GLU 237": "OE1" <-> "OE2" Residue "J GLU 248": "OE1" <-> "OE2" Residue "J GLU 261": "OE1" <-> "OE2" Residue "J GLU 271": "OE1" <-> "OE2" Residue "J GLU 287": "OE1" <-> "OE2" Residue "J GLU 289": "OE1" <-> "OE2" Residue "J GLU 301": "OE1" <-> "OE2" Residue "J GLU 302": "OE1" <-> "OE2" Residue "J GLU 311": "OE1" <-> "OE2" Residue "J GLU 318": "OE1" <-> "OE2" Residue "J GLU 336": "OE1" <-> "OE2" Residue "J GLU 349": "OE1" <-> "OE2" Residue "J GLU 357": "OE1" <-> "OE2" Residue "J GLU 362": "OE1" <-> "OE2" Residue "J GLU 372": "OE1" <-> "OE2" Residue "J GLU 397": "OE1" <-> "OE2" Residue "J GLU 403": "OE1" <-> "OE2" Residue "J ARG 416": "NH1" <-> "NH2" Residue "J GLU 422": "OE1" <-> "OE2" Residue "J ASP 440": "OD1" <-> "OD2" Residue "J ASP 458": "OD1" <-> "OD2" Residue "J GLU 461": "OE1" <-> "OE2" Residue "J GLU 487": "OE1" <-> "OE2" Residue "J PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 548": "NH1" <-> "NH2" Residue "J GLU 720": "OE1" <-> "OE2" Residue "K ARG 53": "NH1" <-> "NH2" Residue "K GLU 68": "OE1" <-> "OE2" Residue "K GLU 81": "OE1" <-> "OE2" Residue "K GLU 87": "OE1" <-> "OE2" Residue "K GLU 168": "OE1" <-> "OE2" Residue "K GLU 242": "OE1" <-> "OE2" Residue "K GLU 243": "OE1" <-> "OE2" Residue "K GLU 290": "OE1" <-> "OE2" Residue "K GLU 301": "OE1" <-> "OE2" Residue "K GLU 326": "OE1" <-> "OE2" Residue "K GLU 331": "OE1" <-> "OE2" Residue "K GLU 404": "OE1" <-> "OE2" Residue "K GLU 421": "OE1" <-> "OE2" Residue "K GLU 470": "OE1" <-> "OE2" Residue "P ARG 53": "NH1" <-> "NH2" Residue "P GLU 68": "OE1" <-> "OE2" Residue "P GLU 81": "OE1" <-> "OE2" Residue "P GLU 87": "OE1" <-> "OE2" Residue "P GLU 168": "OE1" <-> "OE2" Residue "P GLU 242": "OE1" <-> "OE2" Residue "P GLU 243": "OE1" <-> "OE2" Residue "P GLU 290": "OE1" <-> "OE2" Residue "P GLU 301": "OE1" <-> "OE2" Residue "P GLU 326": "OE1" <-> "OE2" Residue "P GLU 331": "OE1" <-> "OE2" Residue "P GLU 404": "OE1" <-> "OE2" Residue "P GLU 421": "OE1" <-> "OE2" Residue "P GLU 470": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 54318 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5164 Classifications: {'peptide': 670} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 646} Chain: "B" Number of atoms: 5164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5164 Classifications: {'peptide': 670} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 646} Chain: "C" Number of atoms: 3874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3874 Classifications: {'peptide': 507} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 481} Chain: "D" Number of atoms: 5164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5164 Classifications: {'peptide': 670} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 646} Chain: "E" Number of atoms: 3874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3874 Classifications: {'peptide': 507} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 481} Chain: "F" Number of atoms: 5164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5164 Classifications: {'peptide': 670} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 646} Chain: "G" Number of atoms: 3874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3874 Classifications: {'peptide': 507} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 481} Chain: "H" Number of atoms: 5164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5164 Classifications: {'peptide': 670} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 646} Chain: "I" Number of atoms: 3874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3874 Classifications: {'peptide': 507} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 481} Chain: "J" Number of atoms: 5164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5164 Classifications: {'peptide': 670} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 646} Chain: "K" Number of atoms: 3874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3874 Classifications: {'peptide': 507} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 481} Chain: "P" Number of atoms: 3874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3874 Classifications: {'peptide': 507} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 481} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.52, per 1000 atoms: 0.38 Number of scatterers: 54318 At special positions: 0 Unit cell: (191.602, 179.695, 189.437, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 312 16.00 O 10290 8.00 N 9528 7.00 C 34188 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.45 Conformation dependent library (CDL) restraints added in 7.3 seconds 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13008 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 264 helices and 78 sheets defined 35.5% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.86 Creating SS restraints... Processing helix chain 'A' and resid 73 through 85 Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 150 through 158 Processing helix chain 'A' and resid 168 through 175 Processing helix chain 'A' and resid 177 through 186 removed outlier: 3.646A pdb=" N LEU A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 212 Processing helix chain 'A' and resid 235 through 253 Processing helix chain 'A' and resid 310 through 326 Processing helix chain 'A' and resid 356 through 365 Proline residue: A 359 - end of helix removed outlier: 3.663A pdb=" N THR A 365 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 459 through 471 Processing helix chain 'A' and resid 481 through 490 removed outlier: 3.638A pdb=" N ARG A 486 " --> pdb=" O ALA A 483 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 489 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 503 through 507 Processing helix chain 'A' and resid 519 through 541 removed outlier: 3.829A pdb=" N GLN A 541 " --> pdb=" O GLN A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 649 removed outlier: 3.759A pdb=" N LYS A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N PHE A 649 " --> pdb=" O GLU A 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 85 Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 124 through 134 Processing helix chain 'B' and resid 150 through 158 Processing helix chain 'B' and resid 168 through 175 Processing helix chain 'B' and resid 177 through 186 removed outlier: 3.645A pdb=" N LEU B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 212 Processing helix chain 'B' and resid 235 through 253 Processing helix chain 'B' and resid 310 through 326 Processing helix chain 'B' and resid 356 through 365 Proline residue: B 359 - end of helix removed outlier: 3.663A pdb=" N THR B 365 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 378 Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'B' and resid 459 through 471 Processing helix chain 'B' and resid 481 through 490 removed outlier: 3.637A pdb=" N ARG B 486 " --> pdb=" O ALA B 483 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 489 " --> pdb=" O ARG B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 496 Processing helix chain 'B' and resid 503 through 507 Processing helix chain 'B' and resid 519 through 541 removed outlier: 3.829A pdb=" N GLN B 541 " --> pdb=" O GLN B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 649 removed outlier: 3.759A pdb=" N LYS B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N PHE B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 48 Processing helix chain 'C' and resid 52 through 60 Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 135 through 151 Processing helix chain 'C' and resid 166 through 186 removed outlier: 6.782A pdb=" N VAL C 170 " --> pdb=" O GLN C 167 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU C 181 " --> pdb=" O ASP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 210 removed outlier: 3.569A pdb=" N SER C 207 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Proline residue: C 208 - end of helix Processing helix chain 'C' and resid 228 through 235 Processing helix chain 'C' and resid 241 through 245 Processing helix chain 'C' and resid 247 through 252 Processing helix chain 'C' and resid 264 through 277 removed outlier: 4.011A pdb=" N TYR C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 304 removed outlier: 4.155A pdb=" N THR C 304 " --> pdb=" O GLU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 323 Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 368 through 383 Processing helix chain 'C' and resid 401 through 405 Processing helix chain 'C' and resid 408 through 421 removed outlier: 3.544A pdb=" N LEU C 415 " --> pdb=" O HIS C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 441 removed outlier: 3.710A pdb=" N ASP C 440 " --> pdb=" O GLY C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 447 No H-bonds generated for 'chain 'C' and resid 445 through 447' Processing helix chain 'C' and resid 465 through 473 Processing helix chain 'C' and resid 479 through 490 Processing helix chain 'C' and resid 494 through 499 removed outlier: 3.772A pdb=" N ARG C 499 " --> pdb=" O PRO C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 524 removed outlier: 4.884A pdb=" N ARG C 512 " --> pdb=" O SER C 509 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU C 522 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA C 523 " --> pdb=" O ASP C 520 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER C 524 " --> pdb=" O VAL C 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 85 Processing helix chain 'D' and resid 101 through 105 Processing helix chain 'D' and resid 117 through 119 No H-bonds generated for 'chain 'D' and resid 117 through 119' Processing helix chain 'D' and resid 124 through 134 Processing helix chain 'D' and resid 150 through 158 Processing helix chain 'D' and resid 168 through 175 Processing helix chain 'D' and resid 177 through 186 removed outlier: 3.646A pdb=" N LEU D 182 " --> pdb=" O ILE D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 212 Processing helix chain 'D' and resid 235 through 253 Processing helix chain 'D' and resid 310 through 326 Processing helix chain 'D' and resid 356 through 365 Proline residue: D 359 - end of helix removed outlier: 3.663A pdb=" N THR D 365 " --> pdb=" O GLU D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 378 Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 459 through 471 Processing helix chain 'D' and resid 481 through 490 removed outlier: 3.638A pdb=" N ARG D 486 " --> pdb=" O ALA D 483 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE D 489 " --> pdb=" O ARG D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 496 Processing helix chain 'D' and resid 503 through 507 Processing helix chain 'D' and resid 519 through 541 removed outlier: 3.828A pdb=" N GLN D 541 " --> pdb=" O GLN D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 649 removed outlier: 3.759A pdb=" N LYS D 648 " --> pdb=" O ALA D 644 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N PHE D 649 " --> pdb=" O GLU D 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 48 Processing helix chain 'E' and resid 52 through 60 Processing helix chain 'E' and resid 66 through 73 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 129 through 131 No H-bonds generated for 'chain 'E' and resid 129 through 131' Processing helix chain 'E' and resid 135 through 151 Processing helix chain 'E' and resid 166 through 186 removed outlier: 6.782A pdb=" N VAL E 170 " --> pdb=" O GLN E 167 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU E 181 " --> pdb=" O ASP E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 210 removed outlier: 3.569A pdb=" N SER E 207 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Proline residue: E 208 - end of helix Processing helix chain 'E' and resid 228 through 235 Processing helix chain 'E' and resid 241 through 245 Processing helix chain 'E' and resid 247 through 252 Processing helix chain 'E' and resid 264 through 277 removed outlier: 4.011A pdb=" N TYR E 277 " --> pdb=" O ASP E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 304 removed outlier: 4.155A pdb=" N THR E 304 " --> pdb=" O GLU E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 323 Processing helix chain 'E' and resid 325 through 327 No H-bonds generated for 'chain 'E' and resid 325 through 327' Processing helix chain 'E' and