Starting phenix.real_space_refine on Mon Mar 11 18:44:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9k_12104/03_2024/7b9k_12104_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9k_12104/03_2024/7b9k_12104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9k_12104/03_2024/7b9k_12104.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9k_12104/03_2024/7b9k_12104.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9k_12104/03_2024/7b9k_12104_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9k_12104/03_2024/7b9k_12104_updated.pdb" } resolution = 3.16 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= 0.007 sd= 0.106 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 360 5.16 5 C 37728 2.51 5 N 9984 2.21 5 O 11064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 220": "OE1" <-> "OE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 501": "OD1" <-> "OD2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 220": "OE1" <-> "OE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "B GLU 436": "OE1" <-> "OE2" Residue "B PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 501": "OD1" <-> "OD2" Residue "B PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 220": "OE1" <-> "OE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 402": "OE1" <-> "OE2" Residue "C GLU 436": "OE1" <-> "OE2" Residue "C PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 501": "OD1" <-> "OD2" Residue "C PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 220": "OE1" <-> "OE2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D GLU 436": "OE1" <-> "OE2" Residue "D PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 501": "OD1" <-> "OD2" Residue "D PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E GLU 249": "OE1" <-> "OE2" Residue "E PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 402": "OE1" <-> "OE2" Residue "E GLU 436": "OE1" <-> "OE2" Residue "E PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 501": "OD1" <-> "OD2" Residue "E PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 220": "OE1" <-> "OE2" Residue "F GLU 249": "OE1" <-> "OE2" Residue "F PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 402": "OE1" <-> "OE2" Residue "F GLU 436": "OE1" <-> "OE2" Residue "F PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 501": "OD1" <-> "OD2" Residue "F PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 220": "OE1" <-> "OE2" Residue "G GLU 249": "OE1" <-> "OE2" Residue "G PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 402": "OE1" <-> "OE2" Residue "G GLU 436": "OE1" <-> "OE2" Residue "G PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 501": "OD1" <-> "OD2" Residue "G PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 220": "OE1" <-> "OE2" Residue "H GLU 249": "OE1" <-> "OE2" Residue "H PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 402": "OE1" <-> "OE2" Residue "H GLU 436": "OE1" <-> "OE2" Residue "H PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 501": "OD1" <-> "OD2" Residue "H PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 220": "OE1" <-> "OE2" Residue "I GLU 249": "OE1" <-> "OE2" Residue "I PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 402": "OE1" <-> "OE2" Residue "I GLU 436": "OE1" <-> "OE2" Residue "I PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 501": "OD1" <-> "OD2" Residue "I PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 220": "OE1" <-> "OE2" Residue "J GLU 249": "OE1" <-> "OE2" Residue "J PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 402": "OE1" <-> "OE2" Residue "J GLU 436": "OE1" <-> "OE2" Residue "J PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 501": "OD1" <-> "OD2" Residue "J PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 220": "OE1" <-> "OE2" Residue "K GLU 249": "OE1" <-> "OE2" Residue "K PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 402": "OE1" <-> "OE2" Residue "K GLU 436": "OE1" <-> "OE2" Residue "K PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 501": "OD1" <-> "OD2" Residue "K PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 220": "OE1" <-> "OE2" Residue "L GLU 249": "OE1" <-> "OE2" Residue "L PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 402": "OE1" <-> "OE2" Residue "L GLU 436": "OE1" <-> "OE2" Residue "L PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 501": "OD1" <-> "OD2" Residue "L PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 220": "OE1" <-> "OE2" Residue "M GLU 249": "OE1" <-> "OE2" Residue "M PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 402": "OE1" <-> "OE2" Residue "M GLU 436": "OE1" <-> "OE2" Residue "M PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 501": "OD1" <-> "OD2" Residue "M PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 220": "OE1" <-> "OE2" Residue "N GLU 249": "OE1" <-> "OE2" Residue "N PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 402": "OE1" <-> "OE2" Residue "N GLU 436": "OE1" <-> "OE2" Residue "N PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 501": "OD1" <-> "OD2" Residue "N PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 220": "OE1" <-> "OE2" Residue "O GLU 249": "OE1" <-> "OE2" Residue "O PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 402": "OE1" <-> "OE2" Residue "O GLU 436": "OE1" <-> "OE2" Residue "O PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 501": "OD1" <-> "OD2" Residue "O PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 220": "OE1" <-> "OE2" Residue "P GLU 249": "OE1" <-> "OE2" Residue "P PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 402": "OE1" <-> "OE2" Residue "P GLU 436": "OE1" <-> "OE2" Residue "P PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 501": "OD1" <-> "OD2" Residue "P PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 220": "OE1" <-> "OE2" Residue "Q GLU 249": "OE1" <-> "OE2" Residue "Q PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 402": "OE1" <-> "OE2" Residue "Q GLU 436": "OE1" <-> "OE2" Residue "Q PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 501": "OD1" <-> "OD2" Residue "Q PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 220": "OE1" <-> "OE2" Residue "R GLU 249": "OE1" <-> "OE2" Residue "R PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 402": "OE1" <-> "OE2" Residue "R GLU 436": "OE1" <-> "OE2" Residue "R PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 501": "OD1" <-> "OD2" Residue "R PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 220": "OE1" <-> "OE2" Residue "S GLU 249": "OE1" <-> "OE2" Residue "S PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 402": "OE1" <-> "OE2" Residue "S GLU 436": "OE1" <-> "OE2" Residue "S PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 501": "OD1" <-> "OD2" Residue "S PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 220": "OE1" <-> "OE2" Residue "T GLU 249": "OE1" <-> "OE2" Residue "T PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 402": "OE1" <-> "OE2" Residue "T GLU 436": "OE1" <-> "OE2" Residue "T PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 