Starting phenix.real_space_refine on Thu Feb 15 05:47:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ywy_14352/02_2024/7ywy_14352.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ywy_14352/02_2024/7ywy_14352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ywy_14352/02_2024/7ywy_14352.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ywy_14352/02_2024/7ywy_14352.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ywy_14352/02_2024/7ywy_14352.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ywy_14352/02_2024/7ywy_14352.pdb" } resolution = 3.4 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 280 5.16 5 C 39788 2.51 5 N 11116 2.21 5 O 12810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b ASP 41": "OD1" <-> "OD2" Residue "b GLU 63": "OE1" <-> "OE2" Residue "b GLU 76": "OE1" <-> "OE2" Residue "b ASP 167": "OD1" <-> "OD2" Residue "b GLU 178": "OE1" <-> "OE2" Residue "b ASP 185": "OD1" <-> "OD2" Residue "b GLU 186": "OE1" <-> "OE2" Residue "b PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 232": "OE1" <-> "OE2" Residue "b ASP 253": "OD1" <-> "OD2" Residue "b ASP 283": "OD1" <-> "OD2" Residue "b ASP 328": "OD1" <-> "OD2" Residue "b GLU 388": "OE1" <-> "OE2" Residue "b ASP 398": "OD1" <-> "OD2" Residue "b GLU 448": "OE1" <-> "OE2" Residue "b ASP 473": "OD1" <-> "OD2" Residue "b TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 484": "OE1" <-> "OE2" Residue "b TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 490": "OD1" <-> "OD2" Residue "G ASP 41": "OD1" <-> "OD2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G GLU 76": "OE1" <-> "OE2" Residue "G ASP 167": "OD1" <-> "OD2" Residue "G GLU 178": "OE1" <-> "OE2" Residue "G ASP 185": "OD1" <-> "OD2" Residue "G GLU 186": "OE1" <-> "OE2" Residue "G PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 232": "OE1" <-> "OE2" Residue "G ASP 253": "OD1" <-> "OD2" Residue "G ASP 283": "OD1" <-> "OD2" Residue "G ASP 328": "OD1" <-> "OD2" Residue "G GLU 388": "OE1" <-> "OE2" Residue "G ASP 398": "OD1" <-> "OD2" Residue "G GLU 448": "OE1" <-> "OE2" Residue "G ASP 473": "OD1" <-> "OD2" Residue "G TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 484": "OE1" <-> "OE2" Residue "G TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 490": "OD1" <-> "OD2" Residue "H ASP 41": "OD1" <-> "OD2" Residue "H GLU 63": "OE1" <-> "OE2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H ASP 167": "OD1" <-> "OD2" Residue "H GLU 178": "OE1" <-> "OE2" Residue "H ASP 185": "OD1" <-> "OD2" Residue "H GLU 186": "OE1" <-> "OE2" Residue "H PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 232": "OE1" <-> "OE2" Residue "H ASP 253": "OD1" <-> "OD2" Residue "H ASP 283": "OD1" <-> "OD2" Residue "H ASP 328": "OD1" <-> "OD2" Residue "H GLU 388": "OE1" <-> "OE2" Residue "H ASP 398": "OD1" <-> "OD2" Residue "H GLU 448": "OE1" <-> "OE2" Residue "H ASP 473": "OD1" <-> "OD2" Residue "H TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 484": "OE1" <-> "OE2" Residue "H TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 490": "OD1" <-> "OD2" Residue "I ASP 41": "OD1" <-> "OD2" Residue "I GLU 63": "OE1" <-> "OE2" Residue "I GLU 76": "OE1" <-> "OE2" Residue "I ASP 167": "OD1" <-> "OD2" Residue "I GLU 178": "OE1" <-> "OE2" Residue "I ASP 185": "OD1" <-> "OD2" Residue "I GLU 186": "OE1" <-> "OE2" Residue "I PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 232": "OE1" <-> "OE2" Residue "I ASP 253": "OD1" <-> "OD2" Residue "I ASP 283": "OD1" <-> "OD2" Residue "I ASP 328": "OD1" <-> "OD2" Residue "I GLU 388": "OE1" <-> "OE2" Residue "I ASP 398": "OD1" <-> "OD2" Residue "I GLU 448": "OE1" <-> "OE2" Residue "I ASP 473": "OD1" <-> "OD2" Residue "I TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 484": "OE1" <-> "OE2" Residue "I TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 490": "OD1" <-> "OD2" Residue "J ASP 41": "OD1" <-> "OD2" Residue "J GLU 63": "OE1" <-> "OE2" Residue "J GLU 76": "OE1" <-> "OE2" Residue "J ASP 167": "OD1" <-> "OD2" Residue "J GLU 178": "OE1" <-> "OE2" Residue "J ASP 185": "OD1" <-> "OD2" Residue "J GLU 186": "OE1" <-> "OE2" Residue "J PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 232": "OE1" <-> "OE2" Residue "J ASP 253": "OD1" <-> "OD2" Residue "J ASP 283": "OD1" <-> "OD2" Residue "J ASP 328": "OD1" <-> "OD2" Residue "J GLU 388": "OE1" <-> "OE2" Residue "J ASP 398": "OD1" <-> "OD2" Residue "J GLU 448": "OE1" <-> "OE2" Residue "J ASP 473": "OD1" <-> "OD2" Residue "J TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 484": "OE1" <-> "OE2" Residue "J TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 490": "OD1" <-> "OD2" Residue "K ASP 41": "OD1" <-> "OD2" Residue "K GLU 63": "OE1" <-> "OE2" Residue "K GLU 76": "OE1" <-> "OE2" Residue "K ASP 167": "OD1" <-> "OD2" Residue "K GLU 178": "OE1" <-> "OE2" Residue "K ASP 185": "OD1" <-> "OD2" Residue "K GLU 186": "OE1" <-> "OE2" Residue "K PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 232": "OE1" <-> "OE2" Residue "K ASP 253": "OD1" <-> "OD2" Residue "K ASP 283": "OD1" <-> "OD2" Residue "K ASP 328": "OD1" <-> "OD2" Residue "K GLU 388": "OE1" <-> "OE2" Residue "K ASP 398": "OD1" <-> "OD2" Residue "K GLU 448": "OE1" <-> "OE2" Residue "K ASP 473": "OD1" <-> "OD2" Residue "K TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 484": "OE1" <-> "OE2" Residue "K TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 490": "OD1" <-> "OD2" Residue "L ASP 41": "OD1" <-> "OD2" Residue "L GLU 63": "OE1" <-> "OE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L ASP 167": "OD1" <-> "OD2" Residue "L GLU 178": "OE1" <-> "OE2" Residue "L ASP 185": "OD1" <-> "OD2" Residue "L GLU 186": "OE1" <-> "OE2" Residue "L PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 232": "OE1" <-> "OE2" Residue "L ASP 253": "OD1" <-> "OD2" Residue "L ASP 283": "OD1" <-> "OD2" Residue "L ASP 328": "OD1" <-> "OD2" Residue "L GLU 388": "OE1" <-> "OE2" Residue "L ASP 398": "OD1" <-> "OD2" Residue "L GLU 448": "OE1" <-> "OE2" Residue "L ASP 473": "OD1" <-> "OD2" Residue "L TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 484": "OE1" <-> "OE2" Residue "L TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 490": "OD1" <-> "OD2" Residue "Z ASP 41": "OD1" <-> "OD2" Residue "Z GLU 63": "OE1" <-> "OE2" Residue "Z GLU 76": "OE1" <-> "OE2" Residue "Z ASP 167": "OD1" <-> "OD2" Residue "Z GLU 178": "OE1" <-> "OE2" Residue "Z ASP 185": "OD1" <-> "OD2" Residue "Z GLU 186": "OE1" <-> "OE2" Residue "Z PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 232": "OE1" <-> "OE2" Residue "Z ASP 253": "OD1" <-> "OD2" Residue "Z ASP 283": "OD1" <-> "OD2" Residue "Z ASP 328": "OD1" <-> "OD2" Residue "Z GLU 388": "OE1" <-> "OE2" Residue "Z ASP 398": "OD1" <-> "OD2" Residue "Z GLU 448": "OE1" <-> "OE2" Residue "Z ASP 473": "OD1" <-> "OD2" Residue "Z TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 484": "OE1" <-> "OE2" Residue "Z TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 490": "OD1" <-> "OD2" Residue "S ASP 41": "OD1" <-> "OD2" Residue "S GLU 63": "OE1" <-> "OE2" Residue "S GLU 76": "OE1" <-> "OE2" Residue "S ASP 167": "OD1" <-> "OD2" Residue "S GLU 178": "OE1" <-> "OE2" Residue "S ASP 185": "OD1" <-> "OD2" Residue "S GLU 186": "OE1" <-> "OE2" Residue "S PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 232": "OE1" <-> "OE2" Residue "S ASP 253": "OD1" <-> "OD2" Residue "S ASP 283": "OD1" <-> "OD2" Residue "S ASP 328": "OD1" <-> "OD2" Residue "S GLU 388": "OE1" <-> "OE2" Residue "S ASP 398": "OD1" <-> "OD2" Residue "S GLU 448": "OE1" <-> "OE2" Residue "S ASP 473": "OD1" <-> "OD2" Residue "S TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 484": "OE1" <-> "OE2" Residue "S TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 490": "OD1" <-> "OD2" Residue "T ASP 41": "OD1" <-> "OD2" Residue "T GLU 63": "OE1" <-> "OE2" Residue "T GLU 76": "OE1" <-> "OE2" Residue "T ASP 167": "OD1" <-> "OD2" Residue "T GLU 178": "OE1" <-> "OE2" Residue "T ASP 185": "OD1" <-> "OD2" Residue "T GLU 186": "OE1" <-> "OE2" Residue "T PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 232": "OE1" <-> "OE2" Residue "T ASP 253": "OD1" <-> "OD2" Residue "T ASP 283": "OD1" <-> "OD2" Residue "T ASP 328": "OD1" <-> "OD2" Residue "T GLU 388": "OE1" <-> "OE2" Residue "T ASP 398": "OD1" <-> "OD2" Residue "T GLU 448": "OE1" <-> "OE2" Residue "T ASP 473": "OD1" <-> "OD2" Residue "T TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 484": "OE1" <-> "OE2" Residue "T TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 490": "OD1" <-> "OD2" Residue "U ASP 41": "OD1" <-> "OD2" Residue "U GLU 63": "OE1" <-> "OE2" Residue "U GLU 76": "OE1" <-> "OE2" Residue "U ASP 167": "OD1" <-> "OD2" Residue "U GLU 178": "OE1" <-> "OE2" Residue "U ASP 185": "OD1" <-> "OD2" Residue "U GLU 186": "OE1" <-> "OE2" Residue "U PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 232": "OE1" <-> "OE2" Residue "U ASP 253": "OD1" <-> "OD2" Residue "U ASP 283": "OD1" <-> "OD2" Residue "U ASP 328": "OD1" <-> "OD2" Residue "U GLU 388": "OE1" <-> "OE2" Residue "U ASP 398": "OD1" <-> "OD2" Residue "U GLU 448": "OE1" <-> "OE2" Residue "U ASP 473": "OD1" <-> "OD2" Residue "U TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 484": "OE1" <-> "OE2" Residue "U TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 490": "OD1" <-> "OD2" Residue "V ASP 41": "OD1" <-> "OD2" Residue "V GLU 63": "OE1" <-> "OE2" Residue "V GLU 76": "OE1" <-> "OE2" Residue "V ASP 167": "OD1" <-> "OD2" Residue "V GLU 178": "OE1" <-> "OE2" Residue "V ASP 185": "OD1" <-> "OD2" Residue "V GLU 186": "OE1" <-> "OE2" Residue "V PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 232": "OE1" <-> "OE2" Residue "V ASP 253": "OD1" <-> "OD2" Residue "V ASP 283": "OD1" <-> "OD2" Residue "V ASP 328": "OD1" <-> "OD2" Residue "V GLU 388": "OE1" <-> "OE2" Residue "V ASP 398": "OD1" <-> "OD2" Residue "V GLU 448": "OE1" <-> "OE2" Residue "V ASP 473": "OD1" <-> "OD2" Residue "V TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 484": "OE1" <-> "OE2" Residue "V TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 490": "OD1" <-> "OD2" Residue "W ASP 41": "OD1" <-> "OD2" Residue "W GLU 63": "OE1" <-> "OE2" Residue "W GLU 76": "OE1" <-> "OE2" Residue "W ASP 167": "OD1" <-> "OD2" Residue "W GLU 178": "OE1" <-> "OE2" Residue "W ASP 185": "OD1" <-> "OD2" Residue "W GLU 186": "OE1" <-> "OE2" Residue "W PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 232": "OE1" <-> "OE2" Residue "W ASP 253": "OD1" <-> "OD2" Residue "W ASP 283": "OD1" <-> "OD2" Residue "W ASP 328": "OD1" <-> "OD2" Residue "W GLU 388": "OE1" <-> "OE2" Residue "W ASP 398": "OD1" <-> "OD2" Residue "W GLU 448": "OE1" <-> "OE2" Residue "W ASP 473": "OD1" <-> "OD2" Residue "W TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 484": "OE1" <-> "OE2" Residue "W TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 490": "OD1" <-> "OD2" Residue "X ASP 41": "OD1" <-> "OD2" Residue "X GLU 63": "OE1" <-> "OE2" Residue "X GLU 76": "OE1" <-> "OE2" Residue "X ASP 167": "OD1" <-> "OD2" Residue "X GLU 178": "OE1" <-> "OE2" Residue "X ASP 185": "OD1" <-> "OD2" Residue "X GLU 186": "OE1" <-> "OE2" Residue "X PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 232": "OE1" <-> "OE2" Residue "X ASP 253": "OD1" <-> "OD2" Residue "X ASP 283": "OD1" <-> "OD2" Residue "X ASP 328": "OD1" <-> "OD2" Residue "X GLU 388": "OE1" <-> "OE2" Residue "X ASP 398": "OD1" <-> "OD2" Residue "X GLU 448": "OE1" <-> "OE2" Residue "X ASP 473": "OD1" <-> "OD2" Residue "X TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 484": "OE1" <-> "OE2" Residue "X TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 490": "OD1" <-> "OD2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 63994 Number of models: 1 Model: "" Number of chains: 28 Chain: "a" Number of atoms: 716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Conformer: "B" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} bond proxies already assigned to first conformer: 667 Chain: "b" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "A" Number of atoms: 716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Conformer: "B" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} bond proxies already assigned to first conformer: 667 Chain: "G" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "B" Number of atoms: 716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Conformer: "B" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} bond proxies already assigned to first conformer: 667 Chain: "H" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "C" Number of atoms: 716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Conformer: "B" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} bond proxies already assigned to first conformer: 667 Chain: "I" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "D" Number of atoms: 716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Conformer: "B" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} bond proxies already assigned to first conformer: 667 Chain: "J" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "E" Number of atoms: 716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Conformer: "B" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} bond proxies already assigned to first conformer: 667 Chain: "K" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "F" Number of atoms: 716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Conformer: "B" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} bond proxies already assigned to first conformer: 667 Chain: "L" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "Y" Number of atoms: 716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Conformer: "B" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} bond proxies already assigned to first conformer: 667 Chain: "Z" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "M" Number of atoms: 716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Conformer: "B" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} bond proxies already assigned to first conformer: 667 Chain: "S" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "N" Number of atoms: 716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Conformer: "B" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} bond proxies already assigned to first conformer: 667 Chain: "T" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "O" Number of atoms: 716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Conformer: "B" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} bond proxies already assigned to first conformer: 667 Chain: "U" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "P" Number of atoms: 716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Conformer: "B" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} bond proxies already assigned to first conformer: 667 Chain: "V" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "Q" Number of atoms: 716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Conformer: "B" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} bond proxies already assigned to first conformer: 667 Chain: "W" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "R" Number of atoms: 716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Conformer: "B" Number of residues, atoms: 88, 689 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} bond proxies already assigned to first conformer: 667 Chain: "X" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Residues with excluded nonbonded symmetry interactions: 42 residue: pdb=" N AGLN a 204 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN a 204 " occ=0.50 residue: pdb=" N AGLN a 221 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN a 221 " occ=0.50 residue: pdb=" N AGLN a 225 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN a 225 " occ=0.50 residue: pdb=" N AGLN A 204 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 204 " occ=0.50 residue: pdb=" N AGLN A 221 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 221 " occ=0.50 residue: pdb=" N AGLN A 225 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 225 " occ=0.50 residue: pdb=" N AGLN B 204 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 204 " occ=0.50 residue: pdb=" N AGLN B 221 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 221 " occ=0.50 residue: pdb=" N AGLN B 225 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 225 " occ=0.50 residue: pdb=" N AGLN C 204 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C 204 " occ=0.50 residue: pdb=" N AGLN C 221 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C 221 " occ=0.50 residue: pdb=" N AGLN C 225 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C 225 " occ=0.50 ... (remaining 30 not shown) Time building chain proxies: 27.75, per 1000 atoms: 0.43 Number of scatterers: 63994 At special positions: 0 Unit cell: (167.776, 166.208, 225.792, 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 280 16.00 O 12810 8.00 N 11116 7.00 C 39788 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=0, symmetry=0 Time building additional restraints: 19.06 Conformation dependent library (CDL) restraints added in 10.9 seconds 17276 Ramachandran restraints generated. 8638 Oldfield, 0 Emsley, 8638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15680 Finding SS restraints... Secondary structure from input PDB file: 392 helices and 84 sheets defined 63.6% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.93 Creating SS restraints... Processing helix chain 'a' and resid 199 through 212 Processing helix chain 'a' and resid 215 through 229 Processing helix chain 'a' and resid 231 through 246 removed outlier: 3.650A pdb=" N LYS a 245 " --> pdb=" O GLY a 241 " (cutoff:3.500A) Processing helix chain 'a' and resid 248 through 251 Processing helix chain 'a' and resid 252 through 266 Processing helix chain 'a' and resid 269 through 284 Processing helix chain 'b' and resid 9 through 28 removed outlier: 3.948A pdb=" N LYS b 15 " --> pdb=" O ASP b 11 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 31 No H-bonds generated for 'chain 'b' and resid 29 through 31' Processing helix chain 'b' and resid 52 through 60 removed outlier: 3.609A pdb=" N VAL b 56 " --> pdb=" O ASP b 52 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU b 59 " --> pdb=" O SER b 55 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE b 60 " --> pdb=" O VAL b 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 64 through 86 removed outlier: 3.769A pdb=" N VAL b 77 " --> pdb=" O MET b 73 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS b 80 " --> pdb=" O GLU b 76 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA b 81 " --> pdb=" O VAL b 77 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN b 82 " --> pdb=" O ALA b 78 " (cutoff:3.500A) Processing helix chain 'b' and resid 88 through 108 removed outlier: 3.919A pdb=" N GLU b 102 " --> pdb=" O ALA b 98 " (cutoff:3.500A) Processing helix chain 'b' and resid 112 through 135 removed outlier: 3.812A pdb=" N LEU b 116 " --> pdb=" O ASN b 112 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER b 135 " --> pdb=" O LEU b 131 " (cutoff:3.500A) Processing helix chain 'b' and resid 140 through 152 Processing helix chain 'b' and resid 155 through 170 removed outlier: 3.717A pdb=" N GLY b 159 " --> pdb=" O ASP b 155 " (cutoff:3.500A) Processing helix chain 'b' and resid 229 through 232 removed outlier: 3.757A pdb=" N GLU b 232 " --> pdb=" O ASN b 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 229 through 232' Processing helix chain 'b' and resid 233 through 242 Processing helix chain 'b' and resid 243 through 245 No H-bonds generated for 'chain 'b' and resid 243 through 245' Processing helix chain 'b' and resid 256 through 268 Processing helix chain 'b' and resid 282 through 297 removed outlier: 3.832A pdb=" N LYS b 286 " --> pdb=" O GLY b 282 " (cutoff:3.500A) Processing helix chain 'b' and resid 308 through 312 removed outlier: 3.692A pdb=" N ALA b 312 " --> pdb=" O LEU b 309 " (cutoff:3.500A) Processing helix chain 'b' and resid 338 through 355 removed outlier: 3.558A pdb=" N ILE b 342 " --> pdb=" O GLU b 338 " (cutoff:3.500A) Processing helix chain 'b' and resid 358 through 374 Processing helix chain 'b' and resid 385 through 410 removed outlier: 3.836A pdb=" N MET b 389 " --> pdb=" O THR b 385 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU b 409 " --> pdb=" O ALA b 405 " (cutoff:3.500A) Processing helix chain 'b' and resid 416 through 425 removed outlier: 4.256A pdb=" N ILE b 420 " --> pdb=" O GLY b 416 " (cutoff:3.500A) Processing helix chain 'b' and resid 433 through 447 removed outlier: 3.679A pdb=" N ASN b 437 " --> pdb=" O ASN b 433 " (cutoff:3.500A) Processing helix chain 'b' and resid 448 through 458 removed outlier: 3.584A pdb=" N ARG b 452 " --> pdb=" O GLU b 448 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS b 458 " --> pdb=" O ILE b 454 " (cutoff:3.500A) Processing helix chain 'b' and resid 461 through 472 removed outlier: 3.698A pdb=" N VAL b 465 " --> pdb=" O GLU b 461 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY b 472 " --> pdb=" O THR b 468 " (cutoff:3.500A) Processing helix chain 'b' and resid 497 through 516 removed outlier: 3.923A pdb=" N THR b 516 " --> pdb=" O GLY b 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 212 Processing helix chain 'A' and resid 215 through 229 Processing helix chain 'A' and resid 231 through 246 removed outlier: 3.651A pdb=" N LYS A 245 " --> pdb=" O GLY A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 251 Processing helix chain 'A' and resid 252 through 266 Processing helix chain 'A' and resid 269 through 284 Processing helix chain 'G' and resid 9 through 28 removed outlier: 3.948A pdb=" N LYS G 15 " --> pdb=" O ASP G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 52 through 60 removed outlier: 3.609A pdb=" N VAL G 56 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE G 60 " --> pdb=" O VAL G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 86 removed outlier: 3.769A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS G 80 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA G 81 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 108 removed outlier: 3.919A pdb=" N GLU G 102 " --> pdb=" O ALA G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 135 removed outlier: 3.812A pdb=" N LEU G 116 " --> pdb=" O ASN G 112 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER G 135 " --> pdb=" O LEU G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 152 Processing helix chain 'G' and resid 155 through 170 removed outlier: 3.717A pdb=" N GLY G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 232 removed outlier: 3.757A pdb=" N GLU G 232 " --> pdb=" O ASN G 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 229 through 232' Processing helix chain 'G' and resid 233 through 242 Processing helix chain 'G' and resid 243 through 245 No H-bonds generated for 'chain 'G' and resid 243 through 245' Processing helix chain 'G' and resid 256 through 268 Processing helix chain 'G' and resid 282 through 297 removed outlier: 3.831A pdb=" N LYS G 286 " --> pdb=" O GLY G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 312 removed outlier: 3.691A pdb=" N ALA G 312 " --> pdb=" O LEU G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 355 removed outlier: 3.558A pdb=" N ILE G 342 " --> pdb=" O GLU G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 374 Processing helix chain 'G' and resid 385 through 410 removed outlier: 3.836A pdb=" N MET G 389 " --> pdb=" O THR G 385 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU G 409 " --> pdb=" O ALA G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 425 removed outlier: 4.256A pdb=" N ILE G 420 " --> pdb=" O GLY G 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 447 removed outlier: 3.678A pdb=" N ASN G 437 " --> pdb=" O ASN G 433 " (cutoff:3.500A) Processing helix chain 'G' and resid 448 through 458 removed outlier: 3.584A pdb=" N ARG G 452 " --> pdb=" O GLU G 448 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS G 458 " --> pdb=" O ILE G 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 472 removed outlier: 3.698A pdb=" N VAL G 465 " --> pdb=" O GLU G 461 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY G 472 " --> pdb=" O THR G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 516 removed outlier: 3.924A pdb=" N THR G 516 " --> pdb=" O GLY G 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 Processing helix chain 'B' and resid 215 through 229 Processing helix chain 'B' and resid 231 through 246 removed outlier: 3.650A pdb=" N LYS B 245 " --> pdb=" O GLY B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 251 Processing helix chain 'B' and resid 252 through 266 Processing helix chain 'B' and resid 269 through 284 Processing helix chain 'H' and resid 9 through 28 removed outlier: 3.948A pdb=" N LYS H 15 " --> pdb=" O ASP H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 52 through 60 removed outlier: 3.609A pdb=" N VAL H 56 " --> pdb=" O ASP H 52 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE H 60 " --> pdb=" O VAL H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 86 removed outlier: 3.769A pdb=" N VAL H 77 " --> pdb=" O MET H 73 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS H 80 " --> pdb=" O GLU H 76 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA H 81 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 108 removed outlier: 3.919A pdb=" N GLU H 102 " --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 135 removed outlier: 3.812A pdb=" N LEU H 116 " --> pdb=" O ASN H 112 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER H 135 " --> pdb=" O LEU H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 152 Processing helix chain 'H' and resid 155 through 170 removed outlier: 3.716A pdb=" N GLY H 159 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 232 removed outlier: 3.757A pdb=" N GLU H 232 " --> pdb=" O ASN H 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 229 through 232' Processing helix chain 'H' and resid 233 through 242 Processing helix chain 'H' and resid 243 through 245 No H-bonds generated for 'chain 'H' and resid 243 through 245' Processing helix chain 'H' and resid 256 through 268 Processing helix chain 'H' and resid 282 through 297 removed outlier: 3.832A pdb=" N LYS H 286 " --> pdb=" O GLY H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 312 removed outlier: 3.692A pdb=" N ALA H 312 " --> pdb=" O LEU H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 355 removed outlier: 3.557A pdb=" N ILE H 342 " --> pdb=" O GLU H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 358 through 374 Processing helix chain 'H' and resid 385 through 410 removed outlier: 3.836A pdb=" N MET H 389 " --> pdb=" O THR H 385 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU H 409 " --> pdb=" O ALA H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 425 removed outlier: 4.256A pdb=" N ILE H 420 " --> pdb=" O GLY H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 447 removed outlier: 3.678A pdb=" N ASN H 437 " --> pdb=" O ASN H 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 448 through 458 removed outlier: 3.584A pdb=" N ARG H 452 " --> pdb=" O GLU H 448 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS H 458 " --> pdb=" O ILE H 454 " (cutoff:3.500A) Processing helix chain 'H' and resid 461 through 472 removed outlier: 3.698A pdb=" N VAL H 465 " --> pdb=" O GLU H 461 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY H 472 " --> pdb=" O THR H 468 " (cutoff:3.500A) Processing helix chain 'H' and resid 497 through 516 removed outlier: 3.923A pdb=" N THR H 516 " --> pdb=" O GLY H 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 215 through 229 Processing helix chain 'C' and resid 231 through 246 removed outlier: 3.650A pdb=" N LYS C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 251 Processing helix chain 'C' and resid 252 through 266 Processing helix chain 'C' and resid 269 through 284 Processing helix chain 'I' and resid 9 through 28 removed outlier: 3.948A pdb=" N LYS I 15 " --> pdb=" O ASP I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 52 through 60 removed outlier: 3.609A pdb=" N VAL I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU I 59 " --> pdb=" O SER I 55 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE I 60 " --> pdb=" O VAL I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 86 removed outlier: 3.769A pdb=" N VAL I 77 " --> pdb=" O MET I 73 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS I 80 " --> pdb=" O GLU I 76 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 108 removed outlier: 3.919A pdb=" N GLU I 102 " --> pdb=" O ALA I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 135 removed outlier: 3.812A pdb=" N LEU I 116 " --> pdb=" O ASN I 112 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER I 135 " --> pdb=" O LEU I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 152 Processing helix chain 'I' and resid 155 through 170 removed outlier: 3.717A pdb=" N GLY I 159 " --> pdb=" O ASP I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 232 removed outlier: 3.757A pdb=" N GLU I 232 " --> pdb=" O ASN I 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 229 through 232' Processing helix chain 'I' and resid 233 through 242 Processing helix chain 'I' and resid 243 through 245 No H-bonds generated for 'chain 'I' and resid 243 through 245' Processing helix chain 'I' and resid 256 through 268 Processing helix chain 'I' and resid 282 through 297 removed outlier: 3.833A pdb=" N LYS I 286 " --> pdb=" O GLY I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 312 removed outlier: 3.691A pdb=" N ALA I 312 " --> pdb=" O LEU I 309 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 355 removed outlier: 3.557A pdb=" N ILE I 342 " --> pdb=" O GLU I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 374 Processing helix chain 'I' and resid 385 through 410 removed outlier: 3.836A pdb=" N MET I 389 " --> pdb=" O THR I 385 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU I 409 " --> pdb=" O ALA I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 416 through 425 removed outlier: 4.256A pdb=" N ILE I 420 " --> pdb=" O GLY I 416 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 447 removed outlier: 3.679A pdb=" N ASN I 437 " --> pdb=" O ASN I 433 " (cutoff:3.500A) Processing helix chain 'I' and resid 448 through 458 removed outlier: 3.584A pdb=" N ARG I 452 " --> pdb=" O GLU I 448 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS I 458 " --> pdb=" O ILE I 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 461 through 472 removed outlier: 3.698A pdb=" N VAL I 465 " --> pdb=" O GLU I 461 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY I 472 " --> pdb=" O THR I 468 " (cutoff:3.500A) Processing helix chain 'I' and resid 497 through 516 removed outlier: 3.923A pdb=" N THR I 516 " --> pdb=" O GLY I 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 212 Processing helix chain 'D' and resid 215 through 229 Processing helix chain 'D' and resid 231 through 246 removed outlier: 3.649A pdb=" N LYS D 245 " --> pdb=" O GLY D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 251 Processing helix chain 'D' and resid 252 through 266 Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'J' and resid 9 through 28 removed outlier: 3.948A pdb=" N LYS J 15 " --> pdb=" O ASP J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 31 No H-bonds generated for 'chain 'J' and resid 29 through 31' Processing helix chain 'J' and resid 52 through 60 removed outlier: 3.610A pdb=" N VAL J 56 " --> pdb=" O ASP J 52 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU J 59 " --> pdb=" O SER J 55 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE J 60 " --> pdb=" O VAL J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 86 removed outlier: 3.770A pdb=" N VAL J 77 " --> pdb=" O MET J 73 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS J 80 " --> pdb=" O GLU J 76 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA J 81 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN J 82 " --> pdb=" O ALA J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 108 removed outlier: 3.919A pdb=" N GLU J 102 " --> pdb=" O ALA J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 135 removed outlier: 3.812A pdb=" N LEU J 116 " --> pdb=" O ASN J 112 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER J 135 " --> pdb=" O LEU J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 152 Processing helix chain 'J' and resid 155 through 170 removed outlier: 3.717A pdb=" N GLY J 159 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 232 removed outlier: 3.756A pdb=" N GLU J 232 " --> pdb=" O ASN J 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 229 through 232' Processing helix chain 'J' and resid 233 through 242 Processing helix chain 'J' and resid 243 through 245 No H-bonds generated for 'chain 'J' and resid 243 through 245' Processing helix chain 'J' and resid 256 through 268 Processing helix chain 'J' and resid 282 through 297 removed outlier: 3.832A pdb=" N LYS J 286 " --> pdb=" O GLY J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 312 removed outlier: 3.692A pdb=" N ALA J 312 " --> pdb=" O LEU J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 355 removed outlier: 3.557A pdb=" N ILE J 342 " --> pdb=" O GLU J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 358 through 374 Processing helix chain 'J' and resid 385 through 410 removed outlier: 3.836A pdb=" N MET J 389 " --> pdb=" O THR J 385 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU J 409 " --> pdb=" O ALA J 405 " (cutoff:3.500A) Processing helix chain 'J' and resid 416 through 425 removed outlier: 4.257A pdb=" N ILE J 420 " --> pdb=" O GLY J 416 " (cutoff:3.500A) Processing helix chain 'J' and resid 433 through 447 removed outlier: 3.679A pdb=" N ASN J 437 " --> pdb=" O ASN J 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 448 through 458 removed outlier: 3.584A pdb=" N ARG J 452 " --> pdb=" O GLU J 448 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS J 458 " --> pdb=" O ILE J 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 461 through 472 removed outlier: 3.698A pdb=" N VAL J 465 " --> pdb=" O GLU J 461 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY J 472 " --> pdb=" O THR J 468 " (cutoff:3.500A) Processing helix chain 'J' and resid 497 through 516 removed outlier: 3.923A pdb=" N THR J 516 " --> pdb=" O GLY J 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 212 Processing helix chain 'E' and resid 215 through 229 Processing helix chain 'E' and resid 231 through 246 removed outlier: 3.650A pdb=" N LYS E 245 " --> pdb=" O GLY E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 251 Processing helix chain 'E' and resid 252 through 266 Processing helix chain 'E' and resid 269 through 284 Processing helix chain 'K' and resid 9 through 28 removed outlier: 3.947A pdb=" N LYS K 15 " --> pdb=" O ASP K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 31 No H-bonds generated for 'chain 'K' and resid 29 through 31' Processing helix chain 'K' and resid 52 through 60 removed outlier: 3.610A pdb=" N VAL K 56 " --> pdb=" O