resid 362 through 364 No H-bonds generated for 'chain 'E' and resid 362 through 364' Processing helix chain 'E' and resid 368 through 383 Processing helix chain 'E' and resid 401 through 405 Processing helix chain 'E' and resid 408 through 421 removed outlier: 3.543A pdb=" N LEU E 415 " --> pdb=" O HIS E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 441 removed outlier: 3.709A pdb=" N ASP E 440 " --> pdb=" O GLY E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 447 No H-bonds generated for 'chain 'E' and resid 445 through 447' Processing helix chain 'E' and resid 465 through 473 Processing helix chain 'E' and resid 479 through 490 Processing helix chain 'E' and resid 494 through 499 removed outlier: 3.772A pdb=" N ARG E 499 " --> pdb=" O PRO E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 524 removed outlier: 4.884A pdb=" N ARG E 512 " --> pdb=" O SER E 509 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU E 522 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA E 523 " --> pdb=" O ASP E 520 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER E 524 " --> pdb=" O VAL E 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 85 Processing helix chain 'F' and resid 101 through 105 Processing helix chain 'F' and resid 117 through 119 No H-bonds generated for 'chain 'F' and resid 117 through 119' Processing helix chain 'F' and resid 124 through 134 Processing helix chain 'F' and resid 150 through 158 Processing helix chain 'F' and resid 168 through 175 Processing helix chain 'F' and resid 177 through 186 removed outlier: 3.646A pdb=" N LEU F 182 " --> pdb=" O ILE F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 212 Processing helix chain 'F' and resid 235 through 253 Processing helix chain 'F' and resid 310 through 326 Processing helix chain 'F' and resid 356 through 365 Proline residue: F 359 - end of helix removed outlier: 3.662A pdb=" N THR F 365 " --> pdb=" O GLU F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 378 Processing helix chain 'F' and resid 386 through 388 No H-bonds generated for 'chain 'F' and resid 386 through 388' Processing helix chain 'F' and resid 459 through 471 Processing helix chain 'F' and resid 481 through 490 removed outlier: 3.639A pdb=" N ARG F 486 " --> pdb=" O ALA F 483 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE F 489 " --> pdb=" O ARG F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 496 Processing helix chain 'F' and resid 503 through 507 Processing helix chain 'F' and resid 519 through 541 removed outlier: 3.829A pdb=" N GLN F 541 " --> pdb=" O GLN F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 649 removed outlier: 3.759A pdb=" N LYS F 648 " --> pdb=" O ALA F 644 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N PHE F 649 " --> pdb=" O GLU F 645 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 48 Processing helix chain 'G' and resid 52 through 60 Processing helix chain 'G' and resid 66 through 73 Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 129 through 131 No H-bonds generated for 'chain 'G' and resid 129 through 131' Processing helix chain 'G' and resid 135 through 151 Processing helix chain 'G' and resid 166 through 186 removed outlier: 6.781A pdb=" N VAL G 170 " --> pdb=" O GLN G 167 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU G 181 " --> pdb=" O ASP G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 210 removed outlier: 3.569A pdb=" N SER G 207 " --> pdb=" O ALA G 204 " (cutoff:3.500A) Proline residue: G 208 - end of helix Processing helix chain 'G' and resid 228 through 235 Processing helix chain 'G' and resid 241 through 245 Processing helix chain 'G' and resid 247 through 252 Processing helix chain 'G' and resid 264 through 277 removed outlier: 4.011A pdb=" N TYR G 277 " --> pdb=" O ASP G 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 304 removed outlier: 4.155A pdb=" N THR G 304 " --> pdb=" O GLU G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 323 Processing helix chain 'G' and resid 325 through 327 No H-bonds generated for 'chain 'G' and resid 325 through 327' Processing helix chain 'G' and resid 362 through 364 No H-bonds generated for 'chain 'G' and resid 362 through 364' Processing helix chain 'G' and resid 368 through 383 Processing helix chain 'G' and resid 401 through 405 Processing helix chain 'G' and resid 408 through 421 removed outlier: 3.544A pdb=" N LEU G 415 " --> pdb=" O HIS G 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 436 through 441 removed outlier: 3.709A pdb=" N ASP G 440 " --> pdb=" O GLY G 436 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 447 No H-bonds generated for 'chain 'G' and resid 445 through 447' Processing helix chain 'G' and resid 465 through 473 Processing helix chain 'G' and resid 479 through 490 Processing helix chain 'G' and resid 494 through 499 removed outlier: 3.772A pdb=" N ARG G 499 " --> pdb=" O PRO G 495 " (cutoff:3.500A) Processing helix chain 'G' and resid 508 through 524 removed outlier: 4.885A pdb=" N ARG G 512 " --> pdb=" O SER G 509 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU G 522 " --> pdb=" O LEU G 519 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA G 523 " --> pdb=" O ASP G 520 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER G 524 " --> pdb=" O VAL G 521 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 85 Processing helix chain 'H' and resid 101 through 105 Processing helix chain 'H' and resid 117 through 119 No H-bonds generated for 'chain 'H' and resid 117 through 119' Processing helix chain 'H' and resid 124 through 134 Processing helix chain 'H' and resid 150 through 158 Processing helix chain 'H' and resid 168 through 175 Processing helix chain 'H' and resid 177 through 186 removed outlier: 3.646A pdb=" N LEU H 182 " --> pdb=" O ILE H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 212 Processing helix chain 'H' and resid 235 through 253 Processing helix chain 'H' and resid 310 through 326 Processing helix chain 'H' and resid 356 through 365 Proline residue: H 359 - end of helix removed outlier: 3.663A pdb=" N THR H 365 " --> pdb=" O GLU H 362 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 378 Processing helix chain 'H' and resid 386 through 388 No H-bonds generated for 'chain 'H' and resid 386 through 388' Processing helix chain 'H' and resid 459 through 471 Processing helix chain 'H' and resid 481 through 490 removed outlier: 3.638A pdb=" N ARG H 486 " --> pdb=" O ALA H 483 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE H 489 " --> pdb=" O ARG H 486 " (cutoff:3.500A) Processing helix chain 'H' and resid 492 through 496 Processing helix chain 'H' and resid 503 through 507 Processing helix chain 'H' and resid 519 through 541 removed outlier: 3.829A pdb=" N GLN H 541 " --> pdb=" O GLN H 537 " (cutoff:3.500A) Processing helix chain 'H' and resid 641 through 649 removed outlier: 3.760A pdb=" N LYS H 648 " --> pdb=" O ALA H 644 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N PHE H 649 " --> pdb=" O GLU H 645 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 48 Processing helix chain 'I' and resid 52 through 60 Processing helix chain 'I' and resid 66 through 73 Processing helix chain 'I' and resid 98 through 100 No H-bonds generated for 'chain 'I' and resid 98 through 100' Processing helix chain 'I' and resid 129 through 131 No H-bonds generated for 'chain 'I' and resid 129 through 131' Processing helix chain 'I' and resid 135 through 151 Processing helix chain 'I' and resid 166 through 186 removed outlier: 6.781A pdb=" N VAL I 170 " --> pdb=" O GLN I 167 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU I 181 " --> pdb=" O ASP I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 210 removed outlier: 3.569A pdb=" N SER I 207 " --> pdb=" O ALA I 204 " (cutoff:3.500A) Proline residue: I 208 - end of helix Processing helix chain 'I' and resid 228 through 235 Processing helix chain 'I' and resid 241 through 245 Processing helix chain 'I' and resid 247 through 252 Processing helix chain 'I' and resid 264 through 277 removed outlier: 4.012A pdb=" N TYR I 277 " --> pdb=" O ASP I 273 " (cutoff:3.500A) Processing helix chain 'I' and resid 300 through 304 removed outlier: 4.156A pdb=" N THR I 304 " --> pdb=" O GLU I 301 " (cutoff:3.500A) Processing helix chain 'I' and resid 316 through 323 Processing helix chain 'I' and resid 325 through 327 No H-bonds generated for 'chain 'I' and resid 325 through 327' Processing helix chain 'I' and resid 362 through 364 No H-bonds generated for 'chain 'I' and resid 362 through 364' Processing helix chain 'I' and resid 368 through 383 Processing helix chain 'I' and resid 401 through 405 Processing helix chain 'I' and resid 408 through 421 removed outlier: 3.544A pdb=" N LEU I 415 " --> pdb=" O HIS I 411 " (cutoff:3.500A) Processing helix chain 'I' and resid 436 through 441 removed outlier: 3.709A pdb=" N ASP I 440 " --> pdb=" O GLY I 436 " (cutoff:3.500A) Processing helix chain 'I' and resid 445 through 447 No H-bonds generated for 'chain 'I' and resid 445 through 447' Processing helix chain 'I' and resid 465 through 473 Processing helix chain 'I' and resid 479 through 490 Processing helix chain 'I' and resid 494 through 499 removed outlier: 3.772A pdb=" N ARG I 499 " --> pdb=" O PRO I 495 " (cutoff:3.500A) Processing helix chain 'I' and resid 508 through 524 removed outlier: 4.884A pdb=" N ARG I 512 " --> pdb=" O SER I 509 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU I 522 " --> pdb=" O LEU I 519 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA I 523 " --> pdb=" O ASP I 520 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER I 524 " --> pdb=" O VAL I 521 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 85 Processing helix chain 'J' and resid 101 through 105 Processing helix chain 'J' and resid 117 through 119 No H-bonds generated for 'chain 'J' and resid 117 through 119' Processing helix chain 'J' and resid 124 through 134 Processing helix chain 'J' and resid 150 through 158 Processing helix chain 'J' and resid 168 through 175 Processing helix chain 'J' and resid 177 through 186 removed outlier: 3.646A pdb=" N LEU J 182 " --> pdb=" O ILE J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 212 Processing helix chain 'J' and resid 235 through 253 Processing helix chain 'J' and resid 310 through 326 Processing helix chain 'J' and resid 356 through 365 Proline residue: J 359 - end of helix removed outlier: 3.662A pdb=" N THR J 365 " --> pdb=" O GLU J 362 " (cutoff:3.500A) Processing helix chain 'J' and resid 369 through 378 Processing helix chain 'J' and resid 386 through 388 No H-bonds generated for 'chain 'J' and resid 386 through 388' Processing helix chain 'J' and resid 459 through 471 Processing helix chain 'J' and resid 481 through 490 removed outlier: 3.637A pdb=" N ARG J 486 " --> pdb=" O ALA J 483 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE J 489 " --> pdb=" O ARG J 486 " (cutoff:3.500A) Processing helix chain 'J' and resid 492 through 496 Processing helix chain 'J' and resid 503 through 507 Processing helix chain 'J' and resid 519 through 541 removed outlier: 3.829A pdb=" N GLN J 541 " --> pdb=" O GLN J 537 " (cutoff:3.500A) Processing helix chain 'J' and resid 641 through 649 removed outlier: 3.758A pdb=" N LYS J 648 " --> pdb=" O ALA J 644 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N PHE J 649 " --> pdb=" O GLU J 645 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 48 Processing helix chain 'K' and resid 52 through 60 Processing helix chain 'K' and resid 66 through 73 Processing helix chain 'K' and resid 98 through 100 No H-bonds generated for 'chain 'K' and resid 98 through 100' Processing helix chain 'K' and resid 129 through 131 No H-bonds generated for 'chain 'K' and resid 129 through 131' Processing helix chain 'K' and resid 135 through 151 Processing helix chain 'K' and resid 166 through 186 removed outlier: 6.781A pdb=" N VAL K 170 " --> pdb=" O GLN K 167 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU K 181 " --> pdb=" O ASP K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 210 removed outlier: 3.568A pdb=" N SER K 207 " --> pdb=" O ALA K 204 " (cutoff:3.500A) Proline residue: K 208 - end of helix Processing helix chain 'K' and resid 