501": "OD1" <-> "OD2" Residue "T PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 220": "OE1" <-> "OE2" Residue "U GLU 249": "OE1" <-> "OE2" Residue "U PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 402": "OE1" <-> "OE2" Residue "U GLU 436": "OE1" <-> "OE2" Residue "U PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 501": "OD1" <-> "OD2" Residue "U PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 220": "OE1" <-> "OE2" Residue "V GLU 249": "OE1" <-> "OE2" Residue "V PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 402": "OE1" <-> "OE2" Residue "V GLU 436": "OE1" <-> "OE2" Residue "V PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 501": "OD1" <-> "OD2" Residue "V PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 220": "OE1" <-> "OE2" Residue "W GLU 249": "OE1" <-> "OE2" Residue "W PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 402": "OE1" <-> "OE2" Residue "W GLU 436": "OE1" <-> "OE2" Residue "W PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 501": "OD1" <-> "OD2" Residue "W PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 220": "OE1" <-> "OE2" Residue "X GLU 249": "OE1" <-> "OE2" Residue "X PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 402": "OE1" <-> "OE2" Residue "X GLU 436": "OE1" <-> "OE2" Residue "X PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 501": "OD1" <-> "OD2" Residue "X PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 59136 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2464 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LA2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2464 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LA2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2464 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LA2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2464 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LA2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2464 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LA2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2464 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LA2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2464 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LA2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2464 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LA2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2464 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LA2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2464 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LA2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2464 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LA2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2464 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LA2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2464 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LA2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2464 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LA2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2464 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LA2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2464 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LA2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2464 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LA2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2464 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LA2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2464 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LA2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2464 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LA2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2464 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LA2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2464 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LA2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2464 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LA2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2464 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LA2:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 22.25, per 1000 atoms: 0.38 Number of scatterers: 59136 At special positions: 0 Unit cell: (188.24, 188.24, 187.2, 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 360 16.00 O 11064 8.00 N 9984 7.00 C 37728 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: 17.25 Conformation dependent library (CDL) restraints added in 7.8 seconds 15024 Ramachandran restraints generated. 7512 Oldfield, 0 Emsley, 7512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14112 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 168 helices and 72 sheets defined 27.2% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.85 Creating SS restraints... Processing helix chain 'A' and resid 407 through 422 removed outlier: 3.735A pdb=" N VAL A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 450 Processing helix chain 'A' and resid 459 through 473 removed outlier: 3.738A pdb=" N ILE A 463 " --> pdb=" O PRO A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 477 No H-bonds generated for 'chain 'A' and resid 475 through 477' Processing helix chain 'A' and resid 519 through 535 removed outlier: 3.740A pdb=" N LYS A 531 " --> pdb=" O MET A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 623 Processing helix chain 'A' and resid 625 through 628 Processing helix chain 'B' and resid 407 through 422 removed outlier: 3.735A pdb=" N VAL B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 450 Processing helix chain 'B' and resid 459 through 473 removed outlier: 3.738A pdb=" N ILE B 463 " --> pdb=" O PRO B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 477 No H-bonds generated for 'chain 'B' and resid 475 through 477' Processing helix chain 'B' and resid 519 through 535 removed outlier: 3.741A pdb=" N LYS B 531 " --> pdb=" O MET B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 623 Processing helix chain 'B' and resid 625 through 628 Processing helix chain 'C' and resid 407 through 422 removed outlier: 3.736A pdb=" N VAL C 421 " --> pdb=" O SER C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 450 Processing helix chain 'C' and resid 459 through 473 removed outlier: 3.737A pdb=" N ILE C 463 " --> pdb=" O PRO C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 477 No H-bonds generated for 'chain 'C' and resid 475 through 477' Processing helix chain 'C' and resid 519 through 535 removed outlier: 3.741A pdb=" N LYS C 531 " --> pdb=" O MET C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 623 Processing helix chain 'C' and resid 625 through 628 Processing helix chain 'D' and resid 407 through 422 removed outlier: 3.734A pdb=" N VAL D 421 " --> pdb=" O SER D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 450 Processing helix chain 'D' and resid 459 through 473 removed outlier: 3.738A pdb=" N ILE D 463 " --> pdb=" O