ASP K 52 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU K 59 " --> pdb=" O SER K 55 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE K 60 " --> pdb=" O VAL K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 86 removed outlier: 3.769A pdb=" N VAL K 77 " --> pdb=" O MET K 73 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS K 80 " --> pdb=" O GLU K 76 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA K 81 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN K 82 " --> pdb=" O ALA K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 108 removed outlier: 3.919A pdb=" N GLU K 102 " --> pdb=" O ALA K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 135 removed outlier: 3.813A pdb=" N LEU K 116 " --> pdb=" O ASN K 112 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER K 135 " --> pdb=" O LEU K 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 152 Processing helix chain 'K' and resid 155 through 170 removed outlier: 3.716A pdb=" N GLY K 159 " --> pdb=" O ASP K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 229 through 232 removed outlier: 3.757A pdb=" N GLU K 232 " --> pdb=" O ASN K 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 229 through 232' Processing helix chain 'K' and resid 233 through 242 Processing helix chain 'K' and resid 243 through 245 No H-bonds generated for 'chain 'K' and resid 243 through 245' Processing helix chain 'K' and resid 256 through 268 Processing helix chain 'K' and resid 282 through 297 removed outlier: 3.832A pdb=" N LYS K 286 " --> pdb=" O GLY K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 312 removed outlier: 3.691A pdb=" N ALA K 312 " --> pdb=" O LEU K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 355 removed outlier: 3.558A pdb=" N ILE K 342 " --> pdb=" O GLU K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 374 Processing helix chain 'K' and resid 385 through 410 removed outlier: 3.835A pdb=" N MET K 389 " --> pdb=" O THR K 385 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU K 409 " --> pdb=" O ALA K 405 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 425 removed outlier: 4.256A pdb=" N ILE K 420 " --> pdb=" O GLY K 416 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 447 removed outlier: 3.678A pdb=" N ASN K 437 " --> pdb=" O ASN K 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 448 through 458 removed outlier: 3.584A pdb=" N ARG K 452 " --> pdb=" O GLU K 448 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS K 458 " --> pdb=" O ILE K 454 " (cutoff:3.500A) Processing helix chain 'K' and resid 461 through 472 removed outlier: 3.698A pdb=" N VAL K 465 " --> pdb=" O GLU K 461 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY K 472 " --> pdb=" O THR K 468 " (cutoff:3.500A) Processing helix chain 'K' and resid 497 through 516 removed outlier: 3.923A pdb=" N THR K 516 " --> pdb=" O GLY K 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 212 Processing helix chain 'F' and resid 215 through 229 Processing helix chain 'F' and resid 231 through 246 removed outlier: 3.650A pdb=" N LYS F 245 " --> pdb=" O GLY F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 251 Processing helix chain 'F' and resid 252 through 266 Processing helix chain 'F' and resid 269 through 284 Processing helix chain 'L' and resid 9 through 28 removed outlier: 3.948A pdb=" N LYS L 15 " --> pdb=" O ASP L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 52 through 60 removed outlier: 3.610A pdb=" N VAL L 56 " --> pdb=" O ASP L 52 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU L 59 " --> pdb=" O SER L 55 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE L 60 " --> pdb=" O VAL L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 86 removed outlier: 3.769A pdb=" N VAL L 77 " --> pdb=" O MET L 73 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS L 80 " --> pdb=" O GLU L 76 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA L 81 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN L 82 " --> pdb=" O ALA L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 108 removed outlier: 3.918A pdb=" N GLU L 102 " --> pdb=" O ALA L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 135 removed outlier: 3.812A pdb=" N LEU L 116 " --> pdb=" O ASN L 112 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER L 135 " --> pdb=" O LEU L 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 152 Processing helix chain 'L' and resid 155 through 170 removed outlier: 3.717A pdb=" N GLY L 159 " --> pdb=" O ASP L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 229 through 232 removed outlier: 3.757A pdb=" N GLU L 232 " --> pdb=" O ASN L 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 229 through 232' Processing helix chain 'L' and resid 233 through 242 Processing helix chain 'L' and resid 243 through 245 No H-bonds generated for 'chain 'L' and resid 243 through 245' Processing helix chain 'L' and resid 256 through 268 Processing helix chain 'L' and resid 282 through 297 removed outlier: 3.832A pdb=" N LYS L 286 " --> pdb=" O GLY L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 312 removed outlier: 3.691A pdb=" N ALA L 312 " --> pdb=" O LEU L 309 " (cutoff:3.500A) Processing helix chain 'L' and resid 338 through 355 removed outlier: 3.557A pdb=" N ILE L 342 " --> pdb=" O GLU L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 358 through 374 Processing helix chain 'L' and resid 385 through 410 removed outlier: 3.836A pdb=" N MET L 389 " --> pdb=" O THR L 385 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU L 409 " --> pdb=" O ALA L 405 " (cutoff:3.500A) Processing helix chain 'L' and resid 416 through 425 removed outlier: 4.256A pdb=" N ILE L 420 " --> pdb=" O GLY L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 433 through 447 removed outlier: 3.678A pdb=" N ASN L 437 " --> pdb=" O ASN L 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 458 removed outlier: 3.584A pdb=" N ARG L 452 " --> pdb=" O GLU L 448 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS L 458 " --> pdb=" O ILE L 454 " (cutoff:3.500A) Processing helix chain 'L' and resid 461 through 472 removed outlier: 3.698A pdb=" N VAL L 465 " --> pdb=" O GLU L 461 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY L 472 " --> pdb=" O THR L 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 497 through 516 removed outlier: 3.923A pdb=" N THR L 516 " --> pdb=" O GLY L 512 " (cutoff:3.500A) Processing helix chain 'Y' and resid 199 through 212 Processing helix chain 'Y' and resid 215 through 229 Processing helix chain 'Y' and resid 231 through 246 removed outlier: 3.650A pdb=" N LYS Y 245 " --> pdb=" O GLY Y 241 " (cutoff:3.500A) Processing helix chain 'Y' and resid 248 through 251 Processing helix chain 'Y' and resid 252 through 266 Processing helix chain 'Y' and resid 269 through 284 Processing helix chain 'Z' and resid 9 through 28 removed outlier: 3.949A pdb=" N LYS Z 15 " --> pdb=" O ASP Z 11 " (cutoff:3.500A) Processing helix chain 'Z' and resid 29 through 31 No H-bonds generated for 'chain 'Z' and resid 29 through 31' Processing helix chain 'Z' and resid 52 through 60 removed outlier: 3.610A pdb=" N VAL Z 56 " --> pdb=" O ASP Z 52 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU Z 59 " --> pdb=" O SER Z 55 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE Z 60 " --> pdb=" O VAL Z 56 " (cutoff:3.500A) Processing helix chain 'Z' and resid 64 through 86 removed outlier: 3.769A pdb=" N VAL Z 77 " --> pdb=" O MET Z 73 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS Z 80 " --> pdb=" O GLU Z 76 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA Z 81 " --> pdb=" O VAL Z 77 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN Z 82 " --> pdb=" O ALA Z 78 " (cutoff:3.500A) Processing helix chain 'Z' and resid 88 through 108 removed outlier: 3.918A pdb=" N GLU Z 102 " --> pdb=" O ALA Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 112 through 135 removed outlier: 3.812A pdb=" N LEU Z 116 " --> pdb=" O ASN Z 112 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER Z 135 " --> pdb=" O LEU Z 131 " (cutoff:3.500A) Processing helix chain 'Z' and resid 140 through 152 Processing helix chain 'Z' and resid 155 through 170 removed outlier: 3.717A pdb=" N GLY Z 159 " --> pdb=" O ASP Z 155 " (cutoff:3.500A) Processing helix chain 'Z' and resid 229 through 232 removed outlier: 3.757A pdb=" N GLU Z 232 " --> pdb=" O ASN Z 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 229 through 232' Processing helix chain 'Z' and resid 233 through 242 Processing helix chain 'Z' and resid 243 through 245 No H-bonds generated for 'chain 'Z' and resid 243 through 245' Processing helix chain 'Z' and resid 256 through 268 Processing helix chain 'Z' and resid 282 through 297 removed outlier: 3.832A pdb=" N LYS Z 286 " --> pdb=" O GLY Z 282 " (cutoff:3.500A) Processing helix chain 'Z' and resid 308 through 312 removed outlier: 3.691A pdb=" N ALA Z 312 " --> pdb=" O LEU Z 309 " (cutoff:3.500A) Processing helix chain 'Z' and resid 338 through 355 removed outlier: 3.558A pdb=" N ILE Z 342 " --> pdb=" O GLU Z 338 " (cutoff:3.500A) Processing helix chain 'Z' and resid 358 through 374 Processing helix chain 'Z' and resid 385 through 410 removed outlier: 3.836A pdb=" N MET Z 389 " --> pdb=" O THR Z 385 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU Z 409 " --> pdb=" O ALA Z 405 " (cutoff:3.500A) Processing helix chain 'Z' and resid 416 through 425 removed outlier: 4.256A pdb=" N ILE Z 420 " --> pdb=" O GLY Z 416 " (cutoff:3.500A) Processing helix chain 'Z' and resid 433 through 447 removed outlier: 3.679A pdb=" N ASN Z 437 " --> pdb=" O ASN Z 433 " (cutoff:3.500A) Processing helix chain 'Z' and resid 448 through 458 removed outlier: 3.584A pdb=" N ARG Z 452 " --> pdb=" O GLU Z 448 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS Z 458 " --> pdb=" O ILE Z 454 " (cutoff:3.500A) Processing helix chain 'Z' and resid 461 through 472 removed outlier: 3.699A pdb=" N VAL Z 465 " --> pdb=" O GLU Z 461 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY Z 472 " --> pdb=" O THR Z 468 " (cutoff:3.500A) Processing helix chain 'Z' and resid 497 through 516 removed outlier: 3.922A pdb=" N THR Z 516 " --> pdb=" O GLY Z 512 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 212 Processing helix chain 'M' and resid 215 through 229 Processing helix chain 'M' and resid 231 through 246 removed outlier: 3.651A pdb=" N LYS M 245 " --> pdb=" O GLY M 241 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 251 Processing helix chain 'M' and resid 252 through 266 Processing helix chain 'M' and resid 269 through 284 Processing helix chain 'S' and resid 9 through 28 removed outlier: 3.948A pdb=" N LYS S 15 " --> pdb=" O ASP S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 52 through 60 removed outlier: 3.609A pdb=" N VAL S 56 " --> pdb=" O ASP S 52 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU S 59 " --> pdb=" O SER S 55 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE S 60 " --> pdb=" O VAL S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 86 removed outlier: 3.768A pdb=" N VAL S 77 " --> pdb=" O MET S 73 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS S 80 " --> pdb=" O GLU S 76 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA S 81 " --> pdb=" O VAL S 77 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN S 82 " --> pdb=" O ALA S 78 " (cutoff:3.500A) Processing helix chain 'S' and resid 88 through 108 removed outlier: 3.919A pdb=" N GLU S 102 " --> pdb=" O ALA S 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 112 through 135 removed outlier: 3.812A pdb=" N LEU S 116 " --> pdb=" O ASN S 112 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER S 135 " --> pdb=" O LEU S 131 " (cutoff:3.500A) Processing helix chain 'S' and resid 140 through 152 Processing helix chain 'S' and resid 155 through 170 removed outlier: 3.717A pdb=" N GLY S 159 " --> pdb=" O ASP S 155 " (cutoff:3.500A) Processing helix chain 'S' and resid 229 through 232 removed outlier: 3.757A pdb=" N GLU S 232 " --> pdb=" O ASN S 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 229 through 232' Processing helix chain 'S' and resid 233 through 242 Processing helix chain 'S' and resid 243 through 245 No H-bonds generated for 'chain 'S' and resid 243 through 245' Processing helix chain 'S' and resid 256 through 268 Processing helix chain 'S' and resid 282 through 297 removed outlier: 3.832A pdb=" N LYS S 286 " --> pdb=" O GLY S 282 " (cutoff:3.500A) Processing helix chain 'S' and resid 308 through 312 removed outlier: 3.692A pdb=" N ALA S 312 " --> pdb=" O LEU S 309 " (cutoff:3.500A) Processing helix chain 'S' and resid 338 through 355 removed outlier: 3.558A pdb=" N ILE S 342 " --> pdb=" O GLU S 338 " (cutoff:3.500A) Processing helix chain 'S' and resid 358 through 374 Processing helix chain 'S' and resid 385 through 410 removed outlier: 3.836A pdb=" N MET S 389 " --> pdb=" O THR S 385 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU S 409 " --> pdb=" O ALA S 405 " (cutoff:3.500A) Processing helix chain 'S' and resid 416 through 425 removed outlier: 4.256A pdb=" N ILE S 420 " --> pdb=" O GLY S 416 " (cutoff:3.500A) Processing helix chain 'S' and resid 433 through 447 removed outlier: 3.678A pdb=" N ASN S 437 " --> pdb=" O ASN S 433 " (cutoff:3.500A) Processing helix chain 'S' and resid 448 through 458 removed outlier: 3.584A pdb=" N ARG S 452 " --> pdb=" O GLU S 448 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS S 458 " --> pdb=" O ILE S 454 " (cutoff:3.500A) Processing helix chain 'S' and resid 461 through 472 removed outlier: 3.698A pdb=" N VAL S 465 " --> pdb=" O GLU S 461 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY S 472 " --> pdb=" O THR S 468 " (cutoff:3.500A) Processing helix chain 'S' and resid 497 through 516 removed outlier: 3.922A pdb=" N THR S 516 " --> pdb=" O GLY S 512 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 212 Processing helix chain 'N' and resid 215 through 229 Processing helix chain 'N' and resid 231 through 246 removed outlier: 3.650A pdb=" N LYS N 245 " --> pdb=" O GLY N 241 " (cutoff:3.500A) Processing helix chain 'N' and resid 248 through 251 Processing helix chain 'N' and resid 252 through 266 Processing helix chain 'N' and resid 269 through 284 Processing helix chain 'T' and resid 9 through 28 removed outlier: 3.948A pdb=" N LYS T 15 " --> pdb=" O ASP T 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 31 No H-bonds generated for 'chain 'T' and resid 29 through 31' Processing helix chain 'T' and resid 52 through 60 removed outlier: 3.609A pdb=" N VAL T 56 " --> pdb=" O ASP T 52 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU T 59 " --> pdb=" O SER T 55 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE T 60 " --> pdb=" O VAL T 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 86 removed outlier: 3.769A pdb=" N VAL T 77 " --> pdb=" O MET T 73 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS T 80 " --> pdb=" O GLU T 76 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA T 81 " --> pdb=" O VAL T 77 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN T 82 " --> pdb=" O ALA T 78 " (cutoff:3.500A) Processing helix chain 'T' and resid 88 through 108 removed outlier: 3.919A pdb=" N GLU T 102 " --> pdb=" O ALA T 98 " (cutoff:3.500A) Processing helix chain 'T' and resid 112 through 135 removed outlier: 3.812A pdb=" N LEU T 116 " --> pdb=" O ASN T 112 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER T 135 " --> pdb=" O LEU T 131 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 152 Processing helix chain 'T' and resid 155 through 170 removed outlier: 3.718A pdb=" N GLY T 159 " --> pdb=" O ASP T 155 " (cutoff:3.500A) Processing helix chain 'T' and resid 229 through 232 removed outlier: 3.756A pdb=" N GLU T 232 " --> pdb=" O ASN T 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 229 through 232' Processing helix chain 'T' and resid 233 through 242 Processing helix chain 'T' and resid 243 through 245 No H-bonds generated for 'chain 'T' and resid 243 through 245' Processing helix chain 'T' and resid 256 through 268 Processing helix chain 'T' and resid 282 through 297 removed outlier: 3.832A pdb=" N LYS T 286 " --> pdb=" O GLY T 282 " (cutoff:3.500A) Processing helix chain 'T' and resid 308 through 312 removed outlier: 3.692A pdb=" N ALA T 312 " --> pdb=" O LEU T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 338 through 355 removed outlier: 3.557A pdb=" N ILE T 342 " --> pdb=" O GLU T 338 " (cutoff:3.500A) Processing helix chain 'T' and resid 358 through 374 Processing helix chain 'T' and resid 385 through 410 removed outlier: 3.836A pdb=" N MET T 389 " --> pdb=" O THR T 385 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU T 409 " --> pdb=" O ALA T 405 " (cutoff:3.500A) Processing helix chain 'T' and resid 416 through 425 removed outlier: 4.257A pdb=" N ILE T 420 " --> pdb=" O GLY T 416 " (cutoff:3.500A) Processing helix chain 'T' and resid 433 through 447 removed outlier: 3.679A pdb=" N ASN T 437 " --> pdb=" O ASN T 433 " (cutoff:3.500A) Processing helix chain 'T' and resid 448 through 458 removed outlier: 3.584A pdb=" N ARG T 452 " --> pdb=" O GLU T 448 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS T 458 " --> pdb=" O ILE T 454 " (cutoff:3.500A) Processing helix chain 'T' and resid 461 through 472 removed outlier: 3.698A pdb=" N VAL T 465 " --> pdb=" O GLU T 461 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY T 472 " --> pdb=" O THR T 468 " (cutoff:3.500A) Processing helix chain 'T' and resid 497 through 516 removed outlier: 3.923A pdb=" N THR T 516 " --> pdb=" O GLY T 512 " (cutoff:3.500A) Processing helix chain 'O' and resid 199 through 212 Processing helix chain 'O' and resid 215 through 229 Processing helix chain 'O' and resid 231 through 246 removed outlier: 3.650A pdb=" N LYS O 245 " --> pdb=" O GLY O 241 " (cutoff:3.500A) Processing helix chain 'O' and resid 248 through 251 Processing helix chain 'O' and resid 252 through 266 Processing helix chain 'O' and resid 269 through 284 Processing helix chain 'U' and resid 9 through 28 removed outlier: 3.948A pdb=" N LYS U 15 " --> pdb=" O ASP U 11 " (cutoff:3.500A) Processing helix chain 'U' and resid 29 through 31 No H-bonds generated for 'chain 'U' and resid 29 through 31' Processing helix chain 'U' and resid 52 through 60 removed outlier: 3.609A pdb=" N VAL U 56 " --> pdb=" O ASP U 52 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU U 59 " --> pdb=" O SER U 55 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE U 60 " --> pdb=" O VAL U 56 " (cutoff:3.500A) Processing helix chain 'U' and resid 64 through 86 removed outlier: 3.769A pdb=" N VAL U 77 " --> pdb=" O MET U 73 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS U 80 " --> pdb=" O GLU U 76 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA U 81 " --> pdb=" O VAL U 77 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN U 82 " --> pdb=" O ALA U 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 88 through 108 removed outlier: 3.919A pdb=" N GLU U 102 " --> pdb=" O ALA U 98 " (cutoff:3.500A) Processing helix chain 'U' and resid 112 through 135 removed outlier: 3.811A pdb=" N LEU U 116 " --> pdb=" O ASN U 112 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER U 135 " --> pdb=" O LEU U 131 " (cutoff:3.500A) Processing helix chain 'U' and resid 140 through 152 Processing helix chain 'U' and resid 155 through 170 removed outlier: 3.717A pdb=" N GLY U 159 " --> pdb=" O ASP U 155 " (cutoff:3.500A) Processing helix chain 'U' and resid 229 through 232 removed outlier: 3.756A pdb=" N GLU U 232 " --> pdb=" O ASN U 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 229 through 232' Processing helix chain 'U' and resid 233 through 242 Processing helix chain 'U' and resid 243 through 245 No H-bonds generated for 'chain 'U' and resid 243 through 245' Processing helix chain 'U' and resid 256 through 268 Processing helix chain 'U' and resid 282 through 297 removed outlier: 3.832A pdb=" N LYS U 286 " --> pdb=" O GLY U 282 " (cutoff:3.500A) Processing helix chain 'U' and resid 308 through 312 removed outlier: 3.692A pdb=" N ALA U 312 " --> pdb=" O LEU U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 338 through 355 removed outlier: 3.558A pdb=" N ILE U 342 " --> pdb=" O GLU U 338 " (cutoff:3.500A) Processing helix chain 'U' and resid 358 through 374 Processing helix chain 'U' and resid 385 through 410 removed outlier: 3.835A pdb=" N MET U 389 " --> pdb=" O THR U 385 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU U 409 " --> pdb=" O ALA U 405 " (cutoff:3.500A) Processing helix chain 'U' and resid 416 through 425 removed outlier: 4.257A pdb=" N ILE U 420 " --> pdb=" O GLY U 416 " (cutoff:3.500A) Processing helix chain 'U' and resid 433 through 447 removed outlier: 3.679A pdb=" N ASN U 437 " --> pdb=" O ASN U 433 " (cutoff:3.500A) Processing helix chain 'U' and resid 448 through 458 removed outlier: 3.584A pdb=" N ARG U 452 " --> pdb=" O GLU U 448 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS U 458 " --> pdb=" O ILE U 454 " (cutoff:3.500A) Processing helix chain 'U' and resid 461 through 472 removed outlier: 3.698A pdb=" N VAL U 465 " --> pdb=" O GLU U 461 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY U 472 " --> pdb=" O THR U 468 " (cutoff:3.500A) Processing helix chain 'U' and resid 497 through 516 removed outlier: 3.923A pdb=" N THR U 516 " --> pdb=" O GLY U 512 " (cutoff:3.500A) Processing helix chain 'P' and resid 199 through 212 Processing helix chain 'P' and resid 215 through 229 Processing helix chain 'P' and resid 231 through 246 removed outlier: 3.650A pdb=" N LYS P 245 " --> pdb=" O GLY P 241 " (cutoff:3.500A) Processing helix chain 'P' and resid 248 through 251 Processing helix chain 'P' and resid 252 through 266 Processing helix chain 'P' and resid 269 through 284 Processing helix chain 'V' and resid 9 through 28 removed outlier: 3.948A pdb=" N LYS V 15 " --> pdb=" O ASP V 11 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 31 No H-bonds generated for 'chain 'V' and resid 29 through 31' Processing helix chain 'V' and resid 52 through 60 removed outlier: 3.610A pdb=" N VAL V 56 " --> pdb=" O ASP V 52 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU V 59 " --> pdb=" O SER V 55 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE V 60 " --> pdb=" O VAL V 56 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 86 removed outlier: 3.769A pdb=" N VAL V 77 " --> pdb=" O MET V 73 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS V 80 " --> pdb=" O GLU V 76 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA V 81 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN V 82 " --> pdb=" O ALA V 78 " (cutoff:3.500A) Processing helix chain 'V' and resid 88 through 108 removed outlier: 3.919A pdb=" N GLU V 102 " --> pdb=" O ALA V 98 " (cutoff:3.500A) Processing helix chain 'V' and resid 112 through 135 removed outlier: 3.812A pdb=" N LEU V 116 " --> pdb=" O ASN V 112 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER V 135 " --> pdb=" O LEU V 131 " (cutoff:3.500A) Processing helix chain 'V' and resid 140 through 152 Processing helix chain 'V' and resid 155 through 170 removed outlier: 3.717A pdb=" N GLY V 159 " --> pdb=" O ASP V 155 " (cutoff:3.500A) Processing helix chain 'V' and resid 229 through 232 removed outlier: 3.757A pdb=" N GLU V 232 " --> pdb=" O ASN V 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 229 through 232' Processing helix chain 'V' and resid 233 through 242 Processing helix chain 'V' and resid 243 through 245 No H-bonds generated for 'chain 'V' and resid 243 through 245' Processing helix chain 'V' and resid 256 through 268 Processing helix chain 'V' and resid 282 through 297 removed outlier: 3.831A pdb=" N LYS V 286 " --> pdb=" O GLY V 282 " (cutoff:3.500A) Processing helix chain 'V' and resid 308 through 312 removed outlier: 3.692A pdb=" N ALA V 312 " --> pdb=" O LEU V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 338 through 355 removed outlier: 3.557A pdb=" N ILE V 342 " --> pdb=" O GLU V 338 " (cutoff:3.500A) Processing helix chain 'V' and resid 358 through 374 Processing helix chain 'V' and resid 385 through 410 removed outlier: 3.835A pdb=" N MET V 389 " --> pdb=" O THR V 385 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU V 409 " --> pdb=" O ALA V 405 " (cutoff:3.500A) Processing helix chain 'V' and resid 416 through 425 removed outlier: 4.256A pdb=" N ILE V 420 " --> pdb=" O GLY V 416 " (cutoff:3.500A) Processing helix chain 'V' and resid 433 through 447 removed outlier: 3.679A pdb=" N ASN V 437 " --> pdb=" O ASN V 433 " (cutoff:3.500A) Processing helix chain 'V' and resid 448 through 458 removed outlier: 3.584A pdb=" N ARG V 452 " --> pdb=" O GLU V 448 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS V 458 " --> pdb=" O ILE V 454 " (cutoff:3.500A) Processing helix chain 'V' and resid 461 through 472 removed outlier: 3.698A pdb=" N VAL V 465 " --> pdb=" O GLU V 461 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY V 472 " --> pdb=" O THR V 468 " (cutoff:3.500A) Processing helix chain 'V' and resid 497 through 516 removed outlier: 3.922A pdb=" N THR V 516 " --> pdb=" O GLY V 512 " (cutoff:3.500A) Processing helix chain 'Q' and resid 199 through 212 Processing helix chain 'Q' and resid 215 through 229 Processing helix chain 'Q' and resid 231 through 246 removed outlier: 3.650A pdb=" N LYS Q 245 " --> pdb=" O GLY Q 241 " (cutoff:3.500A) Processing helix chain 'Q' and resid 248 through 251 Processing helix chain 'Q' and resid 252 through 266 Processing helix chain 'Q' and resid 269 through 284 Processing helix chain 'W' and resid 9 through 28 removed outlier: 3.947A pdb=" N LYS W 15 " --> pdb=" O ASP W 11 " (cutoff:3.500A) Processing helix chain 'W' and resid 29 through 31 No H-bonds generated for 'chain 'W' and resid 29 through 31' Processing helix chain 'W' and resid 52 through 60 removed outlier: 3.609A pdb=" N VAL W 56 " --> pdb=" O ASP W 52 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU W 59 " --> pdb=" O SER W 55 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE W 60 " --> pdb=" O VAL W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 64 through 86 removed outlier: 3.769A pdb=" N VAL W 77 " --> pdb=" O MET W 73 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS W 80 " --> pdb=" O GLU W 76 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA W 81 " --> pdb=" O VAL W 77 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN W 82 " --> pdb=" O ALA W 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 88 through 108 removed outlier: 3.919A pdb=" N GLU W 102 " --> pdb=" O ALA W 98 " (cutoff:3.500A) Processing helix chain 'W' and resid 112 through 135 removed outlier: 3.812A pdb=" N LEU W 116 " --> pdb=" O ASN W 112 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER W 135 " --> pdb=" O LEU W 131 " (cutoff:3.500A) Processing helix chain 'W' and resid 140 through 152 Processing helix chain 'W' and resid 155 through 170 removed outlier: 3.717A pdb=" N GLY W 159 " --> pdb=" O ASP W 155 " (cutoff:3.500A) Processing helix chain 'W' and resid 229 through 232 removed outlier: 3.756A pdb=" N GLU W 232 " --> pdb=" O ASN W 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 229 through 232' Processing helix chain 'W' and resid 233 through 242 Processing helix chain 'W' and resid 243 through 245 No H-bonds generated for 'chain 'W' and resid 243 through 245' Processing helix chain 'W' and resid 256 through 268 Processing helix chain 'W' and resid 282 through 297 removed outlier: 3.832A pdb=" N LYS W 286 " --> pdb=" O GLY W 282 " (cutoff:3.500A) Processing helix chain 'W' and resid 308 through 312 removed outlier: 3.692A pdb=" N ALA W 312 " --> pdb=" O LEU W 309 " (cutoff:3.500A) Processing helix chain 'W' and resid 338 through 355 removed outlier: 3.557A pdb=" N ILE W 342 " --> pdb=" O GLU W 338 " (cutoff:3.500A) Processing helix chain 'W' and resid 358 through 374 Processing helix chain 'W' and resid 385 through 410 removed outlier: 3.836A pdb=" N MET W 389 " --> pdb=" O THR W 385 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU W 409 " --> pdb=" O ALA W 405 " (cutoff:3.500A) Processing helix chain 'W' and resid 416 through 425 removed outlier: 4.257A pdb=" N ILE W 420 " --> pdb=" O GLY W 416 " (cutoff:3.500A) Processing helix chain 'W' and resid 433 through 447 removed outlier: 3.678A pdb=" N ASN W 437 " --> pdb=" O ASN W 433 " (cutoff:3.500A) Processing helix chain 'W' and resid 448 through 458 removed outlier: 3.584A pdb=" N ARG W 452 " --> pdb=" O GLU W 448 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS W 458 " --> pdb=" O ILE W 454 " (cutoff:3.500A) Processing helix chain 'W' and resid 461 through 472 removed outlier: 3.698A pdb=" N VAL W 465 " --> pdb=" O GLU W 461 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY W 472 " --> pdb=" O THR W 468 " (cutoff:3.500A) Processing helix chain 'W' and resid 497 through 516 removed outlier: 3.922A pdb=" N THR W 516 " --> pdb=" O GLY W 512 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 212 Processing helix chain 'R' and resid 215 through 229 Processing helix chain 'R' and resid 231 through 246 removed outlier: 3.649A pdb=" N LYS R 245 " --> pdb=" O GLY R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 251 Processing helix chain 'R' and resid 252 through 266 Processing helix chain 'R' and resid 269 through 284 Processing helix chain 'X' and resid 9 through 28 removed outlier: 3.948A pdb=" N LYS X 15 " --> pdb=" O ASP X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 29 through 31 No H-bonds generated for 'chain 'X' and resid 29 through 31' Processing helix chain 'X' and resid 52 through 60 removed outlier: 3.610A pdb=" N VAL X 56 " --> pdb=" O ASP X 52 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU X 59 " --> pdb=" O SER X 55 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE X 60 " --> pdb=" O VAL X 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 86 removed outlier: 3.769A pdb=" N VAL X 77 " --> pdb=" O MET X 73 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS X 80 " --> pdb=" O GLU X 76 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA X 81 " --> pdb=" O VAL X 77 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN X 82 " --> pdb=" O ALA X 78 " (cutoff:3.500A) Processing helix chain 'X' and resid 88 through 108 removed outlier: 3.919A pdb=" N GLU X 102 " --> pdb=" O ALA X 98 " (cutoff:3.500A) Processing helix chain 'X' and resid 112 through 135 removed outlier: 3.812A pdb=" N LEU X 116 " --> pdb=" O ASN X 112 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER X 135 " --> pdb=" O LEU X 131 " (cutoff:3.500A) Processing helix chain 'X' and resid 140 through 152 Processing helix chain 'X' and resid 155 through 170 removed outlier: 3.717A pdb=" N GLY X 159 " --> pdb=" O ASP X 155 " (cutoff:3.500A) Processing helix chain 'X' and resid 229 through 232 removed outlier: 3.757A pdb=" N GLU X 232 " --> pdb=" O ASN X 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 229 through 232' Processing helix chain 'X' and resid 233 through 242 Processing helix chain 'X' and resid 243 through 245 No H-bonds generated for 'chain 'X' and resid 243 through 245' Processing helix chain 'X' and resid 256 through 268 Processing helix chain 'X' and resid 282 through 297 removed outlier: 3.832A pdb=" N LYS X 286 " --> pdb=" O GLY X 282 " (cutoff:3.500A) Processing helix chain 'X' and resid 308 through 312 removed outlier: 3.691A pdb=" N ALA X 312 " --> pdb=" O LEU X 309 " (cutoff:3.500A) Processing helix chain 'X' and resid 338 through 355 removed outlier: 3.557A pdb=" N ILE X 342 " --> pdb=" O GLU X 338 " (cutoff:3.500A) Processing helix chain 'X' and resid 358 through 374 Processing helix chain 'X' and resid 385 through 410 removed outlier: 3.836A pdb=" N MET X 389 " --> pdb=" O THR X 385 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU X 409 " --> pdb=" O ALA X 405 " (cutoff:3.500A) Processing helix chain 'X' and resid 416 through 425 removed outlier: 4.257A pdb=" N ILE X 420 " --> pdb=" O GLY X 416 " (cutoff:3.500A) Processing helix chain 'X' and resid 433 through 447 removed outlier: 3.678A pdb=" N ASN X 437 " --> pdb=" O ASN X 433 " (cutoff:3.500A) Processing helix chain 'X' and resid 448 through 458 removed outlier: 3.584A pdb=" N ARG X 452 " --> pdb=" O GLU X 448 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS X 458 " --> pdb=" O ILE X 454 " (cutoff:3.500A) Processing helix chain 'X' and resid 461 through 472 removed outlier: 3.699A pdb=" N VAL X 465 " --> pdb=" O GLU X 461 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY X 472 " --> pdb=" O THR X 468 " (cutoff:3.500A) Processing helix chain 'X' and resid 497 through 516 removed outlier: 3.923A pdb=" N THR X 516 " --> pdb=" O GLY X 512 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 4 through 8 removed outlier: 6.005A pdb=" N ASN L 37 " --> pdb=" O THR b 517 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N CYS b 519 " --> pdb=" O ASN L 37 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL L 39 " --> pdb=" O CYS b 519 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'b' and resid 48 through 50 removed outlier: 7.375A pdb=" N ASN b 37 " --> pdb=" O CYS G 519 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N VAL G 521 " --> pdb=" O ASN b 37 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL b 39 " --> pdb=" O VAL G 521 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N ASP G 523 " --> pdb=" O VAL b 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'b' and resid 175 through 179 removed outlier: 3.864A pdb=" N VAL b 381 " --> pdb=" O GLU b 178 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 192 through 195 Processing sheet with id=AA5, first strand: chain 'b' and resid 273 through 277 removed outlier: 6.461A pdb=" N LEU b 247 " --> pdb=" O ALA b 274 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL b 276 " --> pdb=" O LEU b 247 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE b 249 " --> pdb=" O VAL b 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 411 through 413 Processing sheet with id=AA7, first strand: chain 'b' and resid 476 through 479 removed outlier: 3.735A pdb=" N GLU b 484 " --> pdb=" O ASN b 479 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 48 through 50 removed outlier: 7.380A pdb=" N ASN G 37 " --> pdb=" O CYS H 519 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N VAL H 521 " --> pdb=" O ASN G 37 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL G 39 " --> pdb=" O VAL H 521 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ASP H 523 " --> pdb=" O VAL G 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 175 through 179 removed outlier: 3.864A pdb=" N VAL G 381 " --> pdb=" O GLU G 178 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 192 through 195 Processing sheet with id=AB2, first strand: chain 'G' and resid 273 through 277 removed outlier: 6.461A pdb=" N LEU G 247 " --> pdb=" O ALA G 274 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL G 276 " --> pdb=" O LEU G 247 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE G 249 " --> pdb=" O VAL G 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 411 through 413 Processing sheet