228 through 235 Processing helix chain 'K' and resid 241 through 245 Processing helix chain 'K' and resid 247 through 252 Processing helix chain 'K' and resid 264 through 277 removed outlier: 4.011A pdb=" N TYR K 277 " --> pdb=" O ASP K 273 " (cutoff:3.500A) Processing helix chain 'K' and resid 300 through 304 removed outlier: 4.156A pdb=" N THR K 304 " --> pdb=" O GLU K 301 " (cutoff:3.500A) Processing helix chain 'K' and resid 316 through 323 Processing helix chain 'K' and resid 325 through 327 No H-bonds generated for 'chain 'K' and resid 325 through 327' Processing helix chain 'K' and resid 362 through 364 No H-bonds generated for 'chain 'K' and resid 362 through 364' Processing helix chain 'K' and resid 368 through 383 Processing helix chain 'K' and resid 401 through 405 Processing helix chain 'K' and resid 408 through 421 removed outlier: 3.543A pdb=" N LEU K 415 " --> pdb=" O HIS K 411 " (cutoff:3.500A) Processing helix chain 'K' and resid 436 through 441 removed outlier: 3.709A pdb=" N ASP K 440 " --> pdb=" O GLY K 436 " (cutoff:3.500A) Processing helix chain 'K' and resid 445 through 447 No H-bonds generated for 'chain 'K' and resid 445 through 447' Processing helix chain 'K' and resid 465 through 473 Processing helix chain 'K' and resid 479 through 490 Processing helix chain 'K' and resid 494 through 499 removed outlier: 3.771A pdb=" N ARG K 499 " --> pdb=" O PRO K 495 " (cutoff:3.500A) Processing helix chain 'K' and resid 508 through 524 removed outlier: 4.885A pdb=" N ARG K 512 " --> pdb=" O SER K 509 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU K 522 " --> pdb=" O LEU K 519 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA K 523 " --> pdb=" O ASP K 520 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER K 524 " --> pdb=" O VAL K 521 " (cutoff:3.500A) Processing helix chain 'P' and resid 35 through 48 Processing helix chain 'P' and resid 52 through 60 Processing helix chain 'P' and resid 66 through 73 Processing helix chain 'P' and resid 98 through 100 No H-bonds generated for 'chain 'P' and resid 98 through 100' Processing helix chain 'P' and resid 129 through 131 No H-bonds generated for 'chain 'P' and resid 129 through 131' Processing helix chain 'P' and resid 135 through 151 Processing helix chain 'P' and resid 166 through 186 removed outlier: 6.781A pdb=" N VAL P 170 " --> pdb=" O GLN P 167 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU P 181 " --> pdb=" O ASP P 178 " (cutoff:3.500A) Processing helix chain 'P' and resid 202 through 210 removed outlier: 3.569A pdb=" N SER P 207 " --> pdb=" O ALA P 204 " (cutoff:3.500A) Proline residue: P 208 - end of helix Processing helix chain 'P' and resid 228 through 235 Processing helix chain 'P' and resid 241 through 245 Processing helix chain 'P' and resid 247 through 252 Processing helix chain 'P' and resid 264 through 277 removed outlier: 4.012A pdb=" N TYR P 277 " --> pdb=" O ASP P 273 " (cutoff:3.500A) Processing helix chain 'P' and resid 300 through 304 removed outlier: 4.156A pdb=" N THR P 304 " --> pdb=" O GLU P 301 " (cutoff:3.500A) Processing helix chain 'P' and resid 316 through 323 Processing helix chain 'P' and resid 325 through 327 No H-bonds generated for 'chain 'P' and resid 325 through 327' Processing helix chain 'P' and resid 362 through 364 No H-bonds generated for 'chain 'P' and resid 362 through 364' Processing helix chain 'P' and resid 368 through 383 Processing helix chain 'P' and resid 401 through 405 Processing helix chain 'P' and resid 408 through 421 removed outlier: 3.544A pdb=" N LEU P 415 " --> pdb=" O HIS P 411 " (cutoff:3.500A) Processing helix chain 'P' and resid 436 through 441 Processing helix chain 'P' and resid 445 through 447 No H-bonds generated for 'chain 'P' and resid 445 through 447' Processing helix chain 'P' and resid 465 through 473 Processing helix chain 'P' and resid 479 through 490 Processing helix chain 'P' and resid 494 through 499 removed outlier: 3.772A pdb=" N ARG P 499 " --> pdb=" O PRO P 495 " (cutoff:3.500A) Processing helix chain 'P' and resid 508 through 524 removed outlier: 4.885A pdb=" N ARG P 512 " --> pdb=" O SER P 509 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU P 522 " --> pdb=" O LEU P 519 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA P 523 " --> pdb=" O ASP P 520 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER P 524 " --> pdb=" O VAL P 521 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 162 through 164 removed outlier: 3.634A pdb=" N ALA A 138 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS A 88 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL A 68 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A 90 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU A 108 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N HIS A 93 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 110 " --> pdb=" O HIS A 93 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 229 through 232 Processing sheet with id= C, first strand: chain 'A' and resid 287 through 289 removed outlier: 3.635A pdb=" N GLU A 349 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU A 338 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE A 347 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 274 through 276 Processing sheet with id= E, first strand: chain 'A' and resid 292 through 294 removed outlier: 4.069A pdb=" N ILE A 292 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 300 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ARG A 294 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LYS A 298 " --> pdb=" O ARG A 294 " (cutoff:3.500A) removed outlier: 13.757A pdb=" N GLN A 297 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N TYR A 401 " --> pdb=" O GLN A 297 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL A 299 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 452 " --> pdb=" O CYS A 398 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 450 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 419 through 421 removed outlier: 3.586A pdb=" N GLN A 419 " --> pdb=" O ARG A 476 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 602 through 607 removed outlier: 6.519A pdb=" N SER A 626 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARG A 619 " --> pdb=" O ASN A 624 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN A 624 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 661 through 664 removed outlier: 5.652A pdb=" N SER A 664 " --> pdb=" O LEU A 723 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU A 723 " --> pdb=" O SER A 664 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 709 " --> pdb=" O GLU A 726 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 669 through 673 removed outlier: 6.851A pdb=" N VAL A 689 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL A 673 " --> pdb=" O ILE A 687 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE A 687 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N MET A 699 " --> pdb=" O ILE A 687 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL A 689 " --> pdb=" O ASN A 697 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN A 697 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 162 through 164 removed outlier: 3.635A pdb=" N ALA B 138 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS B 88 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL B 68 " --> pdb=" O LYS B 88 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 90 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU B 108 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N HIS B 93 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL B 110 " --> pdb=" O HIS B 93 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 229 through 232 Processing sheet with id= L, first strand: chain 'B' and resid 287 through 289 removed outlier: 3.635A pdb=" N GLU B 349 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU B 338 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE B 347 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 274 through 276 Processing sheet with id= N, first strand: chain 'B' and resid 292 through 294 removed outlier: 4.068A pdb=" N ILE B 292 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 300 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ARG B 294 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LYS B 298 " --> pdb=" O ARG B 294 " (cutoff:3.500A) removed outlier: 13.757A pdb=" N GLN B 297 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 10.611A pdb=" N TYR B 401 " --> pdb=" O GLN B 297 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B 299 " --> pdb=" O ARG B 399 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 452 " --> pdb=" O CYS B 398 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER B 450 " --> pdb=" O VAL B 400 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 419 through 421 removed outlier: 3.587A pdb=" N GLN B 419 " --> pdb=" O ARG B 476 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 602 through 607 removed outlier: 6.519A pdb=" N SER B 626 " --> pdb=" O LEU B 617 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG B 619 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN B 624 " --> pdb=" O ARG B 619 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 661 through 664 removed outlier: 5.652A pdb=" N SER B 664 " --> pdb=" O LEU B 723 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU B 723 " --> pdb=" O SER B 664 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER B 709 " --> pdb=" O GLU B 726 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 669 through 673 removed outlier: 6.851A pdb=" N VAL B 689 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL B 673 " --> pdb=" O ILE B 687 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE B 687 " --> pdb=" O VAL B 673 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N MET B 699 " --> pdb=" O ILE B 687 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL B 689 " --> pdb=" O ASN B 697 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN B 697 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 80 through 82 removed outlier: 4.548A pdb=" N THR C 109 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE C 213 " --> pdb=" O SER C 194 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE C 196 " --> pdb=" O PHE C 213 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE C 215 " --> pdb=" O ILE C 196 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ARG C 259 " --> pdb=" O MET C 216 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 199 through 201 removed outlier: 5.873A pdb=" N TYR C 222 " --> pdb=" O CYS C 200 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'C' and resid 330 through 332 removed outlier: 4.623A pdb=" N VAL C 342 " --> pdb=" O ILE C 332 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL C 355 " --> pdb=" O PRO C 387 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE C 389 " --> pdb=" O VAL C 355 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASN C 357 " --> pdb=" O ILE C 389 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE C 391 " --> pdb=" O ASN C 357 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR C 451 " --> pdb=" O THR C 428 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ILE C 430 " --> pdb=" O THR C 451 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TYR C 453 " --> pdb=" O ILE C 430 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 433 through 435 removed outlier: 6.255A pdb=" N GLU C 459 " --> pdb=" O ALA C 434 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'D' and resid 162 through 164 removed outlier: 3.635A pdb=" N ALA D 138 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS D 88 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL D 68 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL D 90 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU D 108 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N HIS D 93 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL D 110 " --> pdb=" O HIS D 93 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 229 through 232 Processing sheet with id= Y, first strand: chain 'D' and resid 287 through 289 removed outlier: 3.635A pdb=" N GLU D 349 " --> pdb=" O GLU D 336 