PRO D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 477 No H-bonds generated for 'chain 'D' and resid 475 through 477' Processing helix chain 'D' and resid 519 through 535 removed outlier: 3.741A pdb=" N LYS D 531 " --> pdb=" O MET D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 623 Processing helix chain 'D' and resid 625 through 628 Processing helix chain 'E' and resid 407 through 422 removed outlier: 3.735A pdb=" N VAL E 421 " --> pdb=" O SER E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 450 Processing helix chain 'E' and resid 459 through 473 removed outlier: 3.738A pdb=" N ILE E 463 " --> pdb=" O PRO E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 477 No H-bonds generated for 'chain 'E' and resid 475 through 477' Processing helix chain 'E' and resid 519 through 535 removed outlier: 3.741A pdb=" N LYS E 531 " --> pdb=" O MET E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 623 Processing helix chain 'E' and resid 625 through 628 Processing helix chain 'F' and resid 407 through 422 removed outlier: 3.735A pdb=" N VAL F 421 " --> pdb=" O SER F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 450 Processing helix chain 'F' and resid 459 through 473 removed outlier: 3.739A pdb=" N ILE F 463 " --> pdb=" O PRO F 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 477 No H-bonds generated for 'chain 'F' and resid 475 through 477' Processing helix chain 'F' and resid 519 through 535 removed outlier: 3.741A pdb=" N LYS F 531 " --> pdb=" O MET F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 623 Processing helix chain 'F' and resid 625 through 628 Processing helix chain 'G' and resid 407 through 422 removed outlier: 3.735A pdb=" N VAL G 421 " --> pdb=" O SER G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 450 Processing helix chain 'G' and resid 459 through 473 removed outlier: 3.737A pdb=" N ILE G 463 " --> pdb=" O PRO G 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 477 No H-bonds generated for 'chain 'G' and resid 475 through 477' Processing helix chain 'G' and resid 519 through 535 removed outlier: 3.740A pdb=" N LYS G 531 " --> pdb=" O MET G 527 " (cutoff:3.500A) Processing helix chain 'G' and resid 608 through 623 Processing helix chain 'G' and resid 625 through 628 Processing helix chain 'H' and resid 407 through 422 removed outlier: 3.734A pdb=" N VAL H 421 " --> pdb=" O SER H 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 435 through 450 Processing helix chain 'H' and resid 459 through 473 removed outlier: 3.738A pdb=" N ILE H 463 " --> pdb=" O PRO H 459 " (cutoff:3.500A) Processing helix chain 'H' and resid 475 through 477 No H-bonds generated for 'chain 'H' and resid 475 through 477' Processing helix chain 'H' and resid 519 through 535 removed outlier: 3.741A pdb=" N LYS H 531 " --> pdb=" O MET H 527 " (cutoff:3.500A) Processing helix chain 'H' and resid 608 through 623 Processing helix chain 'H' and resid 625 through 628 Processing helix chain 'I' and resid 407 through 422 removed outlier: 3.735A pdb=" N VAL I 421 " --> pdb=" O SER I 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 435 through 450 Processing helix chain 'I' and resid 459 through 473 removed outlier: 3.738A pdb=" N ILE I 463 " --> pdb=" O PRO I 459 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 477 No H-bonds generated for 'chain 'I' and resid 475 through 477' Processing helix chain 'I' and resid 519 through 535 removed outlier: 3.740A pdb=" N LYS I 531 " --> pdb=" O MET I 527 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 623 Processing helix chain 'I' and resid 625 through 628 Processing helix chain 'J' and resid 407 through 422 removed outlier: 3.734A pdb=" N VAL J 421 " --> pdb=" O SER J 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 435 through 450 Processing helix chain 'J' and resid 459 through 473 removed outlier: 3.739A pdb=" N ILE J 463 " --> pdb=" O PRO J 459 " (cutoff:3.500A) Processing helix chain 'J' and resid 475 through 477 No H-bonds generated for 'chain 'J' and resid 475 through 477' Processing helix chain 'J' and resid 519 through 535 removed outlier: 3.741A pdb=" N LYS J 531 " --> pdb=" O MET J 527 " (cutoff:3.500A) Processing helix chain 'J' and resid 608 through 623 Processing helix chain 'J' and resid 625 through 628 Processing helix chain 'K' and resid 407 through 422 removed outlier: 3.734A pdb=" N VAL K 421 " --> pdb=" O SER K 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 435 through 450 Processing helix chain 'K' and resid 459 through 473 removed outlier: 3.738A pdb=" N ILE K 463 " --> pdb=" O PRO K 459 " (cutoff:3.500A) Processing helix chain 'K' and resid 475 through 477 No H-bonds generated for 'chain 'K' and resid 475 through 477' Processing helix chain 'K' and resid 519 through 535 removed outlier: 3.741A pdb=" N LYS K 531 " --> pdb=" O MET K 527 " (cutoff:3.500A) Processing helix chain 'K' and resid 608 through 623 Processing helix chain 'K' and resid 625 through 628 Processing helix chain 'L' and resid 407 through 422 removed outlier: 3.735A pdb=" N VAL L 421 " --> pdb=" O SER L 417 " (cutoff:3.500A) Processing helix chain 'L' and resid 435 through 450 Processing helix chain 'L' and resid 459 through 473 removed outlier: 3.737A pdb=" N ILE L 463 " --> pdb=" O PRO L 459 " (cutoff:3.500A) Processing helix chain 'L' and resid 475 through 477 No H-bonds generated for 'chain 'L' and resid 475 through 477' Processing helix chain 'L' and resid 519 through 535 removed outlier: 3.741A pdb=" N LYS L 531 " --> pdb=" O MET L 527 " (cutoff:3.500A) Processing helix chain 'L' and resid 608 through 623 Processing helix chain 'L' and resid 625 through 628 Processing helix chain 'M' and resid 407 through 422 removed outlier: 3.734A pdb=" N VAL M 421 " --> pdb=" O SER M 417 " (cutoff:3.500A) Processing helix chain 'M' and resid 435 through 450 Processing helix chain 'M' and resid 459 through 473 removed outlier: 3.738A pdb=" N ILE M 463 " --> pdb=" O PRO M 459 " (cutoff:3.500A) Processing helix chain 'M' and resid 475 through 477 No H-bonds generated for 'chain 'M' and resid 475 through 477' Processing helix chain 'M' and resid 519 through 535 removed outlier: 3.741A pdb=" N LYS M 531 " --> pdb=" O MET M 527 " (cutoff:3.500A) Processing helix chain 'M' and resid 608 through 623 Processing helix chain 'M' and resid 625 through 628 Processing helix chain 'N' and resid 407 through 422 removed outlier: 3.735A pdb=" N VAL N 421 " --> pdb=" O SER N 417 " (cutoff:3.500A) Processing helix chain 'N' and resid 435 through 450 Processing helix chain 'N' and resid 459 through 473 removed outlier: 3.738A pdb=" N ILE N 463 " --> pdb=" O PRO N 459 " (cutoff:3.500A) Processing helix chain 'N' and resid 475 through 477 No H-bonds generated for 'chain 'N' and resid 475 through 477' Processing helix chain 'N' and resid 519 through 535 removed outlier: 3.740A pdb=" N LYS N 531 " --> pdb=" O MET N 527 " (cutoff:3.500A) Processing helix chain 'N' and resid 608 through 623 Processing helix chain 'N' and resid 625 