with id=AB4, first strand: chain 'G' and resid 476 through 479 removed outlier: 3.735A pdb=" N GLU G 484 " --> pdb=" O ASN G 479 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 48 through 50 removed outlier: 7.388A pdb=" N ASN H 37 " --> pdb=" O CYS I 519 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N VAL I 521 " --> pdb=" O ASN H 37 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL H 39 " --> pdb=" O VAL I 521 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ASP I 523 " --> pdb=" O VAL H 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 175 through 179 removed outlier: 3.864A pdb=" N VAL H 381 " --> pdb=" O GLU H 178 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 192 through 195 Processing sheet with id=AB8, first strand: chain 'H' and resid 273 through 277 removed outlier: 6.462A pdb=" N LEU H 247 " --> pdb=" O ALA H 274 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N VAL H 276 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE H 249 " --> pdb=" O VAL H 276 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 411 through 413 Processing sheet with id=AC1, first strand: chain 'H' and resid 476 through 479 removed outlier: 3.735A pdb=" N GLU H 484 " --> pdb=" O ASN H 479 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 48 through 50 removed outlier: 7.384A pdb=" N ASN I 37 " --> pdb=" O CYS J 519 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N VAL J 521 " --> pdb=" O ASN I 37 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL I 39 " --> pdb=" O VAL J 521 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N ASP J 523 " --> pdb=" O VAL I 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 175 through 179 removed outlier: 3.863A pdb=" N VAL I 381 " --> pdb=" O GLU I 178 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 192 through 195 Processing sheet with id=AC5, first strand: chain 'I' and resid 273 through 277 removed outlier: 6.462A pdb=" N LEU I 247 " --> pdb=" O ALA I 274 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N VAL I 276 " --> pdb=" O LEU I 247 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE I 249 " --> pdb=" O VAL I 276 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 411 through 413 Processing sheet with id=AC7, first strand: chain 'I' and resid 476 through 479 removed outlier: 3.735A pdb=" N GLU I 484 " --> pdb=" O ASN I 479 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 48 through 50 removed outlier: 7.391A pdb=" N ASN J 37 " --> pdb=" O CYS K 519 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N VAL K 521 " --> pdb=" O ASN J 37 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL J 39 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N ASP K 523 " --> pdb=" O VAL J 39 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 175 through 179 removed outlier: 3.864A pdb=" N VAL J 381 " --> pdb=" O GLU J 178 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 192 through 195 Processing sheet with id=AD2, first strand: chain 'J' and resid 273 through 277 removed outlier: 6.462A pdb=" N LEU J 247 " --> pdb=" O ALA J 274 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N VAL J 276 " --> pdb=" O LEU J 247 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE J 249 " --> pdb=" O VAL J 276 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 411 through 413 Processing sheet with id=AD4, first strand: chain 'J' and resid 476 through 479 removed outlier: 3.735A pdb=" N GLU J 484 " --> pdb=" O ASN J 479 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 48 through 50 removed outlier: 7.362A pdb=" N ASN K 37 " --> pdb=" O CYS L 519 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N VAL L 521 " --> pdb=" O ASN K 37 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL K 39 " --> pdb=" O VAL L 521 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N ASP L 523 " --> pdb=" O VAL K 39 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 175 through 179 removed outlier: 3.863A pdb=" N VAL K 381 " --> pdb=" O GLU K 178 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 192 through 195 Processing sheet with id=AD8, first strand: chain 'K' and resid 273 through 277 removed outlier: 6.461A pdb=" N LEU K 247 " --> pdb=" O ALA K 274 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N VAL K 276 " --> pdb=" O LEU K 247 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE K 249 " --> pdb=" O VAL K 276 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AE1, first strand: chain 'K' and resid 476 through 479 removed outlier: 3.736A pdb=" N GLU K 484 " --> pdb=" O ASN K 479 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 175 through 179 removed outlier: 3.864A pdb=" N VAL L 381 " --> pdb=" O GLU L 178 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 192 through 195 Processing sheet with id=AE4, first strand: chain 'L' and resid 273 through 277 removed outlier: 6.461A pdb=" N LEU L 247 " --> pdb=" O ALA L 274 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL L 276 " --> pdb=" O LEU L 247 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE L 249 " --> pdb=" O VAL L 276 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 411 through 413 Processing sheet with id=AE6, first strand: chain 'L' and resid 476 through 479 removed outlier: 3.735A pdb=" N GLU L 484 " --> pdb=" O ASN L 479 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Z' and resid 4 through 8 removed outlier: 6.005A pdb=" N ASN X 37 " --> pdb=" O THR Z 517 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N CYS Z 519 " --> pdb=" O ASN X 37 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL X 39 " --> pdb=" O CYS Z 519 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Z' and resid 48 through 50 removed outlier: 7.375A pdb=" N ASN Z 37 " --> pdb=" O CYS S 519 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N VAL S 521 " --> pdb=" O ASN Z 37 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL Z 39 " --> pdb=" O VAL S 521 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N ASP S 523 " --> pdb=" O VAL Z 39 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Z' and resid 175 through 179 removed outlier: 3.864A pdb=" N VAL Z 381 " --> pdb=" O GLU Z 178 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Z' and resid 192 through 195 Processing sheet with id=AF2, first strand: chain 'Z' and resid 273 through 277 removed outlier: 6.461A pdb=" N LEU Z 247 " --> pdb=" O ALA Z 274 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N VAL Z 276 " --> pdb=" O LEU Z 247 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE Z 249 " --> pdb=" O VAL Z 276 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Z' and resid 411 through 413 Processing sheet with id=AF4, first strand: chain 'Z' and resid 476 through 479 removed outlier: 3.735A pdb=" N GLU Z 484 " --> pdb=" O ASN Z 479 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 48 through 50 removed outlier: 7.381A pdb=" N ASN S 37 " --> pdb=" O CYS T 519 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N VAL T 521 " --> pdb=" O ASN S 37 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL S 39 " --> pdb=" O VAL T 521 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ASP T 523 " --> pdb=" O VAL S 39 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'S' and resid 175 through 179 removed outlier: 3.863A pdb=" N VAL S 381 " --> pdb=" O GLU S 178 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 192 through 195 Processing sheet with id=AF8, first strand: chain 'S' and resid 273 through 277 removed outlier: 6.461A pdb=" N LEU S 247 " --> pdb=" O ALA S 274 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL S 276 " --> pdb=" O LEU S 247 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE S 249 " --> pdb=" O VAL S 276 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'S' and resid 411 through 413 Processing sheet with id=AG1, first strand: chain 'S' and resid 476 through 479 removed outlier: 3.736A pdb=" N GLU S 484 " --> pdb=" O ASN S 479 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'T' and resid 48 through 50 removed outlier: 7.388A pdb=" N ASN T 37 " --> pdb=" O CYS U 519 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N VAL U 521 " --> pdb=" O ASN T 37 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL T 39 " --> pdb=" O VAL U 521 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ASP U 523 " --> pdb=" O VAL T 39 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'T' and resid 175 through 179 removed outlier: 3.864A pdb=" N VAL T 381 " --> pdb=" O GLU T 178 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'T' and resid 192 through 195 Processing sheet with id=AG5, first strand: chain 'T' and resid 273 through 277 removed outlier: 6.461A pdb=" N LEU T 247 " --> pdb=" O ALA T 274 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N VAL T 276 " --> pdb=" O LEU T 247 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE T 249 " --> pdb=" O VAL T 276 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'T' and resid 411 through 413 Processing sheet with id=AG7, first strand: chain 'T' and resid 476 through 479 removed outlier: 3.735A pdb=" N GLU T 484 " --> pdb=" O ASN T 479 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'U' and resid 48 through 50 removed outlier: 7.384A pdb=" N ASN U 37 " --> pdb=" O CYS V 519 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N VAL V 521 " --> pdb=" O ASN U 37 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL U 39 " --> pdb=" O VAL V 521 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N ASP V 523 " --> pdb=" O VAL U 39 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'U' and resid 175 through 179 removed outlier: 3.864A pdb=" N VAL U 381 " --> pdb=" O GLU U 178 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'U' and resid 192 through 195 Processing sheet with id=AH2, first strand: chain 'U' and resid 273 through 277 removed outlier: 6.461A pdb=" N LEU U 247 " --> pdb=" O ALA U 274 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N VAL U 276 " --> pdb=" O LEU U 247 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE U 249 " --> pdb=" O VAL U 276 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'U' and resid 411 through 413 Processing sheet with id=AH4, first strand: chain 'U' and resid 476 through 479 removed outlier: 3.735A pdb=" N GLU U 484 " --> pdb=" O ASN U 479 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'V' and resid 48 through 50 removed outlier: 7.392A pdb=" N ASN V 37 " --> pdb=" O CYS W 519 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N VAL W 521 " --> pdb=" O ASN V 37 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL V 39 " --> pdb=" O VAL W 521 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N ASP W 523 " --> pdb=" O VAL V 39 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'V' and resid 175 through 179 removed outlier: 3.864A pdb=" N VAL V 381 " --> pdb=" O GLU V 178 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'V' and resid 192 through 195 Processing sheet with id=AH8, first strand: chain 'V' and resid 273 through 277 removed outlier: 6.462A pdb=" N LEU V 247 " --> pdb=" O ALA V 274 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL V 276 " --> pdb=" O LEU V 247 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE V 249 " --> pdb=" O VAL V 276 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'V' and resid 411 through 413 Processing sheet with id=AI1, first strand: chain 'V' and resid 476 through 479 removed outlier: 3.735A pdb=" N GLU V 484 " --> pdb=" O ASN V 479 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'W' and resid 48 through 50 removed outlier: 7.362A pdb=" N ASN W 37 " --> pdb=" O CYS X 519 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N VAL X 521 " --> pdb=" O ASN W 37 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL W 39 " --> pdb=" O VAL X 521 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N ASP X 523 " --> pdb=" O VAL W 39 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'W' and resid 175 through 179 removed outlier: 3.863A pdb=" N VAL W 381 " --> pdb=" O GLU W 178 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'W' and resid 192 through 195 Processing sheet with id=AI5, first strand: chain 'W' and resid 273 through 277 removed outlier: 6.461A pdb=" N LEU W 247 " --> pdb=" O ALA W 274 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL W 276 " --> pdb=" O LEU W 247 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE W 249 " --> pdb=" O VAL W 276 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'W' and resid 411 through 413 Processing sheet with id=AI7, first strand: chain 'W' and resid 476 through 479 removed outlier: 3.735A pdb=" N GLU W 484 " --> pdb=" O ASN W 479 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'X' and resid 175 through 179 removed outlier: 3.864A pdb=" N VAL X 381 " --> pdb=" O GLU X 178 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'X' and resid 192 through 195 Processing sheet with id=AJ1, first strand: chain 'X' and resid 273 through 277 removed outlier: 6.462A pdb=" N LEU X 247 " --> pdb=" O ALA X 274 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL X 276 " --> pdb=" O LEU X 247 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE X 249 " --> pdb=" O VAL X 276 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'X' and resid 411 through 413 Processing sheet with id=AJ3, first strand: chain 'X' and resid 476 through 479 removed outlier: 3.736A pdb=" N GLU X 484 " --> pdb=" O ASN X 479 " (cutoff:3.500A) 4202 hydrogen bonds defined for protein. 12270 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: 26.44 Time building geometry restraints manager: 20.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 21196 1.33 - 1.45: 4990 1.45 - 1.57: 37836 1.57 - 1.69: 0 1.69 - 1.80: 518 Bond restraints: 64540 Sorted by residual: bond pdb=" N VAL S 376 " pdb=" CA VAL S 376 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.11e-02 8.12e+03 1.33e+01 bond pdb=" N VAL V 376 " pdb=" CA VAL V 376 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.11e-02 8.12e+03 1.30e+01 bond pdb=" N VAL W 376 " pdb=" CA VAL W 376 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.11e-02 8.12e+03 1.29e+01 bond pdb=" N VAL Z 376 " pdb=" CA VAL Z 376 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.11e-02 8.12e+03 1.28e+01 bond pdb=" N VAL T 376 " pdb=" CA VAL T 376 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.11e-02 8.12e+03 1.28e+01 ... (remaining 64535 not shown) Histogram of bond angle deviations from ideal: 98.72 - 105.29: 980 105.29 - 111.85: 31665 111.85 - 118.42: 20208 118.42 - 124.98: 34031 124.98 - 131.55: 364 Bond angle restraints: 87248 Sorted by residual: angle pdb=" N GLY Z 9 " pdb=" CA GLY Z 9 " pdb=" C GLY Z 9 " ideal model delta sigma weight residual 110.86 118.18 -7.32 1.84e+00 2.95e-01 1.58e+01 angle pdb=" N GLY U 9 " pdb=" CA GLY U 9 " pdb=" C GLY U 9 " ideal model delta sigma weight residual 110.86 118.17 -7.31 1.84e+00 2.95e-01 1.58e+01 angle pdb=" N GLY S 9 " pdb=" CA GLY S 9 " pdb=" C GLY S 9 " ideal model delta sigma weight residual 110.86 118.15 -7.29 1.84e+00 2.95e-01 1.57e+01 angle pdb=" CG LYS X 160 " pdb=" CD LYS X 160 " pdb=" CE LYS X 160 " ideal model delta sigma weight residual 111.30 120.41 -9.11 2.30e+00 1.89e-01 1.57e+01 angle pdb=" CG LYS T 160 " pdb=" CD LYS T 160 " pdb=" CE LYS T 160 " ideal model delta sigma weight residual 111.30 120.40 -9.10 2.30e+00 1.89e-01 1.57e+01 ... (remaining 87243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 36362 17.62 - 35.23: 2655 35.23 - 52.85: 687 52.85 - 70.46: 266 70.46 - 88.08: 70 Dihedral angle restraints: 40040 sinusoidal: 15596 harmonic: 24444 Sorted by residual: dihedral pdb=" CA ALA L 384 " pdb=" C ALA L 384 " pdb=" N THR L 385 " pdb=" CA THR L 385 " ideal model delta harmonic sigma weight residual -180.00 -152.70 -27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA ALA Z 384 " pdb=" C ALA Z 384 " pdb=" N THR Z 385 " pdb=" CA THR Z 385 " ideal model delta harmonic sigma weight residual -180.00 -152.70 -27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA ALA I 384 " pdb=" C ALA I 384 " pdb=" N THR I 385 " pdb=" CA THR I 385 " ideal model delta harmonic sigma weight residual -180.00 -152.71 -27.29 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 40037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 6048 0.037 - 0.074: 3276 0.074 - 0.111: 852 0.111 - 0.148: 222 0.148 - 0.185: 102 Chirality restraints: 10500 Sorted by residual: chirality pdb=" CA VAL T 376 " pdb=" N VAL T 376 " pdb=" C VAL T 376 " pdb=" CB VAL T 376 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CA VAL L 376 " pdb=" N VAL L 376 " pdb=" C VAL L 376 " pdb=" CB VAL L 376 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA VAL G 376 " pdb=" N VAL G 376 " pdb=" C VAL G 376 " pdb=" CB VAL G 376 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.35e-01 ... (remaining 10497 not shown) Planarity restraints: 11522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA L 373 " -0.023 2.00e-02 2.50e+03 4.59e-02 2.11e+01 pdb=" C ALA L 373 " 0.079 2.00e-02 2.50e+03 pdb=" O ALA L 373 " -0.030 2.00e-02 2.50e+03 pdb=" N GLY L 374 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA T 373 " 0.023 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" C ALA T 373 " -0.079 2.00e-02 2.50e+03 pdb=" O ALA T 373 " 0.030 2.00e-02 2.50e+03 pdb=" N GLY T 374 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA W 373 " -0.023 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" C ALA W 373 " 0.079 2.00e-02 2.50e+03 pdb=" O ALA W 373 " -0.030 2.00e-02 2.50e+03 pdb=" N GLY W 374 " -0.027 2.00e-02 2.50e+03 ... (remaining 11519 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 2986 2.71 - 3.25: 65029 3.25 - 3.80: 95107 3.80 - 4.35: 108120 4.35 - 4.90: 188467 Nonbonded interactions: 459709 Sorted by model distance: nonbonded pdb=" O ILE U 270 " pdb=" CG2 VAL U 271 " model vdw 2.158 3.460 nonbonded pdb=" O ILE V 270 " pdb=" CG2 VAL V 271 " model vdw 2.158 3.460 nonbonded pdb=" O ILE I 270 " pdb=" CG2 VAL I 271 " model vdw 2.158 3.460 nonbonded pdb=" O ILE L 270 " pdb=" CG2 VAL L 271 " model vdw 2.158 3.460 nonbonded pdb=" O ILE Z 270 " pdb=" CG2 VAL Z 271 " model vdw 2.158 3.460 ... (remaining 459704 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 197 through 203 or resid 205 through 220 or resid 222 thro \ ugh 224 or resid 226 through 284)) selection = (chain 'B' and (resid 197 through 203 or resid 205 through 220 or resid 222 thro \ ugh 224 or resid 226 through 284)) selection = (chain 'C' and (resid 197 through 203 or resid 205 through 220 or resid 222 thro \ ugh 224 or resid 226 through 284)) selection = (chain 'D' and (resid 197 through 203 or resid 205 through 220 or resid 222 thro \ ugh 224 or resid 226 through 284)) selection = (chain 'E' and (resid 197 through 203 or resid 205 through 220 or resid 222 thro \ ugh 224 or resid 226 through 284)) selection = (chain 'F' and (resid 197 through 203 or resid 205 through 220 or resid 222 thro \ ugh 224 or resid 226 through 284)) selection = (chain 'M' and (resid 197 through 203 or resid 205 through 220 or resid 222 thro \ ugh 224 or resid 226 through 284)) selection = (chain 'N' and (resid 197 through 203 or resid 205 through 220 or resid 222 thro \ ugh 224 or resid 226 through 284)) selection = (chain 'O' and (resid 197 through 203 or resid 205 through 220 or resid 222 thro \ ugh 224 or resid 226 through 284)) selection = (chain 'P' and (resid 197 through 203 or resid 205 through 220 or resid 222 thro \ ugh 224 or resid 226 through 284)) selection = (chain 'Q' and (resid 197 through 203 or resid 205 through 220 or resid 222 thro \ ugh 224 or resid 226 through 284)) selection = (chain 'R' and (resid 197 through 203 or resid 205 through 220 or resid 222 thro \ ugh 224 or resid 226 through 284)) selection = (chain 'Y' and (resid 197 through 203 or resid 205 through 220 or resid 222 thro \ ugh 224 or resid 226 through 284)) selection = (chain 'a' and (resid 197 through 203 or resid 205 through 220 or resid 222 thro \ ugh 224 or resid 226 through 284)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 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: 0.360 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: 0.040 Extract box with map and model: 4.460 Check model and map are aligned: 0.710 Set scattering table: 0.450 Process input model: 136.500 Find NCS groups from input model: 3.330 Set up NCS constraints: 0.380 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:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 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 : 0.009 0.068 64540 Z= 0.622 Angle : 1.032 10.350 87248 Z= 0.603 Chirality : 0.049 0.185 10500 Planarity : 0.005 0.062 11522 Dihedral : 14.598 88.080 24360 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.76 % Favored : 94.75 % Rotamer: Outliers : 2.10 % Allowed : 3.99 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.09), residues: 8638 helix: 1.15 (0.07), residues: 5068 sheet: 0.40 (0.18), residues: 700 loop : -2.40 (0.10), residues: 2870 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS T 401 PHE 0.014 0.002 PHE V 8 TYR 0.018 0.003 TYR L 199 ARG 0.005 0.001 ARG R 277 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17276 Ramachandran restraints generated. 8638 Oldfield, 0 Emsley, 8638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17276 Ramachandran restraints generated. 8638 Oldfield, 0 Emsley, 8638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1722 residues out of total 6580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1582 time to evaluate : 5.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 27 VAL cc_start: 0.8264 (OUTLIER) cc_final: 0.8007 (t) REVERT: b 89 THR cc_start: 0.8401 (m) cc_final: 0.8176 (p) REVERT: b 105 LYS cc_start: 0.8393 (ttpt) cc_final: 0.7923 (ttmm) REVERT: b 111 MET cc_start: 0.8424 (mtt) cc_final: 0.8177 (mtt) REVERT: b 178 GLU cc_start: 0.6248 (pt0) cc_final: 0.5866 (pt0) REVERT: b 200 LEU cc_start: 0.8553 (mt) cc_final: 0.8280 (mt) REVERT: b 277 LYS cc_start: 0.6844 (mttt) cc_final: 0.6481 (mttt) REVERT: b 286 LYS cc_start: 0.7313 (mttt) cc_final: 0.6692 (ptmt) REVERT: b 307 MET cc_start: 0.5359 (mmp) cc_final: 0.4574 (mmp) REVERT: b 380 LYS cc_start: 0.7294 (mttt) cc_final: 0.6470 (mtmm) REVERT: b 397 GLU cc_start: 0.7131 (tt0) cc_final: 0.6867 (tt0) REVERT: b 404 ARG cc_start: 0.7861 (tpp80) cc_final: 0.7131 (ttp80) REVERT: b 422 VAL cc_start: 0.8974 (t) cc_final: 0.8483 (m) REVERT: b 430 ARG cc_start: 0.8911 (mmt-90) cc_final: 0.8563 (mmt180) REVERT: b 432 GLN cc_start: 0.7570 (mm110) cc_final: 0.7363 (mm-40) REVERT: b 448 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7073 (mt-10) REVERT: b 460 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7385 (tp30) REVERT: b 473 ASP cc_start: 0.8054 (p0) cc_final: 0.7157 (m-30) REVERT: b 490 ASP cc_start: 0.7726 (m-30) cc_final: 0.7205 (m-30) REVERT: b 518 GLU cc_start: 0.8210 (tp30) cc_final: 0.7204 (tp30) REVERT: b 520 MET cc_start: 0.8463 (mtm) cc_final: 0.8089 (mtm) REVERT: G 27 VAL cc_start: 0.8142 (OUTLIER) cc_final: 0.7863 (t) REVERT: G 76 GLU cc_start: 0.8115 (tt0) cc_final: 0.7854 (tt0) REVERT: G 115 ASP cc_start: 0.8480 (m-30) cc_final: 0.8271 (m-30) REVERT: G 307 MET cc_start: 0.6534 (mmp) cc_final: 0.5482 (mmp) REVERT: G 351 GLN cc_start: 0.7197 (tt0) cc_final: 0.6825 (tp-100) REVERT: G 404 ARG cc_start: 0.7111 (tpp80) cc_final: 0.6438 (mtp85) REVERT: G 432 GLN cc_start: 0.7754 (mm110) cc_final: 0.7509 (mm-40) REVERT: G 448 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7597 (mt-10) REVERT: G 460 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7590 (mm-30) REVERT: B 278 GLN cc_start: 0.8100 (mt0) cc_final: 0.7249 (tm-30) REVERT: H 59 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7489 (mm-30) REVERT: H 204 PHE cc_start: 0.7364 (m-80) cc_final: 0.7101 (m-80) REVERT: H 216 GLU cc_start: 0.7523 (pp20) cc_final: 0.7260 (pp20) REVERT: H 267 MET cc_start: 0.6306 (ttt) cc_final: 0.5759 (tpt) REVERT: H 277 LYS cc_start: 0.7356 (mttt) cc_final: 0.6908 (mtmm) REVERT: H 286 LYS cc_start: 0.7759 (mttt) cc_final: 0.6788 (pttt) REVERT: H 325 ILE cc_start: 0.7727 (mt) cc_final: 0.7462 (mm) REVERT: H 380 LYS cc_start: 0.7399 (mttt) cc_final: 0.6730 (mtmm) REVERT: H 395 ARG cc_start: 0.7063 (mtm180) cc_final: 0.6784 (mtm110) REVERT: H 398 ASP cc_start: 0.8686 (t70) cc_final: 0.8394 (t0) REVERT: H 404 ARG cc_start: 0.7226 (tpp80) cc_final: 0.7009 (ttm-80) REVERT: H 426 LEU cc_start: 0.8501 (mt) cc_final: 0.8278 (mp) REVERT: H 448 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7483 (mt-10) REVERT: H 494 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8072 (pt) REVERT: H 495 ASP cc_start: 0.7953 (m-30) cc_final: 0.7633 (m-30) REVERT: H 518 GLU cc_start: 0.8299 (tp30) cc_final: 0.7642 (mm-30) REVERT: H 520 MET cc_start: 0.8306 (mtm) cc_final: 0.8072 (mtm) REVERT: I 105 LYS cc_start: 0.8438 (ttpt) cc_final: 0.8233 (ttmm) REVERT: I 178 GLU cc_start: 0.7109 (pt0) cc_final: 0.6601 (pt0) REVERT: I 193 MET cc_start: 0.7470 (tpp) cc_final: 0.7082 (tpp) REVERT: I 216 GLU cc_start: 0.7133 (pp20) cc_final: 0.6751 (pp20) REVERT: I 252 GLU cc_start: 0.6867 (mp0) cc_final: 0.6456 (mp0) REVERT: I 267 MET cc_start: 0.6625 (ttt) cc_final: 0.6040 (tpt) REVERT: I 277 LYS cc_start: 0.6584 (mttt) cc_final: 0.6346 (mtmm) REVERT: I 307 MET cc_start: 0.5912 (mmp) cc_final: 0.5036 (mmp) REVERT: I 321 LYS cc_start: 0.7523 (tptt) cc_final: 0.7233 (tttt) REVERT: I 351 GLN cc_start: 0.7650 (tt0) cc_final: 0.6905 (tp40) REVERT: I 389 MET cc_start: 0.6816 (ttt) cc_final: 0.6607 (tpp) REVERT: I 460 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7692 (tp30) REVERT: I 473 ASP cc_start: 0.7654 (p0) cc_final: 0.6835 (m-30) REVERT: I 490 ASP cc_start: 0.7206 (m-30) cc_final: 0.6806 (m-30) REVERT: I 520 MET cc_start: 0.8541 (mtm) cc_final: 0.8198 (mtm) REVERT: J 204 PHE cc_start: 0.7025 (m-80) cc_final: 0.6592 (m-80) REVERT: J 233 MET cc_start: 0.5948 (mmm) cc_final: 0.5446 (mmm) REVERT: J 267 MET cc_start: 0.6706 (ttt) cc_final: 0.6423 (tpp) REVERT: J 286 LYS cc_start: 0.6813 (mttt) cc_final: 0.5809 (pttt) REVERT: J 288 MET cc_start: 0.6304 (mtt) cc_final: 0.6098 (mtp) REVERT: J 307 MET cc_start: 0.6027 (mmp) cc_final: 0.4977 (mmp) REVERT: J 380 LYS cc_start: 0.7438 (mttt) cc_final: 0.6868 (mtmm) REVERT: J 404 ARG cc_start: 0.7266 (tpp80) cc_final: 0.7016 (ttm-80) REVERT: J 432 GLN cc_start: 0.7657 (mm110) cc_final: 0.7158 (mt0) REVERT: J 448 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7547 (mt-10) REVERT: J 490 ASP cc_start: 0.7653 (m-30) cc_final: 0.7350 (m-30) REVERT: J 518 GLU cc_start: 0.8143 (tp30) cc_final: 0.7907 (mm-30) REVERT: E 265 LEU cc_start: 0.5733 (mt) cc_final: 0.5514 (mt) REVERT: K 73 MET cc_start: 0.7526 (ttp) cc_final: 0.7212 (ttp) REVERT: K 76 GLU cc_start: 0.7943 (tt0) cc_final: 0.7677 (tt0) REVERT: K 178 GLU cc_start: 0.6997 (pt0) cc_final: 0.6697 (pt0) REVERT: K 193 MET cc_start: 0.6649 (tpp) cc_final: 0.6391 (tpp) REVERT: K 267 MET cc_start: 0.6285 (ttt) cc_final: 0.5669 (tpt) REVERT: K 307 MET cc_start: 0.6276 (mmp) cc_final: 0.5340 (mmp) REVERT: K 330 THR cc_start: 0.7735 (m) cc_final: 0.7141 (p) REVERT: K 351 GLN cc_start: 0.7122 (tt0) cc_final: 0.6313 (tp40) REVERT: K 363 GLU cc_start: 0.6992 (tt0) cc_final: 0.6625 (tm-30) REVERT: K 380 LYS cc_start: 0.7452 (mttt) cc_final: 0.6628 (mtmm) REVERT: K 404 ARG cc_start: 0.7762 (tpp80) cc_final: 0.7256 (mtp85) REVERT: K 432 GLN cc_start: 0.7211 (mm110) cc_final: 0.6949 (mm-40) REVERT: K 448 GLU cc_start: 0.8513 (mt-10) cc_final: 0.7762 (mt-10) REVERT: K 460 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7531 (mm-30) REVERT: K 514 MET cc_start: 0.7923 (ttm) cc_final: 0.7319 (mtm) REVERT: L 69 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7555 (mtm) REVERT: L 73 MET cc_start: 0.8027 (ttp) cc_final: 0.7728 (ttp) REVERT: L 114 MET cc_start: 0.7187 (mmt) cc_final: 0.6685 (mmm) REVERT: L 178 GLU cc_start: 0.6758 (pt0) cc_final: 0.6257 (pt0) REVERT: L 219 PHE cc_start: 0.4542 (m-10) cc_final: 0.4215 (m-80) REVERT: L 307 MET cc_start: 0.6220 (mmp) cc_final: 0.4686 (mmp) REVERT: L 351 GLN cc_start: 0.7483 (tt0) cc_final: 0.7118 (tp40) REVERT: L 380 LYS cc_start: 0.7350 (mttt) cc_final: 0.6813 (mttp) REVERT: L 389 MET cc_start: 0.5937 (ttt) cc_final: 0.5370 (ttt) REVERT: L 432 GLN cc_start: 0.7475 (mm110) cc_final: 0.7167 (mm110) REVERT: L 448 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7954 (mt-10) REVERT: L 482 THR cc_start: 0.7906 (m) cc_final: 0.7604 (p) REVERT: L 490 ASP cc_start: 0.8168 (m-30) cc_final: 0.7853 (m-30) REVERT: L 518 GLU cc_start: 0.8294 (tp30) cc_final: 0.7493 (mm-30) REVERT: Z 18 ARG cc_start: 0.7629 (ttm-80) cc_final: 0.7246 (mtp85) REVERT: Z 27 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.7767 (t) REVERT: Z 59 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7299 (mm-30) REVERT: Z 73 MET cc_start: 0.8284 (ttp) cc_final: 0.8080 (ttp) REVERT: Z 118 ARG cc_start: 0.6430 (mtt180) cc_final: 0.6091 (mmm-85) REVERT: Z 160 LYS cc_start: 0.7955 (tttt) cc_final: 0.7676 (mtpp) REVERT: Z 166 MET cc_start: 0.7686 (ttm) cc_final: 0.7315 (ttt) REVERT: Z 216 GLU cc_start: 0.6728 (pp20) cc_final: 0.6223 (pp20) REVERT: Z 252 GLU cc_start: 0.6953 (mp0) cc_final: 0.6680 (mp0) REVERT: Z 267 MET cc_start: 0.4817 (ttt) cc_final: 0.4375 (ptt) REVERT: Z 321 LYS cc_start: 0.8295 (tptt) cc_final: 0.7985 (mmmt) REVERT: Z 371 LYS cc_start: 0.6941 (tppt) cc_final: 0.6640 (ttmm) REVERT: Z 432 GLN cc_start: 0.7706 (mm110) cc_final: 0.7363 (mm-40) REVERT: Z 473 ASP cc_start: 0.7316 (p0) cc_final: 0.6979 (m-30) REVERT: Z 487 ASN cc_start: 0.8091 (m-40) cc_final: 0.7700 (m-40) REVERT: Z 490 ASP cc_start: 0.7563 (m-30) cc_final: 0.7325 (m-30) REVERT: Z 491 MET cc_start: 0.7822 (mtt) cc_final: 0.7389 (mtt) REVERT: Z 494 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8511 (pt) REVERT: M 238 LEU cc_start: 0.7581 (tp) cc_final: 0.7381 (tp) REVERT: S 11 ASP cc_start: 0.7016 (t0) cc_final: 0.6515 (t0) REVERT: S 63 GLU cc_start: 0.7202 (tp30) cc_final: 0.6088 (pm20) REVERT: S 69 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7336 (mtm) REVERT: S 76 GLU cc_start: 0.7481 (tt0) cc_final: 0.7154 (tp30) REVERT: S 111 MET cc_start: 0.8750 (mtt) cc_final: 0.8460 (mtp) REVERT: S 118 ARG cc_start: 0.6431 (mtt180) cc_final: 0.6115 (mmm-85) REVERT: S 164 GLU cc_start: 0.7856 (tt0) cc_final: 0.7466 (mm-30) REVERT: S 175 ILE cc_start: 0.8424 (mm) cc_final: 0.8219 (mm) REVERT: S 179 ASP cc_start: 0.8751 (m-30) cc_final: 0.8103 (m-30) REVERT: S 207 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7219 (ttpt) REVERT: S 288 MET cc_start: 0.5576 (mtt) cc_final: 0.5070 (mtp) REVERT: S 307 MET cc_start: 0.6516 (mmp) cc_final: 0.6263 (mmp) REVERT: S 321 LYS cc_start: 0.8007 (tptt) cc_final: 0.7638 (mmmm) REVERT: S 380 LYS cc_start: 0.6547 (mttt) cc_final: 0.6288 (mmtp) REVERT: S 390 LYS cc_start: 0.6698 (mtpp) cc_final: 0.6472 (tttm) REVERT: S 473 ASP cc_start: 0.7378 (p0) cc_final: 0.7134 (m-30) REVERT: S 483 GLU cc_start: 0.8384 (mp0) cc_final: 0.6583 (tp30) REVERT: S 518 GLU cc_start: 0.8439 (tp30) cc_final: 0.8099 (mm-30) REVERT: S 523 ASP cc_start: 0.8450 (m-30) cc_final: 0.8205 (m-30) REVERT: N 238 LEU cc_start: 0.7599 (tp) cc_final: 0.7355 (tp) REVERT: T 59 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7081 (mm-30) REVERT: T 76 GLU cc_start: 0.7595 (tt0) cc_final: 0.7168 (tt0) REVERT: T 111 MET cc_start: 0.8991 (mtt) cc_final: 0.8655 (mtt) REVERT: T 160 LYS cc_start: 0.7045 (tttt) cc_final: 0.6823 (mtpp) REVERT: T 179 ASP cc_start: 0.8253 (m-30) cc_final: 0.7651 (m-30) REVERT: T 214 GLU cc_start: 0.6724 (pt0) cc_final: 0.6025 (pt0) REVERT: T 216 GLU cc_start: 0.6924 (pp20) cc_final: 0.6500 (pp20) REVERT: T 321 LYS cc_start: 0.8206 (tptt) cc_final: 0.7771 (mmmt) REVERT: T 345 ARG cc_start: 0.6404 (mmm160) cc_final: 0.6111 (tpt90) REVERT: T 448 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7095 (mt-10) REVERT: T 487 ASN cc_start: 0.7498 (m-40) cc_final: 0.7199 (t0) REVERT: T 490 ASP cc_start: 0.7668 (m-30) cc_final: 0.7310 (m-30) REVERT: T 518 GLU cc_start: 0.8341 (tp30) cc_final: 0.7958 (mm-30) REVERT: U 41 ASP cc_start: 0.8458 (t70) cc_final: 0.7648 (t0) REVERT: U 42 LYS cc_start: 0.7300 (mmtt) cc_final: 0.6849 (mmtm) REVERT: U 132 LYS cc_start: 0.7949 (tttp) cc_final: 0.7746 (mtpt) REVERT: U 160 LYS cc_start: 0.7419 (tttt) cc_final: 0.6888 (mtmm) REVERT: U 166 MET cc_start: 0.7701 (ttm) cc_final: 0.7436 (ttt) REVERT: U 171 LYS cc_start: 0.8621 (mmtp) cc_final: 0.8139 (tppt) REVERT: U 175 ILE cc_start: 0.8206 (mm) cc_final: 0.7912 (mm) REVERT: U 179 ASP cc_start: 0.8588 (m-30) cc_final: 0.8277 (m-30) REVERT: U 193 MET cc_start: 0.7734 (tpp) cc_final: 0.7191 (mmm) REVERT: U 207 LYS cc_start: 0.7208 (OUTLIER) cc_final: 0.6690 (mmtm) REVERT: U 267 MET cc_start: 0.5155 (ttt) cc_final: 0.4952 (ptt) REVERT: U 367 GLU cc_start: 0.6950 (mm-30) cc_final: 0.6564 (mm-30) REVERT: U 371 LYS cc_start: 0.7351 (tppt) cc_final: 0.7060 (ttmm) REVERT: U 378 VAL cc_start: 0.8361 (t) cc_final: 0.8135 (m) REVERT: U 390 LYS cc_start: 0.6646 (mtpp) cc_final: 0.6404 (tttm) REVERT: U 457 ASN cc_start: 0.8375 (m-40) cc_final: 0.8169 (m110) REVERT: U 460 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7333 (mm-30) REVERT: V 61 GLU cc_start: 0.7589 (pt0) cc_final: 0.7351 (pt0) REVERT: V 161 LEU cc_start: 0.6885 (tp) cc_final: 0.6527 (tp) REVERT: V 166 MET cc_start: 0.7345 (ttm) cc_final: 0.6898 (ttm) REVERT: V 179 ASP cc_start: 0.8453 (m-30) cc_final: 0.8198 (m-30) REVERT: V 186 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6754 (tp30) REVERT: V 196 ASP cc_start: 0.8364 (m-30) cc_final: 0.8061 (m-30) REVERT: V 207 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.6827 (mtmt) REVERT: V 216 GLU cc_start: 0.6778 (pp20) cc_final: 0.6253 (pp20) REVERT: V 252 GLU cc_start: 0.7066 (mp0) cc_final: 0.6757 (mp0) REVERT: V 267 MET cc_start: 0.4726 (ttt) cc_final: 0.4390 (ptt) REVERT: V 307 MET cc_start: 0.6017 (mmp) cc_final: 0.5780 (mmp) REVERT: V 378 VAL cc_start: 0.8602 (t) cc_final: 0.8375 (m) REVERT: V 390 LYS cc_start: 0.6958 (mtpp) cc_final: 0.6586 (tttm) REVERT: V 448 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7100 (tt0) REVERT: V 460 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7259 (mm-30) REVERT: V 482 THR cc_start: 0.9280 (m) cc_final: 0.8745 (p) REVERT: V 483 GLU cc_start: 0.8284 (mp0) cc_final: 0.6627 (tp30) REVERT: Q 226 LEU cc_start: 0.7636 (mt) cc_final: 0.7138 (mt) REVERT: W 11 ASP cc_start: 0.7260 (t0) cc_final: 0.6954 (t0) REVERT: W 18 ARG cc_start: 0.7694 (ttm-80) cc_final: 0.7411 (mtp85) REVERT: W 118 ARG cc_start: 0.6605 (mtt180) cc_final: 0.6294 (mmm-85) REVERT: W 129 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7562 (mm-30) REVERT: W 166 MET cc_start: 0.7387 (ttm) cc_final: 0.7166 (ttm) REVERT: W 179 ASP cc_start: 0.8513 (m-30) cc_final: 0.8246 (m-30) REVERT: W 194 GLN cc_start: 0.6496 (tt0) cc_final: 0.6246 (tt0) REVERT: W 214 GLU cc_start: 0.6330 (pt0) cc_final: 0.5872 (pt0) REVERT: W 288 MET cc_start: 0.6060 (mtt) cc_final: 0.5616 (mtp) REVERT: W 321 LYS cc_start: 0.8166 (tptt) cc_final: 0.7686 (mmmt) REVERT: W 380 LYS cc_start: 0.6293 (mttt) cc_final: 0.6022 (mmtp) REVERT: W 400 LEU cc_start: 0.7564 (tp) cc_final: 0.7315 (tt) REVERT: W 432 GLN cc_start: 0.8371 (mm110) cc_final: 0.8045 (mm-40) REVERT: W 482 THR cc_start: 0.8940 (m) cc_final: 0.8677 (p) REVERT: W 483 GLU cc_start: 0.8289 (mp0) cc_final: 0.6835 (mp0) REVERT: W 487 ASN cc_start: 0.8242 (m-40) cc_final: 0.7929 (m-40) REVERT: W 520 MET cc_start: 0.8866 (mtm) cc_final: 0.8650 (mtm) REVERT: R 238 LEU cc_start: 0.8027 (tp) cc_final: 0.7823 (tp) REVERT: X 18 ARG cc_start: 0.7606 (ttm-80) cc_final: 0.7359 (ttp80) REVERT: X 41 ASP cc_start: 0.8306 (t70) cc_final: 0.7699 (t0) REVERT: X 51 LYS cc_start: 0.8613 (mttt) cc_final: 0.8349 (mtmm) REVERT: X 59 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7057 (mm-30) REVERT: X 111 MET cc_start: 0.9150 (mtt) cc_final: 0.8853 (mtp) REVERT: X 115 ASP cc_start: 0.7129 (m-30) cc_final: 0.6707 (m-30) REVERT: X 132 LYS cc_start: 0.7621 (tttp) cc_final: 0.7219 (mtpt) REVERT: X 160 LYS cc_start: 0.7543 (tttt) cc_final: 0.6889 (mtpp) REVERT: X 164 GLU cc_start: 0.7857 (tt0) cc_final: 0.7551 (mm-30) REVERT: X 175 ILE cc_start: 0.8423 (mm) cc_final: 0.8166 (mm) REVERT: X 179 ASP cc_start: 0.8489 (m-30) cc_final: 0.7893 (m-30) REVERT: X 200 LEU cc_start: 0.7447 (mt) cc_final: 0.6945 (mt) REVERT: X 204 PHE cc_start: 0.7972 (m-80) cc_final: 0.7674 (m-10) REVERT: X 207 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7656 (mtmt) REVERT: X 288 MET cc_start: 0.5473 (mtt) cc_final: 0.5252 (mtp) REVERT: X 307 MET cc_start: 0.6318 (mmp) cc_final: 0.6015 (mmp) REVERT: X 329 THR cc_start: 0.7822 (p) cc_final: 0.7403 (t) REVERT: X 390 LYS cc_start: 0.6837 (mtpp) cc_final: 0.6587 (tttp) REVERT: X 428 ASP cc_start: 0.8059 (m-30) cc_final: 0.7734 (m-30) REVERT: X 473 ASP cc_start: 0.7672 (p0) cc_final: 0.7344 (m-30) REVERT: X 483 GLU cc_start: 0.8252 (mp0) cc_final: 0.6798 (tp30) REVERT: X 484 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7117 (pt0) REVERT: X 487 ASN cc_start: 0.7635 (m-40) cc_final: 0.6859 (t0) REVERT: X 490 ASP cc_start: 0.7322 (m-30) cc_final: 0.6652 (m-30) outliers start: 140 outliers final: 25 residues processed: 1662 average time/residue: 0.5821 time to fit residues: 1647.3357 Evaluate side-chains 1232 residues out of total 6580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1196 time to evaluate : 5.