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU D 338 " --> pdb=" O PHE D 347 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE D 347 " --> pdb=" O LEU D 338 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 274 through 276 Processing sheet with id= AA, first strand: chain 'D' and resid 292 through 294 removed outlier: 4.068A pdb=" N ILE D 292 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL D 300 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ARG D 294 " --> pdb=" O LYS D 298 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LYS D 298 " --> pdb=" O ARG D 294 " (cutoff:3.500A) removed outlier: 13.756A pdb=" N GLN D 297 " --> pdb=" O TYR D 401 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N TYR D 401 " --> pdb=" O GLN D 297 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL D 299 " --> pdb=" O ARG D 399 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 452 " --> pdb=" O CYS D 398 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER D 450 " --> pdb=" O VAL D 400 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 419 through 421 removed outlier: 3.587A pdb=" N GLN D 419 " --> pdb=" O ARG D 476 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 602 through 607 removed outlier: 6.519A pdb=" N SER D 626 " --> pdb=" O LEU D 617 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARG D 619 " --> pdb=" O ASN D 624 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN D 624 " --> pdb=" O ARG D 619 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 661 through 664 removed outlier: 5.652A pdb=" N SER D 664 " --> pdb=" O LEU D 723 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU D 723 " --> pdb=" O SER D 664 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER D 709 " --> pdb=" O GLU D 726 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 669 through 673 removed outlier: 6.851A pdb=" N VAL D 689 " --> pdb=" O VAL D 671 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL D 673 " --> pdb=" O ILE D 687 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE D 687 " --> pdb=" O VAL D 673 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N MET D 699 " --> pdb=" O ILE D 687 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL D 689 " --> pdb=" O ASN D 697 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN D 697 " --> pdb=" O VAL D 689 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 80 through 82 removed outlier: 4.548A pdb=" N THR E 109 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE E 213 " --> pdb=" O SER E 194 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE E 196 " --> pdb=" O PHE E 213 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N PHE E 215 " --> pdb=" O ILE E 196 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG E 259 " --> pdb=" O MET E 216 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 199 through 201 removed outlier: 5.875A pdb=" N TYR E 222 " --> pdb=" O CYS E 200 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'E' and resid 330 through 332 removed outlier: 4.623A pdb=" N VAL E 342 " --> pdb=" O ILE E 332 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL E 355 " --> pdb=" O PRO E 387 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE E 389 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASN E 357 " --> pdb=" O ILE E 389 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N PHE E 391 " --> pdb=" O ASN E 357 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR E 451 " --> pdb=" O THR E 428 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE E 430 " --> pdb=" O THR E 451 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TYR E 453 " --> pdb=" O ILE E 430 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'E' and resid 433 through 435 removed outlier: 6.255A pdb=" N GLU E 459 " --> pdb=" O ALA E 434 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'F' and resid 162 through 164 removed outlier: 3.634A pdb=" N ALA F 138 " --> pdb=" O LYS F 65 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS F 88 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL F 68 " --> pdb=" O LYS F 88 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL F 90 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU F 108 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N HIS F 93 " --> pdb=" O GLU F 108 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL F 110 " --> pdb=" O HIS F 93 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'F' and resid 229 through 232 Processing sheet with id= AL, first strand: chain 'F' and resid 287 through 289 removed outlier: 3.635A pdb=" N GLU F 349 " --> pdb=" O GLU F 336 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU F 338 " --> pdb=" O PHE F 347 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N PHE F 347 " --> pdb=" O LEU F 338 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'F' and resid 274 through 276 Processing sheet with id= AN, first strand: chain 'F' and resid 292 through 294 removed outlier: 4.069A pdb=" N ILE F 292 " --> pdb=" O VAL F 300 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL F 300 " --> pdb=" O ILE F 292 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ARG F 294 " --> pdb=" O LYS F 298 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LYS F 298 " --> pdb=" O ARG F 294 " (cutoff:3.500A) removed outlier: 13.757A pdb=" N GLN F 297 " --> pdb=" O TYR F 401 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N TYR F 401 " --> pdb=" O GLN F 297 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL F 299 " --> pdb=" O ARG F 399 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU F 452 " --> pdb=" O CYS F 398 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER F 450 " --> pdb=" O VAL F 400 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'F' and resid 419 through 421 removed outlier: 3.585A pdb=" N GLN F 419 " --> pdb=" O ARG F 476 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'F' and resid 602 through 607 removed outlier: 6.518A pdb=" N SER F 626 " --> pdb=" O LEU F 617 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG F 619 " --> pdb=" O ASN F 624 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN F 624 " --> pdb=" O ARG F 619 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'F' and resid 661 through 664 removed outlier: 5.652A pdb=" N SER F 664 " --> pdb=" O LEU F 723 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU F 723 " --> pdb=" O SER F 664 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER F 709 " --> pdb=" O GLU F 726 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'F' and resid 669 through 673 removed outlier: 6.851A pdb=" N VAL F 689 " --> pdb=" O VAL F 671 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL F 673 " --> pdb=" O ILE F 687 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE F 687 " --> pdb=" O VAL F 673 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N MET F 699 " --> pdb=" O ILE F 687 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL F 689 " --> pdb=" O ASN F 697 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN F 697 " --> pdb=" O VAL F 689 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'G' and resid 80 through 82 removed outlier: 4.549A pdb=" N THR G 109 " --> pdb=" O SER G 82 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE G 213 " --> pdb=" O SER G 194 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE G 196 " --> pdb=" O PHE G 213 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE G 215 " --> pdb=" O ILE G 196 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ARG G 259 " --> pdb=" O MET G 216 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'G' and resid 199 through 201 removed outlier: 5.874A pdb=" N TYR G 222 " --> pdb=" O CYS G 200 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'G' and resid 330 through 332 removed outlier: 4.624A pdb=" N VAL G 342 " --> pdb=" O ILE G 332 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL G 355 " --> pdb=" O PRO G 387 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE G 389 " --> pdb=" O VAL G 355 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ASN G 357 " --> pdb=" O ILE G 389 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N PHE G 391 " --> pdb=" O ASN G 357 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR G 451 " --> pdb=" O THR G 428 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE G 430 " --> pdb=" O THR G 451 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TYR G 453 " --> pdb=" O ILE G 430 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'G' and resid 433 through 435 removed outlier: 6.255A pdb=" N GLU G 459 " --> pdb=" O ALA G 434 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV Processing sheet with id= AW, first strand: chain 'H' and resid 162 through 164 removed outlier: 3.634A pdb=" N ALA H 138 " --> pdb=" O LYS H 65 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS H 88 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL H 68 " --> pdb=" O LYS H 88 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL H 90 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLU H 108 " --> pdb=" O ALA H 91 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N HIS H 93 " --> pdb=" O GLU H 108 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL H 110 " --> pdb=" O HIS H 93 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'H' and resid 229 through 232 Processing sheet with id= AY, first strand: chain 'H' and resid 287 through 289 removed outlier: 3.635A pdb=" N GLU H 349 " --> pdb=" O GLU H 336 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU H 338 " --> pdb=" O PHE H 347 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE H 347 " --> pdb=" O LEU H 338 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'H' and resid 274 through 276 Processing sheet with id= BA, first strand: chain 'H' and resid 292 through 294 removed outlier: 4.069A pdb=" N ILE H 292 " --> pdb=" O VAL H 300 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL H 300 " --> pdb=" O ILE H 292 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ARG H 294 " --> pdb=" O LYS H 298 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LYS H 298 " --> pdb=" O ARG H 294 " (cutoff:3.500A) removed outlier: 13.756A pdb=" N GLN H 297 " --> pdb=" O TYR H 401 " (cutoff:3.500A) removed outlier: 10.611A pdb=" N TYR H 401 " --> pdb=" O GLN H 297 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL H 299 " --> pdb=" O ARG H 399 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU H 452 " --> pdb=" O CYS H 398 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER H 450 " --> pdb=" O VAL H 400 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'H' and resid 419 through 421 removed outlier: 3.586A pdb=" N GLN H 419 " --> pdb=" O ARG H 476 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'H' and resid 602 through 607 removed outlier: 6.519A pdb=" N SER H 626 " --> pdb=" O LEU H 617 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG H 619 " --> pdb=" O ASN H 624 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN H 624 " --> pdb=" O ARG H 619 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'H' and resid 661 through 664 removed outlier: 5.651A pdb=" N SER H 664 " --> pdb=" O LEU H 723 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU H 723 " --> pdb=" O SER H 664 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER H 709 " --> pdb=" O GLU H 726 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'H' and resid 669 through 673 removed outlier: 6.851A pdb=" N VAL H 689 " --> pdb=" O VAL H 671 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL H 673 " --> pdb=" O ILE H 687 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE H 687 " --> pdb=" O VAL H 673 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N MET H 699 " --> pdb=" O ILE H 687 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL H 689 " --> pdb=" O ASN H 697 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN H 697 " --> pdb=" O VAL H 689 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'I' and resid 80 through 82 removed outlier: 4.549A pdb=" N THR I 109 " --> pdb=" O SER I 82 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE I 213 " --> pdb=" O SER I 194 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE I 196 " --> pdb=" O PHE I 213 