through 628 Processing helix chain 'O' and resid 407 through 422 removed outlier: 3.734A pdb=" N VAL O 421 " --> pdb=" O SER O 417 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 450 Processing helix chain 'O' and resid 459 through 473 removed outlier: 3.738A pdb=" N ILE O 463 " --> pdb=" O PRO O 459 " (cutoff:3.500A) Processing helix chain 'O' and resid 475 through 477 No H-bonds generated for 'chain 'O' and resid 475 through 477' Processing helix chain 'O' and resid 519 through 535 removed outlier: 3.741A pdb=" N LYS O 531 " --> pdb=" O MET O 527 " (cutoff:3.500A) Processing helix chain 'O' and resid 608 through 623 Processing helix chain 'O' and resid 625 through 628 Processing helix chain 'P' and resid 407 through 422 removed outlier: 3.735A pdb=" N VAL P 421 " --> pdb=" O SER P 417 " (cutoff:3.500A) Processing helix chain 'P' and resid 435 through 450 Processing helix chain 'P' and resid 459 through 473 removed outlier: 3.738A pdb=" N ILE P 463 " --> pdb=" O PRO P 459 " (cutoff:3.500A) Processing helix chain 'P' and resid 475 through 477 No H-bonds generated for 'chain 'P' and resid 475 through 477' Processing helix chain 'P' and resid 519 through 535 removed outlier: 3.741A pdb=" N LYS P 531 " --> pdb=" O MET P 527 " (cutoff:3.500A) Processing helix chain 'P' and resid 608 through 623 Processing helix chain 'P' and resid 625 through 628 Processing helix chain 'Q' and resid 407 through 422 removed outlier: 3.735A pdb=" N VAL Q 421 " --> pdb=" O SER Q 417 " (cutoff:3.500A) Processing helix chain 'Q' and resid 435 through 450 Processing helix chain 'Q' and resid 459 through 473 removed outlier: 3.738A pdb=" N ILE Q 463 " --> pdb=" O PRO Q 459 " (cutoff:3.500A) Processing helix chain 'Q' and resid 475 through 477 No H-bonds generated for 'chain 'Q' and resid 475 through 477' Processing helix chain 'Q' and resid 519 through 535 removed outlier: 3.741A pdb=" N LYS Q 531 " --> pdb=" O MET Q 527 " (cutoff:3.500A) Processing helix chain 'Q' and resid 608 through 623 Processing helix chain 'Q' and resid 625 through 628 Processing helix chain 'R' and resid 407 through 422 removed outlier: 3.734A pdb=" N VAL R 421 " --> pdb=" O SER R 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 435 through 450 Processing helix chain 'R' and resid 459 through 473 removed outlier: 3.738A pdb=" N ILE R 463 " --> pdb=" O PRO R 459 " (cutoff:3.500A) Processing helix chain 'R' and resid 475 through 477 No H-bonds generated for 'chain 'R' and resid 475 through 477' Processing helix chain 'R' and resid 519 through 535 removed outlier: 3.741A pdb=" N LYS R 531 " --> pdb=" O MET R 527 " (cutoff:3.500A) Processing helix chain 'R' and resid 608 through 623 Processing helix chain 'R' and resid 625 through 628 Processing helix chain 'S' and resid 407 through 422 removed outlier: 3.735A pdb=" N VAL S 421 " --> pdb=" O SER S 417 " (cutoff:3.500A) Processing helix chain 'S' and resid 435 through 450 Processing helix chain 'S' and resid 459 through 473 removed outlier: 3.738A pdb=" N ILE S 463 " --> pdb=" O PRO S 459 " (cutoff:3.500A) Processing helix chain 'S' and resid 475 through 477 No H-bonds generated for 'chain 'S' and resid 475 through 477' Processing helix chain 'S' and resid 519 through 535 removed outlier: 3.740A pdb=" N LYS S 531 " --> pdb=" O MET S 527 " (cutoff:3.500A) Processing helix chain 'S' and resid 608 through 623 Processing helix chain 'S' and resid 625 through 628 Processing helix chain 'T' and resid 407 through 422 removed outlier: 3.734A pdb=" N VAL T 421 " --> pdb=" O SER T 417 " (cutoff:3.500A) Processing helix chain 'T' and resid 435 through 450 Processing helix chain 'T' and resid 459 through 473 removed outlier: 3.738A pdb=" N ILE T 463 " --> pdb=" O PRO T 459 " (cutoff:3.500A) Processing helix chain 'T' and resid 475 through 477 No H-bonds generated for 'chain 'T' and resid 475 through 477' Processing helix chain 'T' and resid 519 through 535 removed outlier: 3.741A pdb=" N LYS T 531 " --> pdb=" O MET T 527 " (cutoff:3.500A) Processing helix chain 'T' and resid 608 through 623 Processing helix chain 'T' and resid 625 through 628 Processing helix chain 'U' and resid 407 through 422 removed outlier: 3.735A pdb=" N VAL U 421 " --> pdb=" O SER U 417 " (cutoff:3.500A) Processing helix chain 'U' and resid 435 through 450 Processing helix chain 'U' and resid 459 through 473 removed outlier: 3.738A pdb=" N ILE U 463 " --> pdb=" O PRO U 459 " (cutoff:3.500A) Processing helix chain 'U' and resid 475 through 477 No H-bonds generated for 'chain 'U' and resid 475 through 477' Processing helix chain 'U' and resid 519 through 535 removed outlier: 3.740A pdb=" N LYS U 531 " --> pdb=" O MET U 527 " (cutoff:3.500A) Processing helix chain 'U' and resid 608 through 623 Processing helix chain 'U' and resid 625 through 628 Processing helix chain 'V' and resid 407 through 422 removed outlier: 3.734A pdb=" N VAL V 421 " --> pdb=" O SER V 417 " (cutoff:3.500A) Processing helix chain 'V' and resid 435 through 450 Processing helix chain 'V' and resid 459 through 473 removed outlier: 3.738A pdb=" N ILE V 463 " --> pdb=" O PRO V 459 " (cutoff:3.500A) Processing helix chain 'V' and resid 475 through 477 No H-bonds generated for 'chain 'V' and resid 475 through 477' Processing helix chain 'V' and resid 519 through 535 removed outlier: 3.741A pdb=" N LYS V 531 " --> pdb=" O MET V 527 " (cutoff:3.500A) Processing helix chain 'V' and resid 608 through 623 Processing helix chain 'V' and resid 625 through 628 Processing helix chain 'W' and resid 407 through 422 removed outlier: 3.734A pdb=" N VAL W 421 " --> pdb=" O SER W 417 " (cutoff:3.500A) Processing helix chain 'W' and resid 435 through 450 Processing helix chain 'W' and resid 459 through 473 removed outlier: 3.738A pdb=" N ILE W 463 " --> pdb=" O PRO W 459 " (cutoff:3.500A) Processing helix chain 'W' and resid 475 through 477 No H-bonds generated for 'chain 'W' and resid 475 through 477' Processing helix chain 'W' and resid 519 through 535 removed outlier: 3.740A pdb=" N LYS W 531 " --> pdb=" O MET W 527 " (cutoff:3.500A) Processing helix chain 'W' and resid 608 through 623 Processing helix chain 'W' and resid 625 through 628 Processing helix chain 'X' and resid 407 through 422 removed outlier: 3.734A pdb=" N VAL X 421 " --> pdb=" O SER X 417 " (cutoff:3.500A) Processing helix chain 'X' and resid 435 through 450 Processing helix chain 'X' and resid 459 through 473 removed outlier: 3.738A pdb=" N ILE X 463 " --> pdb=" O PRO X 459 " (cutoff:3.500A) Processing helix chain 'X' and resid 475 through 477 No H-bonds generated for 'chain 'X' and resid 475 through 477' Processing helix chain 'X' and resid 519 through 535 removed outlier: 3.741A pdb=" N LYS X 531 " --> pdb=" O MET X 527 " (cutoff:3.500A) Processing helix chain 'X' and resid 608 through 623 Processing helix chain 'X' and resid 625 through 628 Processing sheet with id= A, first strand: chain 'A' and resid 247 through 250 removed outlier: 4.189A pdb=" N ILE A 239 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 