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 27 VAL Chi-restraints excluded: chain b residue 270 ILE Chi-restraints excluded: chain b residue 342 ILE Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain H residue 270 ILE Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 494 LEU Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 270 ILE Chi-restraints excluded: chain K residue 270 ILE Chi-restraints excluded: chain K residue 342 ILE Chi-restraints excluded: chain L residue 69 MET Chi-restraints excluded: chain L residue 270 ILE Chi-restraints excluded: chain L residue 292 ILE Chi-restraints excluded: chain L residue 342 ILE Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain Z residue 369 VAL Chi-restraints excluded: chain Z residue 494 LEU Chi-restraints excluded: chain S residue 69 MET Chi-restraints excluded: chain S residue 207 LYS Chi-restraints excluded: chain T residue 69 MET Chi-restraints excluded: chain T residue 369 VAL Chi-restraints excluded: chain U residue 69 MET Chi-restraints excluded: chain U residue 207 LYS Chi-restraints excluded: chain U residue 270 ILE Chi-restraints excluded: chain V residue 27 VAL Chi-restraints excluded: chain V residue 207 LYS Chi-restraints excluded: chain V residue 369 VAL Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 369 VAL Chi-restraints excluded: chain X residue 69 MET Chi-restraints excluded: chain X residue 207 LYS Chi-restraints excluded: chain X residue 369 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 709 optimal weight: 2.9990 chunk 636 optimal weight: 9.9990 chunk 353 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 429 optimal weight: 0.9990 chunk 340 optimal weight: 10.0000 chunk 658 optimal weight: 0.8980 chunk 254 optimal weight: 2.9990 chunk 400 optimal weight: 6.9990 chunk 490 optimal weight: 3.9990 chunk 762 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 457 ASN H 457 ASN I 194 GLN I 457 ASN ** J 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN K 326 ASN K 457 ASN ** Y 204 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 : 0.004 0.064 64540 Z= 0.241 Angle : 0.726 20.750 87248 Z= 0.381 Chirality : 0.044 0.320 10500 Planarity : 0.005 0.055 11522 Dihedral : 5.179 57.863 9230 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.49 % Allowed : 2.58 % Favored : 96.92 % Rotamer: Outliers : 2.46 % Allowed : 8.46 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.82 (0.09), residues: 8638 helix: 1.88 (0.07), residues: 5110 sheet: 0.23 (0.16), residues: 952 loop : -2.18 (0.10), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS Y 242 PHE 0.020 0.002 PHE J 66 TYR 0.017 0.002 TYR T 506 ARG 0.005 0.000 ARG I 404 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17276 Ramachandran restraints generated. 8638 Oldfield, 0 Emsley, 8638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17276 Ramachandran restraints generated. 8638 Oldfield, 0 Emsley, 8638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1330 residues out of total 6580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1166 time to evaluate : 5.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 218 LEU cc_start: 0.6084 (tp) cc_final: 0.5872 (tt) REVERT: b 27 VAL cc_start: 0.7656 (OUTLIER) cc_final: 0.7362 (t) REVERT: b 105 LYS cc_start: 0.8183 (ttpt) cc_final: 0.7789 (ttmm) REVERT: b 178 GLU cc_start: 0.6362 (pt0) cc_final: 0.6103 (pt0) REVERT: b 193 MET cc_start: 0.7895 (tpp) cc_final: 0.7483 (tpt) REVERT: b 252 GLU cc_start: 0.6896 (mp0) cc_final: 0.6690 (mp0) REVERT: b 307 MET cc_start: 0.5016 (mmp) cc_final: 0.3899 (mmp) REVERT: b 351 GLN cc_start: 0.7376 (tt0) cc_final: 0.6426 (tp-100) REVERT: b 352 GLN cc_start: 0.6416 (mt0) cc_final: 0.6070 (mt0) REVERT: b 366 GLN cc_start: 0.6955 (mm110) cc_final: 0.6525 (mm110) REVERT: b 380 LYS cc_start: 0.7107 (mttt) cc_final: 0.6484 (mtmm) REVERT: b 397 GLU cc_start: 0.7322 (tt0) cc_final: 0.7060 (tt0) REVERT: b 404 ARG cc_start: 0.7765 (tpp80) cc_final: 0.7521 (ttm-80) REVERT: b 422 VAL cc_start: 0.9044 (t) cc_final: 0.8525 (m) REVERT: b 430 ARG cc_start: 0.8948 (mmt-90) cc_final: 0.8642 (mmt180) REVERT: b 448 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7533 (mt-10) REVERT: b 470 LYS cc_start: 0.7360 (mttt) cc_final: 0.7114 (mttp) REVERT: b 473 ASP cc_start: 0.8089 (p0) cc_final: 0.7254 (m-30) REVERT: b 520 MET cc_start: 0.8398 (mtm) cc_final: 0.8092 (mtm) REVERT: A 218 LEU cc_start: 0.6535 (tp) cc_final: 0.6053 (tt) REVERT: G 50 THR cc_start: 0.9204 (t) cc_final: 0.8961 (p) REVERT: G 67 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7227 (mt-10) REVERT: G 69 MET cc_start: 0.8212 (mtm) cc_final: 0.7634 (mtm) REVERT: G 102 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7312 (mm-30) REVERT: G 121 ASP cc_start: 0.7250 (m-30) cc_final: 0.6403 (t0) REVERT: G 160 LYS cc_start: 0.7612 (ptmt) cc_final: 0.7223 (ptmm) REVERT: G 267 MET cc_start: 0.7728 (tpt) cc_final: 0.7347 (tpt) REVERT: G 307 MET cc_start: 0.6156 (mmp) cc_final: 0.5083 (mmp) REVERT: G 351 GLN cc_start: 0.7182 (tt0) cc_final: 0.6827 (tp-100) REVERT: G 404 ARG cc_start: 0.7251 (tpp80) cc_final: 0.6616 (mtp85) REVERT: G 430 ARG cc_start: 0.8669 (mmt-90) cc_final: 0.8436 (mmt-90) REVERT: G 432 GLN cc_start: 0.7667 (mm110) cc_final: 0.7327 (mm-40) REVERT: H 69 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8112 (ttm) REVERT: H 105 LYS cc_start: 0.8530 (ttpt) cc_final: 0.7934 (ttmm) REVERT: H 130 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7117 (mm-30) REVERT: H 267 MET cc_start: 0.6051 (ttt) cc_final: 0.5603 (tpt) REVERT: H 307 MET cc_start: 0.5999 (mmp) cc_final: 0.5147 (mmp) REVERT: H 325 ILE cc_start: 0.7932 (mt) cc_final: 0.7640 (mm) REVERT: H 351 GLN cc_start: 0.7499 (tt0) cc_final: 0.6562 (tp40) REVERT: H 380 LYS cc_start: 0.7309 (mttt) cc_final: 0.6763 (mtmm) REVERT: H 398 ASP cc_start: 0.8684 (t70) cc_final: 0.8336 (t0) REVERT: H 403 THR cc_start: 0.8365 (m) cc_final: 0.8051 (m) REVERT: H 404 ARG cc_start: 0.7271 (tpp80) cc_final: 0.7002 (ttm-80) REVERT: H 426 LEU cc_start: 0.8413 (mt) cc_final: 0.8158 (mp) REVERT: H 518 GLU cc_start: 0.7893 (tp30) cc_final: 0.7191 (tp30) REVERT: I 105 LYS cc_start: 0.8368 (ttpt) cc_final: 0.8150 (ttmm) REVERT: I 267 MET cc_start: 0.6855 (ttt) cc_final: 0.6334 (tpt) REVERT: I 307 MET cc_start: 0.5523 (mmp) cc_final: 0.4469 (mmp) REVERT: I 389 MET cc_start: 0.6874 (ttt) cc_final: 0.6646 (tpp) REVERT: I 432 GLN cc_start: 0.7448 (mm-40) cc_final: 0.7179 (mt0) REVERT: I 473 ASP cc_start: 0.7946 (p0) cc_final: 0.7121 (m-30) REVERT: I 490 ASP cc_start: 0.7321 (m-30) cc_final: 0.6921 (m-30) REVERT: J 50 THR cc_start: 0.9245 (t) cc_final: 0.8943 (p) REVERT: J 204 PHE cc_start: 0.6885 (m-80) cc_final: 0.6338 (m-80) REVERT: J 233 MET cc_start: 0.5953 (mmm) cc_final: 0.4939 (mmm) REVERT: J 252 GLU cc_start: 0.7305 (mp0) cc_final: 0.7044 (mp0) REVERT: J 267 MET cc_start: 0.6697 (ttt) cc_final: 0.6325 (tpp) REVERT: J 288 MET cc_start: 0.6336 (mtt) cc_final: 0.6053 (mtp) REVERT: J 307 MET cc_start: 0.5782 (mmp) cc_final: 0.4759 (mmp) REVERT: J 363 GLU cc_start: 0.6429 (tt0) cc_final: 0.6090 (tm-30) REVERT: J 380 LYS cc_start: 0.7397 (mttt) cc_final: 0.6868 (mtmm) REVERT: J 404 ARG cc_start: 0.7232 (tpp80) cc_final: 0.6981 (ttm-80) REVERT: J 432 GLN cc_start: 0.7370 (mm110) cc_final: 0.7003 (mt0) REVERT: J 448 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7881 (mt-10) REVERT: K 76 GLU cc_start: 0.7956 (tt0) cc_final: 0.7555 (tt0) REVERT: K 105 LYS cc_start: 0.8462 (ttpt) cc_final: 0.8160 (ttmm) REVERT: K 121 ASP cc_start: 0.7391 (m-30) cc_final: 0.6463 (t0) REVERT: K 155 ASP cc_start: 0.7053 (t0) cc_final: 0.6101 (m-30) REVERT: K 193 MET cc_start: 0.6774 (tpp) cc_final: 0.6024 (tpt) REVERT: K 267 MET cc_start: 0.6203 (ttt) cc_final: 0.5858 (tpp) REVERT: K 307 MET cc_start: 0.5759 (mmp) cc_final: 0.4645 (mmp) REVERT: K 380 LYS cc_start: 0.7348 (mttt) cc_final: 0.6758 (mtmm) REVERT: K 389 MET cc_start: 0.6865 (ttm) cc_final: 0.6590 (tpp) REVERT: K 404 ARG cc_start: 0.7741 (tpp80) cc_final: 0.7234 (mtp85) REVERT: K 432 GLN cc_start: 0.7257 (mm110) cc_final: 0.6896 (mt0) REVERT: K 448 GLU cc_start: 0.8598 (mt-10) cc_final: 0.7923 (mt-10) REVERT: K 460 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7764 (mm-30) REVERT: L 59 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7293 (mm-30) REVERT: L 114 MET cc_start: 0.6209 (mmt) cc_final: 0.5964 (mmm) REVERT: L 160 LYS cc_start: 0.7236 (ptmt) cc_final: 0.7001 (tttt) REVERT: L 233 MET cc_start: 0.6422 (mmm) cc_final: 0.5442 (mmm) REVERT: L 307 MET cc_start: 0.5940 (mmp) cc_final: 0.4462 (mmp) REVERT: L 380 LYS cc_start: 0.7268 (mttt) cc_final: 0.6745 (mttp) REVERT: L 397 GLU cc_start: 0.7988 (tt0) cc_final: 0.7281 (tm-30) REVERT: L 432 GLN cc_start: 0.7385 (mm110) cc_final: 0.7072 (mt0) REVERT: L 518 GLU cc_start: 0.8060 (tp30) cc_final: 0.7687 (mm-30) REVERT: Y 226 LEU cc_start: 0.7395 (mt) cc_final: 0.7166 (mt) REVERT: Z 18 ARG cc_start: 0.7555 (ttm-80) cc_final: 0.6905 (ttp80) REVERT: Z 41 ASP cc_start: 0.7828 (t70) cc_final: 0.6876 (t0) REVERT: Z 59 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7228 (mm-30) REVERT: Z 73 MET cc_start: 0.8370 (ttp) cc_final: 0.8128 (ttp) REVERT: Z 160 LYS cc_start: 0.7952 (tttt) cc_final: 0.7695 (mtpp) REVERT: Z 164 GLU cc_start: 0.8106 (tt0) cc_final: 0.7727 (tm-30) REVERT: Z 166 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7350 (ttt) REVERT: Z 196 ASP cc_start: 0.8452 (m-30) cc_final: 0.8065 (t0) REVERT: Z 345 ARG cc_start: 0.6880 (mmm160) cc_final: 0.6538 (tpp-160) REVERT: Z 432 GLN cc_start: 0.7699 (mm110) cc_final: 0.7309 (mm-40) REVERT: Z 473 ASP cc_start: 0.7465 (p0) cc_final: 0.7209 (m-30) REVERT: Z 482 THR cc_start: 0.9149 (m) cc_final: 0.8913 (p) REVERT: Z 487 ASN cc_start: 0.8223 (m-40) cc_final: 0.7801 (m-40) REVERT: Z 490 ASP cc_start: 0.7798 (m-30) cc_final: 0.7549 (m-30) REVERT: Z 491 MET cc_start: 0.7933 (mtt) cc_final: 0.7561 (mtt) REVERT: M 238 LEU cc_start: 0.7645 (tp) cc_final: 0.7419 (tp) REVERT: S 11 ASP cc_start: 0.6514 (t0) cc_final: 0.5860 (t0) REVERT: S 73 MET cc_start: 0.7621 (ttp) cc_final: 0.7264 (ttm) REVERT: S 160 LYS cc_start: 0.7214 (ttpp) cc_final: 0.6822 (mtpp) REVERT: S 179 ASP cc_start: 0.8614 (m-30) cc_final: 0.8098 (m-30) REVERT: S 207 LYS cc_start: 0.7382 (mmmm) cc_final: 0.7155 (mtmt) REVERT: S 214 GLU cc_start: 0.6707 (pm20) cc_final: 0.6253 (pm20) REVERT: S 288 MET cc_start: 0.5410 (mtt) cc_final: 0.4845 (mtp) REVERT: S 321 LYS cc_start: 0.7840 (tptt) cc_final: 0.7440 (mmmm) REVERT: S 380 LYS cc_start: 0.6644 (mttt) cc_final: 0.6303 (mmtp) REVERT: S 390 LYS cc_start: 0.6548 (mtpp) cc_final: 0.6280 (tttm) REVERT: N 238 LEU cc_start: 0.7765 (tp) cc_final: 0.7518 (tp) REVERT: T 59 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7484 (mm-30) REVERT: T 82 ASN cc_start: 0.8405 (t0) cc_final: 0.8160 (t0) REVERT: T 179 ASP cc_start: 0.7905 (m-30) cc_final: 0.7562 (m-30) REVERT: T 207 LYS cc_start: 0.7697 (mtpp) cc_final: 0.7048 (mmtm) REVERT: T 345 ARG cc_start: 0.6744 (mmm160) cc_final: 0.6327 (mtp180) REVERT: T 487 ASN cc_start: 0.7880 (m-40) cc_final: 0.7289 (t0) REVERT: U 42 LYS cc_start: 0.7307 (mmtt) cc_final: 0.7064 (mmtm) REVERT: U 132 LYS cc_start: 0.7840 (tttp) cc_final: 0.7534 (ttmm) REVERT: U 160 LYS cc_start: 0.7037 (tttt) cc_final: 0.6797 (mtmm) REVERT: U 166 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.6906 (mtp) REVERT: U 175 ILE cc_start: 0.8492 (mm) cc_final: 0.8166 (mt) REVERT: U 179 ASP cc_start: 0.8135 (m-30) cc_final: 0.7879 (m-30) REVERT: U 207 LYS cc_start: 0.7483 (mmmm) cc_final: 0.7070 (mmtm) REVERT: U 214 GLU cc_start: 0.6718 (pm20) cc_final: 0.6491 (pm20) REVERT: U 267 MET cc_start: 0.4955 (ttt) cc_final: 0.4716 (ptt) REVERT: U 378 VAL cc_start: 0.8673 (t) cc_final: 0.8463 (m) REVERT: U 403 THR cc_start: 0.7898 (m) cc_final: 0.7636 (m) REVERT: U 432 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7681 (mm-40) REVERT: U 482 THR cc_start: 0.9202 (m) cc_final: 0.8797 (p) REVERT: U 487 ASN cc_start: 0.8394 (m-40) cc_final: 0.7637 (t0) REVERT: P 259 GLN cc_start: 0.6410 (pp30) cc_final: 0.5204 (pm20) REVERT: V 5 ASP cc_start: 0.8154 (t70) cc_final: 0.7705 (t0) REVERT: V 61 GLU cc_start: 0.7504 (pt0) cc_final: 0.7270 (pt0) REVERT: V 121 ASP cc_start: 0.7190 (m-30) cc_final: 0.6393 (t0) REVERT: V 161 LEU cc_start: 0.6946 (tp) cc_final: 0.6598 (tp) REVERT: V 166 MET cc_start: 0.7327 (ttm) cc_final: 0.6832 (ttm) REVERT: V 171 LYS cc_start: 0.8845 (mtmt) cc_final: 0.8621 (mtpt) REVERT: V 193 MET cc_start: 0.7240 (mmm) cc_final: 0.6774 (tpt) REVERT: V 207 LYS cc_start: 0.7189 (mmmm) cc_final: 0.6852 (mtmt) REVERT: V 267 MET cc_start: 0.4705 (ttt) cc_final: 0.4325 (ptt) REVERT: V 332 ILE cc_start: 0.6657 (OUTLIER) cc_final: 0.6227 (tp) REVERT: V 390 LYS cc_start: 0.6895 (mtpp) cc_final: 0.6348 (mmmt) REVERT: V 393 LYS cc_start: 0.7185 (tttp) cc_final: 0.6976 (ttpt) REVERT: V 432 GLN cc_start: 0.7493 (mm-40) cc_final: 0.7254 (mm-40) REVERT: V 455 VAL cc_start: 0.8857 (t) cc_final: 0.8645 (t) REVERT: V 482 THR cc_start: 0.9342 (m) cc_final: 0.8830 (p) REVERT: V 483 GLU cc_start: 0.8292 (mp0) cc_final: 0.8085 (mp0) REVERT: W 18 ARG cc_start: 0.7560 (ttm-80) cc_final: 0.7103 (mtp85) REVERT: W 160 LYS cc_start: 0.7067 (ptpp) cc_final: 0.6826 (mtpp) REVERT: W 166 MET cc_start: 0.7426 (ttm) cc_final: 0.6993 (ttt) REVERT: W 179 ASP cc_start: 0.8386 (m-30) cc_final: 0.8145 (m-30) REVERT: W 214 GLU cc_start: 0.6319 (pt0) cc_final: 0.6079 (pt0) REVERT: W 288 MET cc_start: 0.5937 (mtt) cc_final: 0.5484 (mtp) REVERT: W 345 ARG cc_start: 0.5929 (mmm160) cc_final: 0.5544 (mtp180) REVERT: W 380 LYS cc_start: 0.6331 (mttt) cc_final: 0.5925 (mmtp) REVERT: W 408 GLU cc_start: 0.5552 (tt0) cc_final: 0.5289 (tt0) REVERT: W 425 LYS cc_start: 0.7818 (mttp) cc_final: 0.7522 (mttt) REVERT: W 432 GLN cc_start: 0.8393 (mm110) cc_final: 0.8113 (mm-40) REVERT: W 495 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7299 (t70) REVERT: R 207 GLN cc_start: 0.5198 (mt0) cc_final: 0.4964 (mt0) REVERT: R 228 GLN cc_start: 0.6545 (mt0) cc_final: 0.5383 (mm-40) REVERT: X 51 LYS cc_start: 0.8553 (mttt) cc_final: 0.8278 (mtmm) REVERT: X 59 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7376 (mm-30) REVERT: X 111 MET cc_start: 0.9093 (mtt) cc_final: 0.8569 (mtp) REVERT: X 115 ASP cc_start: 0.7194 (m-30) cc_final: 0.6602 (m-30) REVERT: X 160 LYS cc_start: 0.7295 (tttt) cc_final: 0.6841 (mtpp) REVERT: X 179 ASP cc_start: 0.8191 (m-30) cc_final: 0.7891 (m-30) REVERT: X 193 MET cc_start: 0.7104 (mmm) cc_final: 0.6601 (mmm) REVERT: X 196 ASP cc_start: 0.8208 (t0) cc_final: 0.7698 (p0) REVERT: X 288 MET cc_start: 0.5456 (mtt) cc_final: 0.5191 (mtp) REVERT: X 345 ARG cc_start: 0.6548 (mmm160) cc_final: 0.6346 (tpp-160) outliers start: 164 outliers final: 106 residues processed: 1223 average time/residue: 0.5539 time to fit residues: 1165.2209 Evaluate side-chains 1142 residues out of total 6580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1030 time to evaluate : 5.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 27 VAL Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 187 LEU Chi-restraints excluded: chain b residue 227 ILE Chi-restraints excluded: chain b residue 401 HIS Chi-restraints excluded: chain b residue 424 SER Chi-restraints excluded: chain b residue 494 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 80 LYS Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 401 HIS Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 162 ILE Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 284 ARG Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 294 THR Chi-restraints excluded: chain I residue 401 HIS Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 166 MET Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain J residue 401 HIS Chi-restraints excluded: chain J residue 517 THR Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 216 GLU Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 372 LEU Chi-restraints excluded: chain K residue 401 HIS Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain K residue 470 LYS Chi-restraints excluded: chain K residue 494 LEU Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 250 ILE Chi-restraints excluded: chain L residue 294 THR Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 401 HIS Chi-restraints excluded: chain L residue 461 GLU Chi-restraints excluded: chain L residue 523 ASP Chi-restraints excluded: chain Y residue 222 LEU Chi-restraints excluded: chain Z residue 61 GLU Chi-restraints excluded: chain Z residue 166 MET Chi-restraints excluded: chain Z residue 169 VAL Chi-restraints excluded: chain Z residue 289 LEU Chi-restraints excluded: chain Z residue 329 THR Chi-restraints excluded: chain Z residue 332 ILE Chi-restraints excluded: chain Z residue 378 VAL Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain S residue 61 GLU Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 177 VAL Chi-restraints excluded: chain S residue 332 ILE Chi-restraints excluded: chain S residue 401 HIS Chi-restraints excluded: chain S residue 424 SER Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 187 LEU Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain T residue 292 ILE Chi-restraints excluded: chain T residue 329 THR Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 424 SER Chi-restraints excluded: chain T residue 494 LEU Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 166 MET Chi-restraints excluded: chain U residue 169 VAL Chi-restraints excluded: chain U residue 177 VAL Chi-restraints excluded: chain U residue 187 LEU Chi-restraints excluded: chain U residue 381 VAL Chi-restraints excluded: chain V residue 27 VAL Chi-restraints excluded: chain V residue 169 VAL Chi-restraints excluded: chain V residue 187 LEU Chi-restraints excluded: chain V residue 194 GLN Chi-restraints excluded: chain V residue 292 ILE Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 401 HIS Chi-restraints excluded: chain V residue 447 MET Chi-restraints excluded: chain W residue 61 GLU Chi-restraints excluded: chain W residue 169 VAL Chi-restraints excluded: chain W residue 289 LEU Chi-restraints excluded: chain W residue 332 ILE Chi-restraints excluded: chain W residue 378 VAL Chi-restraints excluded: chain W residue 401 HIS Chi-restraints excluded: chain W residue 495 ASP Chi-restraints excluded: chain X residue 27 VAL Chi-restraints excluded: chain X residue 169 VAL Chi-restraints excluded: chain X residue 177 VAL Chi-restraints excluded: chain X residue 187 LEU Chi-restraints excluded: chain X residue 378 VAL Chi-restraints excluded: chain X residue 401 HIS Chi-restraints excluded: chain X residue 494 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 423 optimal weight: 30.0000 chunk 236 optimal weight: 7.9990 chunk 634 optimal weight: 9.9990 chunk 519 optimal weight: 0.1980 chunk 210 optimal weight: 20.0000 chunk 764 optimal weight: 6.9990 chunk 825 optimal weight: 9.9990 chunk 680 optimal weight: 4.9990 chunk 757 optimal weight: 6.9990 chunk 260 optimal weight: 2.9990 chunk 613 optimal weight: 2.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 GLN H 82 ASN K 457 ASN L 351 GLN ** Y 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 505 GLN ** P 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 259 GLN ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 194 GLN ** R 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 64540 Z= 0.325 Angle : 0.710 17.598 87248 Z= 0.378 Chirality : 0.044 0.242 10500 Planarity : 0.005 0.056 11522 Dihedral : 4.761 58.434 9160 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.77 % Favored : 95.76 % Rotamer: Outliers : 3.71 % Allowed : 11.60 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.89 (0.09), residues: 8638 helix: 1.98 (0.07), residues: 5096 sheet: 0.21 (0.17), residues: 826 loop : -2.10 (0.10), residues: 2716 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS N 227 PHE 0.019 0.002 PHE V 8 TYR 0.022 0.002 TYR Z 506 ARG 0.005 0.001 ARG S 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17276 Ramachandran restraints generated. 8638 Oldfield, 0 Emsley, 8638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17276 Ramachandran restraints generated. 8638 Oldfield, 0 Emsley, 8638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1314 residues out of total 6580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1067 time to evaluate : 5.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 208 GLN cc_start: 0.6525 (tp40) cc_final: 0.6012 (tt0) REVERT: b 105 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7836 (ttmm) REVERT: b 178 GLU cc_start: 0.7039 (pt0) cc_final: 0.6837 (pt0) REVERT: b 286 LYS cc_start: 0.7295 (mttt) cc_final: 0.6504 (ptmt) REVERT: b 307 MET cc_start: 0.5334 (mmp) cc_final: 0.4127 (mmp) REVERT: b 351 GLN cc_start: 0.7694 (tt0) cc_final: 0.6849 (tp-100) REVERT: b 352 GLN cc_start: 0.6413 (mt0) cc_final: 0.6091 (mt0) REVERT: b 366 GLN cc_start: 0.6864 (mm110) cc_final: 0.6323 (mm110) REVERT: b 380 LYS cc_start: 0.7377 (mttt) cc_final: 0.6700 (mtmm) REVERT: b 395 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7460 (mtm110) REVERT: b 397 GLU cc_start: 0.7368 (tt0) cc_final: 0.7086 (tt0) REVERT: b 404 ARG cc_start: 0.7592 (tpp80) cc_final: 0.7135 (ttp80) REVERT: b 430 ARG cc_start: 0.8935 (mmt-90) cc_final: 0.8544 (mmt180) REVERT: b 432 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7373 (mt0) REVERT: b 520 MET cc_start: 0.8435 (mtm) cc_final: 0.8173 (mtm) REVERT: G 69 MET cc_start: 0.8257 (mtm) cc_final: 0.7936 (mtm) REVERT: G 121 ASP cc_start: 0.7801 (m-30) cc_final: 0.7175 (t0) REVERT: G 267 MET cc_start: 0.7630 (tpt) cc_final: 0.7265 (tpt) REVERT: G 307 MET cc_start: 0.6435 (mmp) cc_final: 0.5338 (mmp) REVERT: G 351 GLN cc_start: 0.7404 (tt0) cc_final: 0.7176 (tp-100) REVERT: G 367 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6999 (mm-30) REVERT: G 380 LYS cc_start: 0.7202 (mttt) cc_final: 0.6820 (mttp) REVERT: G 389 MET cc_start: 0.6938 (ttt) cc_final: 0.6686 (tpp) REVERT: G 432 GLN cc_start: 0.7760 (mm110) cc_final: 0.7405 (mm-40) REVERT: G 520 MET cc_start: 0.8494 (mtm) cc_final: 0.8158 (mtm) REVERT: B 238 LEU cc_start: 0.7742 (tp) cc_final: 0.7535 (tp) REVERT: H 105 LYS cc_start: 0.8429 (ttpt) cc_final: 0.7868 (ttmm) REVERT: H 130 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7237 (mm-30) REVERT: H 307 MET cc_start: 0.5416 (mmp) cc_final: 0.4611 (mmp) REVERT: H 325 ILE cc_start: 0.7951 (mt) cc_final: 0.7643 (mm) REVERT: H 351 GLN cc_start: 0.7387 (tt0) cc_final: 0.6469 (tp-100) REVERT: H 380 LYS cc_start: 0.7376 (mttt) cc_final: 0.6783 (mtmm) REVERT: H 398 ASP cc_start: 0.8650 (t70) cc_final: 0.8302 (t0) REVERT: H 403 THR cc_start: 0.8393 (m) cc_final: 0.8078 (m) REVERT: H 404 ARG cc_start: 0.7314 (tpp80) cc_final: 0.7091 (ttm-80) REVERT: H 483 GLU cc_start: 0.6863 (mp0) cc_final: 0.6605 (mp0) REVERT: H 495 ASP cc_start: 0.8058 (m-30) cc_final: 0.7836 (t0) REVERT: C 218 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6358 (tt) REVERT: I 105 LYS cc_start: 0.8471 (ttpt) cc_final: 0.8099 (ttmm) REVERT: I 187 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8049 (tt) REVERT: I 267 MET cc_start: 0.6781 (ttt) cc_final: 0.6380 (tpt) REVERT: I 307 MET cc_start: 0.5623 (mmp) cc_final: 0.4273 (mmp) REVERT: I 321 LYS cc_start: 0.7299 (tptt) cc_final: 0.6945 (tttt) REVERT: I 389 MET cc_start: 0.6958 (ttt) cc_final: 0.6677 (tpp) REVERT: I 432 GLN cc_start: 0.7515 (mm-40) cc_final: 0.7059 (mt0) REVERT: I 448 GLU cc_start: 0.8509 (mt-10) cc_final: 0.7841 (mt-10) REVERT: I 490 ASP cc_start: 0.7621 (m-30) cc_final: 0.6764 (m-30) REVERT: I 514 MET cc_start: 0.7740 (ttm) cc_final: 0.7225 (mtp) REVERT: D 207 GLN cc_start: 0.7742 (tp40) cc_final: 0.7132 (mm-40) REVERT: J 204 PHE cc_start: 0.7065 (m-80) cc_final: 0.6562 (m-80) REVERT: J 233 MET cc_start: 0.6412 (mmm) cc_final: 0.5385 (mmm) REVERT: J 267 MET cc_start: 0.6697 (ttt) cc_final: 0.6244 (tpp) REVERT: J 288 MET cc_start: 0.6386 (mtt) cc_final: 0.6100 (mtp) REVERT: J 307 MET cc_start: 0.5783 (mmp) cc_final: 0.4631 (mmp) REVERT: J 352 GLN cc_start: 0.6238 (mt0) cc_final: 0.6021 (mt0) REVERT: J 380 LYS cc_start: 0.7428 (mttt) cc_final: 0.6989 (mtmm) REVERT: J 389 MET cc_start: 0.7344 (tpp) cc_final: 0.7076 (tpp) REVERT: J 404 ARG cc_start: 0.7167 (tpp80) cc_final: 0.6841 (ttm-80) REVERT: J 432 GLN cc_start: 0.7589 (mm110) cc_final: 0.7258 (mt0) REVERT: K 105 LYS cc_start: 0.8580 (ttpt) cc_final: 0.8137 (ttmm) REVERT: K 121 ASP cc_start: 0.7706 (m-30) cc_final: 0.7382 (m-30) REVERT: K 155 ASP cc_start: 0.7077 (t0) cc_final: 0.6191 (m-30) REVERT: K 267 MET cc_start: 0.6283 (ttt) cc_final: 0.5988 (tpp) REVERT: K 307 MET cc_start: 0.5503 (mmp) cc_final: 0.4645 (mmp) REVERT: K 330 THR cc_start: 0.7563 (m) cc_final: 0.6959 (p) REVERT: K 380 LYS cc_start: 0.7436 (mttt) cc_final: 0.6907 (mtmm) REVERT: K 401 HIS cc_start: 0.7982 (OUTLIER) cc_final: 0.7594 (t-170) REVERT: K 404 ARG cc_start: 0.7725 (tpp80) cc_final: 0.7259 (mtp85) REVERT: K 432 GLN cc_start: 0.7309 (mm110) cc_final: 0.6842 (mt0) REVERT: K 523 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7777 (t0) REVERT: L 59 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7457 (mm-30) REVERT: L 160 LYS cc_start: 0.7361 (ptmt) cc_final: 0.7000 (ptmm) REVERT: L 178 GLU cc_start: 0.6898 (pt0) cc_final: 0.6521 (pt0) REVERT: L 193 MET cc_start: 0.6861 (mmm) cc_final: 0.6403 (mmm) REVERT: L 233 MET cc_start: 0.6737 (mmm) cc_final: 0.5372 (mmm) REVERT: L 307 MET cc_start: 0.5110 (mmp) cc_final: 0.4095 (mmp) REVERT: L 326 ASN cc_start: 0.7436 (t0) cc_final: 0.7062 (t0) REVERT: L 327 LYS cc_start: 0.7425 (ttpp) cc_final: 0.7153 (ttpp) REVERT: L 395 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6845 (mtp180) REVERT: L 397 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7126 (tm-30) REVERT: L 518 GLU cc_start: 0.8235 (tp30) cc_final: 0.7838 (mm-30) REVERT: Y 228 GLN cc_start: 0.5183 (mm-40) cc_final: 0.4918 (mt0) REVERT: Z 18 ARG cc_start: 0.7693 (ttm-80) cc_final: 0.6967 (ttp80) REVERT: Z 42 LYS cc_start: 0.7105 (mmtt) cc_final: 0.6839 (mmtt) REVERT: Z 59 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7143 (mm-30) REVERT: Z 160 LYS cc_start: 0.8152 (tttt) cc_final: 0.7880 (mtpp) REVERT: Z 196 ASP cc_start: 0.8395 (m-30) cc_final: 0.8060 (p0) REVERT: Z 345 ARG cc_start: 0.6870 (mmm160) cc_final: 0.6621 (mtp85) REVERT: Z 371 LYS cc_start: 0.7075 (tppt) cc_final: 0.6663 (ttmm) REVERT: Z 432 GLN cc_start: 0.7735 (mm110) cc_final: 0.7409 (mm-40) REVERT: Z 482 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8837 (p) REVERT: Z 491 MET cc_start: 0.7498 (mtt) cc_final: 0.7264 (mtt) REVERT: M 238 LEU cc_start: 0.7966 (tp) cc_final: 0.7758 (tp) REVERT: S 118 ARG cc_start: 0.6556 (mtt180) cc_final: 0.6278 (mmm-85) REVERT: S 160 LYS cc_start: 0.7354 (ttpp) cc_final: 0.7016 (mtpp) REVERT: S 179 ASP cc_start: 0.8630 (m-30) cc_final: 0.8254 (m-30) REVERT: S 193 MET cc_start: 0.7642 (mmm) cc_final: 0.7062 (mmt) REVERT: S 207 LYS cc_start: 0.7561 (mmmm) cc_final: 0.7306 (mtmt) REVERT: S 214 GLU cc_start: 0.6962 (pm20) cc_final: 0.6551 (pm20) REVERT: S 288 MET cc_start: 0.5534 (mtt) cc_final: 0.4944 (mtp) REVERT: S 321 LYS cc_start: 0.7785 (tptt) cc_final: 0.7412 (mmmm) REVERT: S 380 LYS cc_start: 0.6837 (mttt) cc_final: 0.6365 (mmtp) REVERT: S 401 HIS cc_start: 0.6251 (OUTLIER) cc_final: 0.5918 (t-170) REVERT: N 222 LEU cc_start: 0.6349 (OUTLIER) cc_final: 0.6110 (mt) REVERT: N 238 LEU cc_start: 0.7744 (tp) cc_final: 0.7504 (tp) REVERT: T 82 ASN cc_start: 0.8323 (t0) cc_final: 0.8098 (t0) REVERT: T 179 ASP cc_start: 0.7827 (m-30) cc_final: 0.7549 (m-30) REVERT: T 193 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.6780 (tpp) REVERT: T 207 LYS cc_start: 0.7607 (mtpp) cc_final: 0.6738 (mmtm) REVERT: T 404 ARG cc_start: 0.8127 (tpp80) cc_final: 0.7853 (ttm-80) REVERT: T 482 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8824 (p) REVERT: T 487 ASN cc_start: 0.8172 (m-40) cc_final: 0.7460 (t0) REVERT: U 42 LYS cc_start: 0.7347 (mmtt) cc_final: 0.7071 (mmtm) REVERT: U 67 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7585 (mt-10) REVERT: U 87 ASP cc_start: 0.8718 (t0) cc_final: 0.8470 (t0) REVERT: U 111 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8423 (mtt) REVERT: U 160 LYS cc_start: 0.7532 (tttt) cc_final: 0.7328 (mtpp) REVERT: U 166 MET cc_start: 0.7726 (ttm) cc_final: 0.7053 (mtp) REVERT: U 207 LYS cc_start: 0.7756 (mmmm) cc_final: 0.7227 (mmtm) REVERT: U 267 MET cc_start: 0.5622 (ttt) cc_final: 0.5246 (ptt) REVERT: U 378 VAL cc_start: 0.8662 (t) cc_final: 0.8411 (m) REVERT: U 403 THR cc_start: 0.7807 (m) cc_final: 0.7568 (m) REVERT: U 482 THR cc_start: 0.9279 (m) cc_final: 0.8881 (p) REVERT: V 5 ASP cc_start: 0.8244 (t70) cc_final: 0.7845 (t0) REVERT: V 61 GLU cc_start: 0.7539 (pt0) cc_final: 0.7249 (pt0) REVERT: V 121 ASP cc_start: 0.7341 (m-30) cc_final: 0.7001 (m-30) REVERT: V 171 LYS cc_start: 0.8805 (mtmt) cc_final: 0.8528 (mtpt) REVERT: V 186 GLU cc_start: 0.6703 (mt-10) cc_final: 0.6431 (tp30) REVERT: V 193 MET cc_start: 0.7162 (mmm) cc_final: 0.6557 (tpt) REVERT: V 204 PHE cc_start: 0.7616 (m-80) cc_final: 0.7406 (m-80) REVERT: V 207 LYS cc_start: 0.7211 (mmmm) cc_final: 0.6866 (mtmt) REVERT: V 267 MET cc_start: 0.4771 (ttt) cc_final: 0.4399 (ptt) REVERT: V 332 ILE cc_start: 0.7095 (OUTLIER) cc_final: 0.6702 (tp) REVERT: V 390 LYS cc_start: 0.6917 (mtpp) cc_final: 0.6414 (mmmt) REVERT: V 393 LYS cc_start: 0.7434 (tttp) cc_final: 0.7217 (ttpt) REVERT: V 432 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7388 (mm-40) REVERT: V 455 VAL cc_start: 0.8865 (t) cc_final: 0.8642 (t) REVERT: V 482 THR cc_start: 0.9299 (OUTLIER) cc_final: 0.8920 (p) REVERT: V 520 MET cc_start: 0.8207 (mtm) cc_final: 0.7921 (mtp) REVERT: W 18 ARG cc_start: 0.7656 (ttm-80) cc_final: 0.7033 (ttp80) REVERT: W 105 LYS cc_start: 0.8108 (ttpt) cc_final: 0.7800 (ttmm) REVERT: W 160 LYS cc_start: 0.7237 (ptpp) cc_final: 0.7022 (mtpp) REVERT: W 179 ASP cc_start: 0.8367 (m-30) cc_final: 0.7948 (m-30) REVERT: W 267 MET cc_start: 0.5336 (ptm) cc_final: 0.5050 (ptt) REVERT: W 288 MET cc_start: 0.5953 (mtt) cc_final: 0.5631 (mtp) REVERT: W 345 ARG cc_start: 0.5945 (mmm160) cc_final: 0.5569 (mmp80) REVERT: W 380 LYS cc_start: 0.6424 (mttt) cc_final: 0.5984 (mmtp) REVERT: W 408 GLU cc_start: 0.5742 (tt0) cc_final: 0.5464 (tt0) REVERT: W 432 GLN cc_start: 0.8316 (mm110) cc_final: 0.7998 (mm-40) REVERT: W 495 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.7186 (t70) REVERT: R 228 GLN cc_start: 0.6550 (mt0) cc_final: 0.5531 (mm-40) REVERT: R 259 GLN cc_start: 0.5463 (pp30) cc_final: 0.5168 (pp30) REVERT: X 59 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7335 (mm-30) REVERT: X 111 MET cc_start: 0.8837 (mtt) cc_final: 0.8502 (mtp) REVERT: X 115 ASP cc_start: 0.7261 (m-30) cc_final: 0.6622 (m-30) REVERT: X 160 LYS cc_start: 0.7868 (tttt) cc_final: 0.7456 (mtpp) REVERT: X 187 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7849 (tp) REVERT: X 196 ASP cc_start: 0.8198 (t0) cc_final: 0.7763 (p0) REVERT: X 200 LEU cc_start: 0.7539 (mt) cc_final: 0.7098 (mt) REVERT: X 288 MET cc_start: 0.5480 (mtt) cc_final: 0.5258 (mtt) REVERT: X 482 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8691 (p) REVERT: X 487 ASN cc_start: 0.8009 (m-40) cc_final: 0.7536 (t0) outliers start: 247 outliers final: 171 residues processed: 1183 average time/residue: 0.5512 time to fit residues: 1124.4520 Evaluate side-chains 1211 residues out of total 6580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1022 time to evaluate : 5.