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N PHE I 215 " --> pdb=" O ILE I 196 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG I 259 " --> pdb=" O MET I 216 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'I' and resid 199 through 201 removed outlier: 5.873A pdb=" N TYR I 222 " --> pdb=" O CYS I 200 " (cutoff:3.500A) No H-bonds generated for sheet with id= BG Processing sheet with id= BH, first strand: chain 'I' and resid 330 through 332 removed outlier: 4.624A pdb=" N VAL I 342 " --> pdb=" O ILE I 332 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL I 355 " --> pdb=" O PRO I 387 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE I 389 " --> pdb=" O VAL I 355 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASN I 357 " --> pdb=" O ILE I 389 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE I 391 " --> pdb=" O ASN I 357 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR I 451 " --> pdb=" O THR I 428 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE I 430 " --> pdb=" O THR I 451 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TYR I 453 " --> pdb=" O ILE I 430 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'I' and resid 433 through 435 removed outlier: 6.255A pdb=" N GLU I 459 " --> pdb=" O ALA I 434 " (cutoff:3.500A) No H-bonds generated for sheet with id= BI Processing sheet with id= BJ, first strand: chain 'J' and resid 162 through 164 removed outlier: 3.635A pdb=" N ALA J 138 " --> pdb=" O LYS J 65 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS J 88 " --> pdb=" O ILE J 66 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL J 68 " --> pdb=" O LYS J 88 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL J 90 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLU J 108 " --> pdb=" O ALA J 91 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N HIS J 93 " --> pdb=" O GLU J 108 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL J 110 " --> pdb=" O HIS J 93 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'J' and resid 229 through 232 Processing sheet with id= BL, first strand: chain 'J' and resid 287 through 289 removed outlier: 3.636A pdb=" N GLU J 349 " --> pdb=" O GLU J 336 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU J 338 " --> pdb=" O PHE J 347 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE J 347 " --> pdb=" O LEU J 338 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'J' and resid 274 through 276 Processing sheet with id= BN, first strand: chain 'J' and resid 292 through 294 removed outlier: 4.069A pdb=" N ILE J 292 " --> pdb=" O VAL J 300 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL J 300 " --> pdb=" O ILE J 292 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ARG J 294 " --> pdb=" O LYS J 298 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LYS J 298 " --> pdb=" O ARG J 294 " (cutoff:3.500A) removed outlier: 13.757A pdb=" N GLN J 297 " --> pdb=" O TYR J 401 " (cutoff:3.500A) removed outlier: 10.612A pdb=" N TYR J 401 " --> pdb=" O GLN J 297 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL J 299 " --> pdb=" O ARG J 399 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU J 452 " --> pdb=" O CYS J 398 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER J 450 " --> pdb=" O VAL J 400 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'J' and resid 419 through 421 removed outlier: 3.585A pdb=" N GLN J 419 " --> pdb=" O ARG J 476 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'J' and resid 602 through 607 removed outlier: 6.519A pdb=" N SER J 626 " --> pdb=" O LEU J 617 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARG J 619 " --> pdb=" O ASN J 624 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN J 624 " --> pdb=" O ARG J 619 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'J' and resid 661 through 664 removed outlier: 5.652A pdb=" N SER J 664 " --> pdb=" O LEU J 723 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU J 723 " --> pdb=" O SER J 664 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER J 709 " --> pdb=" O GLU J 726 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'J' and resid 669 through 673 removed outlier: 6.851A pdb=" N VAL J 689 " --> pdb=" O VAL J 671 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL J 673 " --> pdb=" O ILE J 687 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE J 687 " --> pdb=" O VAL J 673 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N MET J 699 " --> pdb=" O ILE J 687 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL J 689 " --> pdb=" O ASN J 697 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASN J 697 " --> pdb=" O VAL J 689 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'K' and resid 80 through 82 removed outlier: 4.548A pdb=" N THR K 109 " --> pdb=" O SER K 82 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE K 213 " --> pdb=" O SER K 194 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE K 196 " --> pdb=" O PHE K 213 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N PHE K 215 " --> pdb=" O ILE K 196 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG K 259 " --> pdb=" O MET K 216 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'K' and resid 199 through 201 removed outlier: 5.873A pdb=" N TYR K 222 " --> pdb=" O CYS K 200 " (cutoff:3.500A) No H-bonds generated for sheet with id= BT Processing sheet with id= BU, first strand: chain 'K' and resid 330 through 332 removed outlier: 4.624A pdb=" N VAL K 342 " --> pdb=" O ILE K 332 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL K 355 " --> pdb=" O PRO K 387 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE K 389 " --> pdb=" O VAL K 355 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASN K 357 " --> pdb=" O ILE K 389 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE K 391 " --> pdb=" O ASN K 357 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR K 451 " --> pdb=" O THR K 428 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE K 430 " --> pdb=" O THR K 451 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TYR K 453 " --> pdb=" O ILE K 430 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'K' and resid 433 through 435 removed outlier: 6.256A pdb=" N GLU K 459 " --> pdb=" O ALA K 434 " (cutoff:3.500A) No H-bonds generated for sheet with id= BV Processing sheet with id= BW, first strand: chain 'P' and resid 80 through 82 removed outlier: 4.548A pdb=" N THR P 109 " --> pdb=" O SER P 82 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE P 213 " --> pdb=" O SER P 194 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE P 196 " --> pdb=" O PHE P 213 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N PHE P 215 " --> pdb=" O ILE P 196 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ARG P 259 " --> pdb=" O MET P 216 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'P' and resid 199 through 201 removed outlier: 5.874A pdb=" N TYR P 222 " --> pdb=" O CYS P 200 " (cutoff:3.500A) No H-bonds generated for sheet with id= BX Processing sheet with id= BY, first strand: chain 'P' and resid 330 through 332 removed outlier: 4.623A pdb=" N VAL P 342 " --> pdb=" O ILE P 332 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL P 355 " --> pdb=" O PRO P 387 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE P 389 " --> pdb=" O VAL P 355 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASN P 357 " --> pdb=" O ILE P 389 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE P 391 " --> pdb=" O ASN P 357 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR P 451 " --> pdb=" O THR P 428 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ILE P 430 " --> pdb=" O THR P 451 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TYR P 453 " --> pdb=" O ILE P 430 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'P' and resid 433 through 435 removed outlier: 6.227A pdb=" N GLU P 459 " --> pdb=" O ALA P 434 " (cutoff:3.500A) No H-bonds generated for sheet with id= BZ 2120 hydrogen bonds defined for protein. 5433 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: 22.26 Time building geometry restraints manager: 17.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 10205 1.32 - 1.45: 13040 1.45 - 1.57: 31553 1.57 - 1.70: 0 1.70 - 1.83: 504 Bond restraints: 55302 Sorted by residual: bond pdb=" C LYS F 694 " pdb=" N MET F 695 " ideal model delta sigma weight residual 1.334 1.448 -0.114 1.63e-02 3.76e+03 4.87e+01 bond pdb=" C LYS B 694 " pdb=" N MET B 695 " ideal model delta sigma weight residual 1.334 1.448 -0.114 1.63e-02 3.76e+03 4.86e+01 bond pdb=" C LYS J 694 " pdb=" N MET J 695 " ideal model delta sigma weight residual 1.334 1.448 -0.113 1.63e-02 3.76e+03 4.85e+01 bond pdb=" C LYS A 694 " pdb=" N MET A 695 " ideal model delta sigma weight residual 1.334 1.447 -0.113 1.63e-02 3.76e+03 4.82e+01 bond pdb=" C LYS D 694 " pdb=" N MET D 695 " ideal model delta sigma weight residual 1.334 1.447 -0.113 1.63e-02 3.76e+03 4.82e+01 ... (remaining 55297 not shown) Histogram of bond angle deviations from ideal: 89.14 - 98.19: 6 98.19 - 107.25: 2056 107.25 - 116.31: 35240 116.31 - 125.37: 36697 125.37 - 134.42: 803 Bond angle restraints: 74802 Sorted by residual: angle pdb=" N LYS P 433 " pdb=" CA LYS P 433 " pdb=" C LYS P 433 " ideal model delta sigma weight residual 110.28 120.02 -9.74 1.48e+00 4.57e-01 4.33e+01 angle pdb=" N PHE D 409 " pdb=" CA PHE D 409 " pdb=" C PHE D 409 " ideal model delta sigma weight residual 113.97 105.72 8.25 1.28e+00 6.10e-01 4.16e+01 angle pdb=" N PHE H 409 " pdb=" CA PHE H 409 " pdb=" C PHE H 409 " ideal model delta sigma weight residual 113.97 105.76 8.21 1.28e+00 6.10e-01 4.12e+01 angle pdb=" N PHE A 409 " pdb=" CA PHE A 409 " pdb=" C PHE A 409 " ideal model delta sigma weight residual 113.97 105.76 8.21 1.28e+00 6.10e-01 4.11e+01 angle pdb=" N PHE F 409 " pdb=" CA PHE F 409 " pdb=" C PHE F 409 " ideal model delta sigma weight residual 113.97 105.78 8.19 1.28e+00 6.10e-01 4.09e+01 ... (remaining 74797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 31033 17.17 - 34.35: 2077 34.35 - 51.52: 358 51.52 - 68.69: 96 68.69 - 85.86: 42 Dihedral angle restraints: 33606 sinusoidal: 13380 harmonic: 20226 Sorted by residual: dihedral pdb=" C ARG P 432 " pdb=" N ARG P 432 " pdb=" CA ARG P 432 " pdb=" CB ARG P 432 " ideal model delta harmonic sigma weight residual -122.60 -136.26 13.66 0 2.50e+00 1.60e-01 2.98e+01 dihedral pdb=" C ASP F 567 " pdb=" N ASP F 567 " pdb=" CA ASP F 567 " pdb=" CB ASP F 567 " ideal model delta harmonic sigma weight residual -122.60 -135.44 12.84 0 2.50e+00 1.60e-01 2.64e+01 dihedral pdb=" C ASP H 567 " pdb=" N ASP H 567 " pdb=" CA ASP H 567 " pdb=" CB ASP H 567 " ideal model delta harmonic sigma weight residual -122.60 -135.43 12.83 0 2.50e+00 1.60e-01 2.63e+01 ... (remaining 33603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 7202 0.106 - 0.211: 1107 0.211 - 0.317: 174 0.317 - 0.422: 6 0.422 - 0.528: 1 Chirality restraints: 8490 Sorted by residual: chirality pdb=" CA ARG P 432 " pdb=" N ARG P 432 " pdb=" C ARG P 432 " pdb=" CB ARG P 432 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" CA ASP H 567 " pdb=" N ASP H 567 " pdb=" C ASP H 567 " pdb=" CB ASP H 567 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA ASP F 567 " pdb=" N ASP F 567 " pdb=" C ASP F 567 " pdb=" CB ASP F 567 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 8487 not shown) Planarity restraints: 9774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU H 461 " 0.024 2.00e-02 2.50e+03 4.86e-02 2.36e+01 pdb=" CD GLU H 461 " -0.084 2.00e-02 2.50e+03 pdb=" OE1 GLU H 461 " 0.030 2.00e-02 2.50e+03 pdb=" OE2 GLU H 461 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 461 " -0.024 2.00e-02 2.50e+03 4.86e-02 2.36e+01 pdb=" CD GLU A 461 " 0.084 2.00e-02 2.50e+03 pdb=" OE1 GLU A 461 " -0.030 2.00e-02 2.50e+03 pdb=" OE2 GLU A 461 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 461 " -0.024 2.00e-02 2.50e+03 4.86e-02 2.36e+01 pdb=" CD GLU B 461 " 0.084 2.00e-02 2.50e+03 pdb=" OE1 GLU B 461 " -0.030 2.00e-02 2.50e+03 pdb=" OE2 GLU B 461 " -0.030 2.00e-02 2.50e+03 ... (remaining 9771 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 3478 2.73 - 3.28: 55184 3.28 - 3.82: 88385 3.82 - 4.36: 116449 4.36 - 4.90: 191303 Nonbonded interactions: 454799 Sorted by model distance: nonbonded pdb=" N GLU G 309 " pdb=" OE1 GLU G 309 " model vdw 2.192 2.520 nonbonded pdb=" N GLU C 309 " pdb=" OE1 GLU C 309 " model vdw 2.193 2.520 nonbonded pdb=" N GLU I 309 " pdb=" OE1 GLU I 309 " model vdw 2.193 2.520 nonbonded pdb=" N GLU P 309 " pdb=" OE1 GLU P 309 " model vdw 2.193 2.520 nonbonded pdb=" N GLU E 309 " pdb=" OE1 GLU E 309 " model vdw 2.193 2.520 ... (remaining 454794 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 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 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: 0.060 Extract box with map and model: 11.150 Check model and map are aligned: 0.610 Set scattering table: 0.380 Process input model: 111.810 Find NCS groups from input model: 2.730 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 : 0.008 0.114 55302 Z= 0.547 Angle : 1.102 9.744 74802 Z= 0.789 Chirality : 0.076 0.528 8490 Planarity : 0.006 0.089 9774 Dihedral : 12.531 85.864 20598 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.41 % Allowed : 2.20 % Favored : 97.39 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.10), residues: 7038 helix: 0.90 (0.10), residues: 2586 sheet: 0.75 (0.13), residues: 1350 loop : -0.24 (0.11), residues: 3102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP H 233 HIS 0.018 0.002 HIS F 480 PHE 0.043 0.003 PHE F 494 TYR 0.046 0.004 TYR F 214 ARG 0.008 0.001 ARG J 325 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 716 time to evaluate : 4.635 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: A 466 MET cc_start: 0.8363 (tpp) cc_final: 0.7943 (tpp) REVERT: A 716 ASP cc_start: 0.7077 (m-30) cc_final: 0.6871 (m-30) REVERT: B 105 MET cc_start: 0.8119 (mtp) cc_final: 0.7901 (ttm) REVERT: B 155 CYS cc_start: 0.8379 (m) cc_final: 0.7304 (m) REVERT: B 394 TRP cc_start: 0.7794 (t-100) cc_final: 0.7552 (t-100) REVERT: B 691 GLU cc_start: 0.6187 (tm-30) cc_final: 0.5880 (tm-30) REVERT: B 713 GLN cc_start: 0.7303 (mm-40) cc_final: 0.6973 (mm-40) REVERT: B 716 ASP cc_start: 0.7293 (m-30) cc_final: 0.7016 (m-30) REVERT: D 713 GLN cc_start: 0.7066 (mm-40) cc_final: 0.6768 (mm110) REVERT: F 155 CYS cc_start: 0.8613 (m) cc_final: 0.8379 (m) REVERT: F 713 GLN cc_start: 0.7073 (mm-40) cc_final: 0.6780 (mm110) REVERT: H 155 CYS cc_start: 0.8620 (m) cc_final: 0.7981 (m) REVERT: H 466 MET cc_start: 0.8364 (tpp) cc_final: 0.8008 (tpp) REVERT: H 716 ASP cc_start: 0.7123 (m-30) cc_final: 0.6920 (m-30) REVERT: J 155 CYS cc_start: 0.8430 (m) cc_final: 0.7260 (m) REVERT: J 394 TRP cc_start: 0.7809 (t-100) cc_final: 0.7567 (t-100) REVERT: J 691 GLU cc_start: 0.6209 (tm-30) cc_final: 0.5902 (tm-30) REVERT: J 713 GLN cc_start: 0.7309 (mm-40) cc_final: 0.6983 (mm-40) REVERT: J 716 ASP cc_start: 0.7299 (m-30) cc_final: 0.7019 (m-30) outliers start: 24 outliers final: 0 residues processed: 734 average time/residue: 1.5656 time to fit residues: 1408.3084 Evaluate side-chains 450 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 450 time to evaluate : 4.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 702 random chunks: chunk 592 optimal weight: 5.9990 chunk 532 optimal weight: 4.9990 chunk 295 optimal weight: 10.0000 chunk 181 optimal weight: 3.9990 chunk 358 optimal weight: 5.9990 chunk 284 optimal weight: 8.9990 chunk 550 optimal weight: 10.0000 chunk 212 optimal weight: 5.9990 chunk 334 optimal weight: 10.0000 chunk 409 optimal weight: 0.4980 chunk 637 optimal weight: 2.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 172 GLN A 190 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 HIS B 190 ASN ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN D 190 ASN D 425 HIS F 172 GLN F 190 ASN F 425 HIS G 147 GLN H 149 ASN H 172 GLN H 190 ASN ** H 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 425 HIS I 147 GLN J 190 ASN ** J 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 55302 Z= 0.413 Angle : 0.602 6.820 74802 Z= 0.326 Chirality : 0.048 0.209 8490 Planarity : 0.004 0.034 9774 Dihedral : 4.733 36.295 7746 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.72 % Allowed : 7.14 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.10), residues: 7038 helix: 1.01 (0.10), residues: 2622 sheet: 0.88 (0.13), residues: 1386 loop : -0.31 (0.11), residues: 3030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 531 HIS 0.009 0.001 HIS E 137 PHE 0.032 0.002 PHE D 503 TYR 0.018 0.002 TYR C 206 ARG 0.008 0.001 ARG D 268 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 440 time to evaluate : 4.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 MET cc_start: 0.8471 (tpp) cc_final: 0.8171 (tpp) REVERT: A 650 MET cc_start: 0.9376 (mmp) cc_final: 0.8543 (mmp) REVERT: A 716 ASP cc_start: 0.7062 (m-30) cc_final: 0.6845 (m-30) REVERT: B 713 GLN cc_start: 0.7347 (mm-40) cc_final: 0.7018 (mm-40) REVERT: B 716 ASP cc_start: 0.7311 (m-30) cc_final: 0.7044 (m-30) REVERT: C 37 GLU cc_start: 0.8047 (tp30) cc_final: 0.7722 (tp30) REVERT: C 485 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7312 (tm-30) REVERT: E 466 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8372 (ttpp) REVERT: G 37 GLU cc_start: 0.8003 (tp30) cc_final: 0.7649 (tp30) REVERT: H 466 MET cc_start: 0.8473 (tpp) cc_final: 0.8172 (tpp) REVERT: H 650 MET cc_start: 0.9375 (mmp) cc_final: 0.8532 (mmp) REVERT: H 716 ASP cc_start: 0.7055 (m-30) cc_final: 0.6841 (m-30) REVERT: I 37 GLU cc_start: 0.8020 (tp30) cc_final: 0.7683 (tp30) REVERT: J 713 GLN cc_start: 0.7350 (mm-40) cc_final: 0.7025 (mm-40) REVERT: J 716 ASP cc_start: 0.7317 (m-30) cc_final: 0.7047 (m-30) REVERT: K 37 GLU cc_start: 0.8043 (tp30) cc_final: 0.7724 (tp30) REVERT: K 485 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7310 (tm-30) REVERT: P 485 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7625 (tm-30) outliers start: 101 outliers final: 33 residues processed: 508 average time/residue: 1.4908 time to fit residues: 939.3542 Evaluate side-chains 430 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 393 time to evaluate : 4.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 448 CYS Chi-restraints excluded: chain C residue 485 GLU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 544 GLN Chi-restraints excluded: chain D residue 576 ASN Chi-restraints excluded: chain D residue 693 MET Chi-restraints excluded: chain E residue 448 CYS Chi-restraints excluded: chain E residue 466 LYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 281 ASN Chi-restraints excluded: chain F residue 544 GLN Chi-restraints excluded: chain F residue 576 ASN Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 281 ASN Chi-restraints excluded: chain H residue 308 LEU Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 281 ASN Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 448 CYS Chi-restraints excluded: chain K residue 485 GLU Chi-restraints excluded: chain P residue 448 CYS Chi-restraints excluded: chain P residue 485 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 702 random chunks: chunk 354 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 530 optimal weight: 3.9990 chunk 434 optimal weight: 0.0970 chunk 175 optimal weight: 1.9990 chunk 638 optimal weight: 0.0980 chunk 689 optimal weight: 0.6980 chunk 568 optimal weight: 7.9990 chunk 633 optimal weight: 0.6980 chunk 217 optimal weight: 1.9990 chunk 512 optimal weight: 0.4980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN A 344 ASN ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN C 236 ASN D 425 HIS E 236 ASN E 321 HIS F 425 HIS G 236 ASN H 296 ASN H 344 ASN I 236 ASN ** J 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 344 ASN K 236 ASN P 236 ASN P 321 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 55302 Z= 0.137 Angle : 0.474 6.985 74802 Z= 0.257 Chirality : 0.042 0.193 8490 Planarity : 0.003 0.031 9774 Dihedral : 4.280 22.843 7746 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.09 % Allowed : 8.90 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.10), residues: 7038 helix: 1.29 (0.11), residues: 2610 sheet: 0.79 (0.13), residues: 1350 loop : -0.27 (0.11), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 596 HIS 0.007 0.001 HIS E 137 PHE 0.030 0.001 PHE D 503 TYR 0.024 0.001 TYR B 455 ARG 0.004 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 430 time to evaluate : 4.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 MET cc_start: 0.8466 (tpp) cc_final: 0.8231 (tpp) REVERT: A 650 MET cc_start: 0.9366 (mmp) cc_final: 0.8574 (mmp) REVERT: A 716 ASP cc_start: 0.7072 (m-30) cc_final: 0.6859 (m-30) REVERT: B 499 ILE cc_start: 0.7541 (pp) cc_final: 0.7302 (pp) REVERT: B 713 GLN cc_start: 0.7361 (mm-40) cc_final: 0.7041 (mm110) REVERT: C 37 GLU cc_start: 0.8006 (tp30) cc_final: 0.7639 (tp30) REVERT: C 466 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8351 (ttpp) REVERT: C 480 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8045 (mm-30) REVERT: D 695 MET cc_start: 0.4477 (tpp) cc_final: 0.4193 (tpp) REVERT: H 466 MET cc_start: 0.8467 (tpp) cc_final: 0.8232 (tpp) REVERT: H 650 MET cc_start: 0.9366 (mmp) cc_final: 0.8735 (mmp) REVERT: H 695 MET cc_start: 0.4065 (tpp) cc_final: 0.3822 (tpp) REVERT: H 716 ASP cc_start: 0.7070 (m-30) cc_final: 0.6848 (m-30) REVERT: I 37 GLU cc_start: 0.7992 (tp30) cc_final: 0.7776 (tp30) REVERT: J 124 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7411 (mtp) REVERT: J 499 ILE cc_start: 0.7366 (pp) cc_final: 0.7131 (pp) REVERT: J 713 GLN cc_start: 0.7364 (mm-40) cc_final: 0.7048 (mm110) REVERT: J 716 ASP cc_start: 0.7258 (m-30) cc_final: 0.7045 (m-30) REVERT: K 37 GLU cc_start: 0.8005 (tp30) cc_final: 0.7640 (tp30) REVERT: K 466 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8352 (ttpp) REVERT: K 480 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7953 (mm-30) REVERT: P 485 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7591 (tm-30) outliers start: 64 outliers final: 11 residues processed: 464 average time/residue: 1.3991 time to fit residues: 815.2053 Evaluate side-chains 412 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 397 time to evaluate : 4.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 466 LYS Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 544 GLN Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain J residue 124 MET Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 464 LYS Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 466 LYS Chi-restraints excluded: chain P residue 485 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 702 random chunks: chunk 630 optimal weight: 0.9990 chunk 480 optimal weight: 1.9990 chunk 331 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 304 optimal weight: 4.9990 chunk 428 optimal weight: 8.9990 chunk 640 optimal weight: 4.9990 chunk 678 optimal weight: 4.9990 chunk 334 optimal weight: 10.0000 chunk 607 optimal weight: 9.9990 chunk 182 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN D 425 HIS F 425 HIS H 149 ASN H 296 ASN ** J 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 286 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 55302 Z= 0.319 Angle : 0.521 6.716 74802 Z= 0.282 Chirality : 0.045 0.160 8490 Planarity : 0.004 0.032 9774 Dihedral : 4.360 24.617 7746 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.55 % Allowed : 9.63 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.10), residues: 7038 helix: 1.19 (0.10), residues: 2628 sheet: 0.74 (0.13), residues: 1458 loop : -0.26 (0.11), residues: 2952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 531 HIS 0.007 0.001 HIS E 137 PHE 0.032 0.002 PHE D 503 TYR 0.025 0.001 TYR A 455 ARG 0.004 0.000 ARG I 376 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 404 time to evaluate : 4.695 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: A 650 MET cc_start: 0.9401 (mmp) cc_final: 0.8544 (mmp) REVERT: A 716 ASP cc_start: 0.7098 (m-30) cc_final: 0.6876 (m-30) REVERT: B 499 ILE cc_start: 0.7549 (pp) cc_final: 0.7319 (pp) REVERT: C 37 GLU cc_start: 0.8011 (tp30) cc_final: 0.7651 (tp30) REVERT: C 466 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8371 (ttpp) REVERT: C 480 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8043 (mm-30) REVERT: C 485 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7266 (tm-30) REVERT: E 466 LYS cc_start: 0.8612 (pptt) cc_final: 0.8306 (ttpp) REVERT: H 650 MET cc_start: 0.9401 (mmp) cc_final: 0.8545 (mmp) REVERT: H 695 MET cc_start: 0.4086 (tpp) cc_final: 0.3862 (tpp) REVERT: H 716 ASP cc_start: 0.7097 (m-30) cc_final: 0.6876 (m-30) REVERT: I 37 GLU cc_start: 0.8006 (tp30) cc_final: 0.7658 (tp30) REVERT: J 499 ILE cc_start: 0.7541 (pp) cc_final: 0.7311 (pp) REVERT: J 713 GLN cc_start: 0.7383 (mm-40) cc_final: 0.7065 (mm110) REVERT: J 716 ASP cc_start: 0.7215 (m-30) cc_final: 0.6990 (m-30) REVERT: K 37 GLU cc_start: 0.8011 (tp30) cc_final: 0.7655 (tp30) REVERT: K 466 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8371 (ttpp) REVERT: K 480 GLU cc_start: 0.8417 (mm-30) cc_final: 0.7967 (mm-30) REVERT: K 485 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7290 (tm-30) REVERT: P 485 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7590 (tm-30) outliers start: 91 outliers final: 34 residues processed: 457 average time/residue: 1.3675 time to fit residues: 789.3810 Evaluate side-chains 418 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 379 time to evaluate : 4.