223 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU A 242 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL A 221 " --> pdb=" O GLU A 242 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 425 through 433 removed outlier: 4.049A pdb=" N THR A 549 " --> pdb=" O ALA A 571 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY A 497 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N SER A 552 " --> pdb=" O GLY A 497 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA A 499 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 579 through 584 Processing sheet with id= D, first strand: chain 'B' and resid 247 through 250 removed outlier: 4.189A pdb=" N ILE B 239 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU B 223 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU B 242 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL B 221 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 425 through 433 removed outlier: 4.050A pdb=" N THR B 549 " --> pdb=" O ALA B 571 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY B 497 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N SER B 552 " --> pdb=" O GLY B 497 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA B 499 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 579 through 584 Processing sheet with id= G, first strand: chain 'C' and resid 247 through 250 removed outlier: 4.189A pdb=" N ILE C 239 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU C 223 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU C 242 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL C 221 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 425 through 433 removed outlier: 4.049A pdb=" N THR C 549 " --> pdb=" O ALA C 571 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY C 497 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N SER C 552 " --> pdb=" O GLY C 497 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA C 499 " --> pdb=" O SER C 552 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 579 through 584 Processing sheet with id= J, first strand: chain 'D' and resid 247 through 250 removed outlier: 4.188A pdb=" N ILE D 239 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU D 223 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU D 242 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL D 221 " --> pdb=" O GLU D 242 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 425 through 433 removed outlier: 4.048A pdb=" N THR D 549 " --> pdb=" O ALA D 571 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY D 497 " --> pdb=" O ILE D 550 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N SER D 552 " --> pdb=" O GLY D 497 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA D 499 " --> pdb=" O SER D 552 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 579 through 584 Processing sheet with id= M, first strand: chain 'E' and resid 247 through 250 removed outlier: 4.189A pdb=" N ILE E 239 " --> pdb=" O VAL E 250 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU E 223 " --> pdb=" O THR E 240 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU E 242 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL E 221 " --> pdb=" O GLU E 242 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 425 through 433 removed outlier: 4.049A pdb=" N THR E 549 " --> pdb=" O ALA E 571 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY E 497 " --> pdb=" O ILE E 550 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N SER E 552 " --> pdb=" O GLY E 497 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA E 499 " --> pdb=" O SER E 552 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 579 through 584 Processing sheet with id= P, first strand: chain 'F' and resid 247 through 250 removed outlier: 4.189A pdb=" N ILE F 239 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU F 223 " --> pdb=" O THR F 240 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU F 242 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL F 221 " --> pdb=" O GLU F 242 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 425 through 433 removed outlier: 4.049A pdb=" N THR F 549 " --> pdb=" O ALA F 571 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY F 497 " --> pdb=" O ILE F 550 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N SER F 552 " --> pdb=" O GLY F 497 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA F 499 " --> pdb=" O SER F 552 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 579 through 584 Processing sheet with id= S, first strand: chain 'G' and resid 247 through 250 removed outlier: 4.190A pdb=" N ILE G 239 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU G 223 " --> pdb=" O THR G 240 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU G 242 " --> pdb=" O VAL G 221 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL G 221 " --> pdb=" O GLU G 242 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 425 through 433 removed outlier: 4.049A pdb=" N THR G 549 " --> pdb=" O ALA G 571 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY G 497 " --> pdb=" O ILE G 550 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N SER G 552 " --> pdb=" O GLY G 497 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA G 499 " --> pdb=" O SER G 552 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 579 through 584 Processing sheet with id= V, first strand: chain 'H' and resid 247 through 250 removed outlier: 4.190A pdb=" N ILE H 239 " --> pdb=" O VAL H 250 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU H 223 " --> pdb=" O THR H 240 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU H 242 " --> pdb=" O VAL H 221 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL H 221 " --> pdb=" O GLU H 242 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 425 through 433 removed outlier: 4.049A pdb=" N THR H 549 " --> pdb=" O ALA H 571 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY H 497 " --> pdb=" O ILE H 550 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N SER H 552 " --> pdb=" O GLY H 497 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA H 499 " --> pdb=" O SER H 552 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 579 through 584 Processing sheet with id= Y, first strand: chain 'I' and resid 247 through 250 removed outlier: 4.189A pdb=" N ILE I 239 " --> pdb=" O VAL I 250 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU I 223 " --> pdb=" O THR I 240 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU I 242 " --> pdb=" O VAL I 221 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL I 221 " --> pdb=" O GLU I 242 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 425 through 433 removed outlier: 4.049A pdb=" N THR I 549 " --> pdb=" O ALA I 571 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY I 497 " --> pdb=" O ILE I 550 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N SER I 552 " --> pdb=" O GLY I 497 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA I 499 " --> pdb=" O SER I 552 