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 11 ASP Chi-restraints excluded: chain b residue 60 ILE Chi-restraints excluded: chain b residue 76 GLU Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 130 GLU Chi-restraints excluded: chain b residue 160 LYS Chi-restraints excluded: chain b residue 187 LEU Chi-restraints excluded: chain b residue 227 ILE Chi-restraints excluded: chain b residue 254 VAL Chi-restraints excluded: chain b residue 267 MET Chi-restraints excluded: chain b residue 271 VAL Chi-restraints excluded: chain b residue 332 ILE Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 401 HIS Chi-restraints excluded: chain b residue 424 SER Chi-restraints excluded: chain b residue 482 THR Chi-restraints excluded: chain b residue 494 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain G residue 401 HIS Chi-restraints excluded: chain G residue 424 SER Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 80 LYS Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 296 THR Chi-restraints excluded: chain H residue 387 VAL Chi-restraints excluded: chain H residue 401 HIS Chi-restraints excluded: chain H residue 510 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 162 ILE Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 284 ARG Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 296 THR Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 401 HIS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 166 MET Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 294 THR Chi-restraints excluded: chain J residue 296 THR Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain J residue 401 HIS Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 517 THR Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 216 GLU Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 296 THR Chi-restraints excluded: chain K residue 372 LEU Chi-restraints excluded: chain K residue 387 VAL Chi-restraints excluded: chain K residue 401 HIS Chi-restraints excluded: chain K residue 403 THR Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain K residue 424 SER Chi-restraints excluded: chain K residue 470 LYS Chi-restraints excluded: chain K residue 494 LEU Chi-restraints excluded: chain K residue 523 ASP Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 250 ILE Chi-restraints excluded: chain L residue 271 VAL Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 395 ARG Chi-restraints excluded: chain L residue 397 GLU Chi-restraints excluded: chain L residue 401 HIS Chi-restraints excluded: chain L residue 407 VAL Chi-restraints excluded: chain Z residue 61 GLU Chi-restraints excluded: chain Z residue 77 VAL Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain Z residue 169 VAL Chi-restraints excluded: chain Z residue 187 LEU Chi-restraints excluded: chain Z residue 193 MET Chi-restraints excluded: chain Z residue 263 VAL Chi-restraints excluded: chain Z residue 329 THR Chi-restraints excluded: chain Z residue 332 ILE Chi-restraints excluded: chain Z residue 378 VAL Chi-restraints excluded: chain Z residue 401 HIS Chi-restraints excluded: chain Z residue 463 SER Chi-restraints excluded: chain Z residue 482 THR Chi-restraints excluded: chain Z residue 516 THR Chi-restraints excluded: chain M residue 222 LEU Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain S residue 61 GLU Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 177 VAL Chi-restraints excluded: chain S residue 292 ILE Chi-restraints excluded: chain S residue 307 MET Chi-restraints excluded: chain S residue 332 ILE Chi-restraints excluded: chain S residue 378 VAL Chi-restraints excluded: chain S residue 401 HIS Chi-restraints excluded: chain S residue 422 VAL Chi-restraints excluded: chain S residue 424 SER Chi-restraints excluded: chain S residue 463 SER Chi-restraints excluded: chain N residue 222 LEU Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 187 LEU Chi-restraints excluded: chain T residue 193 MET Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain T residue 292 ILE Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 378 VAL Chi-restraints excluded: chain T residue 401 HIS Chi-restraints excluded: chain T residue 424 SER Chi-restraints excluded: chain T residue 463 SER Chi-restraints excluded: chain T residue 482 THR Chi-restraints excluded: chain T residue 494 LEU Chi-restraints excluded: chain T residue 517 THR Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain O residue 278 GLN Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 111 MET Chi-restraints excluded: chain U residue 169 VAL Chi-restraints excluded: chain U residue 177 VAL Chi-restraints excluded: chain U residue 187 LEU Chi-restraints excluded: chain U residue 381 VAL Chi-restraints excluded: chain U residue 401 HIS Chi-restraints excluded: chain U residue 422 VAL Chi-restraints excluded: chain U residue 463 SER Chi-restraints excluded: chain P residue 259 GLN Chi-restraints excluded: chain V residue 27 VAL Chi-restraints excluded: chain V residue 169 VAL Chi-restraints excluded: chain V residue 187 LEU Chi-restraints excluded: chain V residue 194 GLN Chi-restraints excluded: chain V residue 307 MET Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 378 VAL Chi-restraints excluded: chain V residue 401 HIS Chi-restraints excluded: chain V residue 447 MET Chi-restraints excluded: chain V residue 463 SER Chi-restraints excluded: chain V residue 482 THR Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 61 GLU Chi-restraints excluded: chain W residue 169 VAL Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain W residue 289 LEU Chi-restraints excluded: chain W residue 332 ILE Chi-restraints excluded: chain W residue 378 VAL Chi-restraints excluded: chain W residue 381 VAL Chi-restraints excluded: chain W residue 401 HIS Chi-restraints excluded: chain W residue 463 SER Chi-restraints excluded: chain W residue 494 LEU Chi-restraints excluded: chain W residue 495 ASP Chi-restraints excluded: chain X residue 27 VAL Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain X residue 169 VAL Chi-restraints excluded: chain X residue 177 VAL Chi-restraints excluded: chain X residue 187 LEU Chi-restraints excluded: chain X residue 307 MET Chi-restraints excluded: chain X residue 378 VAL Chi-restraints excluded: chain X residue 401 HIS Chi-restraints excluded: chain X residue 422 VAL Chi-restraints excluded: chain X residue 463 SER Chi-restraints excluded: chain X residue 482 THR Chi-restraints excluded: chain X residue 494 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 755 optimal weight: 8.9990 chunk 574 optimal weight: 7.9990 chunk 396 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 364 optimal weight: 40.0000 chunk 513 optimal weight: 20.0000 chunk 766 optimal weight: 20.0000 chunk 811 optimal weight: 20.0000 chunk 400 optimal weight: 0.8980 chunk 726 optimal weight: 7.9990 chunk 218 optimal weight: 9.9990 overall best weight: 7.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 203 GLN a 206 GLN b 290 GLN B 206 GLN B 208 GLN C 206 GLN C 242 HIS I 290 GLN J 290 GLN E 242 HIS K 290 GLN K 457 ASN L 290 GLN ** L 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 432 GLN ** N 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 253 GLN ** Q 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 242 HIS ** R 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 432 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.098 64540 Z= 0.574 Angle : 0.851 16.161 87248 Z= 0.454 Chirality : 0.051 0.303 10500 Planarity : 0.006 0.075 11522 Dihedral : 5.123 58.657 9159 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.57 % Favored : 94.94 % Rotamer: Outliers : 4.44 % Allowed : 13.82 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.32 (0.09), residues: 8638 helix: 1.49 (0.07), residues: 5054 sheet: 0.05 (0.17), residues: 924 loop : -2.31 (0.10), residues: 2660 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS M 227 PHE 0.022 0.003 PHE V 8 TYR 0.031 0.004 TYR T 506 ARG 0.009 0.001 ARG K 452 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17276 Ramachandran restraints generated. 8638 Oldfield, 0 Emsley, 8638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17276 Ramachandran restraints generated. 8638 Oldfield, 0 Emsley, 8638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1396 residues out of total 6580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 1100 time to evaluate : 5.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 59 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7245 (mm-30) REVERT: b 105 LYS cc_start: 0.8344 (ttpt) cc_final: 0.7886 (ttmm) REVERT: b 112 ASN cc_start: 0.8086 (t0) cc_final: 0.7822 (t0) REVERT: b 160 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7528 (ttmm) REVERT: b 164 GLU cc_start: 0.7345 (tp30) cc_final: 0.7102 (tp30) REVERT: b 178 GLU cc_start: 0.7105 (pt0) cc_final: 0.6625 (pt0) REVERT: b 205 ILE cc_start: 0.6304 (mt) cc_final: 0.6014 (mt) REVERT: b 286 LYS cc_start: 0.7482 (mttt) cc_final: 0.6816 (ptmt) REVERT: b 307 MET cc_start: 0.4960 (mmp) cc_final: 0.4147 (mmp) REVERT: b 351 GLN cc_start: 0.7673 (tt0) cc_final: 0.6907 (tp-100) REVERT: b 352 GLN cc_start: 0.6515 (mt0) cc_final: 0.6183 (mt0) REVERT: b 366 GLN cc_start: 0.7032 (mm110) cc_final: 0.6607 (mm110) REVERT: b 380 LYS cc_start: 0.7191 (mttt) cc_final: 0.6672 (mtmm) REVERT: b 397 GLU cc_start: 0.7386 (tt0) cc_final: 0.7077 (tt0) REVERT: b 404 ARG cc_start: 0.7853 (tpp80) cc_final: 0.7196 (ttp80) REVERT: b 430 ARG cc_start: 0.8900 (mmt-90) cc_final: 0.8622 (mmt-90) REVERT: b 432 GLN cc_start: 0.7602 (mm-40) cc_final: 0.7334 (mt0) REVERT: G 112 ASN cc_start: 0.8553 (t0) cc_final: 0.8322 (t0) REVERT: G 121 ASP cc_start: 0.7932 (m-30) cc_final: 0.7357 (t0) REVERT: G 267 MET cc_start: 0.7548 (tpt) cc_final: 0.7289 (tpp) REVERT: G 307 MET cc_start: 0.5876 (mmp) cc_final: 0.5227 (mmp) REVERT: G 367 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7041 (mm-30) REVERT: G 380 LYS cc_start: 0.7298 (mttt) cc_final: 0.6369 (mtmm) REVERT: G 432 GLN cc_start: 0.7990 (mm110) cc_final: 0.7685 (tt0) REVERT: B 238 LEU cc_start: 0.7845 (tp) cc_final: 0.7628 (tp) REVERT: H 59 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7197 (mm-30) REVERT: H 73 MET cc_start: 0.8012 (ttm) cc_final: 0.7788 (ttm) REVERT: H 105 LYS cc_start: 0.8489 (ttpt) cc_final: 0.7922 (ttmm) REVERT: H 130 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7269 (mm-30) REVERT: H 286 LYS cc_start: 0.8014 (mttt) cc_final: 0.7035 (pttt) REVERT: H 307 MET cc_start: 0.5441 (mmp) cc_final: 0.4585 (mmp) REVERT: H 321 LYS cc_start: 0.7534 (tptt) cc_final: 0.7330 (tptm) REVERT: H 325 ILE cc_start: 0.7992 (mt) cc_final: 0.7683 (mm) REVERT: H 351 GLN cc_start: 0.7461 (tt0) cc_final: 0.6667 (tp-100) REVERT: H 380 LYS cc_start: 0.7380 (mttt) cc_final: 0.6667 (mtmm) REVERT: H 398 ASP cc_start: 0.8637 (t70) cc_final: 0.8292 (t0) REVERT: H 404 ARG cc_start: 0.7317 (tpp80) cc_final: 0.7106 (ttm-80) REVERT: H 494 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8426 (pp) REVERT: I 105 LYS cc_start: 0.8531 (ttpt) cc_final: 0.8202 (ttmm) REVERT: I 187 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7929 (tt) REVERT: I 233 MET cc_start: 0.6013 (mmm) cc_final: 0.5599 (mmp) REVERT: I 267 MET cc_start: 0.6644 (ttt) cc_final: 0.6377 (tpp) REVERT: I 307 MET cc_start: 0.5597 (mmp) cc_final: 0.4477 (mmp) REVERT: I 321 LYS cc_start: 0.7327 (tptt) cc_final: 0.6858 (tttt) REVERT: I 380 LYS cc_start: 0.7750 (mttt) cc_final: 0.7470 (mttp) REVERT: I 432 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7192 (mt0) REVERT: I 451 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8420 (tp) REVERT: I 482 THR cc_start: 0.8799 (m) cc_final: 0.8520 (p) REVERT: I 490 ASP cc_start: 0.7786 (m-30) cc_final: 0.7426 (m-30) REVERT: D 207 GLN cc_start: 0.7707 (tp40) cc_final: 0.7218 (mm-40) REVERT: J 69 MET cc_start: 0.8494 (mtm) cc_final: 0.7932 (mtm) REVERT: J 186 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7171 (pt0) REVERT: J 204 PHE cc_start: 0.7140 (m-80) cc_final: 0.6594 (m-80) REVERT: J 233 MET cc_start: 0.6400 (mmm) cc_final: 0.6072 (mmp) REVERT: J 288 MET cc_start: 0.6454 (mtt) cc_final: 0.6108 (mtp) REVERT: J 307 MET cc_start: 0.6399 (mmp) cc_final: 0.5144 (mmp) REVERT: J 380 LYS cc_start: 0.7623 (mttt) cc_final: 0.6985 (mttt) REVERT: J 404 ARG cc_start: 0.7466 (tpp80) cc_final: 0.7186 (ttm-80) REVERT: J 432 GLN cc_start: 0.7572 (mm110) cc_final: 0.7261 (mt0) REVERT: K 105 LYS cc_start: 0.8555 (ttpt) cc_final: 0.8243 (ttmm) REVERT: K 112 ASN cc_start: 0.8368 (t0) cc_final: 0.8091 (t0) REVERT: K 118 ARG cc_start: 0.6986 (mtt180) cc_final: 0.6538 (mmm-85) REVERT: K 121 ASP cc_start: 0.7857 (m-30) cc_final: 0.7513 (m-30) REVERT: K 178 GLU cc_start: 0.7108 (pt0) cc_final: 0.6741 (pt0) REVERT: K 267 MET cc_start: 0.6320 (ttt) cc_final: 0.5998 (tpp) REVERT: K 307 MET cc_start: 0.5330 (mmp) cc_final: 0.4422 (mmp) REVERT: K 321 LYS cc_start: 0.7622 (tptt) cc_final: 0.7310 (tptm) REVERT: K 330 THR cc_start: 0.7604 (m) cc_final: 0.6929 (p) REVERT: K 351 GLN cc_start: 0.7726 (tt0) cc_final: 0.7256 (tp40) REVERT: K 380 LYS cc_start: 0.7650 (mttt) cc_final: 0.7164 (mtmm) REVERT: K 387 VAL cc_start: 0.6200 (OUTLIER) cc_final: 0.5994 (p) REVERT: K 404 ARG cc_start: 0.8050 (tpp80) cc_final: 0.7515 (mtp85) REVERT: K 432 GLN cc_start: 0.7416 (mm110) cc_final: 0.6970 (mt0) REVERT: L 59 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7348 (mm-30) REVERT: L 105 LYS cc_start: 0.8462 (ttpt) cc_final: 0.8075 (ttmm) REVERT: L 307 MET cc_start: 0.5315 (mmp) cc_final: 0.4439 (mmp) REVERT: L 326 ASN cc_start: 0.7629 (t0) cc_final: 0.7076 (t0) REVERT: L 397 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7304 (tm-30) REVERT: Z 11 ASP cc_start: 0.7740 (t0) cc_final: 0.7049 (t0) REVERT: Z 18 ARG cc_start: 0.7716 (ttm-80) cc_final: 0.6982 (ttp80) REVERT: Z 59 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7220 (mm-30) REVERT: Z 160 LYS cc_start: 0.8340 (tttt) cc_final: 0.8130 (mtpp) REVERT: Z 164 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8098 (tm-30) REVERT: Z 193 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6898 (ttm) REVERT: Z 196 ASP cc_start: 0.8376 (m-30) cc_final: 0.8050 (p0) REVERT: Z 207 LYS cc_start: 0.7663 (mtpt) cc_final: 0.7375 (mmtm) REVERT: Z 222 LEU cc_start: 0.4977 (OUTLIER) cc_final: 0.4705 (mt) REVERT: Z 253 ASP cc_start: 0.7431 (t70) cc_final: 0.7039 (t70) REVERT: Z 371 LYS cc_start: 0.7164 (tppt) cc_final: 0.6934 (ttmm) REVERT: Z 432 GLN cc_start: 0.7811 (mm110) cc_final: 0.7560 (mm-40) REVERT: Z 482 THR cc_start: 0.9138 (m) cc_final: 0.8898 (p) REVERT: Z 491 MET cc_start: 0.7523 (mtt) cc_final: 0.7221 (mtp) REVERT: M 222 LEU cc_start: 0.6252 (OUTLIER) cc_final: 0.6034 (mt) REVERT: M 228 GLN cc_start: 0.6530 (mp10) cc_final: 0.5617 (mm-40) REVERT: S 11 ASP cc_start: 0.7483 (t0) cc_final: 0.7180 (t0) REVERT: S 118 ARG cc_start: 0.6988 (mtt180) cc_final: 0.6250 (mmm-85) REVERT: S 160 LYS cc_start: 0.7447 (ttpp) cc_final: 0.7208 (mtpp) REVERT: S 207 LYS cc_start: 0.7460 (mmmm) cc_final: 0.7249 (mtmt) REVERT: S 214 GLU cc_start: 0.7374 (pm20) cc_final: 0.6951 (pm20) REVERT: S 222 LEU cc_start: 0.5246 (OUTLIER) cc_final: 0.4935 (mt) REVERT: S 267 MET cc_start: 0.7273 (pmm) cc_final: 0.7021 (pmm) REVERT: S 321 LYS cc_start: 0.7772 (tptt) cc_final: 0.7491 (mmmm) REVERT: S 371 LYS cc_start: 0.7516 (tppt) cc_final: 0.7107 (ttmm) REVERT: S 447 MET cc_start: 0.8713 (mtt) cc_final: 0.8353 (mtt) REVERT: N 228 GLN cc_start: 0.5827 (OUTLIER) cc_final: 0.4172 (mm-40) REVERT: N 238 LEU cc_start: 0.7879 (tp) cc_final: 0.7632 (tp) REVERT: T 82 ASN cc_start: 0.8387 (t0) cc_final: 0.8152 (t0) REVERT: T 130 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6648 (mm-30) REVERT: T 179 ASP cc_start: 0.7929 (m-30) cc_final: 0.7713 (m-30) REVERT: T 487 ASN cc_start: 0.8277 (m-40) cc_final: 0.7455 (t0) REVERT: U 42 LYS cc_start: 0.7272 (mmtt) cc_final: 0.7013 (mmtm) REVERT: U 115 ASP cc_start: 0.7080 (m-30) cc_final: 0.6692 (m-30) REVERT: U 160 LYS cc_start: 0.7848 (tttt) cc_final: 0.7526 (mtpp) REVERT: U 166 MET cc_start: 0.7694 (ttm) cc_final: 0.7189 (mtp) REVERT: U 207 LYS cc_start: 0.7894 (mmmm) cc_final: 0.7475 (mmtm) REVERT: U 267 MET cc_start: 0.5520 (ttt) cc_final: 0.5136 (ptt) REVERT: U 371 LYS cc_start: 0.7548 (tppt) cc_final: 0.7235 (ttmm) REVERT: U 378 VAL cc_start: 0.8494 (t) cc_final: 0.8237 (m) REVERT: U 447 MET cc_start: 0.8449 (mtt) cc_final: 0.7969 (mtt) REVERT: U 482 THR cc_start: 0.9378 (OUTLIER) cc_final: 0.9064 (p) REVERT: U 488 MET cc_start: 0.8620 (mmm) cc_final: 0.8341 (mtp) REVERT: P 226 LEU cc_start: 0.7077 (mt) cc_final: 0.6844 (mt) REVERT: P 253 GLN cc_start: 0.6750 (OUTLIER) cc_final: 0.5999 (mp-120) REVERT: V 5 ASP cc_start: 0.8278 (t0) cc_final: 0.7886 (t0) REVERT: V 61 GLU cc_start: 0.7612 (pt0) cc_final: 0.7241 (pt0) REVERT: V 121 ASP cc_start: 0.7428 (m-30) cc_final: 0.7023 (m-30) REVERT: V 193 MET cc_start: 0.7467 (mmm) cc_final: 0.6794 (tpt) REVERT: V 332 ILE cc_start: 0.6620 (OUTLIER) cc_final: 0.6409 (tp) REVERT: V 338 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6920 (pm20) REVERT: V 390 LYS cc_start: 0.7075 (mtpp) cc_final: 0.6456 (mmmt) REVERT: V 393 LYS cc_start: 0.7667 (tttp) cc_final: 0.7336 (ttpt) REVERT: V 432 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7475 (mm-40) REVERT: V 461 GLU cc_start: 0.8017 (tt0) cc_final: 0.7662 (tt0) REVERT: V 488 MET cc_start: 0.8086 (mmm) cc_final: 0.7580 (mmm) REVERT: Q 238 LEU cc_start: 0.7617 (tp) cc_final: 0.7360 (tp) REVERT: W 105 LYS cc_start: 0.8171 (ttpt) cc_final: 0.7820 (ttmm) REVERT: W 118 ARG cc_start: 0.6428 (mtt180) cc_final: 0.5953 (mmm-85) REVERT: W 179 ASP cc_start: 0.8464 (m-30) cc_final: 0.7990 (m-30) REVERT: W 214 GLU cc_start: 0.6932 (pm20) cc_final: 0.6471 (pm20) REVERT: W 288 MET cc_start: 0.5583 (mtt) cc_final: 0.5337 (mtp) REVERT: W 345 ARG cc_start: 0.5984 (mmm160) cc_final: 0.5720 (mmp80) REVERT: W 380 LYS cc_start: 0.6541 (mttt) cc_final: 0.5788 (mmtp) REVERT: W 408 GLU cc_start: 0.6259 (tt0) cc_final: 0.5943 (tt0) REVERT: W 432 GLN cc_start: 0.8302 (mm110) cc_final: 0.8069 (mm-40) REVERT: W 495 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7237 (t70) REVERT: R 228 GLN cc_start: 0.6544 (mt0) cc_final: 0.5500 (mm-40) REVERT: X 59 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7335 (mm-30) REVERT: X 73 MET cc_start: 0.8529 (ttp) cc_final: 0.8014 (ttp) REVERT: X 111 MET cc_start: 0.8956 (mtt) cc_final: 0.8572 (mtp) REVERT: X 118 ARG cc_start: 0.6717 (mtt180) cc_final: 0.6363 (mmm-85) REVERT: X 160 LYS cc_start: 0.7922 (tttt) cc_final: 0.7511 (mtpp) REVERT: X 187 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7780 (tp) REVERT: X 193 MET cc_start: 0.7248 (mmt) cc_final: 0.6956 (mmt) REVERT: X 196 ASP cc_start: 0.8221 (t0) cc_final: 0.7789 (p0) REVERT: X 288 MET cc_start: 0.5073 (mtt) cc_final: 0.4837 (mtt) REVERT: X 390 LYS cc_start: 0.7007 (mtpp) cc_final: 0.6393 (ttpp) REVERT: X 482 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8768 (p) REVERT: X 487 ASN cc_start: 0.7854 (m-40) cc_final: 0.7486 (t0) outliers start: 296 outliers final: 214 residues processed: 1267 average time/residue: 0.5625 time to fit residues: 1226.9534 Evaluate side-chains 1296 residues out of total 6580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1062 time to evaluate : 5.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 11 ASP Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 60 ILE Chi-restraints excluded: chain b residue 73 MET Chi-restraints excluded: chain b residue 76 GLU Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 130 GLU Chi-restraints excluded: chain b residue 160 LYS Chi-restraints excluded: chain b residue 187 LEU Chi-restraints excluded: chain b residue 227 ILE Chi-restraints excluded: chain b residue 254 VAL Chi-restraints excluded: chain b residue 267 MET Chi-restraints excluded: chain b residue 271 VAL Chi-restraints excluded: chain b residue 296 THR Chi-restraints excluded: chain b residue 332 ILE Chi-restraints excluded: chain b residue 401 HIS Chi-restraints excluded: chain b residue 422 VAL Chi-restraints excluded: chain b residue 424 SER Chi-restraints excluded: chain b residue 463 SER Chi-restraints excluded: chain b residue 494 LEU Chi-restraints excluded: chain b residue 509 SER Chi-restraints excluded: chain b residue 510 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain G residue 401 HIS Chi-restraints excluded: chain G residue 424 SER Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 80 LYS Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 296 THR Chi-restraints excluded: chain H residue 401 HIS Chi-restraints excluded: chain H residue 463 SER Chi-restraints excluded: chain H residue 494 LEU Chi-restraints excluded: chain H residue 510 VAL Chi-restraints excluded: chain H residue 516 THR Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 162 ILE Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 284 ARG Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 294 THR Chi-restraints excluded: chain I residue 381 VAL Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 422 VAL Chi-restraints excluded: chain I residue 451 LEU Chi-restraints excluded: chain I residue 454 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 294 THR Chi-restraints excluded: chain J residue 296 THR Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain J residue 401 HIS Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 451 LEU Chi-restraints excluded: chain J residue 517 THR Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 216 GLU Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 296 THR Chi-restraints excluded: chain K residue 369 VAL Chi-restraints excluded: chain K residue 372 LEU Chi-restraints excluded: chain K residue 381 VAL Chi-restraints excluded: chain K residue 387 VAL Chi-restraints excluded: chain K residue 397 GLU Chi-restraints excluded: chain K residue 401 HIS Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain K residue 424 SER Chi-restraints excluded: chain K residue 470 LYS Chi-restraints excluded: chain K residue 494 LEU Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 227 ILE Chi-restraints excluded: chain L residue 250 ILE Chi-restraints excluded: chain L residue 271 VAL Chi-restraints excluded: chain L residue 296 THR Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 397 GLU Chi-restraints excluded: chain L residue 401 HIS Chi-restraints excluded: chain L residue 461 GLU Chi-restraints excluded: chain L residue 499 VAL Chi-restraints excluded: chain Z residue 27 VAL Chi-restraints excluded: chain Z residue 61 GLU Chi-restraints excluded: chain Z residue 77 VAL Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain Z residue 169 VAL Chi-restraints excluded: chain Z residue 187 LEU Chi-restraints excluded: chain Z residue 193 MET Chi-restraints excluded: chain Z residue 222 LEU Chi-restraints excluded: chain Z residue 300 VAL Chi-restraints excluded: chain Z residue 329 THR Chi-restraints excluded: chain Z residue 378 VAL Chi-restraints excluded: chain Z residue 401 HIS Chi-restraints excluded: chain Z residue 454 ILE Chi-restraints excluded: chain Z residue 463 SER Chi-restraints excluded: chain Z residue 494 LEU Chi-restraints excluded: chain Z residue 497 THR Chi-restraints excluded: chain Z residue 516 THR Chi-restraints excluded: chain M residue 222 LEU Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain S residue 61 GLU Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 177 VAL Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain S residue 222 LEU Chi-restraints excluded: chain S residue 292 ILE Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 332 ILE Chi-restraints excluded: chain S residue 378 VAL Chi-restraints excluded: chain S residue 401 HIS Chi-restraints excluded: chain S residue 422 VAL Chi-restraints excluded: chain S residue 424 SER Chi-restraints excluded: chain S residue 454 ILE Chi-restraints excluded: chain S residue 463 SER Chi-restraints excluded: chain N residue 228 GLN Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 187 LEU Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 292 ILE Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 378 VAL Chi-restraints excluded: chain T residue 401 HIS Chi-restraints excluded: chain T residue 424 SER Chi-restraints excluded: chain T residue 463 SER Chi-restraints excluded: chain T residue 482 THR Chi-restraints excluded: chain T residue 494 LEU Chi-restraints excluded: chain T residue 517 THR Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain O residue 278 GLN Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 169 VAL Chi-restraints excluded: chain U residue 174 VAL Chi-restraints excluded: chain U residue 177 VAL Chi-restraints excluded: chain U residue 187 LEU Chi-restraints excluded: chain U residue 300 VAL Chi-restraints excluded: chain U residue 381 VAL Chi-restraints excluded: chain U residue 401 HIS Chi-restraints excluded: chain U residue 422 VAL Chi-restraints excluded: chain U residue 463 SER Chi-restraints excluded: chain U residue 482 THR Chi-restraints excluded: chain U residue 515 ILE Chi-restraints excluded: chain U residue 516 THR Chi-restraints excluded: chain P residue 253 GLN Chi-restraints excluded: chain V residue 27 VAL Chi-restraints excluded: chain V residue 107 VAL Chi-restraints excluded: chain V residue 169 VAL Chi-restraints excluded: chain V residue 187 LEU Chi-restraints excluded: chain V residue 300 VAL Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 333 ILE Chi-restraints excluded: chain V residue 378 VAL Chi-restraints excluded: chain V residue 401 HIS Chi-restraints excluded: chain V residue 463 SER Chi-restraints excluded: chain V residue 499 VAL Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 61 GLU Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 169 VAL Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain W residue 289 LEU Chi-restraints excluded: chain W residue 378 VAL Chi-restraints excluded: chain W residue 381 VAL Chi-restraints excluded: chain W residue 422 VAL Chi-restraints excluded: chain W residue 463 SER Chi-restraints excluded: chain W residue 494 LEU Chi-restraints excluded: chain W residue 495 ASP Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain X residue 27 VAL Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain X residue 162 ILE Chi-restraints excluded: chain X residue 169 VAL Chi-restraints excluded: chain X residue 177 VAL Chi-restraints excluded: chain X residue 187 LEU Chi-restraints excluded: chain X residue 378 VAL Chi-restraints excluded: chain X residue 381 VAL Chi-restraints excluded: chain X residue 401 HIS Chi-restraints excluded: chain X residue 422 VAL Chi-restraints excluded: chain X residue 463 SER Chi-restraints excluded: chain X residue 482 THR Chi-restraints excluded: chain X residue 494 LEU Chi-restraints excluded: chain X residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 676 optimal weight: 5.9990 chunk 460 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 604 optimal weight: 30.0000 chunk 335 optimal weight: 0.8980 chunk 692 optimal weight: 10.0000 chunk 561 optimal weight: 10.0000 chunk 0 optimal weight: 80.0000 chunk 414 optimal weight: 0.7980 chunk 728 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 203 GLN J 112 ASN ** Y 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 228 GLN ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 242 HIS ** N 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 242 HIS ** Q 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 290 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 64540 Z= 0.231 Angle : 0.677 18.327 87248 Z= 0.354 Chirality : 0.042 0.247 10500 Planarity : 0.004 0.051 11522 Dihedral : 4.754 52.464 9159 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.47 % Allowed : 3.12 % Favored : 96.41 % Rotamer: Outliers : 3.62 % Allowed : 15.89 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.09), residues: 8638 helix: 2.02 (0.07), residues: 5110 sheet: 0.70 (0.17), residues: 826 loop : -2.10 (0.10), residues: 2702 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS Y 242 PHE 0.013 0.002 PHE X 66 TYR 0.016 0.002 TYR b 476 ARG 0.007 0.000 ARG T 345 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17276 Ramachandran restraints generated. 8638 Oldfield, 0 Emsley, 8638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17276 Ramachandran restraints generated. 8638 Oldfield, 0 Emsley, 8638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1306 residues out of total 6580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1065 time to evaluate : 5.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 67 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7486 (mt-10) REVERT: b 105 LYS cc_start: 0.8361 (ttpt) cc_final: 0.7910 (ttmm) REVERT: b 160 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7372 (ttmm) REVERT: b 164 GLU cc_start: 0.7253 (tp30) cc_final: 0.7016 (tp30) REVERT: b 178 GLU cc_start: 0.6993 (pt0) cc_final: 0.6551 (pt0) REVERT: b 205 ILE cc_start: 0.6279 (mt) cc_final: 0.6027 (mt) REVERT: b 286 LYS cc_start: 0.7527 (mttt) cc_final: 0.6609 (ptmt) REVERT: b 307 MET cc_start: 0.4879 (mmp) cc_final: 0.4104 (mmp) REVERT: b 321 LYS cc_start: 0.6934 (tptt) cc_final: 0.6484 (tttt) REVERT: b 351 GLN cc_start: 0.7733 (tt0) cc_final: 0.6996 (tp-100) REVERT: b 352 GLN cc_start: 0.6528 (mt0) cc_final: 0.6225 (mt0) REVERT: b 366 GLN cc_start: 0.6924 (mm110) cc_final: 0.6484 (mm110) REVERT: b 380 LYS cc_start: 0.7063 (mttt) cc_final: 0.6487 (mtmm) REVERT: b 397 GLU cc_start: 0.7378 (tt0) cc_final: 0.7080 (tt0) REVERT: b 404 ARG cc_start: 0.7559 (tpp80) cc_final: 0.7148 (ttp80) REVERT: b 407 VAL cc_start: 0.8103 (p) cc_final: 0.7880 (p) REVERT: G 69 MET cc_start: 0.8178 (mtm) cc_final: 0.7842 (mtm) REVERT: G 121 ASP cc_start: 0.7855 (m-30) cc_final: 0.7302 (t0) REVERT: G 164 GLU cc_start: 0.7670 (tp30) cc_final: 0.7368 (tp30) REVERT: G 267 MET cc_start: 0.7517 (tpt) cc_final: 0.7097 (tpt) REVERT: G 307 MET cc_start: 0.5808 (mmp) cc_final: 0.5221 (mmp) REVERT: G 367 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6991 (mm-30) REVERT: G 380 LYS cc_start: 0.7318 (mttt) cc_final: 0.6349 (mtmm) REVERT: G 494 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8047 (pp) REVERT: B 238 LEU cc_start: 0.7906 (tp) cc_final: 0.7650 (tp) REVERT: H 73 MET cc_start: 0.7941 (ttm) cc_final: 0.7691 (ttm) REVERT: H 105 LYS cc_start: 0.8450 (ttpt) cc_final: 0.7866 (ttmm) REVERT: H 130 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7183 (mm-30) REVERT: H 286 LYS cc_start: 0.7787 (mttt) cc_final: 0.6859 (ptmt) REVERT: H 307 MET cc_start: 0.5397 (mmp) cc_final: 0.4452 (mmp) REVERT: H 321 LYS cc_start: 0.7477 (tptt) cc_final: 0.7255 (tptm) REVERT: H 325 ILE cc_start: 0.7950 (mt) cc_final: 0.7639 (mm) REVERT: H 351 GLN cc_start: 0.7391 (tt0) cc_final: 0.6705 (tp40) REVERT: H 366 GLN cc_start: 0.7199 (mt0) cc_final: 0.6914 (mt0) REVERT: H 380 LYS cc_start: 0.7337 (mttt) cc_final: 0.6653 (mtmm) REVERT: H 398 ASP cc_start: 0.8603 (t70) cc_final: 0.8245 (t0) REVERT: H 403 THR cc_start: 0.8407 (m) cc_final: 0.8090 (m) REVERT: H 404 ARG cc_start: 0.7252 (tpp80) cc_final: 0.7044 (ttm-80) REVERT: H 473 ASP cc_start: 0.7655 (p0) cc_final: 0.6879 (m-30) REVERT: C 207 GLN cc_start: 0.3807 (mm-40) cc_final: 0.3603 (mm-40) REVERT: I 105 LYS cc_start: 0.8429 (ttpt) cc_final: 0.8020 (ttmm) REVERT: I 187 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8092 (tt) REVERT: I 233 MET cc_start: 0.6122 (mmm) cc_final: 0.5702 (mmp) REVERT: I 267 MET cc_start: 0.6530 (ttt) cc_final: 0.6231 (tpp) REVERT: I 307 MET cc_start: 0.5510 (mmp) cc_final: 0.4371 (mmt) REVERT: I 321 LYS cc_start: 0.7350 (tptt) cc_final: 0.6819 (tttt) REVERT: I 389 MET cc_start: 0.7087 (tpp) cc_final: 0.6732 (tpp) REVERT: I 432 GLN cc_start: 0.7715 (mm-40) cc_final: 0.7293 (mt0) REVERT: I 514 MET cc_start: 0.7493 (ttm) cc_final: 0.7218 (mtp) REVERT: I 523 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.8046 (t0) REVERT: D 207 GLN cc_start: 0.7812 (tp40) cc_final: 0.7170 (mm110) REVERT: J 69 MET cc_start: 0.8333 (mtm) cc_final: 0.7788 (mtm) REVERT: J 204 PHE cc_start: 0.6996 (m-80) cc_final: 0.6584 (m-80) REVERT: J 288 MET cc_start: 0.6232 (mtt) cc_final: 0.5989 (mtp) REVERT: J 307 MET cc_start: 0.6188 (mmp) cc_final: 0.4930 (mmp) REVERT: J 380 LYS cc_start: 0.7614 (mttt) cc_final: 0.7163 (mtmm) REVERT: J 404 ARG cc_start: 0.7386 (tpp80) cc_final: 0.7179 (ttm-80) REVERT: J 432 GLN cc_start: 0.7536 (mm110) cc_final: 0.7317 (mt0) REVERT: J 494 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8113 (pp) REVERT: K 69 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7643 (mtm) REVERT: K 105 LYS cc_start: 0.8372 (ttpt) cc_final: 0.8103 (ttmm) REVERT: K 112 ASN cc_start: 0.8005 (t0) cc_final: 0.7778 (t0) REVERT: K 121 ASP cc_start: 0.7756 (m-30) cc_final: 0.7391 (m-30) REVERT: K 178 GLU cc_start: 0.7018 (pt0) cc_final: 0.6675 (pt0) REVERT: K 267 MET cc_start: 0.6219 (ttt) cc_final: 0.5910 (tpp) REVERT: K 307 MET cc_start: 0.5254 (mmp) cc_final: 0.4367 (mmp) REVERT: K 321 LYS cc_start: 0.7527 (tptt) cc_final: 0.7212 (tptm) REVERT: K 351 GLN cc_start: 0.7735 (tt0) cc_final: 0.7467 (tp40) REVERT: K 380 LYS cc_start: 0.7517 (mttt) cc_final: 0.7009 (mtmm) REVERT: K 387 VAL cc_start: 0.5938 (OUTLIER) cc_final: 0.5690 (p) REVERT: K 404 ARG cc_start: 0.8026 (tpp80) cc_final: 0.7549 (mtp85) REVERT: K 422 VAL cc_start: 0.9026 (t) cc_final: 0.8528 (m) REVERT: K 432 GLN cc_start: 0.7202 (mm110) cc_final: 0.6863 (mt0) REVERT: K 514 MET cc_start: 0.7591 (mtp) cc_final: 0.7048 (mtt) REVERT: L 59 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7575 (mm-30) REVERT: L 105 LYS cc_start: 0.8320 (ttpt) cc_final: 0.7936 (ttmm) REVERT: L 307 MET cc_start: 0.5242 (mmp) cc_final: 0.4387 (mmp) REVERT: L 326 ASN cc_start: 0.7104 (t0) cc_final: 0.6677 (t0) REVERT: L 397 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: Y 228 GLN cc_start: 0.6505 (OUTLIER) cc_final: 0.6197 (mm-40) REVERT: Z 18 ARG cc_start: 0.7465 (ttm-80) cc_final: 0.6812 (ttp80) REVERT: Z 59 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7182 (mm-30) REVERT: Z 63 GLU cc_start: 0.7373 (tp30) cc_final: 0.6882 (pm20) REVERT: Z 193 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6720 (ttm) REVERT: Z 207 LYS cc_start: 0.7475 (mtpt) cc_final: 0.6874 (mmtm) REVERT: Z 267 MET cc_start: 0.6576 (ptp) cc_final: 0.6314 (ptm) REVERT: Z 345 ARG cc_start: 0.6915 (mmm160) cc_final: 0.6673 (mtp85) REVERT: Z 432 GLN cc_start: 0.7560 (mm110) cc_final: 0.7266 (mm-40) REVERT: Z 482 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8892 (p) REVERT: Z 491 MET cc_start: 0.7469 (mtt) cc_final: 0.7160 (mtp) REVERT: M 222 LEU cc_start: 0.6024 (OUTLIER) cc_final: 0.5818 (mt) REVERT: S 128 VAL cc_start: 0.8264 (t) cc_final: 0.7941 (t) REVERT: S 204 PHE cc_start: 0.8087 (m-10) cc_final: 0.7753 (m-80) REVERT: S 207 LYS cc_start: 0.7521 (mmmm) cc_final: 0.7217 (mtpt) REVERT: S 267 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6402 (ptm) REVERT: S 288 MET cc_start: 0.5995 (mtm) cc_final: 0.5545 (mtp) REVERT: S 321 LYS cc_start: 0.7834 (tptt) cc_final: 0.7488 (mmmm) REVERT: S 488 MET cc_start: 0.8686 (mmm) cc_final: 0.7788 (mmm) REVERT: S 494 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7890 (pp) REVERT: N 222 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6706 (mt) REVERT: N 228 GLN cc_start: 0.6087 (OUTLIER) cc_final: 0.4471 (mm-40) REVERT: N 238 LEU cc_start: 0.7848 (tp) cc_final: 0.7533 (tp) REVERT: T 179 ASP cc_start: 0.7911 (m-30) cc_final: 0.7687 (m-30) REVERT: T 487 ASN cc_start: 0.8214 (m-40) cc_final: 0.7408 (t0) REVERT: U 160 LYS cc_start: 0.7765 (tttt) cc_final: 0.7502 (mtpp) REVERT: U 166 MET cc_start: 0.7700 (ttm) cc_final: 0.7042 (mtp) REVERT: U 207 LYS cc_start: 0.7993 (mmmm) cc_final: 0.7443 (mmtm) REVERT: U 267 MET cc_start: 0.5509 (ttt) cc_final: 0.5142 (ptt) REVERT: U 378 VAL cc_start: 0.8569 (t) cc_final: 0.8287 (m) REVERT: U 447 MET cc_start: 0.8214 (mtt) cc_final: 0.7725 (mtt) REVERT: U 482 THR cc_start: 0.9339 (OUTLIER) cc_final: 0.8957 (p) REVERT: U 488 MET cc_start: 0.8615 (mmm) cc_final: 0.8381 (mtp) REVERT: V 61 GLU cc_start: 0.7588 (pt0) cc_final: 0.7249 (pt0) REVERT: V 87 ASP cc_start: 0.8323 (t0) cc_final: 0.8035 (t0) REVERT: V 121 ASP cc_start: 0.7290 (m-30) cc_final: 0.6940 (m-30) REVERT: V 129 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6422 (mt-10) REVERT: V 171 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8503 (mtpt) REVERT: V 193 MET cc_start: 0.7394 (mmm) cc_final: 0.6561 (tpt) REVERT: V 222 LEU cc_start: 0.4441 (OUTLIER) cc_final: 0.4168 (mt) REVERT: V 332 ILE cc_start: 0.7153 (OUTLIER) cc_final: 0.6803 (tp) REVERT: V 338 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6797 (pm20) REVERT: V 390 LYS cc_start: 0.7043 (mtpp) cc_final: 0.6404 (mmmt) REVERT: V 393 LYS cc_start: 0.7454 (tttp) cc_final: 0.7175 (ttpt) REVERT: V 432 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7342 (mm-40) REVERT: V 455 VAL cc_start: 0.8567 (t) cc_final: 0.8322 (t) REVERT: Q 238 LEU cc_start: 0.7558 (tp) cc_final: 0.7308 (tp) REVERT: W 105 LYS cc_start: 0.8105 (ttpt) cc_final: 0.7799 (ttmm) REVERT: W 179 ASP cc_start: 0.8556 (m-30) cc_final: 0.8037 (m-30) REVERT: W 214 GLU cc_start: 0.6839 (pm20) cc_final: 0.6384 (pm20) REVERT: W 345 ARG cc_start: 0.5933 (mmm160) cc_final: 0.5706 (mtp85) REVERT: W 380 LYS cc_start: 0.6417 (mttt) cc_final: 0.5946 (mmtp) REVERT: W 432 GLN cc_start: 0.8183 (mm110) cc_final: 0.7957 (mm-40) REVERT: W 495 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7201 (t70) REVERT: R 228 GLN cc_start: 0.6535 (mt0) cc_final: 0.5551 (mm-40) REVERT: R 259 GLN cc_start: 0.5292 (pp30) cc_final: 0.4607 (pm20) REVERT: X 59 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7257 (mm-30) REVERT: X 160 LYS cc_start: 0.7791 (tttt) cc_final: 0.7343 (mtpp) REVERT: X 185 ASP cc_start: 0.6662 (m-30) cc_final: 0.6424 (m-30) REVERT: X 187 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7803 (tp) REVERT: X 193 MET cc_start: 0.7251 (mmt) cc_final: 0.6674 (tpt) REVERT: X 196 ASP cc_start: 0.8213 (t0) cc_final: 0.7851 (p0) REVERT: X 233 MET cc_start: 0.6898 (mmm) cc_final: 0.6521 (mmp) REVERT: X 288 MET cc_start: 0.4982 (mtt) cc_final: 0.4725 (mtt) REVERT: X 371 LYS cc_start: 0.7415 (tptt) cc_final: 0.7045 (ttmm) REVERT: X 487 ASN cc_start: 0.7745 (m-40) cc_final: 0.7430 (t0) outliers start: 241 outliers final: 168 residues processed: 1192 average time/residue: 0.5584 time to fit residues: 1150.9983 Evaluate side-chains 1226 residues out of total 6580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1036 time to evaluate : 5.