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 466 LYS Chi-restraints excluded: chain C residue 485 GLU Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 281 ASN Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 544 GLN Chi-restraints excluded: chain F residue 706 THR Chi-restraints excluded: chain H residue 281 ASN Chi-restraints excluded: chain H residue 350 MET Chi-restraints excluded: chain H residue 706 THR Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 281 ASN Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 464 LYS Chi-restraints excluded: chain J residue 706 THR Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 466 LYS Chi-restraints excluded: chain K residue 485 GLU Chi-restraints excluded: chain P residue 485 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 702 random chunks: chunk 565 optimal weight: 9.9990 chunk 385 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 505 optimal weight: 0.9990 chunk 279 optimal weight: 2.9990 chunk 579 optimal weight: 10.0000 chunk 469 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 346 optimal weight: 10.0000 chunk 609 optimal weight: 8.9990 chunk 171 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 ASN D 425 HIS E 236 ASN F 351 ASN F 425 HIS H 190 ASN ** J 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 55302 Z= 0.174 Angle : 0.478 10.660 74802 Z= 0.258 Chirality : 0.043 0.210 8490 Planarity : 0.004 0.030 9774 Dihedral : 4.206 23.337 7746 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.23 % Allowed : 10.25 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.10), residues: 7038 helix: 1.22 (0.11), residues: 2610 sheet: 0.75 (0.13), residues: 1488 loop : -0.20 (0.11), residues: 2940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 284 HIS 0.007 0.001 HIS P 137 PHE 0.034 0.001 PHE F 503 TYR 0.012 0.001 TYR P 206 ARG 0.006 0.000 ARG H 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 389 time to evaluate : 4.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 650 MET cc_start: 0.9384 (mmp) cc_final: 0.8569 (mmp) REVERT: A 716 ASP cc_start: 0.7124 (m-30) cc_final: 0.6894 (m-30) REVERT: B 174 MET cc_start: 0.7739 (mmt) cc_final: 0.7501 (mpm) REVERT: B 499 ILE cc_start: 0.7554 (pp) cc_final: 0.7314 (pp) REVERT: B 641 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8070 (ttm-80) REVERT: C 37 GLU cc_start: 0.8002 (tp30) cc_final: 0.7622 (tp30) REVERT: C 466 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8366 (ttpp) REVERT: C 480 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8026 (mm-30) REVERT: C 485 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7233 (tm-30) REVERT: E 466 LYS cc_start: 0.8633 (pptt) cc_final: 0.8301 (ttpp) REVERT: F 666 MET cc_start: 0.7517 (pmm) cc_final: 0.7279 (pmm) REVERT: H 650 MET cc_start: 0.9386 (mmp) cc_final: 0.8568 (mmp) REVERT: H 695 MET cc_start: 0.4040 (tpp) cc_final: 0.3835 (tpp) REVERT: H 716 ASP cc_start: 0.7133 (m-30) cc_final: 0.6892 (m-30) REVERT: J 499 ILE cc_start: 0.7547 (pp) cc_final: 0.7304 (pp) REVERT: J 713 GLN cc_start: 0.7383 (mm-40) cc_final: 0.7062 (mm110) REVERT: J 716 ASP cc_start: 0.7254 (m-30) cc_final: 0.7000 (m-30) REVERT: K 37 GLU cc_start: 0.8002 (tp30) cc_final: 0.7629 (tp30) REVERT: K 466 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8366 (ttpp) REVERT: K 480 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7977 (mm-30) REVERT: K 485 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7234 (tm-30) REVERT: P 485 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7574 (tm-30) outliers start: 72 outliers final: 26 residues processed: 436 average time/residue: 1.4062 time to fit residues: 772.0457 Evaluate side-chains 410 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 378 time to evaluate : 4.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 419 GLN Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 466 LYS Chi-restraints excluded: chain C residue 485 GLU Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 706 THR Chi-restraints excluded: chain H residue 706 THR Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 419 GLN Chi-restraints excluded: chain J residue 464 LYS Chi-restraints excluded: chain J residue 576 ASN Chi-restraints excluded: chain J residue 706 THR Chi-restraints excluded: chain J residue 725 VAL Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 466 LYS Chi-restraints excluded: chain K residue 485 GLU Chi-restraints excluded: chain P residue 485 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 702 random chunks: chunk 228 optimal weight: 9.9990 chunk 611 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 398 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 679 optimal weight: 0.0570 chunk 563 optimal weight: 8.9990 chunk 314 optimal weight: 30.0000 chunk 56 optimal weight: 6.9990 chunk 224 optimal weight: 10.0000 chunk 356 optimal weight: 5.9990 overall best weight: 3.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 ASN D 425 HIS F 351 ASN F 425 HIS H 296 ASN H 576 ASN ** J 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 55302 Z= 0.396 Angle : 0.550 8.453 74802 Z= 0.297 Chirality : 0.046 0.181 8490 Planarity : 0.004 0.034 9774 Dihedral : 4.401 25.385 7746 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.43 % Allowed : 10.52 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.10), residues: 7038 helix: 1.11 (0.10), residues: 2598 sheet: 0.66 (0.13), residues: 1500 loop : -0.28 (0.11), residues: 2940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 284 HIS 0.007 0.001 HIS I 137 PHE 0.035 0.002 PHE D 347 TYR 0.019 0.002 TYR P 417 ARG 0.004 0.001 ARG H 154 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 390 time to evaluate : 4.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.2058 (mmp) cc_final: 0.1552 (mmt) REVERT: A 716 ASP cc_start: 0.7275 (m-30) cc_final: 0.7019 (m-30) REVERT: B 174 MET cc_start: 0.7774 (mmt) cc_final: 0.7567 (mpm) REVERT: C 37 GLU cc_start: 0.8029 (tp30) cc_final: 0.7661 (tp30) REVERT: C 480 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8046 (mm-30) REVERT: C 485 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7283 (tm-30) REVERT: F 466 MET cc_start: 0.8360 (tpp) cc_final: 0.8083 (tpp) REVERT: H 229 MET cc_start: 0.2121 (mmp) cc_final: 0.1600 (mmt) REVERT: H 650 MET cc_start: 0.9394 (mmp) cc_final: 0.8533 (mmp) REVERT: H 695 MET cc_start: 0.4044 (tpp) cc_final: 0.3774 (tpp) REVERT: H 716 ASP cc_start: 0.7266 (m-30) cc_final: 0.7009 (m-30) REVERT: J 713 GLN cc_start: 0.7397 (mm-40) cc_final: 0.7063 (mm110) REVERT: J 716 ASP cc_start: 0.7301 (m-30) cc_final: 0.7049 (m-30) REVERT: K 37 GLU cc_start: 0.8031 (tp30) cc_final: 0.7665 (tp30) REVERT: K 480 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8000 (mm-30) REVERT: K 485 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7283 (tm-30) REVERT: P 485 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7523 (tm-30) outliers start: 84 outliers final: 44 residues processed: 444 average time/residue: 1.3853 time to fit residues: 777.1683 Evaluate side-chains 423 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 376 time to evaluate : 4.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 419 GLN Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 448 CYS Chi-restraints excluded: chain C residue 485 GLU Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain E residue 448 CYS Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 706 THR Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 281 ASN Chi-restraints excluded: chain H residue 706 THR Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 419 GLN Chi-restraints excluded: chain J residue 464 LYS Chi-restraints excluded: chain J residue 658 THR Chi-restraints excluded: chain J residue 706 THR Chi-restraints excluded: chain J residue 725 VAL Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 448 CYS Chi-restraints excluded: chain K residue 485 GLU Chi-restraints excluded: chain P residue 448 CYS Chi-restraints excluded: chain P residue 485 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 702 random chunks: chunk 654 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 386 optimal weight: 0.8980 chunk 496 optimal weight: 0.7980 chunk 384 optimal weight: 3.9990 chunk 571 optimal weight: 5.9990 chunk 379 optimal weight: 0.8980 chunk 676 optimal weight: 0.7980 chunk 423 optimal weight: 7.9990 chunk 412 optimal weight: 3.9990 chunk 312 optimal weight: 20.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 419 GLN ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN H 419 GLN ** J 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 55302 Z= 0.161 Angle : 0.482 11.243 74802 Z= 0.258 Chirality : 0.043 0.190 8490 Planarity : 0.003 0.031 9774 Dihedral : 4.155 23.105 7746 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.08 % Allowed : 11.03 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.10), residues: 7038 helix: 1.17 (0.11), residues: 2598 sheet: 0.74 (0.13), residues: 1488 loop : -0.24 (0.11), residues: 2952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 284 HIS 0.007 0.001 HIS P 137 PHE 0.037 0.001 PHE J 347 TYR 0.012 0.001 TYR E 206 ARG 0.005 0.000 ARG H 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 391 time to evaluate : 4.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.2167 (mmp) cc_final: 0.1877 (mmt) REVERT: A 650 MET cc_start: 0.9314 (mmp) cc_final: 0.8682 (mmp) REVERT: A 716 ASP cc_start: 0.7274 (m-30) cc_final: 0.7012 (m-30) REVERT: B 641 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8115 (ttm-80) REVERT: C 37 GLU cc_start: 0.7999 (tp30) cc_final: 0.7614 (tp30) REVERT: C 480 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8026 (mm-30) REVERT: C 485 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7215 (tm-30) REVERT: F 466 MET cc_start: 0.8324 (tpp) cc_final: 0.8046 (tpp) REVERT: H 229 MET cc_start: 0.2093 (mmp) cc_final: 0.1817 (mmt) REVERT: H 650 MET cc_start: 0.9380 (mmp) cc_final: 0.8564 (mmp) REVERT: H 695 MET cc_start: 0.4002 (tpp) cc_final: 0.3767 (tpp) REVERT: H 716 ASP cc_start: 0.7280 (m-30) cc_final: 0.7017 (m-30) REVERT: J 641 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8075 (ttm-80) REVERT: J 713 GLN cc_start: 0.7395 (mm-40) cc_final: 0.7058 (mm110) REVERT: J 716 ASP cc_start: 0.7294 (m-30) cc_final: 0.7041 (m-30) REVERT: K 37 GLU cc_start: 0.7999 (tp30) cc_final: 0.7617 (tp30) REVERT: K 480 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7968 (mm-30) REVERT: K 485 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7214 (tm-30) REVERT: P 485 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7530 (tm-30) outliers start: 63 outliers final: 33 residues processed: 435 average time/residue: 1.4049 time to fit residues: 768.8440 Evaluate side-chains 412 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 374 time to evaluate : 4.