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 579 through 584 Processing sheet with id= AB, first strand: chain 'J' and resid 247 through 250 removed outlier: 4.189A pdb=" N ILE J 239 " --> pdb=" O VAL J 250 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU J 223 " --> pdb=" O THR J 240 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU J 242 " --> pdb=" O VAL J 221 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL J 221 " --> pdb=" O GLU J 242 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 425 through 433 removed outlier: 4.048A pdb=" N THR J 549 " --> pdb=" O ALA J 571 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY J 497 " --> pdb=" O ILE J 550 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N SER J 552 " --> pdb=" O GLY J 497 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA J 499 " --> pdb=" O SER J 552 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 579 through 584 Processing sheet with id= AE, first strand: chain 'K' and resid 247 through 250 removed outlier: 4.188A pdb=" N ILE K 239 " --> pdb=" O VAL K 250 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU K 223 " --> pdb=" O THR K 240 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLU K 242 " --> pdb=" O VAL K 221 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL K 221 " --> pdb=" O GLU K 242 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 425 through 433 removed outlier: 4.049A pdb=" N THR K 549 " --> pdb=" O ALA K 571 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY K 497 " --> pdb=" O ILE K 550 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N SER K 552 " --> pdb=" O GLY K 497 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA K 499 " --> pdb=" O SER K 552 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'K' and resid 579 through 584 Processing sheet with id= AH, first strand: chain 'L' and resid 247 through 250 removed outlier: 4.189A pdb=" N ILE L 239 " --> pdb=" O VAL L 250 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU L 223 " --> pdb=" O THR L 240 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU L 242 " --> pdb=" O VAL L 221 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL L 221 " --> pdb=" O GLU L 242 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 425 through 433 removed outlier: 4.048A pdb=" N THR L 549 " --> pdb=" O ALA L 571 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY L 497 " --> pdb=" O ILE L 550 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N SER L 552 " --> pdb=" O GLY L 497 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA L 499 " --> pdb=" O SER L 552 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 579 through 584 Processing sheet with id= AK, first strand: chain 'M' and resid 247 through 250 removed outlier: 4.190A pdb=" N ILE M 239 " --> pdb=" O VAL M 250 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU M 223 " --> pdb=" O THR M 240 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU M 242 " --> pdb=" O VAL M 221 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL M 221 " --> pdb=" O GLU M 242 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'M' and resid 425 through 433 removed outlier: 4.049A pdb=" N THR M 549 " --> pdb=" O ALA M 571 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY M 497 " --> pdb=" O ILE M 550 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N SER M 552 " --> pdb=" O GLY M 497 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA M 499 " --> pdb=" O SER M 552 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'M' and resid 579 through 584 Processing sheet with id= AN, first strand: chain 'N' and resid 247 through 250 removed outlier: 4.189A pdb=" N ILE N 239 " --> pdb=" O VAL N 250 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU N 223 " --> pdb=" O THR N 240 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU N 242 " --> pdb=" O VAL N 221 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL N 221 " --> pdb=" O GLU N 242 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'N' and resid 425 through 433 removed outlier: 4.049A pdb=" N THR N 549 " --> pdb=" O ALA N 571 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY N 497 " --> pdb=" O ILE N 550 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N SER N 552 " --> pdb=" O GLY N 497 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA N 499 " --> pdb=" O SER N 552 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'N' and resid 579 through 584 Processing sheet with id= AQ, first strand: chain 'O' and resid 247 through 250 removed outlier: 4.189A pdb=" N ILE O 239 " --> pdb=" O VAL O 250 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU O 223 " --> pdb=" O THR O 240 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU O 242 " --> pdb=" O VAL O 221 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL O 221 " --> pdb=" O GLU O 242 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'O' and resid 425 through 433 removed outlier: 4.048A pdb=" N THR O 549 " --> pdb=" O ALA O 571 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY O 497 " --> pdb=" O ILE O 550 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N SER O 552 " --> pdb=" O GLY O 497 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA O 499 " --> pdb=" O SER O 552 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'O' and resid 579 through 584 Processing sheet with id= AT, first strand: chain 'P' and resid 247 through 250 removed outlier: 4.189A pdb=" N ILE P 239 " --> pdb=" O VAL P 250 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU P 223 " --> pdb=" O THR P 240 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU P 242 " --> pdb=" O VAL P 221 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL P 221 " --> pdb=" O GLU P 242 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'P' and resid 425 through 433 removed outlier: 4.048A pdb=" N THR P 549 " --> pdb=" O ALA P 571 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY P 497 " --> pdb=" O ILE P 550 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N SER P 552 " --> pdb=" O GLY P 497 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA P 499 " --> pdb=" O SER P 552 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'P' and resid 579 through 584 Processing sheet with id= AW, first strand: chain 'Q' and resid 247 through 250 removed outlier: 4.189A pdb=" N ILE Q 239 " --> pdb=" O VAL Q 250 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU Q 223 " --> pdb=" O THR Q 240 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU Q 242 " --> pdb=" O VAL Q 221 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL Q 221 " --> pdb=" O GLU Q 242 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'Q' and resid 425 through 433 removed outlier: 4.049A pdb=" N THR Q 549 " --> pdb=" O ALA Q 571 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY Q 497 " --> pdb=" O ILE Q 550 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N SER Q 552 " --> pdb=" O GLY Q 497 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA Q 499 " --> pdb=" O