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 60 ILE Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 160 LYS Chi-restraints excluded: chain b residue 187 LEU Chi-restraints excluded: chain b residue 227 ILE Chi-restraints excluded: chain b residue 267 MET Chi-restraints excluded: chain b residue 271 VAL Chi-restraints excluded: chain b residue 401 HIS Chi-restraints excluded: chain b residue 424 SER Chi-restraints excluded: chain b residue 482 THR Chi-restraints excluded: chain b residue 494 LEU Chi-restraints excluded: chain b residue 510 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 401 HIS Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 424 SER Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 80 LYS Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 401 HIS Chi-restraints excluded: chain H residue 509 SER Chi-restraints excluded: chain H residue 510 VAL Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 160 LYS Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 284 ARG Chi-restraints excluded: chain I residue 296 THR Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 387 VAL Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 401 HIS Chi-restraints excluded: chain I residue 515 ILE Chi-restraints excluded: chain I residue 523 ASP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain J residue 401 HIS Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 494 LEU Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 216 GLU Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 296 THR Chi-restraints excluded: chain K residue 372 LEU Chi-restraints excluded: chain K residue 387 VAL Chi-restraints excluded: chain K residue 401 HIS Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain K residue 424 SER Chi-restraints excluded: chain K residue 463 SER Chi-restraints excluded: chain K residue 470 LYS Chi-restraints excluded: chain K residue 494 LEU Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 250 ILE Chi-restraints excluded: chain L residue 271 VAL Chi-restraints excluded: chain L residue 381 VAL Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 397 GLU Chi-restraints excluded: chain L residue 401 HIS Chi-restraints excluded: chain L residue 407 VAL Chi-restraints excluded: chain L residue 442 VAL Chi-restraints excluded: chain Y residue 206 GLN Chi-restraints excluded: chain Y residue 222 LEU Chi-restraints excluded: chain Y residue 228 GLN Chi-restraints excluded: chain Z residue 61 GLU Chi-restraints excluded: chain Z residue 77 VAL Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain Z residue 129 GLU Chi-restraints excluded: chain Z residue 169 VAL Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain Z residue 187 LEU Chi-restraints excluded: chain Z residue 193 MET Chi-restraints excluded: chain Z residue 329 THR Chi-restraints excluded: chain Z residue 332 ILE Chi-restraints excluded: chain Z residue 378 VAL Chi-restraints excluded: chain Z residue 401 HIS Chi-restraints excluded: chain Z residue 482 THR Chi-restraints excluded: chain M residue 222 LEU Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain S residue 61 GLU Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 177 VAL Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain S residue 206 ASN Chi-restraints excluded: chain S residue 267 MET Chi-restraints excluded: chain S residue 332 ILE Chi-restraints excluded: chain S residue 378 VAL Chi-restraints excluded: chain S residue 401 HIS Chi-restraints excluded: chain S residue 422 VAL Chi-restraints excluded: chain S residue 424 SER Chi-restraints excluded: chain S residue 463 SER Chi-restraints excluded: chain S residue 494 LEU Chi-restraints excluded: chain N residue 222 LEU Chi-restraints excluded: chain N residue 228 GLN Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 187 LEU Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 292 ILE Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 378 VAL Chi-restraints excluded: chain T residue 401 HIS Chi-restraints excluded: chain T residue 424 SER Chi-restraints excluded: chain T residue 494 LEU Chi-restraints excluded: chain T residue 517 THR Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain O residue 278 GLN Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 169 VAL Chi-restraints excluded: chain U residue 177 VAL Chi-restraints excluded: chain U residue 187 LEU Chi-restraints excluded: chain U residue 381 VAL Chi-restraints excluded: chain U residue 401 HIS Chi-restraints excluded: chain U residue 482 THR Chi-restraints excluded: chain U residue 515 ILE Chi-restraints excluded: chain P residue 253 GLN Chi-restraints excluded: chain V residue 27 VAL Chi-restraints excluded: chain V residue 129 GLU Chi-restraints excluded: chain V residue 169 VAL Chi-restraints excluded: chain V residue 187 LEU Chi-restraints excluded: chain V residue 194 GLN Chi-restraints excluded: chain V residue 222 LEU Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 401 HIS Chi-restraints excluded: chain V residue 447 MET Chi-restraints excluded: chain V residue 463 SER Chi-restraints excluded: chain V residue 494 LEU Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 61 GLU Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 169 VAL Chi-restraints excluded: chain W residue 206 ASN Chi-restraints excluded: chain W residue 240 VAL Chi-restraints excluded: chain W residue 289 LEU Chi-restraints excluded: chain W residue 417 VAL Chi-restraints excluded: chain W residue 495 ASP Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain X residue 27 VAL Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain X residue 162 ILE Chi-restraints excluded: chain X residue 169 VAL Chi-restraints excluded: chain X residue 177 VAL Chi-restraints excluded: chain X residue 187 LEU Chi-restraints excluded: chain X residue 263 VAL Chi-restraints excluded: chain X residue 367 GLU Chi-restraints excluded: chain X residue 378 VAL Chi-restraints excluded: chain X residue 381 VAL Chi-restraints excluded: chain X residue 401 HIS Chi-restraints excluded: chain X residue 494 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 273 optimal weight: 10.0000 chunk 731 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 476 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 chunk 812 optimal weight: 6.9990 chunk 674 optimal weight: 0.9990 chunk 376 optimal weight: 10.0000 chunk 67 optimal weight: 50.0000 chunk 268 optimal weight: 10.0000 chunk 426 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 203 GLN E 203 GLN K 457 ASN ** Y 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 228 GLN Y 242 HIS ** Y 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 ASN ** O 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 206 GLN ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 290 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 64540 Z= 0.324 Angle : 0.701 14.938 87248 Z= 0.367 Chirality : 0.044 0.225 10500 Planarity : 0.004 0.052 11522 Dihedral : 4.721 47.791 9157 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.03 % Favored : 95.49 % Rotamer: Outliers : 4.47 % Allowed : 16.27 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.09), residues: 8638 helix: 2.05 (0.07), residues: 5082 sheet: 0.69 (0.18), residues: 798 loop : -2.17 (0.10), residues: 2758 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS S 401 PHE 0.014 0.002 PHE J 8 TYR 0.018 0.002 TYR L 478 ARG 0.006 0.000 ARG L 404 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17276 Ramachandran restraints generated. 8638 Oldfield, 0 Emsley, 8638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17276 Ramachandran restraints generated. 8638 Oldfield, 0 Emsley, 8638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1348 residues out of total 6580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1050 time to evaluate : 5.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 59 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7380 (mm-30) REVERT: b 105 LYS cc_start: 0.8468 (ttpt) cc_final: 0.8126 (ttmm) REVERT: b 160 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7422 (ttmm) REVERT: b 164 GLU cc_start: 0.7221 (tp30) cc_final: 0.6974 (tp30) REVERT: b 286 LYS cc_start: 0.7590 (mttt) cc_final: 0.6687 (ptmt) REVERT: b 307 MET cc_start: 0.5036 (mmp) cc_final: 0.4312 (mmp) REVERT: b 321 LYS cc_start: 0.6873 (tptt) cc_final: 0.6496 (tttt) REVERT: b 351 GLN cc_start: 0.7812 (tt0) cc_final: 0.7031 (tp40) REVERT: b 352 GLN cc_start: 0.6546 (mt0) cc_final: 0.6239 (mt0) REVERT: b 366 GLN cc_start: 0.6917 (mm110) cc_final: 0.6489 (mm110) REVERT: b 380 LYS cc_start: 0.7122 (mttt) cc_final: 0.6591 (mtmm) REVERT: b 397 GLU cc_start: 0.7402 (tt0) cc_final: 0.7099 (tt0) REVERT: b 404 ARG cc_start: 0.7564 (tpp80) cc_final: 0.7142 (ttp80) REVERT: b 407 VAL cc_start: 0.8197 (p) cc_final: 0.7938 (p) REVERT: G 121 ASP cc_start: 0.7900 (m-30) cc_final: 0.7324 (t0) REVERT: G 267 MET cc_start: 0.7407 (tpt) cc_final: 0.7199 (tpt) REVERT: G 307 MET cc_start: 0.5934 (mmp) cc_final: 0.5328 (mmp) REVERT: G 367 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6975 (mm-30) REVERT: G 380 LYS cc_start: 0.7306 (mttt) cc_final: 0.6295 (mtmm) REVERT: G 494 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8089 (pp) REVERT: G 520 MET cc_start: 0.8522 (mtm) cc_final: 0.8253 (mtm) REVERT: B 238 LEU cc_start: 0.7927 (tp) cc_final: 0.7674 (tp) REVERT: H 59 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7213 (mm-30) REVERT: H 73 MET cc_start: 0.7970 (ttm) cc_final: 0.7611 (ttm) REVERT: H 105 LYS cc_start: 0.8280 (ttpt) cc_final: 0.7839 (ttmm) REVERT: H 130 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7107 (mm-30) REVERT: H 286 LYS cc_start: 0.7853 (mttt) cc_final: 0.6899 (ptmt) REVERT: H 307 MET cc_start: 0.5591 (mmp) cc_final: 0.4650 (mmp) REVERT: H 321 LYS cc_start: 0.7476 (tptt) cc_final: 0.7018 (tttt) REVERT: H 325 ILE cc_start: 0.7961 (mt) cc_final: 0.7649 (mm) REVERT: H 366 GLN cc_start: 0.7222 (mt0) cc_final: 0.6944 (mt0) REVERT: H 380 LYS cc_start: 0.7352 (mttt) cc_final: 0.6624 (mtmm) REVERT: H 398 ASP cc_start: 0.8605 (t70) cc_final: 0.8237 (t0) REVERT: H 403 THR cc_start: 0.8432 (m) cc_final: 0.8116 (m) REVERT: H 404 ARG cc_start: 0.7268 (tpp80) cc_final: 0.7055 (ttm-80) REVERT: H 473 ASP cc_start: 0.7789 (p0) cc_final: 0.7018 (m-30) REVERT: I 105 LYS cc_start: 0.8418 (ttpt) cc_final: 0.8032 (ttmm) REVERT: I 186 GLU cc_start: 0.7599 (mt-10) cc_final: 0.6804 (pt0) REVERT: I 187 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7954 (tt) REVERT: I 233 MET cc_start: 0.6116 (mmm) cc_final: 0.5689 (mmp) REVERT: I 267 MET cc_start: 0.6528 (ttt) cc_final: 0.6215 (tpp) REVERT: I 307 MET cc_start: 0.5683 (mmp) cc_final: 0.4506 (mmt) REVERT: I 321 LYS cc_start: 0.7213 (tptt) cc_final: 0.6745 (tttt) REVERT: I 366 GLN cc_start: 0.7509 (mm110) cc_final: 0.7210 (mm110) REVERT: I 389 MET cc_start: 0.7051 (tpp) cc_final: 0.6713 (tpp) REVERT: I 432 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7303 (mt0) REVERT: I 482 THR cc_start: 0.8780 (m) cc_final: 0.8474 (p) REVERT: I 514 MET cc_start: 0.7954 (ttm) cc_final: 0.7750 (mtp) REVERT: I 523 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7749 (t0) REVERT: D 207 GLN cc_start: 0.7693 (tp40) cc_final: 0.7160 (mm110) REVERT: J 69 MET cc_start: 0.8452 (mtm) cc_final: 0.7943 (mtm) REVERT: J 204 PHE cc_start: 0.7012 (m-80) cc_final: 0.6603 (m-80) REVERT: J 233 MET cc_start: 0.6136 (mmm) cc_final: 0.5830 (mmp) REVERT: J 307 MET cc_start: 0.5050 (mmp) cc_final: 0.3971 (mmp) REVERT: J 380 LYS cc_start: 0.7638 (mttt) cc_final: 0.7208 (mtmm) REVERT: J 404 ARG cc_start: 0.7406 (tpp80) cc_final: 0.7189 (ttm-80) REVERT: J 432 GLN cc_start: 0.7516 (mm110) cc_final: 0.7268 (mt0) REVERT: J 494 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8193 (pp) REVERT: K 105 LYS cc_start: 0.8430 (ttpt) cc_final: 0.8130 (ttmm) REVERT: K 112 ASN cc_start: 0.8100 (t0) cc_final: 0.7872 (t0) REVERT: K 121 ASP cc_start: 0.7772 (m-30) cc_final: 0.7410 (m-30) REVERT: K 178 GLU cc_start: 0.7024 (pt0) cc_final: 0.6714 (pt0) REVERT: K 267 MET cc_start: 0.6257 (ttt) cc_final: 0.5980 (tpp) REVERT: K 307 MET cc_start: 0.5413 (mmp) cc_final: 0.4573 (mmp) REVERT: K 330 THR cc_start: 0.7507 (m) cc_final: 0.6958 (p) REVERT: K 380 LYS cc_start: 0.7502 (mttt) cc_final: 0.7012 (mtmm) REVERT: K 387 VAL cc_start: 0.5960 (OUTLIER) cc_final: 0.5714 (p) REVERT: K 404 ARG cc_start: 0.8035 (tpp80) cc_final: 0.7564 (mtp85) REVERT: K 422 VAL cc_start: 0.9030 (t) cc_final: 0.8489 (m) REVERT: K 432 GLN cc_start: 0.7184 (mm110) cc_final: 0.6790 (mt0) REVERT: K 514 MET cc_start: 0.7817 (mtp) cc_final: 0.7591 (mtp) REVERT: L 59 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7589 (mm-30) REVERT: L 307 MET cc_start: 0.5428 (mmp) cc_final: 0.4558 (mmp) REVERT: L 326 ASN cc_start: 0.7474 (t0) cc_final: 0.6967 (t0) REVERT: L 397 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7196 (tm-30) REVERT: Y 228 GLN cc_start: 0.6805 (OUTLIER) cc_final: 0.6174 (mm-40) REVERT: Y 259 GLN cc_start: 0.5773 (pp30) cc_final: 0.4776 (pm20) REVERT: Z 18 ARG cc_start: 0.7592 (ttm-80) cc_final: 0.6979 (ttp80) REVERT: Z 59 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7185 (mm-30) REVERT: Z 63 GLU cc_start: 0.7397 (tp30) cc_final: 0.6917 (pm20) REVERT: Z 164 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8039 (mm-30) REVERT: Z 193 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6792 (ttm) REVERT: Z 207 LYS cc_start: 0.7484 (mtpt) cc_final: 0.6938 (mmtm) REVERT: Z 222 LEU cc_start: 0.5088 (OUTLIER) cc_final: 0.4870 (mt) REVERT: Z 267 MET cc_start: 0.6533 (ptp) cc_final: 0.6330 (ptm) REVERT: Z 345 ARG cc_start: 0.6903 (mmm160) cc_final: 0.6667 (mtp85) REVERT: Z 371 LYS cc_start: 0.7096 (tppt) cc_final: 0.6811 (ttmm) REVERT: Z 432 GLN cc_start: 0.7544 (mm110) cc_final: 0.7267 (mm-40) REVERT: Z 482 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8941 (p) REVERT: Z 491 MET cc_start: 0.7489 (mtt) cc_final: 0.7170 (mtp) REVERT: M 222 LEU cc_start: 0.5932 (OUTLIER) cc_final: 0.5707 (mt) REVERT: M 228 GLN cc_start: 0.6806 (mp10) cc_final: 0.5066 (mm-40) REVERT: S 128 VAL cc_start: 0.8255 (t) cc_final: 0.7958 (t) REVERT: S 193 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6670 (tpt) REVERT: S 204 PHE cc_start: 0.8009 (m-10) cc_final: 0.7639 (m-80) REVERT: S 207 LYS cc_start: 0.7526 (mmmm) cc_final: 0.7219 (mtpt) REVERT: S 222 LEU cc_start: 0.5217 (OUTLIER) cc_final: 0.4859 (mt) REVERT: S 267 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6512 (ptm) REVERT: S 288 MET cc_start: 0.6178 (mtm) cc_final: 0.5536 (mtp) REVERT: S 488 MET cc_start: 0.8775 (mmm) cc_final: 0.7935 (mmm) REVERT: S 494 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7895 (pp) REVERT: N 222 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6281 (mt) REVERT: N 228 GLN cc_start: 0.6058 (OUTLIER) cc_final: 0.4461 (mm-40) REVERT: N 238 LEU cc_start: 0.7773 (tp) cc_final: 0.7456 (tp) REVERT: T 130 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6388 (mm-30) REVERT: T 179 ASP cc_start: 0.7967 (m-30) cc_final: 0.7733 (m-30) REVERT: T 404 ARG cc_start: 0.8217 (tpp80) cc_final: 0.7790 (tpp80) REVERT: T 487 ASN cc_start: 0.8229 (m-40) cc_final: 0.7407 (t0) REVERT: U 115 ASP cc_start: 0.6897 (m-30) cc_final: 0.6540 (m-30) REVERT: U 160 LYS cc_start: 0.7760 (tttt) cc_final: 0.7544 (mtpp) REVERT: U 166 MET cc_start: 0.7645 (ttm) cc_final: 0.7110 (mtp) REVERT: U 207 LYS cc_start: 0.7995 (mmmm) cc_final: 0.7508 (mmtm) REVERT: U 267 MET cc_start: 0.5536 (ttt) cc_final: 0.5148 (ptt) REVERT: U 378 VAL cc_start: 0.8464 (t) cc_final: 0.8174 (m) REVERT: U 447 MET cc_start: 0.8301 (mtt) cc_final: 0.7821 (mtt) REVERT: U 482 THR cc_start: 0.9372 (OUTLIER) cc_final: 0.9038 (p) REVERT: U 488 MET cc_start: 0.8588 (mmm) cc_final: 0.8382 (mtp) REVERT: V 61 GLU cc_start: 0.7609 (pt0) cc_final: 0.7247 (pt0) REVERT: V 87 ASP cc_start: 0.8350 (t0) cc_final: 0.8062 (t0) REVERT: V 121 ASP cc_start: 0.7312 (m-30) cc_final: 0.6980 (m-30) REVERT: V 129 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6443 (mt-10) REVERT: V 171 LYS cc_start: 0.8713 (mtmt) cc_final: 0.8273 (mtpt) REVERT: V 172 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8307 (mp0) REVERT: V 178 GLU cc_start: 0.7563 (pt0) cc_final: 0.7294 (pt0) REVERT: V 193 MET cc_start: 0.7451 (mmm) cc_final: 0.6578 (tpt) REVERT: V 222 LEU cc_start: 0.4490 (OUTLIER) cc_final: 0.4237 (mt) REVERT: V 267 MET cc_start: 0.5161 (ptm) cc_final: 0.4929 (ptt) REVERT: V 332 ILE cc_start: 0.7271 (OUTLIER) cc_final: 0.6931 (tp) REVERT: V 338 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6883 (pm20) REVERT: V 390 LYS cc_start: 0.7124 (mtpp) cc_final: 0.6468 (mmmt) REVERT: V 393 LYS cc_start: 0.7508 (tttp) cc_final: 0.7193 (ttpt) REVERT: V 432 GLN cc_start: 0.7574 (mm-40) cc_final: 0.7292 (mm-40) REVERT: V 470 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7137 (mttt) REVERT: Q 238 LEU cc_start: 0.7580 (tp) cc_final: 0.7329 (tp) REVERT: W 105 LYS cc_start: 0.8156 (ttpt) cc_final: 0.7816 (ttmm) REVERT: W 214 GLU cc_start: 0.6839 (pm20) cc_final: 0.6396 (pm20) REVERT: W 345 ARG cc_start: 0.5926 (mmm160) cc_final: 0.5711 (mtp85) REVERT: W 380 LYS cc_start: 0.6362 (mttt) cc_final: 0.5886 (mmtp) REVERT: W 432 GLN cc_start: 0.8221 (mm110) cc_final: 0.8012 (mm-40) REVERT: W 495 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7228 (t70) REVERT: R 228 GLN cc_start: 0.6449 (mt0) cc_final: 0.5561 (mm-40) REVERT: R 259 GLN cc_start: 0.5387 (pp30) cc_final: 0.4441 (pm20) REVERT: X 59 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7253 (mm-30) REVERT: X 160 LYS cc_start: 0.7867 (tttt) cc_final: 0.7470 (mtpp) REVERT: X 185 ASP cc_start: 0.6862 (m-30) cc_final: 0.6634 (m-30) REVERT: X 196 ASP cc_start: 0.8227 (t0) cc_final: 0.7843 (p0) REVERT: X 233 MET cc_start: 0.6762 (mmm) cc_final: 0.6269 (mmp) REVERT: X 288 MET cc_start: 0.5002 (mtt) cc_final: 0.4753 (mtt) REVERT: X 371 LYS cc_start: 0.7408 (tptt) cc_final: 0.7173 (ttmm) REVERT: X 420 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7921 (tt) REVERT: X 482 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8752 (p) REVERT: X 487 ASN cc_start: 0.7862 (m-40) cc_final: 0.7459 (t0) outliers start: 298 outliers final: 231 residues processed: 1217 average time/residue: 0.5394 time to fit residues: 1136.2351 Evaluate side-chains 1294 residues out of total 6580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1035 time to evaluate : 5.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 11 ASP Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 60 ILE Chi-restraints excluded: chain b residue 61 GLU Chi-restraints excluded: chain b residue 76 GLU Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 160 LYS Chi-restraints excluded: chain b residue 187 LEU Chi-restraints excluded: chain b residue 227 ILE Chi-restraints excluded: chain b residue 267 MET Chi-restraints excluded: chain b residue 381 VAL Chi-restraints excluded: chain b residue 401 HIS Chi-restraints excluded: chain b residue 422 VAL Chi-restraints excluded: chain b residue 424 SER Chi-restraints excluded: chain b residue 482 THR Chi-restraints excluded: chain b residue 494 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain G residue 401 HIS Chi-restraints excluded: chain G residue 424 SER Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 80 LYS Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 296 THR Chi-restraints excluded: chain H residue 401 HIS Chi-restraints excluded: chain H residue 463 SER Chi-restraints excluded: chain H residue 509 SER Chi-restraints excluded: chain H residue 510 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 162 ILE Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 284 ARG Chi-restraints excluded: chain I residue 296 THR Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 387 VAL Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 422 VAL Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 515 ILE Chi-restraints excluded: chain I residue 523 ASP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 292 ILE Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 494 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 22 VAL Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 216 GLU Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 296 THR Chi-restraints excluded: chain K residue 372 LEU Chi-restraints excluded: chain K residue 381 VAL Chi-restraints excluded: chain K residue 387 VAL Chi-restraints excluded: chain K residue 397 GLU Chi-restraints excluded: chain K residue 401 HIS Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain K residue 424 SER Chi-restraints excluded: chain K residue 454 ILE Chi-restraints excluded: chain K residue 463 SER Chi-restraints excluded: chain K residue 470 LYS Chi-restraints excluded: chain K residue 494 LEU Chi-restraints excluded: chain K residue 515 ILE Chi-restraints excluded: chain K residue 516 THR Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 69 MET Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 250 ILE Chi-restraints excluded: chain L residue 271 VAL Chi-restraints excluded: chain L residue 332 ILE Chi-restraints excluded: chain L residue 381 VAL Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 397 GLU Chi-restraints excluded: chain L residue 401 HIS Chi-restraints excluded: chain L residue 407 VAL Chi-restraints excluded: chain L residue 442 VAL Chi-restraints excluded: chain L residue 461 GLU Chi-restraints excluded: chain L residue 509 SER Chi-restraints excluded: chain Y residue 222 LEU Chi-restraints excluded: chain Y residue 228 GLN Chi-restraints excluded: chain Z residue 61 GLU Chi-restraints excluded: chain Z residue 77 VAL Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain Z residue 129 GLU Chi-restraints excluded: chain Z residue 169 VAL Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain Z residue 187 LEU Chi-restraints excluded: chain Z residue 193 MET Chi-restraints excluded: chain Z residue 222 LEU Chi-restraints excluded: chain Z residue 329 THR Chi-restraints excluded: chain Z residue 332 ILE Chi-restraints excluded: chain Z residue 378 VAL Chi-restraints excluded: chain Z residue 401 HIS Chi-restraints excluded: chain Z residue 407 VAL Chi-restraints excluded: chain Z residue 454 ILE Chi-restraints excluded: chain Z residue 463 SER Chi-restraints excluded: chain Z residue 482 THR Chi-restraints excluded: chain Z residue 494 LEU Chi-restraints excluded: chain Z residue 516 THR Chi-restraints excluded: chain M residue 222 LEU Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain S residue 61 GLU Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 175 ILE Chi-restraints excluded: chain S residue 177 VAL Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain S residue 193 MET Chi-restraints excluded: chain S residue 206 ASN Chi-restraints excluded: chain S residue 222 LEU Chi-restraints excluded: chain S residue 267 MET Chi-restraints excluded: chain S residue 292 ILE Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 332 ILE Chi-restraints excluded: chain S residue 378 VAL Chi-restraints excluded: chain S residue 401 HIS Chi-restraints excluded: chain S residue 422 VAL Chi-restraints excluded: chain S residue 424 SER Chi-restraints excluded: chain S residue 447 MET Chi-restraints excluded: chain S residue 463 SER Chi-restraints excluded: chain S residue 494 LEU Chi-restraints excluded: chain N residue 222 LEU Chi-restraints excluded: chain N residue 228 GLN Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 129 GLU Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 187 LEU Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 206 ASN Chi-restraints excluded: chain T residue 292 ILE Chi-restraints excluded: chain T residue 329 THR Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 336 VAL Chi-restraints excluded: chain T residue 378 VAL Chi-restraints excluded: chain T residue 401 HIS Chi-restraints excluded: chain T residue 407 VAL Chi-restraints excluded: chain T residue 424 SER Chi-restraints excluded: chain T residue 463 SER Chi-restraints excluded: chain T residue 482 THR Chi-restraints excluded: chain T residue 494 LEU Chi-restraints excluded: chain T residue 517 THR Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain O residue 278 GLN Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 169 VAL Chi-restraints excluded: chain U residue 174 VAL Chi-restraints excluded: chain U residue 177 VAL Chi-restraints excluded: chain U residue 187 LEU Chi-restraints excluded: chain U residue 249 ILE Chi-restraints excluded: chain U residue 381 VAL Chi-restraints excluded: chain U residue 401 HIS Chi-restraints excluded: chain U residue 422 VAL Chi-restraints excluded: chain U residue 463 SER Chi-restraints excluded: chain U residue 482 THR Chi-restraints excluded: chain U residue 515 ILE Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain V residue 27 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 107 VAL Chi-restraints excluded: chain V residue 129 GLU Chi-restraints excluded: chain V residue 169 VAL Chi-restraints excluded: chain V residue 175 ILE Chi-restraints excluded: chain V residue 187 LEU Chi-restraints excluded: chain V residue 222 LEU Chi-restraints excluded: chain V residue 300 VAL Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 378 VAL Chi-restraints excluded: chain V residue 401 HIS Chi-restraints excluded: chain V residue 447 MET Chi-restraints excluded: chain V residue 463 SER Chi-restraints excluded: chain V residue 470 LYS Chi-restraints excluded: chain V residue 494 LEU Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 61 GLU Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 169 VAL Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain W residue 206 ASN Chi-restraints excluded: chain W residue 229 ASN Chi-restraints excluded: chain W residue 240 VAL Chi-restraints excluded: chain W residue 289 LEU Chi-restraints excluded: chain W residue 332 ILE Chi-restraints excluded: chain W residue 378 VAL Chi-restraints excluded: chain W residue 417 VAL Chi-restraints excluded: chain W residue 494 LEU Chi-restraints excluded: chain W residue 495 ASP Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain X residue 27 VAL Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain X residue 162 ILE Chi-restraints excluded: chain X residue 169 VAL Chi-restraints excluded: chain X residue 177 VAL Chi-restraints excluded: chain X residue 263 VAL Chi-restraints excluded: chain X residue 367 GLU Chi-restraints excluded: chain X residue 378 VAL Chi-restraints excluded: chain X residue 401 HIS Chi-restraints excluded: chain X residue 420 ILE Chi-restraints excluded: chain X residue 422 VAL Chi-restraints excluded: chain X residue 463 SER Chi-restraints excluded: chain X residue 482 THR Chi-restraints excluded: chain X residue 494 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 783 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 463 optimal weight: 20.0000 chunk 593 optimal weight: 4.9990 chunk 459 optimal weight: 20.0000 chunk 684 optimal weight: 0.9980 chunk 453 optimal weight: 0.6980 chunk 809 optimal weight: 5.9990 chunk 506 optimal weight: 5.9990 chunk 493 optimal weight: 2.9990 chunk 373 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 208 GLN ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 228 GLN ** Y 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 432 GLN ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 64540 Z= 0.199 Angle : 0.646 15.162 87248 Z= 0.335 Chirality : 0.041 0.234 10500 Planarity : 0.004 0.049 11522 Dihedral : 4.542 38.221 9157 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.02 % Favored : 96.55 % Rotamer: Outliers : 3.71 % Allowed : 17.15 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.09), residues: 8638 helix: 2.28 (0.07), residues: 5110 sheet: 0.87 (0.17), residues: 896 loop : -2.00 (0.11), residues: 2632 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS O 227 PHE 0.010 0.001 PHE S 66 TYR 0.016 0.002 TYR K 476 ARG 0.004 0.000 ARG L 404 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17276 Ramachandran restraints generated. 8638 Oldfield, 0 Emsley, 8638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17276 Ramachandran restraints generated. 8638 Oldfield, 0 Emsley, 8638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1307 residues out of total 6580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1060 time to evaluate : 5.