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 419 GLN Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 448 CYS Chi-restraints excluded: chain C residue 485 GLU Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 706 THR Chi-restraints excluded: chain H residue 658 THR Chi-restraints excluded: chain H residue 706 THR Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 419 GLN Chi-restraints excluded: chain J residue 641 ARG Chi-restraints excluded: chain J residue 658 THR Chi-restraints excluded: chain J residue 706 THR Chi-restraints excluded: chain J residue 725 VAL Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 485 GLU Chi-restraints excluded: chain P residue 485 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 702 random chunks: chunk 418 optimal weight: 20.0000 chunk 270 optimal weight: 3.9990 chunk 404 optimal weight: 3.9990 chunk 203 optimal weight: 40.0000 chunk 132 optimal weight: 8.9990 chunk 131 optimal weight: 7.9990 chunk 430 optimal weight: 10.0000 chunk 460 optimal weight: 7.9990 chunk 334 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 531 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 576 ASN ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN F 351 ASN H 172 GLN ** J 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 55302 Z= 0.510 Angle : 0.610 12.793 74802 Z= 0.327 Chirality : 0.049 0.200 8490 Planarity : 0.005 0.037 9774 Dihedral : 4.491 26.051 7746 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.47 % Allowed : 11.05 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.10), residues: 7038 helix: 0.96 (0.10), residues: 2604 sheet: 0.55 (0.13), residues: 1530 loop : -0.32 (0.11), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 531 HIS 0.008 0.001 HIS I 137 PHE 0.042 0.002 PHE J 347 TYR 0.028 0.002 TYR E 417 ARG 0.007 0.001 ARG F 539 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 375 time to evaluate : 4.693 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: A 229 MET cc_start: 0.2135 (mmp) cc_final: 0.1713 (mmt) REVERT: A 716 ASP cc_start: 0.7324 (m-30) cc_final: 0.7069 (m-30) REVERT: B 229 MET cc_start: 0.3264 (mmm) cc_final: 0.2507 (mmp) REVERT: B 641 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8210 (ttm-80) REVERT: C 37 GLU cc_start: 0.8050 (tp30) cc_final: 0.7683 (tp30) REVERT: C 480 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8051 (mm-30) REVERT: F 666 MET cc_start: 0.7631 (pmm) cc_final: 0.7411 (pmm) REVERT: H 229 MET cc_start: 0.2112 (mmp) cc_final: 0.1695 (mmt) REVERT: H 650 MET cc_start: 0.9402 (mmp) cc_final: 0.8534 (mmp) REVERT: H 716 ASP cc_start: 0.7327 (m-30) cc_final: 0.7070 (m-30) REVERT: J 229 MET cc_start: 0.3295 (mmm) cc_final: 0.2563 (mmp) REVERT: J 350 MET cc_start: 0.7505 (tmt) cc_final: 0.7098 (tmt) REVERT: J 641 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8208 (ttm-80) REVERT: J 713 GLN cc_start: 0.7416 (mm-40) cc_final: 0.7077 (mm110) REVERT: J 716 ASP cc_start: 0.7343 (m-30) cc_final: 0.7068 (m-30) REVERT: K 37 GLU cc_start: 0.8047 (tp30) cc_final: 0.7685 (tp30) REVERT: K 480 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8008 (mm-30) REVERT: P 485 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7498 (tm-30) outliers start: 86 outliers final: 48 residues processed: 437 average time/residue: 1.3499 time to fit residues: 748.4535 Evaluate side-chains 416 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 365 time to evaluate : 4.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 419 GLN Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 448 CYS Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 281 ASN Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 706 THR Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 174 MET Chi-restraints excluded: chain H residue 658 THR Chi-restraints excluded: chain H residue 706 THR Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 281 ASN Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 419 GLN Chi-restraints excluded: chain J residue 641 ARG Chi-restraints excluded: chain J residue 658 THR Chi-restraints excluded: chain J residue 706 THR Chi-restraints excluded: chain J residue 725 VAL Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 448 CYS Chi-restraints excluded: chain P residue 485 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 702 random chunks: chunk 615 optimal weight: 7.9990 chunk 648 optimal weight: 0.8980 chunk 591 optimal weight: 2.9990 chunk 630 optimal weight: 2.9990 chunk 379 optimal weight: 0.7980 chunk 274 optimal weight: 0.9990 chunk 495 optimal weight: 0.7980 chunk 193 optimal weight: 9.9990 chunk 569 optimal weight: 3.9990 chunk 596 optimal weight: 9.9990 chunk 628 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 GLN ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 HIS D 296 ASN D 611 GLN E 236 ASN F 169 HIS F 351 ASN ** J 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 611 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 55302 Z= 0.182 Angle : 0.513 14.282 74802 Z= 0.274 Chirality : 0.043 0.184 8490 Planarity : 0.004 0.033 9774 Dihedral : 4.251 23.901 7746 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.92 % Allowed : 11.65 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.10), residues: 7038 helix: 1.08 (0.11), residues: 2592 sheet: 0.63 (0.13), residues: 1518 loop : -0.26 (0.11), residues: 2928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 284 HIS 0.006 0.001 HIS P 137 PHE 0.040 0.001 PHE B 347 TYR 0.012 0.001 TYR P 206 ARG 0.005 0.000 ARG I 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 378 time to evaluate : 4.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.2353 (mmp) cc_final: 0.1890 (mmt) REVERT: A 716 ASP cc_start: 0.7335 (m-30) cc_final: 0.7074 (m-30) REVERT: B 229 MET cc_start: 0.3219 (mmm) cc_final: 0.2579 (mmp) REVERT: C 37 GLU cc_start: 0.7989 (tp30) cc_final: 0.7615 (tp30) REVERT: C 480 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8020 (mm-30) REVERT: D 128 MET cc_start: 0.7666 (mpp) cc_final: 0.7415 (mpp) REVERT: D 466 MET cc_start: 0.8312 (tpp) cc_final: 0.7935 (tpp) REVERT: H 124 MET cc_start: 0.7529 (mmm) cc_final: 0.7317 (mmm) REVERT: H 229 MET cc_start: 0.2356 (mmp) cc_final: 0.1890 (mmt) REVERT: H 716 ASP cc_start: 0.7368 (m-30) cc_final: 0.7115 (m-30) REVERT: J 229 MET cc_start: 0.3222 (mmm) cc_final: 0.2574 (mmp) REVERT: J 713 GLN cc_start: 0.7368 (mm-40) cc_final: 0.7014 (mm110) REVERT: J 716 ASP cc_start: 0.7363 (m-30) cc_final: 0.7110 (m-30) REVERT: K 37 GLU cc_start: 0.7987 (tp30) cc_final: 0.7615 (tp30) REVERT: K 480 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7976 (mm-30) REVERT: P 485 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7504 (tm-30) outliers start: 54 outliers final: 39 residues processed: 418 average time/residue: 1.3891 time to fit residues: 733.3878 Evaluate side-chains 411 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 371 time to evaluate : 5.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 419 GLN Chi-restraints excluded: chain B residue 544 GLN Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 448 CYS Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 281 ASN Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 706 THR Chi-restraints excluded: chain H residue 658 THR Chi-restraints excluded: chain H residue 706 THR Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 281 ASN Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 419 GLN Chi-restraints excluded: chain J residue 544 GLN Chi-restraints excluded: chain J residue 658 THR Chi-restraints excluded: chain J residue 706 THR Chi-restraints excluded: chain J residue 725 VAL Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 448 CYS Chi-restraints excluded: chain P residue 485 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 702 random chunks: chunk 414 optimal weight: 0.8980 chunk 666 optimal weight: 0.6980 chunk 406 optimal weight: 0.8980 chunk 316 optimal weight: 7.9990 chunk 463 optimal weight: 3.9990 chunk 699 optimal weight: 0.7980 chunk 643 optimal weight: 0.8980 chunk 556 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 430 optimal weight: 8.9990 chunk 341 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 611 GLN ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN D 611 GLN ** J 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 611 GLN K 115 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 55302 Z= 0.153 Angle : 0.508 14.858 74802 Z= 0.269 Chirality : 0.043 0.191 8490 Planarity : 0.003 0.033 9774 Dihedral : 4.113 22.886 7746 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.77 % Allowed : 11.89 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.10), residues: 7038 helix: 1.11 (0.11), residues: 2598 sheet: 0.75 (0.13), residues: 1464 loop : -0.23 (0.11), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 284 HIS 0.006 0.001 HIS E 137 PHE 0.042 0.001 PHE J 347 TYR 0.011 0.001 TYR E 206 ARG 0.016 0.000 ARG D 295 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 383 time to evaluate : 4.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.2036 (mmp) cc_final: 0.1655 (mmt) REVERT: A 716 ASP cc_start: 0.7365 (m-30) cc_final: 0.7113 (m-30) REVERT: B 229 MET cc_start: 0.3274 (mmm) cc_final: 0.2275 (mmp) REVERT: B 273 GLN cc_start: 0.7914 (tp40) cc_final: 0.7496 (tp40) REVERT: C 37 GLU cc_start: 0.7997 (tp30) cc_final: 0.7618 (tp30) REVERT: D 466 MET cc_start: 0.8191 (tpp) cc_final: 0.7832 (tpp) REVERT: H 124 MET cc_start: 0.7593 (mmm) cc_final: 0.7343 (mmm) REVERT: H 229 MET cc_start: 0.2038 (mmp) cc_final: 0.1654 (mmt) REVERT: H 650 MET cc_start: 0.9298 (mmp) cc_final: 0.8728 (mmp) REVERT: H 716 ASP cc_start: 0.7331 (m-30) cc_final: 0.7090 (m-30) REVERT: J 229 MET cc_start: 0.3292 (mmm) cc_final: 0.2284 (mmp) REVERT: J 713 GLN cc_start: 0.7338 (mm-40) cc_final: 0.6984 (mm110) REVERT: J 716 ASP cc_start: 0.7341 (m-30) cc_final: 0.7100 (m-30) REVERT: K 37 GLU cc_start: 0.7999 (tp30) cc_final: 0.7618 (tp30) REVERT: P 485 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7488 (tm-30) outliers start: 45 outliers final: 31 residues processed: 418 average time/residue: 1.3961 time to fit residues: 736.2013 Evaluate side-chains 404 residues out of total 5856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 372 time to evaluate : 4.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 419 GLN Chi-restraints excluded: chain B residue 658 THR Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 448 CYS Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 706 THR Chi-restraints excluded: chain H residue 658 THR Chi-restraints excluded: chain H residue 706 THR Chi-restraints excluded: chain J residue 189 VAL Chi-restraints excluded: chain J residue 281 ASN Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 419 GLN Chi-restraints excluded: chain J residue 658 THR Chi-restraints excluded: chain J residue 706 THR Chi-restraints excluded: chain J residue 725 VAL Chi-restraints excluded: chain K residue 308 LEU Chi-restraints excluded: chain K residue 448 CYS Chi-restraints excluded: chain P residue 485 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 702 random chunks: chunk 442 optimal weight: 5.9990 chunk 593 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 513 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 154 optimal weight: 0.8980 chunk 557 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 chunk 572 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 102 optimal weight: 0.5980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 GLN ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN D 296 ASN D 611 GLN F 172 GLN H 611 GLN ** J 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 611 GLN K 115 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.144568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.086585 restraints weight = 105057.782| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.18 r_work: 0.2846 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 55302 Z= 0.290 Angle : 0.548 15.781 74802 Z= 0.292 Chirality : 0.045 0.191 8490 Planarity : 0.004 0.035 9774 Dihedral : 4.263 24.561 7746 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.80 % Allowed : 11.92 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.10), residues: 7038 helix: 1.07 (0.11), residues: 2592 sheet: 0.61 (0.13), residues: 1530 loop : -0.25 (0.11), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 284 HIS 0.007 0.001 HIS I 137 PHE 0.040 0.002 PHE A 347 TYR 0.019 0.001 TYR P 417 ARG 0.007 0.000 ARG B 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16762.70 seconds wall clock time: 292 minutes 42.79 seconds (17562.79 seconds total)