SER Q 552 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'Q' and resid 579 through 584 Processing sheet with id= AZ, first strand: chain 'R' and resid 247 through 250 removed outlier: 4.190A pdb=" N ILE R 239 " --> pdb=" O VAL R 250 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU R 223 " --> pdb=" O THR R 240 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU R 242 " --> pdb=" O VAL R 221 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL R 221 " --> pdb=" O GLU R 242 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'R' and resid 425 through 433 removed outlier: 4.049A pdb=" N THR R 549 " --> pdb=" O ALA R 571 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY R 497 " --> pdb=" O ILE R 550 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N SER R 552 " --> pdb=" O GLY R 497 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA R 499 " --> pdb=" O SER R 552 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'R' and resid 579 through 584 Processing sheet with id= BC, first strand: chain 'S' and resid 247 through 250 removed outlier: 4.189A pdb=" N ILE S 239 " --> pdb=" O VAL S 250 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU S 223 " --> pdb=" O THR S 240 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU S 242 " --> pdb=" O VAL S 221 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL S 221 " --> pdb=" O GLU S 242 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'S' and resid 425 through 433 removed outlier: 4.049A pdb=" N THR S 549 " --> pdb=" O ALA S 571 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY S 497 " --> pdb=" O ILE S 550 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N SER S 552 " --> pdb=" O GLY S 497 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA S 499 " --> pdb=" O SER S 552 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'S' and resid 579 through 584 Processing sheet with id= BF, first strand: chain 'T' and resid 247 through 250 removed outlier: 4.189A pdb=" N ILE T 239 " --> pdb=" O VAL T 250 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU T 223 " --> pdb=" O THR T 240 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU T 242 " --> pdb=" O VAL T 221 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL T 221 " --> pdb=" O GLU T 242 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'T' and resid 425 through 433 removed outlier: 4.049A pdb=" N THR T 549 " --> pdb=" O ALA T 571 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY T 497 " --> pdb=" O ILE T 550 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N SER T 552 " --> pdb=" O GLY T 497 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA T 499 " --> pdb=" O SER T 552 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'T' and resid 579 through 584 Processing sheet with id= BI, first strand: chain 'U' and resid 247 through 250 removed outlier: 4.189A pdb=" N ILE U 239 " --> pdb=" O VAL U 250 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU U 223 " --> pdb=" O THR U 240 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU U 242 " --> pdb=" O VAL U 221 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL U 221 " --> pdb=" O GLU U 242 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'U' and resid 425 through 433 removed outlier: 4.049A pdb=" N THR U 549 " --> pdb=" O ALA U 571 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY U 497 " --> pdb=" O ILE U 550 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N SER U 552 " --> pdb=" O GLY U 497 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA U 499 " --> pdb=" O SER U 552 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'U' and resid 579 through 584 Processing sheet with id= BL, first strand: chain 'V' and resid 247 through 250 removed outlier: 4.189A pdb=" N ILE V 239 " --> pdb=" O VAL V 250 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU V 223 " --> pdb=" O THR V 240 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU V 242 " --> pdb=" O VAL V 221 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL V 221 " --> pdb=" O GLU V 242 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'V' and resid 425 through 433 removed outlier: 4.049A pdb=" N THR V 549 " --> pdb=" O ALA V 571 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY V 497 " --> pdb=" O ILE V 550 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N SER V 552 " --> pdb=" O GLY V 497 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA V 499 " --> pdb=" O SER V 552 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'V' and resid 579 through 584 Processing sheet with id= BO, first strand: chain 'W' and resid 247 through 250 removed outlier: 4.189A pdb=" N ILE W 239 " --> pdb=" O VAL W 250 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU W 223 " --> pdb=" O THR W 240 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU W 242 " --> pdb=" O VAL W 221 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL W 221 " --> pdb=" O GLU W 242 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'W' and resid 425 through 433 removed outlier: 4.049A pdb=" N THR W 549 " --> pdb=" O ALA W 571 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLY W 497 " --> pdb=" O ILE W 550 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N SER W 552 " --> pdb=" O GLY W 497 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA W 499 " --> pdb=" O SER W 552 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'W' and resid 579 through 584 Processing sheet with id= BR, first strand: chain 'X' and resid 247 through 250 removed outlier: 4.188A pdb=" N ILE X 239 " --> pdb=" O VAL X 250 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU X 223 " --> pdb=" O THR X 240 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU X 242 " --> pdb=" O VAL X 221 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL X 221 " --> pdb=" O GLU X 242 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'X' and resid 425 through 433 removed outlier: 4.048A pdb=" N THR X 549 " --> pdb=" O ALA X 571 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY X 497 " --> pdb=" O ILE X 550 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N SER X 552 " --> pdb=" O GLY X 497 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA X 499 " --> pdb=" O SER X 552 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'X' and resid 579 through 584 2160 hydrogen bonds defined for protein. 6192 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: 18.14 Time building geometry restraints manager: 18.