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 105 LYS cc_start: 0.8284 (ttpt) cc_final: 0.7945 (ttmm) REVERT: b 132 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7798 (tttt) REVERT: b 160 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7400 (ttmm) REVERT: b 164 GLU cc_start: 0.7204 (tp30) cc_final: 0.6966 (tp30) REVERT: b 286 LYS cc_start: 0.7537 (mttt) cc_final: 0.6653 (ptmt) REVERT: b 307 MET cc_start: 0.4981 (mmp) cc_final: 0.4282 (mmp) REVERT: b 321 LYS cc_start: 0.6805 (tptt) cc_final: 0.6425 (tttt) REVERT: b 351 GLN cc_start: 0.7887 (tt0) cc_final: 0.7052 (tp40) REVERT: b 352 GLN cc_start: 0.6513 (mt0) cc_final: 0.6216 (mt0) REVERT: b 366 GLN cc_start: 0.6792 (mm110) cc_final: 0.6544 (mm110) REVERT: b 380 LYS cc_start: 0.6942 (mttt) cc_final: 0.6420 (mtmm) REVERT: b 397 GLU cc_start: 0.7651 (tt0) cc_final: 0.7355 (tt0) REVERT: b 404 ARG cc_start: 0.7562 (tpp80) cc_final: 0.7165 (ttp80) REVERT: G 121 ASP cc_start: 0.7711 (m-30) cc_final: 0.7109 (t0) REVERT: G 233 MET cc_start: 0.6865 (mmm) cc_final: 0.6407 (mmp) REVERT: G 286 LYS cc_start: 0.7801 (mttt) cc_final: 0.7014 (pttp) REVERT: G 307 MET cc_start: 0.5935 (mmp) cc_final: 0.5346 (mmp) REVERT: G 367 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6969 (mm-30) REVERT: G 380 LYS cc_start: 0.7279 (mttt) cc_final: 0.6275 (mtmm) REVERT: G 494 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8101 (pp) REVERT: B 238 LEU cc_start: 0.7932 (tp) cc_final: 0.7692 (tp) REVERT: H 59 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7164 (mm-30) REVERT: H 73 MET cc_start: 0.7939 (ttm) cc_final: 0.7649 (ttm) REVERT: H 105 LYS cc_start: 0.8240 (ttpt) cc_final: 0.7835 (ttmm) REVERT: H 130 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7129 (mm-30) REVERT: H 286 LYS cc_start: 0.7791 (mttt) cc_final: 0.6858 (ptmt) REVERT: H 321 LYS cc_start: 0.7392 (tptt) cc_final: 0.7043 (tttt) REVERT: H 366 GLN cc_start: 0.7215 (mt0) cc_final: 0.6932 (mt0) REVERT: H 380 LYS cc_start: 0.7324 (mttt) cc_final: 0.6619 (mtmm) REVERT: H 398 ASP cc_start: 0.8588 (t70) cc_final: 0.8207 (t0) REVERT: H 403 THR cc_start: 0.8204 (m) cc_final: 0.7868 (m) REVERT: H 404 ARG cc_start: 0.7214 (tpp80) cc_final: 0.7012 (ttm-80) REVERT: H 473 ASP cc_start: 0.7714 (p0) cc_final: 0.6917 (m-30) REVERT: C 206 GLN cc_start: 0.5472 (tp-100) cc_final: 0.5252 (tp-100) REVERT: C 259 GLN cc_start: 0.6982 (mt0) cc_final: 0.5819 (pm20) REVERT: I 105 LYS cc_start: 0.8314 (ttpt) cc_final: 0.7920 (ttmm) REVERT: I 233 MET cc_start: 0.6368 (mmm) cc_final: 0.5832 (mmp) REVERT: I 267 MET cc_start: 0.6269 (ttt) cc_final: 0.5958 (tpp) REVERT: I 307 MET cc_start: 0.5644 (mmp) cc_final: 0.4487 (mmp) REVERT: I 321 LYS cc_start: 0.7200 (tptt) cc_final: 0.6720 (tttt) REVERT: I 366 GLN cc_start: 0.7461 (mm110) cc_final: 0.7147 (mm110) REVERT: I 389 MET cc_start: 0.6969 (tpp) cc_final: 0.6681 (tpp) REVERT: I 432 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7178 (mt0) REVERT: I 514 MET cc_start: 0.7452 (ttm) cc_final: 0.7210 (mtp) REVERT: I 523 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8058 (t0) REVERT: D 207 GLN cc_start: 0.7541 (tp40) cc_final: 0.7048 (mm-40) REVERT: J 69 MET cc_start: 0.8276 (mtm) cc_final: 0.7725 (mtm) REVERT: J 87 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8205 (m-30) REVERT: J 204 PHE cc_start: 0.7044 (m-80) cc_final: 0.6739 (m-80) REVERT: J 288 MET cc_start: 0.6378 (mtp) cc_final: 0.5998 (mtp) REVERT: J 307 MET cc_start: 0.4970 (mmp) cc_final: 0.3855 (mmp) REVERT: J 380 LYS cc_start: 0.7580 (mttt) cc_final: 0.7031 (mtmm) REVERT: J 404 ARG cc_start: 0.7322 (tpp80) cc_final: 0.7073 (ttm-80) REVERT: J 473 ASP cc_start: 0.8048 (p0) cc_final: 0.7210 (m-30) REVERT: J 494 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8203 (pp) REVERT: K 105 LYS cc_start: 0.8334 (ttpt) cc_final: 0.8032 (ttmm) REVERT: K 121 ASP cc_start: 0.7706 (m-30) cc_final: 0.7326 (m-30) REVERT: K 155 ASP cc_start: 0.7144 (t0) cc_final: 0.6238 (m-30) REVERT: K 178 GLU cc_start: 0.6978 (pt0) cc_final: 0.6670 (pt0) REVERT: K 267 MET cc_start: 0.6234 (ttt) cc_final: 0.5982 (tpp) REVERT: K 307 MET cc_start: 0.5392 (mmp) cc_final: 0.4563 (mmp) REVERT: K 321 LYS cc_start: 0.7433 (tppt) cc_final: 0.6560 (tttt) REVERT: K 380 LYS cc_start: 0.7510 (mttt) cc_final: 0.7031 (mtmm) REVERT: K 387 VAL cc_start: 0.5756 (OUTLIER) cc_final: 0.5472 (p) REVERT: K 404 ARG cc_start: 0.8078 (tpp80) cc_final: 0.7647 (mtp85) REVERT: K 422 VAL cc_start: 0.9041 (t) cc_final: 0.8546 (m) REVERT: K 432 GLN cc_start: 0.7066 (mm110) cc_final: 0.6696 (mt0) REVERT: K 514 MET cc_start: 0.7579 (mtp) cc_final: 0.7147 (mtt) REVERT: L 59 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7533 (mm-30) REVERT: L 307 MET cc_start: 0.5401 (mmp) cc_final: 0.4540 (mmp) REVERT: L 326 ASN cc_start: 0.7055 (t0) cc_final: 0.6733 (t0) REVERT: L 397 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: Y 228 GLN cc_start: 0.6976 (OUTLIER) cc_final: 0.6369 (mm-40) REVERT: Y 259 GLN cc_start: 0.5859 (pp30) cc_final: 0.5163 (pm20) REVERT: Z 18 ARG cc_start: 0.7455 (ttm-80) cc_final: 0.6783 (ttp80) REVERT: Z 59 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7176 (mm-30) REVERT: Z 63 GLU cc_start: 0.7275 (tp30) cc_final: 0.6907 (pm20) REVERT: Z 164 GLU cc_start: 0.8275 (tm-30) cc_final: 0.8020 (mm-30) REVERT: Z 193 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6655 (ttm) REVERT: Z 199 TYR cc_start: 0.7747 (p90) cc_final: 0.7516 (p90) REVERT: Z 207 LYS cc_start: 0.7482 (mtpt) cc_final: 0.6884 (mmtm) REVERT: Z 222 LEU cc_start: 0.5046 (OUTLIER) cc_final: 0.4812 (mt) REVERT: Z 267 MET cc_start: 0.6239 (ptp) cc_final: 0.6021 (ptt) REVERT: Z 371 LYS cc_start: 0.7051 (tppt) cc_final: 0.6778 (ttmm) REVERT: Z 432 GLN cc_start: 0.7416 (mm110) cc_final: 0.7179 (mm-40) REVERT: Z 482 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8937 (p) REVERT: Z 491 MET cc_start: 0.7437 (mtt) cc_final: 0.7117 (mtp) REVERT: M 228 GLN cc_start: 0.6827 (mp10) cc_final: 0.5137 (mm-40) REVERT: S 128 VAL cc_start: 0.8215 (t) cc_final: 0.7890 (t) REVERT: S 172 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8310 (mp0) REVERT: S 193 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.6561 (tpt) REVERT: S 204 PHE cc_start: 0.8094 (m-10) cc_final: 0.7767 (m-80) REVERT: S 207 LYS cc_start: 0.7515 (mmmm) cc_final: 0.7228 (mtpt) REVERT: S 222 LEU cc_start: 0.5222 (OUTLIER) cc_final: 0.4838 (mt) REVERT: S 267 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6549 (ptm) REVERT: S 288 MET cc_start: 0.5959 (mtm) cc_final: 0.5537 (mtp) REVERT: S 317 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6576 (mp) REVERT: S 488 MET cc_start: 0.8654 (mmm) cc_final: 0.7862 (mmm) REVERT: S 494 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7799 (pp) REVERT: N 222 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.6191 (mt) REVERT: N 228 GLN cc_start: 0.6042 (OUTLIER) cc_final: 0.4501 (mm-40) REVERT: N 238 LEU cc_start: 0.7757 (tp) cc_final: 0.7433 (tp) REVERT: T 179 ASP cc_start: 0.7839 (m-30) cc_final: 0.7570 (m-30) REVERT: T 317 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6796 (mp) REVERT: T 408 GLU cc_start: 0.6364 (tm-30) cc_final: 0.6034 (tm-30) REVERT: T 482 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8690 (p) REVERT: T 487 ASN cc_start: 0.8194 (m-40) cc_final: 0.7365 (t0) REVERT: U 160 LYS cc_start: 0.7719 (tttt) cc_final: 0.7503 (mtpp) REVERT: U 166 MET cc_start: 0.7561 (ttm) cc_final: 0.7004 (mtp) REVERT: U 207 LYS cc_start: 0.7995 (mmmm) cc_final: 0.7512 (mmtm) REVERT: U 226 LYS cc_start: 0.8958 (mtpt) cc_final: 0.8178 (tttp) REVERT: U 267 MET cc_start: 0.5514 (ttt) cc_final: 0.5088 (ptt) REVERT: U 332 ILE cc_start: 0.7793 (mm) cc_final: 0.7528 (tp) REVERT: U 378 VAL cc_start: 0.8431 (t) cc_final: 0.8122 (m) REVERT: U 447 MET cc_start: 0.8037 (mtt) cc_final: 0.7827 (mtm) REVERT: U 482 THR cc_start: 0.9336 (OUTLIER) cc_final: 0.8983 (p) REVERT: U 488 MET cc_start: 0.8592 (mmm) cc_final: 0.8360 (mtp) REVERT: V 61 GLU cc_start: 0.7644 (pt0) cc_final: 0.7327 (pt0) REVERT: V 87 ASP cc_start: 0.8286 (t0) cc_final: 0.7929 (t0) REVERT: V 121 ASP cc_start: 0.7201 (m-30) cc_final: 0.6790 (m-30) REVERT: V 129 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6333 (tt0) REVERT: V 164 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7639 (mm-30) REVERT: V 171 LYS cc_start: 0.8663 (mtmt) cc_final: 0.8305 (mtpt) REVERT: V 172 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8319 (mp0) REVERT: V 193 MET cc_start: 0.7370 (mmm) cc_final: 0.6485 (tpt) REVERT: V 222 LEU cc_start: 0.4383 (OUTLIER) cc_final: 0.4067 (mt) REVERT: V 267 MET cc_start: 0.5552 (ptm) cc_final: 0.5274 (ptt) REVERT: V 332 ILE cc_start: 0.7339 (OUTLIER) cc_final: 0.6990 (tp) REVERT: V 338 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6777 (pm20) REVERT: V 390 LYS cc_start: 0.7077 (mtpp) cc_final: 0.6419 (mmmt) REVERT: V 393 LYS cc_start: 0.7379 (tttp) cc_final: 0.7125 (ttpt) REVERT: V 432 GLN cc_start: 0.7552 (mm-40) cc_final: 0.7311 (mm-40) REVERT: V 455 VAL cc_start: 0.8528 (t) cc_final: 0.8285 (t) REVERT: V 470 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7084 (mttt) REVERT: Q 238 LEU cc_start: 0.7582 (tp) cc_final: 0.7333 (tp) REVERT: W 105 LYS cc_start: 0.8229 (ttpt) cc_final: 0.7953 (ttmm) REVERT: W 214 GLU cc_start: 0.6798 (pm20) cc_final: 0.6325 (pm20) REVERT: W 380 LYS cc_start: 0.6262 (mttt) cc_final: 0.5792 (mmtp) REVERT: W 432 GLN cc_start: 0.8146 (mm110) cc_final: 0.7943 (mm-40) REVERT: W 495 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7158 (t70) REVERT: R 228 GLN cc_start: 0.6388 (mt0) cc_final: 0.5529 (mm-40) REVERT: R 259 GLN cc_start: 0.5519 (pp30) cc_final: 0.5214 (pp30) REVERT: X 160 LYS cc_start: 0.7847 (tttt) cc_final: 0.7453 (mtpp) REVERT: X 196 ASP cc_start: 0.8228 (t0) cc_final: 0.7886 (p0) REVERT: X 233 MET cc_start: 0.6748 (mmm) cc_final: 0.6194 (mmp) REVERT: X 253 ASP cc_start: 0.7382 (t70) cc_final: 0.6860 (t70) REVERT: X 288 MET cc_start: 0.4940 (mtt) cc_final: 0.4699 (mtt) REVERT: X 482 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8675 (p) REVERT: X 487 ASN cc_start: 0.7810 (m-40) cc_final: 0.7396 (t0) outliers start: 247 outliers final: 182 residues processed: 1202 average time/residue: 0.5339 time to fit residues: 1113.5184 Evaluate side-chains 1240 residues out of total 6580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1030 time to evaluate : 5.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 60 ILE Chi-restraints excluded: chain b residue 61 GLU Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 160 LYS Chi-restraints excluded: chain b residue 187 LEU Chi-restraints excluded: chain b residue 227 ILE Chi-restraints excluded: chain b residue 267 MET Chi-restraints excluded: chain b residue 381 VAL Chi-restraints excluded: chain b residue 401 HIS Chi-restraints excluded: chain b residue 424 SER Chi-restraints excluded: chain b residue 494 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain G residue 401 HIS Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 424 SER Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain G residue 509 SER Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 80 LYS Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 401 HIS Chi-restraints excluded: chain H residue 407 VAL Chi-restraints excluded: chain H residue 463 SER Chi-restraints excluded: chain H residue 509 SER Chi-restraints excluded: chain H residue 510 VAL Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 284 ARG Chi-restraints excluded: chain I residue 296 THR Chi-restraints excluded: chain I residue 387 VAL Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 401 HIS Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 515 ILE Chi-restraints excluded: chain I residue 523 ASP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 494 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 216 GLU Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 387 VAL Chi-restraints excluded: chain K residue 397 GLU Chi-restraints excluded: chain K residue 401 HIS Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain K residue 424 SER Chi-restraints excluded: chain K residue 470 LYS Chi-restraints excluded: chain K residue 494 LEU Chi-restraints excluded: chain K residue 516 THR Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 250 ILE Chi-restraints excluded: chain L residue 271 VAL Chi-restraints excluded: chain L residue 366 GLN Chi-restraints excluded: chain L residue 381 VAL Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 397 GLU Chi-restraints excluded: chain L residue 401 HIS Chi-restraints excluded: chain L residue 407 VAL Chi-restraints excluded: chain L residue 442 VAL Chi-restraints excluded: chain L residue 509 SER Chi-restraints excluded: chain Y residue 222 LEU Chi-restraints excluded: chain Y residue 228 GLN Chi-restraints excluded: chain Z residue 61 GLU Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain Z residue 187 LEU Chi-restraints excluded: chain Z residue 193 MET Chi-restraints excluded: chain Z residue 222 LEU Chi-restraints excluded: chain Z residue 229 ASN Chi-restraints excluded: chain Z residue 332 ILE Chi-restraints excluded: chain Z residue 378 VAL Chi-restraints excluded: chain Z residue 401 HIS Chi-restraints excluded: chain Z residue 407 VAL Chi-restraints excluded: chain Z residue 454 ILE Chi-restraints excluded: chain Z residue 482 THR Chi-restraints excluded: chain Z residue 494 LEU Chi-restraints excluded: chain Z residue 516 THR Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain S residue 61 GLU Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 177 VAL Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain S residue 193 MET Chi-restraints excluded: chain S residue 206 ASN Chi-restraints excluded: chain S residue 222 LEU Chi-restraints excluded: chain S residue 267 MET Chi-restraints excluded: chain S residue 292 ILE Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 317 LEU Chi-restraints excluded: chain S residue 332 ILE Chi-restraints excluded: chain S residue 378 VAL Chi-restraints excluded: chain S residue 401 HIS Chi-restraints excluded: chain S residue 422 VAL Chi-restraints excluded: chain S residue 424 SER Chi-restraints excluded: chain S residue 447 MET Chi-restraints excluded: chain S residue 454 ILE Chi-restraints excluded: chain S residue 494 LEU Chi-restraints excluded: chain N residue 222 LEU Chi-restraints excluded: chain N residue 228 GLN Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 129 GLU Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 187 LEU Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 206 ASN Chi-restraints excluded: chain T residue 292 ILE Chi-restraints excluded: chain T residue 317 LEU Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 336 VAL Chi-restraints excluded: chain T residue 378 VAL Chi-restraints excluded: chain T residue 401 HIS Chi-restraints excluded: chain T residue 482 THR Chi-restraints excluded: chain T residue 494 LEU Chi-restraints excluded: chain T residue 515 ILE Chi-restraints excluded: chain T residue 517 THR Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain O residue 278 GLN Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 177 VAL Chi-restraints excluded: chain U residue 249 ILE Chi-restraints excluded: chain U residue 300 VAL Chi-restraints excluded: chain U residue 381 VAL Chi-restraints excluded: chain U residue 401 HIS Chi-restraints excluded: chain U residue 463 SER Chi-restraints excluded: chain U residue 482 THR Chi-restraints excluded: chain U residue 515 ILE Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain V residue 27 VAL Chi-restraints excluded: chain V residue 107 VAL Chi-restraints excluded: chain V residue 129 GLU Chi-restraints excluded: chain V residue 187 LEU Chi-restraints excluded: chain V residue 194 GLN Chi-restraints excluded: chain V residue 222 LEU Chi-restraints excluded: chain V residue 300 VAL Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 378 VAL Chi-restraints excluded: chain V residue 401 HIS Chi-restraints excluded: chain V residue 420 ILE Chi-restraints excluded: chain V residue 463 SER Chi-restraints excluded: chain V residue 470 LYS Chi-restraints excluded: chain V residue 494 LEU Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 61 GLU Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 196 ASP Chi-restraints excluded: chain W residue 206 ASN Chi-restraints excluded: chain W residue 229 ASN Chi-restraints excluded: chain W residue 240 VAL Chi-restraints excluded: chain W residue 332 ILE Chi-restraints excluded: chain W residue 378 VAL Chi-restraints excluded: chain W residue 463 SER Chi-restraints excluded: chain W residue 494 LEU Chi-restraints excluded: chain W residue 495 ASP Chi-restraints excluded: chain X residue 27 VAL Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain X residue 151 SER Chi-restraints excluded: chain X residue 162 ILE Chi-restraints excluded: chain X residue 169 VAL Chi-restraints excluded: chain X residue 177 VAL Chi-restraints excluded: chain X residue 263 VAL Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 367 GLU Chi-restraints excluded: chain X residue 378 VAL Chi-restraints excluded: chain X residue 401 HIS Chi-restraints excluded: chain X residue 463 SER Chi-restraints excluded: chain X residue 482 THR Chi-restraints excluded: chain X residue 494 LEU Chi-restraints excluded: chain X residue 515 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 500 optimal weight: 5.9990 chunk 323 optimal weight: 20.0000 chunk 483 optimal weight: 20.0000 chunk 243 optimal weight: 20.0000 chunk 159 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 514 optimal weight: 9.9990 chunk 551 optimal weight: 0.8980 chunk 400 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 636 optimal weight: 9.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 203 GLN B 206 GLN H 290 GLN J 432 GLN ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 457 ASN ** Y 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 228 GLN ** Y 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 64540 Z= 0.320 Angle : 0.700 15.238 87248 Z= 0.364 Chirality : 0.044 0.220 10500 Planarity : 0.004 0.053 11522 Dihedral : 4.608 36.069 9157 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.30 % Favored : 95.25 % Rotamer: Outliers : 4.29 % Allowed : 17.00 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.09), residues: 8638 helix: 2.16 (0.07), residues: 5096 sheet: 0.82 (0.19), residues: 728 loop : -2.07 (0.10), residues: 2814 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS W 401 PHE 0.014 0.002 PHE J 8 TYR 0.018 0.002 TYR T 506 ARG 0.005 0.000 ARG W 345 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17276 Ramachandran restraints generated. 8638 Oldfield, 0 Emsley, 8638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17276 Ramachandran restraints generated. 8638 Oldfield, 0 Emsley, 8638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1333 residues out of total 6580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1047 time to evaluate : 5.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 59 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7428 (mm-30) REVERT: b 105 LYS cc_start: 0.8452 (ttpt) cc_final: 0.8127 (ttmm) REVERT: b 132 LYS cc_start: 0.8261 (ttmm) cc_final: 0.8056 (tttt) REVERT: b 160 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7457 (ttmm) REVERT: b 164 GLU cc_start: 0.7231 (tp30) cc_final: 0.6987 (tp30) REVERT: b 219 PHE cc_start: 0.5313 (m-80) cc_final: 0.5025 (m-80) REVERT: b 286 LYS cc_start: 0.7629 (mttt) cc_final: 0.6773 (ptmt) REVERT: b 307 MET cc_start: 0.5159 (mmp) cc_final: 0.4430 (mmp) REVERT: b 321 LYS cc_start: 0.6863 (tptt) cc_final: 0.6457 (tttt) REVERT: b 351 GLN cc_start: 0.7710 (tt0) cc_final: 0.6979 (tp40) REVERT: b 352 GLN cc_start: 0.6537 (mt0) cc_final: 0.6226 (mt0) REVERT: b 366 GLN cc_start: 0.6732 (mm110) cc_final: 0.6477 (mm110) REVERT: b 380 LYS cc_start: 0.6921 (mttt) cc_final: 0.6357 (mtmm) REVERT: b 397 GLU cc_start: 0.7400 (tt0) cc_final: 0.7105 (tt0) REVERT: b 404 ARG cc_start: 0.7547 (tpp80) cc_final: 0.7102 (ttp80) REVERT: G 121 ASP cc_start: 0.7872 (m-30) cc_final: 0.7296 (t0) REVERT: G 233 MET cc_start: 0.6868 (mmm) cc_final: 0.6390 (mmp) REVERT: G 307 MET cc_start: 0.6095 (mmp) cc_final: 0.5467 (mmp) REVERT: G 367 GLU cc_start: 0.7304 (mm-30) cc_final: 0.6955 (mm-30) REVERT: G 380 LYS cc_start: 0.7229 (mttt) cc_final: 0.6370 (mtmm) REVERT: G 494 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8080 (pp) REVERT: G 520 MET cc_start: 0.8589 (mtm) cc_final: 0.8282 (mtm) REVERT: B 238 LEU cc_start: 0.7960 (tp) cc_final: 0.7729 (tp) REVERT: H 59 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7210 (mm-30) REVERT: H 73 MET cc_start: 0.7972 (ttm) cc_final: 0.7596 (ttm) REVERT: H 105 LYS cc_start: 0.8311 (ttpt) cc_final: 0.7869 (ttmm) REVERT: H 130 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7066 (mm-30) REVERT: H 321 LYS cc_start: 0.7444 (tptt) cc_final: 0.7069 (tttt) REVERT: H 325 ILE cc_start: 0.7761 (mt) cc_final: 0.7502 (mm) REVERT: H 366 GLN cc_start: 0.7235 (mt0) cc_final: 0.6952 (mt0) REVERT: H 380 LYS cc_start: 0.7344 (mttt) cc_final: 0.6698 (mtmm) REVERT: H 398 ASP cc_start: 0.8595 (t70) cc_final: 0.8214 (t0) REVERT: H 403 THR cc_start: 0.8424 (m) cc_final: 0.8108 (m) REVERT: H 473 ASP cc_start: 0.7790 (p0) cc_final: 0.7000 (m-30) REVERT: I 105 LYS cc_start: 0.8404 (ttpt) cc_final: 0.8018 (ttmm) REVERT: I 186 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7037 (pt0) REVERT: I 233 MET cc_start: 0.6320 (mmm) cc_final: 0.5038 (mmm) REVERT: I 267 MET cc_start: 0.6138 (ttt) cc_final: 0.5823 (tpp) REVERT: I 307 MET cc_start: 0.5840 (mmp) cc_final: 0.4810 (mmp) REVERT: I 321 LYS cc_start: 0.7054 (tptt) cc_final: 0.6515 (tttt) REVERT: I 366 GLN cc_start: 0.7460 (mm110) cc_final: 0.7152 (mm110) REVERT: I 380 LYS cc_start: 0.7482 (mttt) cc_final: 0.7024 (mmtp) REVERT: I 389 MET cc_start: 0.7048 (tpp) cc_final: 0.6771 (tpp) REVERT: I 432 GLN cc_start: 0.7799 (mm-40) cc_final: 0.7236 (mt0) REVERT: I 514 MET cc_start: 0.7905 (ttm) cc_final: 0.7672 (mtp) REVERT: I 523 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7941 (t0) REVERT: D 207 GLN cc_start: 0.7510 (tp40) cc_final: 0.7017 (mm-40) REVERT: J 69 MET cc_start: 0.8439 (mtm) cc_final: 0.7930 (mtm) REVERT: J 87 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8253 (m-30) REVERT: J 204 PHE cc_start: 0.6988 (m-80) cc_final: 0.6620 (m-80) REVERT: J 233 MET cc_start: 0.6081 (mmp) cc_final: 0.5361 (mmp) REVERT: J 288 MET cc_start: 0.6513 (mtp) cc_final: 0.6114 (mtp) REVERT: J 307 MET cc_start: 0.5157 (mmp) cc_final: 0.4710 (mmm) REVERT: J 380 LYS cc_start: 0.7625 (mttt) cc_final: 0.7082 (mtmm) REVERT: J 404 ARG cc_start: 0.7385 (tpp80) cc_final: 0.7147 (ttm-80) REVERT: J 494 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8304 (pp) REVERT: K 112 ASN cc_start: 0.8082 (t0) cc_final: 0.7863 (t0) REVERT: K 121 ASP cc_start: 0.7742 (m-30) cc_final: 0.7368 (m-30) REVERT: K 178 GLU cc_start: 0.7019 (pt0) cc_final: 0.6729 (pt0) REVERT: K 267 MET cc_start: 0.6301 (ttt) cc_final: 0.6039 (tpp) REVERT: K 307 MET cc_start: 0.5788 (mmp) cc_final: 0.5021 (mmp) REVERT: K 321 LYS cc_start: 0.7456 (tppt) cc_final: 0.6577 (tttt) REVERT: K 380 LYS cc_start: 0.7526 (mttt) cc_final: 0.7049 (mtmm) REVERT: K 387 VAL cc_start: 0.5933 (OUTLIER) cc_final: 0.5670 (p) REVERT: K 404 ARG cc_start: 0.8088 (tpp80) cc_final: 0.7655 (mtp85) REVERT: K 422 VAL cc_start: 0.9034 (t) cc_final: 0.8489 (m) REVERT: K 430 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.7504 (mpt180) REVERT: K 432 GLN cc_start: 0.7144 (mm110) cc_final: 0.6732 (mt0) REVERT: K 514 MET cc_start: 0.7819 (mtp) cc_final: 0.7619 (mtp) REVERT: L 307 MET cc_start: 0.5607 (mmp) cc_final: 0.4724 (mmp) REVERT: L 326 ASN cc_start: 0.7508 (t0) cc_final: 0.7143 (t0) REVERT: L 397 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: Y 228 GLN cc_start: 0.6780 (OUTLIER) cc_final: 0.6553 (mm-40) REVERT: Y 259 GLN cc_start: 0.5903 (pp30) cc_final: 0.5228 (pm20) REVERT: Z 18 ARG cc_start: 0.7767 (ttm-80) cc_final: 0.7089 (ttp80) REVERT: Z 59 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7174 (mm-30) REVERT: Z 63 GLU cc_start: 0.7350 (tp30) cc_final: 0.6946 (pm20) REVERT: Z 193 MET cc_start: 0.7115 (OUTLIER) cc_final: 0.6771 (ttm) REVERT: Z 207 LYS cc_start: 0.7491 (mtpt) cc_final: 0.6939 (mmtm) REVERT: Z 222 LEU cc_start: 0.5065 (OUTLIER) cc_final: 0.4821 (mt) REVERT: Z 267 MET cc_start: 0.6282 (ptp) cc_final: 0.6056 (ptt) REVERT: Z 371 LYS cc_start: 0.7088 (tppt) cc_final: 0.6840 (ttmm) REVERT: Z 432 GLN cc_start: 0.7482 (mm110) cc_final: 0.7210 (mm-40) REVERT: Z 491 MET cc_start: 0.7523 (mtt) cc_final: 0.7196 (mtp) REVERT: M 228 GLN cc_start: 0.6841 (OUTLIER) cc_final: 0.5173 (mm-40) REVERT: S 172 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8366 (mp0) REVERT: S 193 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6539 (tpt) REVERT: S 207 LYS cc_start: 0.7599 (mmmm) cc_final: 0.7259 (mtpt) REVERT: S 222 LEU cc_start: 0.5335 (OUTLIER) cc_final: 0.4948 (mt) REVERT: S 267 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6634 (ptm) REVERT: S 288 MET cc_start: 0.6150 (mtm) cc_final: 0.5565 (mtp) REVERT: S 371 LYS cc_start: 0.7397 (tppt) cc_final: 0.7084 (ttmm) REVERT: S 488 MET cc_start: 0.8772 (mmm) cc_final: 0.7979 (mmm) REVERT: S 494 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7766 (pp) REVERT: N 228 GLN cc_start: 0.6046 (OUTLIER) cc_final: 0.4513 (mm-40) REVERT: N 238 LEU cc_start: 0.7773 (tp) cc_final: 0.7489 (tp) REVERT: T 76 GLU cc_start: 0.7673 (tt0) cc_final: 0.7334 (tt0) REVERT: T 179 ASP cc_start: 0.7863 (m-30) cc_final: 0.7574 (m-30) REVERT: T 267 MET cc_start: 0.5771 (ptt) cc_final: 0.5198 (tmm) REVERT: T 317 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7092 (mp) REVERT: T 404 ARG cc_start: 0.8212 (tpp80) cc_final: 0.7935 (ttm110) REVERT: T 408 GLU cc_start: 0.6303 (tm-30) cc_final: 0.6011 (tm-30) REVERT: T 487 ASN cc_start: 0.8238 (m-40) cc_final: 0.7396 (t0) REVERT: U 115 ASP cc_start: 0.6905 (m-30) cc_final: 0.6547 (m-30) REVERT: U 160 LYS cc_start: 0.7779 (tttt) cc_final: 0.7545 (mtpp) REVERT: U 166 MET cc_start: 0.7644 (ttm) cc_final: 0.7155 (mtp) REVERT: U 207 LYS cc_start: 0.7988 (mmmm) cc_final: 0.7515 (mmtm) REVERT: U 267 MET cc_start: 0.5320 (ttt) cc_final: 0.4920 (ptt) REVERT: U 378 VAL cc_start: 0.8455 (t) cc_final: 0.8149 (m) REVERT: U 447 MET cc_start: 0.8297 (mtt) cc_final: 0.7802 (mtt) REVERT: U 482 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.8965 (p) REVERT: U 488 MET cc_start: 0.8640 (mmm) cc_final: 0.8433 (mtp) REVERT: P 222 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6403 (mt) REVERT: V 61 GLU cc_start: 0.7645 (pt0) cc_final: 0.7295 (pt0) REVERT: V 87 ASP cc_start: 0.8304 (t0) cc_final: 0.7953 (t0) REVERT: V 121 ASP cc_start: 0.7305 (m-30) cc_final: 0.6927 (m-30) REVERT: V 171 LYS cc_start: 0.8662 (mtmt) cc_final: 0.8297 (mtpt) REVERT: V 172 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8371 (mp0) REVERT: V 193 MET cc_start: 0.7472 (mmm) cc_final: 0.6568 (tpt) REVERT: V 222 LEU cc_start: 0.4434 (OUTLIER) cc_final: 0.4173 (mt) REVERT: V 267 MET cc_start: 0.5542 (ptm) cc_final: 0.5306 (ptt) REVERT: V 332 ILE cc_start: 0.7404 (OUTLIER) cc_final: 0.7062 (tp) REVERT: V 338 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6842 (pm20) REVERT: V 390 LYS cc_start: 0.7106 (mtpp) cc_final: 0.6422 (mmmt) REVERT: V 393 LYS cc_start: 0.7435 (tttp) cc_final: 0.7141 (ttpt) REVERT: V 432 GLN cc_start: 0.7585 (mm-40) cc_final: 0.7324 (mm-40) REVERT: V 470 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7049 (mttt) REVERT: Q 238 LEU cc_start: 0.7602 (tp) cc_final: 0.7352 (tp) REVERT: W 105 LYS cc_start: 0.8161 (ttpt) cc_final: 0.7820 (ttmm) REVERT: W 214 GLU cc_start: 0.6808 (pm20) cc_final: 0.6380 (pm20) REVERT: W 317 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6445 (mp) REVERT: W 380 LYS cc_start: 0.6371 (mttt) cc_final: 0.5915 (mmtp) REVERT: W 432 GLN cc_start: 0.8205 (mm110) cc_final: 0.8004 (mm-40) REVERT: W 495 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7237 (t70) REVERT: R 228 GLN cc_start: 0.6409 (mt0) cc_final: 0.5543 (mm-40) REVERT: X 160 LYS cc_start: 0.7895 (tttt) cc_final: 0.7497 (mtpp) REVERT: X 193 MET cc_start: 0.7037 (OUTLIER) cc_final: 0.6347 (tpt) REVERT: X 196 ASP cc_start: 0.8251 (t0) cc_final: 0.7880 (p0) REVERT: X 233 MET cc_start: 0.6752 (mmm) cc_final: 0.6178 (mmp) REVERT: X 288 MET cc_start: 0.4977 (mtt) cc_final: 0.4737 (mtt) REVERT: X 371 LYS cc_start: 0.7537 (tptt) cc_final: 0.7148 (ttmm) REVERT: X 482 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8716 (p) REVERT: X 487 ASN cc_start: 0.7854 (m-40) cc_final: 0.7412 (t0) outliers start: 286 outliers final: 231 residues processed: 1217 average time/residue: 0.5557 time to fit residues: 1173.6842 Evaluate side-chains 1294 residues out of total 6580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1034 time to evaluate : 5.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 11 ASP Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 60 ILE Chi-restraints excluded: chain b residue 61 GLU Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 160 LYS Chi-restraints excluded: chain b residue 187 LEU Chi-restraints excluded: chain b residue 227 ILE Chi-restraints excluded: chain b residue 267 MET Chi-restraints excluded: chain b residue 381 VAL Chi-restraints excluded: chain b residue 401 HIS Chi-restraints excluded: chain b residue 424 SER Chi-restraints excluded: chain b residue 482 THR Chi-restraints excluded: chain b residue 494 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain G residue 397 GLU Chi-restraints excluded: chain G residue 401 HIS Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 424 SER Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain G residue 509 SER Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 523 ASP Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 80 LYS Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 401 HIS Chi-restraints excluded: chain H residue 407 VAL Chi-restraints excluded: chain H residue 463 SER Chi-restraints excluded: chain H residue 509 SER Chi-restraints excluded: chain H residue 510 VAL Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 162 ILE Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 284 ARG Chi-restraints excluded: chain I residue 296 THR Chi-restraints excluded: chain I residue 387 VAL Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 515 ILE Chi-restraints excluded: chain I residue 523 ASP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 292 ILE Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 494 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 216 GLU Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 296 THR Chi-restraints excluded: chain K residue 372 LEU Chi-restraints excluded: chain K residue 381 VAL Chi-restraints excluded: chain K residue 387 VAL Chi-restraints excluded: chain K residue 397 GLU Chi-restraints excluded: chain K residue 401 HIS Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain K residue 424 SER Chi-restraints excluded: chain K residue 430 ARG Chi-restraints excluded: chain K residue 454 ILE Chi-restraints excluded: chain K residue 463 SER Chi-restraints excluded: chain K residue 470 LYS Chi-restraints excluded: chain K residue 494 LEU Chi-restraints excluded: chain K residue 516 THR Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 69 MET Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 135 SER Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 250 ILE Chi-restraints excluded: chain L residue 271 VAL Chi-restraints excluded: chain L residue 381 VAL Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 397 GLU Chi-restraints excluded: chain L residue 401 HIS Chi-restraints excluded: chain L residue 407 VAL Chi-restraints excluded: chain L residue 422 VAL Chi-restraints excluded: chain L residue 442 VAL Chi-restraints excluded: chain L residue 461 GLU Chi-restraints excluded: chain L residue 509 SER Chi-restraints excluded: chain Y residue 222 LEU Chi-restraints excluded: chain Y residue 228 GLN Chi-restraints excluded: chain Z residue 61 GLU Chi-restraints excluded: chain Z residue 77 VAL Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain Z residue 129 GLU Chi-restraints excluded: chain Z residue 151 SER Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain Z residue 187 LEU Chi-restraints excluded: chain Z residue 193 MET Chi-restraints excluded: chain Z residue 222 LEU Chi-restraints excluded: chain Z residue 300 VAL Chi-restraints excluded: chain Z residue 329 THR Chi-restraints excluded: chain Z residue 332 ILE Chi-restraints excluded: chain Z residue 378 VAL Chi-restraints excluded: chain Z residue 401 HIS Chi-restraints excluded: chain Z residue 407 VAL Chi-restraints excluded: chain Z residue 454 ILE Chi-restraints excluded: chain Z residue 463 SER Chi-restraints excluded: chain Z residue 494 LEU Chi-restraints excluded: chain Z residue 516 THR Chi-restraints excluded: chain M residue 222 LEU Chi-restraints excluded: chain M residue 228 GLN Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain S residue 61 GLU Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 175 ILE Chi-restraints excluded: chain S residue 177 VAL Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain S residue 193 MET Chi-restraints excluded: chain S residue 206 ASN Chi-restraints excluded: chain S residue 222 LEU Chi-restraints excluded: chain S residue 267 MET Chi-restraints excluded: chain S residue 292 ILE Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 332 ILE Chi-restraints excluded: chain S residue 378 VAL Chi-restraints excluded: chain S residue 401 HIS Chi-restraints excluded: chain S residue 422 VAL Chi-restraints excluded: chain S residue 424 SER Chi-restraints excluded: chain S residue 432 GLN Chi-restraints excluded: chain S residue 447 MET Chi-restraints excluded: chain S residue 454 ILE Chi-restraints excluded: chain S residue 463 SER Chi-restraints excluded: chain S residue 494 LEU Chi-restraints excluded: chain N residue 226 LEU Chi-restraints excluded: chain N residue 228 GLN Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 129 GLU Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 151 SER Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 187 LEU Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 206 ASN Chi-restraints excluded: chain T residue 292 ILE Chi-restraints excluded: chain T residue 317 LEU Chi-restraints excluded: chain T residue 329 THR Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 336 VAL Chi-restraints excluded: chain T residue 378 VAL Chi-restraints excluded: chain T residue 401 HIS Chi-restraints excluded: chain T residue 417 VAL Chi-restraints excluded: chain T residue 424 SER Chi-restraints excluded: chain T residue 463 SER Chi-restraints excluded: chain T residue 482 THR Chi-restraints excluded: chain T residue 494 LEU Chi-restraints excluded: chain T residue 515 ILE Chi-restraints excluded: chain T residue 517 THR Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain O residue 278 GLN Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 177 VAL Chi-restraints excluded: chain U residue 187 LEU Chi-restraints excluded: chain U residue 249 ILE Chi-restraints excluded: chain U residue 300 VAL Chi-restraints excluded: chain U residue 381 VAL Chi-restraints excluded: chain U residue 401 HIS Chi-restraints excluded: chain U residue 422 VAL Chi-restraints excluded: chain U residue 463 SER Chi-restraints excluded: chain U residue 482 THR Chi-restraints excluded: chain U residue 515 ILE Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain V residue 27 VAL Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain V residue 107 VAL Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 175 ILE Chi-restraints excluded: chain V residue 187 LEU Chi-restraints excluded: chain V residue 222 LEU Chi-restraints excluded: chain V residue 300 VAL Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 378 VAL Chi-restraints excluded: chain V residue 401 HIS Chi-restraints excluded: chain V residue 463 SER Chi-restraints excluded: chain V residue 470 LYS Chi-restraints excluded: chain V residue 494 LEU Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 61 GLU Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 151 SER Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 196 ASP Chi-restraints excluded: chain W residue 206 ASN Chi-restraints excluded: chain W residue 229 ASN Chi-restraints excluded: chain W residue 240 VAL Chi-restraints excluded: chain W residue 317 LEU Chi-restraints excluded: chain W residue 332 ILE Chi-restraints excluded: chain W residue 378 VAL Chi-restraints excluded: chain W residue 422 VAL Chi-restraints excluded: chain W residue 463 SER Chi-restraints excluded: chain W residue 494 LEU Chi-restraints excluded: chain W residue 495 ASP Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain X residue 27 VAL Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain X residue 151 SER Chi-restraints excluded: chain X residue 162 ILE Chi-restraints excluded: chain X residue 169 VAL Chi-restraints excluded: chain X residue 177 VAL Chi-restraints excluded: chain X residue 193 MET Chi-restraints excluded: chain X residue 263 VAL Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 367 GLU Chi-restraints excluded: chain X residue 378 VAL Chi-restraints excluded: chain X residue 401 HIS Chi-restraints excluded: chain X residue 463 SER Chi-restraints excluded: chain X residue 482 THR Chi-restraints excluded: chain X residue 494 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 736 optimal weight: 0.7980 chunk 775 optimal weight: 0.8980 chunk 707 optimal weight: 9.9990 chunk 754 optimal weight: 20.0000 chunk 454 optimal weight: 0.9990 chunk 328 optimal weight: 2.9990 chunk 592 optimal weight: 1.9990 chunk 231 optimal weight: 7.9990 chunk 681 optimal weight: 3.9990 chunk 713 optimal weight: 0.9990 chunk 751 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 457 ASN L 290 GLN ** Y 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 228 GLN ** Y 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 253 GLN ** N 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 64540 Z= 0.169 Angle : 0.639 15.938 87248 Z= 0.328 Chirality : 0.041 0.218 10500 Planarity : 0.004 0.048 11522 Dihedral : 4.422 35.766 9157 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.40 % Allowed : 2.64 % Favored : 96.96 % Rotamer: Outliers : 3.14 % Allowed : 18.17 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.09), residues: 8638 helix: 2.39 (0.07), residues: 5138 sheet: 0.90 (0.17), residues: 896 loop : -1.91 (0.11), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS Y 227 PHE 0.010 0.001 PHE T 66 TYR 0.014 0.001 TYR K 476 ARG 0.005 0.000 ARG Z 345 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17276 Ramachandran restraints generated. 8638 Oldfield, 0 Emsley, 8638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17276 Ramachandran restraints generated. 8638 Oldfield, 0 Emsley, 8638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1251 residues out of total 6580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1042 time to evaluate : 5.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 77 VAL cc_start: 0.8717 (t) cc_final: 0.8481 (t) REVERT: b 105 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7887 (ttmm) REVERT: b 160 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7408 (ttmm) REVERT: b 164 GLU cc_start: 0.7198 (tp30) cc_final: 0.6965 (tp30) REVERT: b 307 MET cc_start: 0.4884 (mmp) cc_final: 0.4188 (mmp) REVERT: b 321 LYS cc_start: 0.6777 (tptt) cc_final: 0.6461 (tttt) REVERT: b 351 GLN cc_start: 0.7859 (tt0) cc_final: 0.7066 (tp40) REVERT: b 352 GLN cc_start: 0.6496 (mt0) cc_final: 0.6197 (mt0) REVERT: b 366 GLN cc_start: 0.6718 (mm110) cc_final: 0.6449 (mm110) REVERT: b 380 LYS cc_start: 0.6937 (mttt) cc_final: 0.6448 (mtmm) REVERT: b 389 MET cc_start: 0.7035 (ttp) cc_final: 0.6594 (ttt) REVERT: b 397 GLU cc_start: 0.7559 (tt0) cc_final: 0.7235 (tt0) REVERT: b 404 ARG cc_start: 0.7476 (tpp80) cc_final: 0.7127 (ttp80) REVERT: G 121 ASP cc_start: 0.7086 (m-30) cc_final: 0.6374 (t0) REVERT: G 233 MET cc_start: 0.6866 (mmm) cc_final: 0.6404 (mmp) REVERT: G 286 LYS cc_start: 0.7848 (mttt) cc_final: 0.7116 (pttp) REVERT: G 307 MET cc_start: 0.6002 (mmp) cc_final: 0.5409 (mmp) REVERT: G 367 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6936 (mm-30) REVERT: G 380 LYS cc_start: 0.7257 (mttt) cc_final: 0.6436 (mtmm) REVERT: G 494 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8030 (pp) REVERT: B 238 LEU cc_start: 0.7972 (tp) cc_final: 0.7743 (tp) REVERT: H 59 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7171 (mm-30) REVERT: H 73 MET cc_start: 0.8047 (ttm) cc_final: 0.7753 (ttm) REVERT: H 105 LYS cc_start: 0.8261 (ttpt) cc_final: 0.7826 (ttmm) REVERT: H 130 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7039 (mm-30) REVERT: H 321 LYS cc_start: 0.7378 (tptt) cc_final: 0.6990 (tttt) REVERT: H 325 ILE cc_start: 0.7735 (mt) cc_final: 0.7478 (mm) REVERT: H 366 GLN cc_start: 0.7177 (mt0) cc_final: 0.6884 (mt0) REVERT: H 380 LYS cc_start: 0.7307 (mttt) cc_final: 0.6688 (mtmm) REVERT: H 398 ASP cc_start: 0.8557 (t70) cc_final: 0.8187 (t0) REVERT: H 403 THR cc_start: 0.8078 (m) cc_final: 0.7737 (m) REVERT: H 473 ASP cc_start: 0.7800 (p0) cc_final: 0.6875 (m-30) REVERT: I 105 LYS cc_start: 0.8315 (ttpt) cc_final: 0.7903 (ttmm) REVERT: I 194 GLN cc_start: 0.7071 (tt0) cc_final: 0.6810 (tt0) REVERT: I 233 MET cc_start: 0.6275 (mmm) cc_final: 0.4927 (mmm) REVERT: I 267 MET cc_start: 0.6118 (ttt) cc_final: 0.5814 (tpp) REVERT: I 307 MET cc_start: 0.5738 (mmp) cc_final: 0.4723 (mmp) REVERT: I 321 LYS cc_start: 0.6998 (tptt) cc_final: 0.6454 (tttt) REVERT: I 389 MET cc_start: 0.6729 (tpp) cc_final: 0.6433 (tpp) REVERT: I 432 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7174 (mt0) REVERT: I 523 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8001 (t0) REVERT: J 69 MET cc_start: 0.8218 (mtm) cc_final: 0.7642 (mtm) REVERT: J 87 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8236 (m-30) REVERT: J 204 PHE cc_start: 0.7011 (m-80) cc_final: 0.6748 (m-80) REVERT: J 233 MET cc_start: 0.6268 (mmp) cc_final: 0.5536 (mmp) REVERT: J 286 LYS cc_start: 0.6933 (mttt) cc_final: 0.6417 (mtmt) REVERT: J 288 MET cc_start: 0.6638 (mtp) cc_final: 0.6216 (mtp) REVERT: J 307 MET cc_start: 0.5273 (mmp) cc_final: 0.4879 (mmm) REVERT: J 380 LYS cc_start: 0.7575 (mttt) cc_final: 0.7044 (mtmm) REVERT: J 404 ARG cc_start: 0.7281 (tpp80) cc_final: 0.7019 (ttm-80) REVERT: J 494 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8151 (pp) REVERT: K 59 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7472 (mm-30) REVERT: K 121 ASP cc_start: 0.7650 (m-30) cc_final: 0.7275 (m-30) REVERT: K 178 GLU cc_start: 0.6958 (pt0) cc_final: 0.6700 (pt0) REVERT: K 267 MET cc_start: 0.6274 (ttt) cc_final: 0.6033 (tpp) REVERT: K 307 MET cc_start: 0.5714 (mmp) cc_final: 0.4950 (mmp) REVERT: K 321 LYS cc_start: 0.7387 (tppt) cc_final: 0.6519 (tttt) REVERT: K 380 LYS cc_start: 0.7503 (mttt) cc_final: 0.7028 (mtmm) REVERT: K 404 ARG cc_start: 0.8103 (tpp80) cc_final: 0.7670 (mtp85) REVERT: K 422 VAL cc_start: 0.9038 (t) cc_final: 0.8539 (m) REVERT: K 432 GLN cc_start: 0.7027 (mm110) cc_final: 0.6659 (mt0) REVERT: K 483 GLU cc_start: 0.7642 (mp0) cc_final: 0.7377 (mp0) REVERT: K 514 MET cc_start: 0.7420 (mtp) cc_final: 0.6977 (mtt) REVERT: L 59 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7513 (mm-30) REVERT: L 307 MET cc_start: 0.5468 (mmp) cc_final: 0.4622 (mmp) REVERT: L 326 ASN cc_start: 0.6983 (t0) cc_final: 0.6714 (t0) REVERT: L 368 ARG cc_start: 0.7121 (ttm170) cc_final: 0.6027 (ttm-80) REVERT: L 397 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7317 (tm-30) REVERT: Y 222 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6133 (mt) REVERT: Y 228 GLN cc_start: 0.6604 (OUTLIER) cc_final: 0.6305 (mm-40) REVERT: Z 18 ARG cc_start: 0.7398 (ttm-80) cc_final: 0.6726 (ttp80) REVERT: Z 59 GLU cc_start: 0.7263 (mm-30) cc_final: 0.7023 (mm-30) REVERT: Z 63 GLU cc_start: 0.7185 (tp30) cc_final: 0.6900 (pm20) REVERT: Z 193 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6742 (ttm) REVERT: Z 207 LYS cc_start: 0.7488 (mtpt) cc_final: 0.6929 (mmtm) REVERT: Z 222 LEU cc_start: 0.4914 (OUTLIER) cc_final: 0.4653 (mt) REVERT: Z 371 LYS cc_start: 0.7025 (tppt) cc_final: 0.6754 (ttmm) REVERT: Z 408 GLU cc_start: 0.6213 (tm-30) cc_final: 0.5909 (tm-30) REVERT: Z 432 GLN cc_start: 0.7323 (mm110) cc_final: 0.7083 (mm-40) REVERT: Z 491 MET cc_start: 0.7430 (mtt) cc_final: 0.7106 (mtp) REVERT: M 228 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.5166 (mm-40) REVERT: S 172 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8360 (mp0) REVERT: S 204 PHE cc_start: 0.7925 (m-10) cc_final: 0.7483 (m-10) REVERT: S 207 LYS cc_start: 0.7546 (mmmm) cc_final: 0.7341 (mtmt) REVERT: S 214 GLU cc_start: 0.6992 (pm20) cc_final: 0.6523 (pm20) REVERT: S 222 LEU cc_start: 0.5460 (OUTLIER) cc_final: 0.5064 (mt) REVERT: S 267 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6594 (ptm) REVERT: S 288 MET cc_start: 0.5908 (mtm) cc_final: 0.5499 (mtp) REVERT: S 389 MET cc_start: 0.6326 (ttt) cc_final: 0.6094 (ttt) REVERT: S 488 MET cc_start: 0.8752 (mmm) cc_final: 0.7726 (mmm) REVERT: N 228 GLN cc_start: 0.6026 (OUTLIER) cc_final: 0.4505 (mm-40) REVERT: N 238 LEU cc_start: 0.7673 (tp) cc_final: 0.7460 (tp) REVERT: T 179 ASP cc_start: 0.7874 (m-30) cc_final: 0.7572 (m-30) REVERT: T 204 PHE cc_start: 0.7674 (m-80) cc_final: 0.7154 (m-80) REVERT: T 267 MET cc_start: 0.5407 (ptt) cc_final: 0.4707 (tmm) REVERT: T 408 GLU cc_start: 0.6216 (tm-30) cc_final: 0.5944 (tm-30) REVERT: T 487 ASN cc_start: 0.8185 (m-40) cc_final: 0.7335 (t0) REVERT: U 69 MET cc_start: 0.7913 (ttp) cc_final: 0.7678 (ttp) REVERT: U 77 VAL cc_start: 0.8444 (t) cc_final: 0.8234 (t) REVERT: U 160 LYS cc_start: 0.7713 (tttt) cc_final: 0.7480 (mtpp) REVERT: U 166 MET cc_start: 0.7579 (ttm) cc_final: 0.7071 (mtp) REVERT: U 171 LYS cc_start: 0.8636 (mtmt) cc_final: 0.8423 (mtpt) REVERT: U 207 LYS cc_start: 0.7943 (mmmm) cc_final: 0.7549 (mmtm) REVERT: U 226 LYS cc_start: 0.8932 (mtpt) cc_final: 0.8021 (tttp) REVERT: U 267 MET cc_start: 0.5325 (ttt) cc_final: 0.4969 (ptt) REVERT: U 378 VAL cc_start: 0.8307 (t) cc_final: 0.7976 (m) REVERT: U 482 THR cc_start: 0.9314 (OUTLIER) cc_final: 0.8946 (p) REVERT: U 488 MET cc_start: 0.8575 (mmm) cc_final: 0.8325 (mtp) REVERT: P 222 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6541 (mt) REVERT: P 253 GLN cc_start: 0.6659 (mp10) cc_final: 0.6014 (mp10) REVERT: V 61 GLU cc_start: 0.7640 (pt0) cc_final: 0.7320 (pt0) REVERT: V 87 ASP cc_start: 0.8229 (t0) cc_final: 0.7817 (t0) REVERT: V 121 ASP cc_start: 0.7221 (m-30) cc_final: 0.6855 (m-30) REVERT: V 129 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.6284 (tt0) REVERT: V 164 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7475 (mm-30) REVERT: V 171 LYS cc_start: 0.8637 (mtmt) cc_final: 0.8269 (mtpt) REVERT: V 172 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8363 (mp0) REVERT: V 193 MET cc_start: 0.7359 (mmm) cc_final: 0.6455 (tpt) REVERT: V 222 LEU cc_start: 0.4760 (OUTLIER) cc_final: 0.4381 (mt) REVERT: V 332 ILE cc_start: 0.7330 (OUTLIER) cc_final: 0.6981 (tp) REVERT: V 390 LYS cc_start: 0.7028 (mtpp) cc_final: 0.6358 (mmmt) REVERT: V 393 LYS cc_start: 0.7171 (tttp) cc_final: 0.6967 (ttpt) REVERT: V 432 GLN cc_start: 0.7547 (mm-40) cc_final: 0.7327 (mm-40) REVERT: V 455 VAL cc_start: 0.8502 (t) cc_final: 0.8260 (t) REVERT: V 470 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7055 (mttt) REVERT: V 488 MET cc_start: 0.7960 (mmm) cc_final: 0.7708 (mmm) REVERT: Q 238 LEU cc_start: 0.7585 (tp) cc_final: 0.7341 (tp) REVERT: W 105 LYS cc_start: 0.8178 (ttpt) cc_final: 0.7922 (ttmm) REVERT: W 214 GLU cc_start: 0.6800 (pm20) cc_final: 0.6269 (pm20) REVERT: W 380 LYS cc_start: 0.6236 (mttt) cc_final: 0.5776 (mmtp) REVERT: W 389 MET cc_start: 0.6236 (ttt) cc_final: 0.5996 (ttt) REVERT: W 432 GLN cc_start: 0.8100 (mm110) cc_final: 0.7890 (mm-40) REVERT: W 495 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7133 (t0) REVERT: R 228 GLN cc_start: 0.6648 (mt0) cc_final: 0.5740 (mm-40) REVERT: X 160 LYS cc_start: 0.7851 (tttt) cc_final: 0.7461 (mtpp) REVERT: X 196 ASP cc_start: 0.8235 (t0) cc_final: 0.7939 (p0) REVERT: X 233 MET cc_start: 0.6746 (mmm) cc_final: 0.6174 (mmp) REVERT: X 253 ASP cc_start: 0.7293 (t70) cc_final: 0.6766 (t70) REVERT: X 288 MET cc_start: 0.4898 (mtt) cc_final: 0.4654 (mtt) REVERT: X 420 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7883 (tt) REVERT: X 482 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8705 (p) REVERT: X 487 ASN cc_start: 0.7889 (m-40) cc_final: 0.7399 (t0) outliers start: 209 outliers final: 161 residues processed: 1153 average time/residue: 0.5475 time to fit residues: 1098.8240 Evaluate side-chains 1209 residues out of total 6580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1024 time to evaluate : 5.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 11 ASP Chi-restraints excluded: chain b residue 60 ILE Chi-restraints excluded: chain b residue 61 GLU Chi-restraints excluded: chain b residue 160 LYS Chi-restraints excluded: chain b residue 187 LEU Chi-restraints excluded: chain b residue 227 ILE Chi-restraints excluded: chain b residue 267 MET Chi-restraints excluded: chain b residue 381 VAL Chi-restraints excluded: chain b residue 401 HIS Chi-restraints excluded: chain b residue 424 SER Chi-restraints excluded: chain b residue 482 THR Chi-restraints excluded: chain b residue 494 LEU Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain G residue 401 HIS Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 424 SER Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain G residue 509 SER Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 523 ASP Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 401 HIS Chi-restraints excluded: chain H residue 407 VAL Chi-restraints excluded: chain H residue 509 SER Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 162 ILE Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 284 ARG Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 401 HIS Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 523 ASP Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 494 LEU Chi-restraints excluded: chain J residue 523 ASP Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 381 VAL Chi-restraints excluded: chain K residue 387 VAL Chi-restraints excluded: chain K residue 397 GLU Chi-restraints excluded: chain K residue 401 HIS Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain K residue 424 SER Chi-restraints excluded: chain K residue 470 LYS Chi-restraints excluded: chain K residue 494 LEU Chi-restraints excluded: chain K residue 516 THR Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 250 ILE Chi-restraints excluded: chain L residue 271 VAL Chi-restraints excluded: chain L residue 332 ILE Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 397 GLU Chi-restraints excluded: chain L residue 401 HIS Chi-restraints excluded: chain L residue 407 VAL Chi-restraints excluded: chain L residue 442 VAL Chi-restraints excluded: chain Y residue 222 LEU Chi-restraints excluded: chain Y residue 228 GLN Chi-restraints excluded: chain Z residue 61 GLU Chi-restraints excluded: chain Z residue 129 GLU Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain Z residue 187 LEU Chi-restraints excluded: chain Z residue 193 MET Chi-restraints excluded: chain Z residue 222 LEU Chi-restraints excluded: chain Z residue 300 VAL Chi-restraints excluded: chain Z residue 332 ILE Chi-restraints excluded: chain Z residue 401 HIS Chi-restraints excluded: chain Z residue 407 VAL Chi-restraints excluded: chain Z residue 494 LEU Chi-restraints excluded: chain Z residue 516 THR Chi-restraints excluded: chain M residue 222 LEU Chi-restraints excluded: chain M residue 228 GLN Chi-restraints excluded: chain M residue 253 GLN Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 61 GLU Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 177 VAL Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain S residue 206 ASN Chi-restraints excluded: chain S residue 222 LEU Chi-restraints excluded: chain S residue 267 MET Chi-restraints excluded: chain S residue 292 ILE Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 332 ILE Chi-restraints excluded: chain S residue 378 VAL Chi-restraints excluded: chain S residue 401 HIS Chi-restraints excluded: chain S residue 424 SER Chi-restraints excluded: chain S residue 454 ILE Chi-restraints excluded: chain S residue 463 SER Chi-restraints excluded: chain S residue 494 LEU Chi-restraints excluded: chain N residue 226 LEU Chi-restraints excluded: chain N residue 228 GLN Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 129 GLU Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 187 LEU Chi-restraints excluded: chain T residue 206 ASN Chi-restraints excluded: chain T residue 292 ILE Chi-restraints excluded: chain T residue 329 THR Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 336 VAL Chi-restraints excluded: chain T residue 378 VAL Chi-restraints excluded: chain T residue 401 HIS Chi-restraints excluded: chain T residue 424 SER Chi-restraints excluded: chain T residue 482 THR Chi-restraints excluded: chain T residue 494 LEU Chi-restraints excluded: chain T residue 515 ILE Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain O residue 278 GLN Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 177 VAL Chi-restraints excluded: chain U residue 249 ILE Chi-restraints excluded: chain U residue 300 VAL Chi-restraints excluded: chain U residue 381 VAL Chi-restraints excluded: chain U residue 401 HIS Chi-restraints excluded: chain U residue 422 VAL Chi-restraints excluded: chain U residue 463 SER Chi-restraints excluded: chain U residue 482 THR Chi-restraints excluded: chain U residue 513 LEU Chi-restraints excluded: chain U residue 515 ILE Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain V residue 129 GLU Chi-restraints excluded: chain V residue 187 LEU Chi-restraints excluded: chain V residue 194 GLN Chi-restraints excluded: chain V residue 222 LEU Chi-restraints excluded: chain V residue 300 VAL Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 378 VAL Chi-restraints excluded: chain V residue 401 HIS Chi-restraints excluded: chain V residue 470 LYS Chi-restraints excluded: chain V residue 494 LEU Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain W residue 61 GLU Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 196 ASP Chi-restraints excluded: chain W residue 206 ASN Chi-restraints excluded: chain W residue 229 ASN Chi-restraints excluded: chain W residue 378 VAL Chi-restraints excluded: chain W residue 463 SER Chi-restraints excluded: chain W residue 494 LEU Chi-restraints excluded: chain W residue 495 ASP Chi-restraints excluded: chain X residue 27 VAL Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain X residue 162 ILE Chi-restraints excluded: chain X residue 169 VAL Chi-restraints excluded: chain X residue 177 VAL Chi-restraints excluded: chain X residue 193 MET Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 401 HIS Chi-restraints excluded: chain X residue 420 ILE Chi-restraints excluded: chain X residue 482 THR Chi-restraints excluded: chain X residue 494 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 495 optimal weight: 1.9990 chunk 797 optimal weight: 2.9990 chunk 486 optimal weight: 0.1980 chunk 378 optimal weight: 0.5980 chunk 554 optimal weight: 1.9990 chunk 836 optimal weight: 5.9990 chunk 770 optimal weight: 0.2980 chunk 666 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 514 optimal weight: 7.9990 chunk 408 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 457 ASN ** Y 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.183 64540 Z= 0.210 Angle : 0.708 59.192 87248 Z= 0.376 Chirality : 0.041 0.583 10500 Planarity : 0.004 0.146 11522 Dihedral : 4.408 35.761 9156 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.70 % Favored : 96.89 % Rotamer: Outliers : 3.11 % Allowed : 18.23 % Favored : 78.66 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.09), residues: 8638 helix: 2.40 (0.07), residues: 5138 sheet: 0.90 (0.17), residues: 896 loop : -1.90 (0.11), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS Y 227 PHE 0.009 0.001 PHE I 195 TYR 0.014 0.001 TYR K 476 ARG 0.004 0.000 ARG Z 345 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17276 Ramachandran restraints generated. 8638 Oldfield, 0 Emsley, 8638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17276 Ramachandran restraints generated. 8638 Oldfield, 0 Emsley, 8638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1233 residues out of total 6580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1026 time to evaluate : 5.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 77 VAL cc_start: 0.8726 (t) cc_final: 0.8473 (t) REVERT: b 105 LYS cc_start: 0.8220 (ttpt) cc_final: 0.7884 (ttmm) REVERT: b 160 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7407 (ttmm) REVERT: b 164 GLU cc_start: 0.7200 (tp30) cc_final: 0.6964 (tp30) REVERT: b 307 MET cc_start: 0.4885 (mmp) cc_final: 0.4179 (mmp) REVERT: b 321 LYS cc_start: 0.6776 (tptt) cc_final: 0.6461 (tttt) REVERT: b 351 GLN cc_start: 0.7855 (tt0) cc_final: 0.7067 (tp40) REVERT: b 352 GLN cc_start: 0.6495 (mt0) cc_final: 0.6197 (mt0) REVERT: b 380 LYS cc_start: 0.6943 (mttt) cc_final: 0.6448 (mtmm) REVERT: b 389 MET cc_start: 0.7037 (ttp) cc_final: 0.6592 (ttt) REVERT: b 397 GLU cc_start: 0.7554 (tt0) cc_final: 0.7236 (tt0) REVERT: b 404 ARG cc_start: 0.7480 (tpp80) cc_final: 0.7125 (ttp80) REVERT: G 121 ASP cc_start: 0.7097 (m-30) cc_final: 0.6372 (t0) REVERT: G 233 MET cc_start: 0.6871 (mmm) cc_final: 0.6403 (mmp) REVERT: G 286 LYS cc_start: 0.7844 (mttt) cc_final: 0.7115 (pttp) REVERT: G 307 MET cc_start: 0.5999 (mmp) cc_final: 0.5409 (mmp) REVERT: G 367 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6936 (mm-30) REVERT: G 380 LYS cc_start: 0.7232 (mttt) cc_final: 0.6404 (mtmm) REVERT: G 494 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8028 (pp) REVERT: B 238 LEU cc_start: 0.7968 (tp) cc_final: 0.7743 (tp) REVERT: H 59 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7171 (mm-30) REVERT: H 73 MET cc_start: 0.8046 (ttm) cc_final: 0.7753 (ttm) REVERT: H 105 LYS cc_start: 0.8262 (ttpt) cc_final: 0.7827 (ttmm) REVERT: H 130 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7037 (mm-30) REVERT: H 321 LYS cc_start: 0.7379 (tptt) cc_final: 0.6990 (tttt) REVERT: H 325 ILE cc_start: 0.7739 (mt) cc_final: 0.7475 (mm) REVERT: H 366 GLN cc_start: 0.7176 (mt0) cc_final: 0.6883 (mt0) REVERT: H 380 LYS cc_start: 0.7309 (mttt) cc_final: 0.6686 (mtmm) REVERT: H 398 ASP cc_start: 0.8556 (t70) cc_final: 0.8186 (t0) REVERT: H 403 THR cc_start: 0.8077 (m) cc_final: 0.7736 (m) REVERT: H 473 ASP cc_start: 0.7798 (p0) cc_final: 0.6875 (m-30) REVERT: I 105 LYS cc_start: 0.8333 (ttpt) cc_final: 0.7901 (ttmm) REVERT: I 194 GLN cc_start: 0.7069 (tt0) cc_final: 0.6806 (tt0) REVERT: I 233 MET cc_start: 0.6272 (mmm) cc_final: 0.4928 (mmm) REVERT: I 267 MET cc_start: 0.6116 (ttt) cc_final: 0.5814 (tpp) REVERT: I 307 MET cc_start: 0.5738 (mmp) cc_final: 0.4722 (mmp) REVERT: I 321 LYS cc_start: 0.6991 (tptt) cc_final: 0.6454 (tttt) REVERT: I 389 MET cc_start: 0.6729 (tpp) cc_final: 0.6428 (tpp) REVERT: I 432 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7178 (mt0) REVERT: I 523 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.8000 (t0) REVERT: J 69 MET cc_start: 0.8204 (mtm) cc_final: 0.7641 (mtm) REVERT: J 87 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.8236 (m-30) REVERT: J 204 PHE cc_start: 0.7011 (m-80) cc_final: 0.6742 (m-80) REVERT: J 233 MET cc_start: 0.6258 (mmp) cc_final: 0.5534 (mmp) REVERT: J 286 LYS cc_start: 0.6930 (mttt) cc_final: 0.6416 (mtmt) REVERT: J 288 MET cc_start: 0.6641 (mtp) cc_final: 0.6214 (mtp) REVERT: J 380 LYS cc_start: 0.7577 (mttt) cc_final: 0.7042 (mtmm) REVERT: J 404 ARG cc_start: 0.7282 (tpp80) cc_final: 0.7019 (ttm-80) REVERT: J 494 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8150 (pp) REVERT: K 59 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7470 (mm-30) REVERT: K 121 ASP cc_start: 0.7646 (m-30) cc_final: 0.7270 (m-30) REVERT: K 178 GLU cc_start: 0.6957 (pt0) cc_final: 0.6707 (pt0) REVERT: K 267 MET cc_start: 0.6275 (ttt) cc_final: 0.6032 (tpp) REVERT: K 307 MET cc_start: 0.5714 (mmp) cc_final: 0.4936 (mmp) REVERT: K 321 LYS cc_start: 0.7391 (tppt) cc_final: 0.6520 (tttt) REVERT: K 380 LYS cc_start: 0.7500 (mttt) cc_final: 0.7029 (mtmm) REVERT: K 404 ARG cc_start: 0.8106 (tpp80) cc_final: 0.7670 (mtp85) REVERT: K 422 VAL cc_start: 0.9038 (t) cc_final: 0.8538 (m) REVERT: K 432 GLN cc_start: 0.7026 (mm110) cc_final: 0.6816 (mt0) REVERT: K 483 GLU cc_start: 0.7642 (mp0) cc_final: 0.7373 (mp0) REVERT: K 514 MET cc_start: 0.7422 (mtp) cc_final: 0.6975 (mtt) REVERT: L 59 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7513 (mm-30) REVERT: L 307 MET cc_start: 0.5468 (mmp) cc_final: 0.4621 (mmp) REVERT: L 326 ASN cc_start: 0.6989 (t0) cc_final: 0.6709 (t0) REVERT: L 368 ARG cc_start: 0.7120 (ttm170) cc_final: 0.6031 (ttm-80) REVERT: L 397 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7316 (tm-30) REVERT: Y 222 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6137 (mt) REVERT: Y 228 GLN cc_start: 0.7027 (mt0) cc_final: 0.6371 (mm-40) REVERT: Z 16 MET cc_start: 0.8330 (mtm) cc_final: 0.7843 (mtp) REVERT: Z 18 ARG cc_start: 0.7393 (ttm-80) cc_final: 0.6725 (ttp80) REVERT: Z 59 GLU cc_start: 0.7260 (mm-30) cc_final: 0.7025 (mm-30) REVERT: Z 63 GLU cc_start: 0.7184 (tp30) cc_final: 0.6900 (pm20) REVERT: Z 193 MET cc_start: 0.7119 (OUTLIER) cc_final: 0.6736 (ttm) REVERT: Z 207 LYS cc_start: 0.7491 (mtpt) cc_final: 0.6932 (mmtm) REVERT: Z 222 LEU cc_start: 0.4917 (OUTLIER) cc_final: 0.4654 (mt) REVERT: Z 371 LYS cc_start: 0.7019 (tppt) cc_final: 0.6754 (ttmm) REVERT: Z 432 GLN cc_start: 0.7314 (mm110) cc_final: 0.7083 (mm-40) REVERT: Z 491 MET cc_start: 0.7429 (mtt) cc_final: 0.7106 (mtp) REVERT: M 228 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.5166 (mm-40) REVERT: S 172 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8360 (mp0) REVERT: S 187 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8113 (tt) REVERT: S 204 PHE cc_start: 0.7918 (m-10) cc_final: 0.7484 (m-10) REVERT: S 207 LYS cc_start: 0.7556 (mmmm) cc_final: 0.7341 (mtmt) REVERT: S 214 GLU cc_start: 0.6993 (pm20) cc_final: 0.6524 (pm20) REVERT: S 222 LEU cc_start: 0.5459 (OUTLIER) cc_final: 0.5064 (mt) REVERT: S 267 MET cc_start: 0.7183 (OUTLIER) cc_final: 0.6594 (ptm) REVERT: S 288 MET cc_start: 0.5906 (mtm) cc_final: 0.5501 (mtp) REVERT: S 488 MET cc_start: 0.8751 (mmm) cc_final: 0.7728 (mmm) REVERT: N 228 GLN cc_start: 0.6029 (OUTLIER) cc_final: 0.4505 (mm-40) REVERT: N 238 LEU cc_start: 0.7669 (tp) cc_final: 0.7460 (tp) REVERT: T 179 ASP cc_start: 0.7881 (m-30) cc_final: 0.7572 (m-30) REVERT: T 204 PHE cc_start: 0.7667 (m-80) cc_final: 0.7151 (m-80) REVERT: T 267 MET cc_start: 0.5408 (ptt) cc_final: 0.4711 (tmm) REVERT: T 408 GLU cc_start: 0.6216 (tm-30) cc_final: 0.5941 (tm-30) REVERT: T 487 ASN cc_start: 0.8185 (m-40) cc_final: 0.7335 (t0) REVERT: U 77 VAL cc_start: 0.8445 (t) cc_final: 0.8235 (t) REVERT: U 160 LYS cc_start: 0.7711 (tttt) cc_final: 0.7480 (mtpp) REVERT: U 166 MET cc_start: 0.7579 (ttm) cc_final: 0.7070 (mtp) REVERT: U 171 LYS cc_start: 0.8640 (mtmt) cc_final: 0.8424 (mtpt) REVERT: U 207 LYS cc_start: 0.7943 (mmmm) cc_final: 0.7549 (mmtm) REVERT: U 226 LYS cc_start: 0.8933 (mtpt) cc_final: 0.8021 (tttp) REVERT: U 267 MET cc_start: 0.5322 (ttt) cc_final: 0.4968 (ptt) REVERT: U 378 VAL cc_start: 0.8303 (t) cc_final: 0.7975 (m) REVERT: U 482 THR cc_start: 0.9316 (OUTLIER) cc_final: 0.8946 (p) REVERT: U 488 MET cc_start: 0.8579 (mmm) cc_final: 0.8323 (mtp) REVERT: P 253 GLN cc_start: 0.6664 (mp10) cc_final: 0.6016 (mp10) REVERT: V 61 GLU cc_start: 0.7634 (pt0) cc_final: 0.7319 (pt0) REVERT: V 87 ASP cc_start: 0.8229 (t0) cc_final: 0.7815 (t0) REVERT: V 121 ASP cc_start: 0.7200 (m-30) cc_final: 0.6854 (m-30) REVERT: V 129 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.6284 (tt0) REVERT: V 164 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7586 (mm-30) REVERT: V 171 LYS cc_start: 0.8635 (mtmt) cc_final: 0.8269 (mtpt) REVERT: V 172 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8364 (mp0) REVERT: V 193 MET cc_start: 0.7355 (mmm) cc_final: 0.6453 (tpt) REVERT: V 222 LEU cc_start: 0.4764 (OUTLIER) cc_final: 0.4380 (mt) REVERT: V 332 ILE cc_start: 0.7335 (OUTLIER) cc_final: 0.6981 (tp) REVERT: V 390 LYS cc_start: 0.7023 (mtpp) cc_final: 0.6358 (mmmt) REVERT: V 393 LYS cc_start: 0.7174 (tttp) cc_final: 0.6967 (ttpt) REVERT: V 432 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7325 (mm-40) REVERT: V 455 VAL cc_start: 0.8496 (t) cc_final: 0.8257 (t) REVERT: V 470 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7052 (mttt) REVERT: V 488 MET cc_start: 0.7956 (mmm) cc_final: 0.7710 (mmm) REVERT: Q 238 LEU cc_start: 0.7586 (tp) cc_final: 0.7340 (tp) REVERT: W 105 LYS cc_start: 0.8184 (ttpt) cc_final: 0.7921 (ttmm) REVERT: W 214 GLU cc_start: 0.6793 (pm20) cc_final: 0.6294 (pm20) REVERT: W 380 LYS cc_start: 0.6231 (mttt) cc_final: 0.5775 (mmtp) REVERT: W 389 MET cc_start: 0.6237 (ttt) cc_final: 0.6002 (ttt) REVERT: W 432 GLN cc_start: 0.8091 (mm110) cc_final: 0.7890 (mm-40) REVERT: W 495 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.7133 (t0) REVERT: R 228 GLN cc_start: 0.6651 (mt0) cc_final: 0.5741 (mm-40) REVERT: X 160 LYS cc_start: 0.7847 (tttt) cc_final: 0.7460 (mtpp) REVERT: X 196 ASP cc_start: 0.8232 (t0) cc_final: 0.7939 (p0) REVERT: X 233 MET cc_start: 0.6746 (mmm) cc_final: 0.6171 (mmp) REVERT: X 253 ASP cc_start: 0.7296 (t70) cc_final: 0.6765 (t70) REVERT: X 288 MET cc_start: 0.4891 (mtt) cc_final: 0.4654 (mtt) REVERT: X 420 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7877 (tt) REVERT: X 482 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8706 (p) REVERT: X 487 ASN cc_start: 0.7879 (m-40) cc_final: 0.7409 (t0) outliers start: 207 outliers final: 176 residues processed: 1134 average time/residue: 0.5497 time to fit residues: 1085.0112 Evaluate side-chains 1227 residues out of total 6580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1028 time to evaluate : 5.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 11 ASP Chi-restraints excluded: chain b residue 60 ILE Chi-restraints excluded: chain b residue 61 GLU Chi-restraints excluded: chain b residue 160 LYS Chi-restraints excluded: chain b residue 187 LEU Chi-restraints excluded: chain b residue 227 ILE Chi-restraints excluded: chain b residue 267 MET Chi-restraints excluded: chain b residue 381 VAL Chi-restraints excluded: chain b residue 401 HIS Chi-restraints excluded: chain b residue 424 SER Chi-restraints excluded: chain b residue 482 THR Chi-restraints excluded: chain b residue 494 LEU Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 387 VAL Chi-restraints excluded: chain G residue 401 HIS Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 424 SER Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain G residue 509 SER Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 523 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 271 VAL Chi-restraints excluded: chain H residue 401 HIS Chi-restraints excluded: chain H residue 407 VAL Chi-restraints excluded: chain H residue 509 SER Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 162 ILE Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain I residue 187 LEU Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 284 ARG Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 401 HIS Chi-restraints excluded: chain I residue 422 VAL Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 523 ASP Chi-restraints excluded: chain J residue 87 ASP Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 160 LYS Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 247 LEU Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain J residue 407 VAL Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain J residue 494 LEU Chi-restraints excluded: chain J residue 523 ASP Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain K residue 87 ASP Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 381 VAL Chi-restraints excluded: chain K residue 387 VAL Chi-restraints excluded: chain K residue 397 GLU Chi-restraints excluded: chain K residue 401 HIS Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain K residue 424 SER Chi-restraints excluded: chain K residue 470 LYS Chi-restraints excluded: chain K residue 494 LEU Chi-restraints excluded: chain K residue 516 THR Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 69 MET Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 250 ILE Chi-restraints excluded: chain L residue 271 VAL Chi-restraints excluded: chain L residue 332 ILE Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 397 GLU Chi-restraints excluded: chain L residue 401 HIS Chi-restraints excluded: chain L residue 407 VAL Chi-restraints excluded: chain L residue 442 VAL Chi-restraints excluded: chain Y residue 222 LEU Chi-restraints excluded: chain Z residue 61 GLU Chi-restraints excluded: chain Z residue 129 GLU Chi-restraints excluded: chain Z residue 177 VAL Chi-restraints excluded: chain Z residue 187 LEU Chi-restraints excluded: chain Z residue 193 MET Chi-restraints excluded: chain Z residue 222 LEU Chi-restraints excluded: chain Z residue 229 ASN Chi-restraints excluded: chain Z residue 300 VAL Chi-restraints excluded: chain Z residue 329 THR Chi-restraints excluded: chain Z residue 332 ILE Chi-restraints excluded: chain Z residue 401 HIS Chi-restraints excluded: chain Z residue 407 VAL Chi-restraints excluded: chain Z residue 494 LEU Chi-restraints excluded: chain Z residue 516 THR Chi-restraints excluded: chain M residue 222 LEU Chi-restraints excluded: chain M residue 228 GLN Chi-restraints excluded: chain M residue 253 GLN Chi-restraints excluded: chain M residue 279 LEU Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain S residue 61 GLU Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 177 VAL Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain S residue 206 ASN Chi-restraints excluded: chain S residue 222 LEU Chi-restraints excluded: chain S residue 267 MET Chi-restraints excluded: chain S residue 292 ILE Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 332 ILE Chi-restraints excluded: chain S residue 378 VAL Chi-restraints excluded: chain S residue 401 HIS Chi-restraints excluded: chain S residue 424 SER Chi-restraints excluded: chain S residue 454 ILE Chi-restraints excluded: chain S residue 463 SER Chi-restraints excluded: chain S residue 494 LEU Chi-restraints excluded: chain N residue 226 LEU Chi-restraints excluded: chain N residue 228 GLN Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 129 GLU Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 187 LEU Chi-restraints excluded: chain T residue 206 ASN Chi-restraints excluded: chain T residue 292 ILE Chi-restraints excluded: chain T residue 329 THR Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 336 VAL Chi-restraints excluded: chain T residue 378 VAL Chi-restraints excluded: chain T residue 401 HIS Chi-restraints excluded: chain T residue 417 VAL Chi-restraints excluded: chain T residue 424 SER Chi-restraints excluded: chain T residue 482 THR Chi-restraints excluded: chain T residue 494 LEU Chi-restraints excluded: chain T residue 515 ILE Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain O residue 278 GLN Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 177 VAL Chi-restraints excluded: chain U residue 249 ILE Chi-restraints excluded: chain U residue 300 VAL Chi-restraints excluded: chain U residue 381 VAL Chi-restraints excluded: chain U residue 401 HIS Chi-restraints excluded: chain U residue 422 VAL Chi-restraints excluded: chain U residue 463 SER Chi-restraints excluded: chain U residue 482 THR Chi-restraints excluded: chain U residue 513 LEU Chi-restraints excluded: chain U residue 515 ILE Chi-restraints excluded: chain P residue 228 GLN Chi-restraints excluded: chain V residue 107 VAL Chi-restraints excluded: chain V residue 129 GLU Chi-restraints excluded: chain V residue 187 LEU Chi-restraints excluded: chain V residue 194 GLN Chi-restraints excluded: chain V residue 222 LEU Chi-restraints excluded: chain V residue 300 VAL Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 378 VAL Chi-restraints excluded: chain V residue 401 HIS Chi-restraints excluded: chain V residue 470 LYS Chi-restraints excluded: chain V residue 494 LEU Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain W residue 61 GLU Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 196 ASP Chi-restraints excluded: chain W residue 206 ASN Chi-restraints excluded: chain W residue 229 ASN Chi-restraints excluded: chain W residue 332 ILE Chi-restraints excluded: chain W residue 378 VAL Chi-restraints excluded: chain W residue 417 VAL Chi-restraints excluded: chain W residue 463 SER Chi-restraints excluded: chain W residue 494 LEU Chi-restraints excluded: chain W residue 495 ASP Chi-restraints excluded: chain X residue 27 VAL Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain X residue 151 SER Chi-restraints excluded: chain X residue 162 ILE Chi-restraints excluded: chain X residue 169 VAL Chi-restraints excluded: chain X residue 177 VAL Chi-restraints excluded: chain X residue 193 MET Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 401 HIS Chi-restraints excluded: chain X residue 420 ILE Chi-restraints excluded: chain X residue 482 THR Chi-restraints excluded: chain X residue 494 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 529 optimal weight: 2.9990 chunk 709 optimal weight: 2.9990 chunk 204 optimal weight: 8.9990 chunk 614 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 185 optimal weight: 50.0000 chunk 667 optimal weight: 9.9990 chunk 279 optimal weight: 5.9990 chunk 685 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 457 ASN ** Y 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 259 GLN ** Q 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.236923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.180285 restraints weight = 304402.850| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 6.31 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3925 r_free = 0.3925 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3925 r_free = 0.3925 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.183 64540 Z= 0.210 Angle : 0.708 59.192 87248 Z= 0.376 Chirality : 0.041 0.583 10500 Planarity : 0.004 0.146 11522 Dihedral : 4.408 35.761 9156 Min Nonbonded Distance : 1.503 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.70 % Favored : 96.89 % Rotamer: Outliers : 3.02 % Allowed : 18.32 % Favored : 78.66 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.09), residues: 8638 helix: 2.40 (0.07), residues: 5138 sheet: 0.90 (0.17), residues: 896 loop : -1.90 (0.11), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS Y 227 PHE 0.009 0.001 PHE I 195 TYR 0.014 0.001 TYR K 476 ARG 0.004 0.000 ARG Z 345 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16753.60 seconds wall clock time: 293 minutes 6.55 seconds (17586.55 seconds total)