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 19437 1.34 - 1.46: 10955 1.46 - 1.58: 29032 1.58 - 1.70: 0 1.70 - 1.82: 648 Bond restraints: 60072 Sorted by residual: bond pdb=" N GLN M 544 " pdb=" CA GLN M 544 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.27e-02 6.20e+03 7.35e+00 bond pdb=" N GLN U 544 " pdb=" CA GLN U 544 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.27e-02 6.20e+03 7.34e+00 bond pdb=" N GLN J 544 " pdb=" CA GLN J 544 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.27e-02 6.20e+03 7.28e+00 bond pdb=" N GLN G 544 " pdb=" CA GLN G 544 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.27e-02 6.20e+03 7.23e+00 bond pdb=" N GLN V 544 " pdb=" CA GLN V 544 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.27e-02 6.20e+03 7.21e+00 ... (remaining 60067 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.68: 2016 106.68 - 113.53: 34454 113.53 - 120.38: 21498 120.38 - 127.23: 22552 127.23 - 134.08: 552 Bond angle restraints: 81072 Sorted by residual: angle pdb=" N ASP X 213 " pdb=" CA ASP X 213 " pdb=" C ASP X 213 " ideal model delta sigma weight residual 107.20 114.18 -6.98 1.70e+00 3.46e-01 1.69e+01 angle pdb=" N ASP D 213 " pdb=" CA ASP D 213 " pdb=" C ASP D 213 " ideal model delta sigma weight residual 107.20 114.15 -6.95 1.70e+00 3.46e-01 1.67e+01 angle pdb=" N ASP U 213 " pdb=" CA ASP U 213 " pdb=" C ASP U 213 " ideal model delta sigma weight residual 107.20 114.15 -6.95 1.70e+00 3.46e-01 1.67e+01 angle pdb=" N ASP W 213 " pdb=" CA ASP W 213 " pdb=" C ASP W 213 " ideal model delta sigma weight residual 107.20 114.14 -6.94 1.70e+00 3.46e-01 1.67e+01 angle pdb=" N ASP P 213 " pdb=" CA ASP P 213 " pdb=" C ASP P 213 " ideal model delta sigma weight residual 107.20 114.14 -6.94 1.70e+00 3.46e-01 1.67e+01 ... (remaining 81067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.53: 35400 26.53 - 53.05: 1296 53.05 - 79.58: 72 79.58 - 106.11: 48 106.11 - 132.64: 48 Dihedral angle restraints: 36864 sinusoidal: 15096 harmonic: 21768 Sorted by residual: dihedral pdb=" CA GLU J 260 " pdb=" C GLU J 260 " pdb=" N LEU J 261 " pdb=" CA LEU J 261 " ideal model delta harmonic sigma weight residual 180.00 152.83 27.17 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA GLU P 260 " pdb=" C GLU P 260 " pdb=" N LEU P 261 " pdb=" CA LEU P 261 " ideal model delta harmonic sigma weight residual 180.00 152.84 27.16 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA GLU E 260 " pdb=" C GLU E 260 " pdb=" N LEU E 261 " pdb=" CA LEU E 261 " ideal model delta harmonic sigma weight residual 180.00 152.84 27.16 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 36861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 6753 0.045 - 0.090: 1884 0.090 - 0.134: 867 0.134 - 0.179: 0 0.179 - 0.224: 24 Chirality restraints: 9528 Sorted by residual: chirality pdb=" C6 LA2 W 245 " pdb=" C5 LA2 W 245 " pdb=" C7 LA2 W 245 " pdb=" S6 LA2 W 245 " both_signs ideal model delta sigma weight residual False 2.99 2.77 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C6 LA2 V 245 " pdb=" C5 LA2 V 245 " pdb=" C7 LA2 V 245 " pdb=" S6 LA2 V 245 " both_signs ideal model delta sigma weight residual False 2.99 2.77 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C6 LA2 T 245 " pdb=" C5 LA2 T 245 " pdb=" C7 LA2 T 245 " pdb=" S6 LA2 T 245 " both_signs ideal model delta sigma weight residual False 2.99 2.77 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 9525 not shown) Planarity restraints: 10368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LA2 C 245 " 0.155 2.00e-02 2.50e+03 1.33e-01 2.19e+02 pdb=" NZ LA2 C 245 " -0.215 2.00e-02 2.50e+03 pdb=" C1 LA2 C 245 " -0.033 2.00e-02 2.50e+03 pdb=" C2 LA2 C 245 " -0.030 2.00e-02 2.50e+03 pdb=" O1 LA2 C 245 " 0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LA2 V 245 " -0.155 2.00e-02 2.50e+03 1.32e-01 2.19e+02 pdb=" NZ LA2 V 245 " 0.215 2.00e-02 2.50e+03 pdb=" C1 LA2 V 245 " 0.033 2.00e-02 2.50e+03 pdb=" C2 LA2 V 245 " 0.030 2.00e-02 2.50e+03 pdb=" O1 LA2 V 245 " -0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LA2 O 245 " -0.155 2.00e-02 2.50e+03 1.32e-01 2.19e+02 pdb=" NZ LA2 O 245 " 0.215 2.00e-02 2.50e+03 pdb=" C1 LA2 O 245 " 0.034 2.00e-02 2.50e+03 pdb=" C2 LA2 O 245 " 0.030 2.00e-02 2.50e+03 pdb=" O1 LA2 O 245 " -0.124 2.00e-02 2.50e+03 ... (remaining 10365 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 2471 2.71 - 3.26: 59548 3.26 - 3.81: 97262 3.81 - 4.35: 125638 4.35 - 4.90: 212980 Nonbonded interactions: 497899 Sorted by model distance: nonbonded pdb=" N GLU N 399 " pdb=" OE1 GLU N 399 " model vdw 2.168 2.520 nonbonded pdb=" N GLU T 399 " pdb=" OE1 GLU T 399 " model vdw 2.168 2.520 nonbonded pdb=" N GLU X 399 " pdb=" OE1 GLU X 399 " model vdw 2.168 2.520 nonbonded pdb=" N GLU J 399 " pdb=" OE1 GLU J 399 " model vdw 2.168 2.520 nonbonded pdb=" N GLU Q 399 " pdb=" OE1 GLU Q 399 " model vdw 2.168 2.520 ... (remaining 497894 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 7.980 Check model and map are aligned: 0.680 Set scattering table: 0.400 Process input model: 115.270 Find NCS groups from input model: 3.060 Set up NCS constraints: 0.490 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 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 : 0.005 0.035 60072 Z= 0.318 Angle : 0.660 6.983 81072 Z= 0.399 Chirality : 0.048 0.224 9528 Planarity : 0.008 0.133 10368 Dihedral : 14.960 132.635 22752 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.11 % Allowed : 7.00 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -3.10 (0.08), residues: 7512 helix: -0.64 (0.10), residues: 2136 sheet: -1.32 (0.13), residues: 1128 loop : -3.19 (0.08), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 584 HIS 0.002 0.001 HIS U 425 PHE 0.013 0.002 PHE X 561 TYR 0.005 0.002 TYR B 493 ARG 0.002 0.000 ARG K 476 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15024 Ramachandran restraints generated. 7512 Oldfield, 0 Emsley, 7512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15024 Ramachandran restraints generated. 7512 Oldfield, 0 Emsley, 7512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 803 time to evaluate : 4.996 Fit side-chains REVERT: A 248 MET cc_start: 0.7003 (mtm) cc_final: 0.6722 (mtm) REVERT: A 276 MET cc_start: 0.6602 (mmt) cc_final: 0.6270 (mmt) REVERT: A 408 ILE cc_start: 0.8602 (pt) cc_final: 0.8276 (mt) REVERT: A 432 THR cc_start: 0.8966 (m) cc_final: 0.8689 (p) REVERT: A 464 MET cc_start: 0.8570 (mtp) cc_final: 0.8317 (mtm) REVERT: A 580 MET cc_start: 0.8709 (tpp) cc_final: 0.8140 (mmt) REVERT: B 580 MET cc_start: 0.8813 (tpp) cc_final: 0.8227 (mmt) REVERT: C 248 MET cc_start: 0.7172 (mtm) cc_final: 0.6822 (mtm) REVERT: C 276 MET cc_start: 0.6453 (mmt) cc_final: 0.6104 (mmt) REVERT: C 408 ILE cc_start: 0.8678 (pt) cc_final: 0.8377 (mt) REVERT: C 432 THR cc_start: 0.8956 (m) cc_final: 0.8739 (p) REVERT: C 451 ARG cc_start: 0.8474 (mtp180) cc_final: 0.8230 (mtp85) REVERT: C 464 MET cc_start: 0.8680 (mtp) cc_final: 0.8429 (mtm) REVERT: C 580 MET cc_start: 0.8709 (tpp) cc_final: 0.8369 (mmt) REVERT: D 276 MET cc_start: 0.6637 (mmt) cc_final: 0.6425 (mmt) REVERT: D 408 ILE cc_start: 0.8585 (pt) cc_final: 0.8364 (mt) REVERT: D 432 THR cc_start: 0.8945 (m) cc_final: 0.8739 (p) REVERT: D 464 MET cc_start: 0.8641 (mtp) cc_final: 0.8360 (mtm) REVERT: D 580 MET cc_start: 0.8695 (tpp) cc_final: 0.8354 (mmt) REVERT: D 630 MET cc_start: 0.8146 (mmm) cc_final: 0.7884 (mmm) REVERT: E 408 ILE cc_start: 0.8321 (pt) cc_final: 0.7923 (mt) REVERT: E 464 MET cc_start: 0.8659 (mtp) cc_final: 0.8231 (mtp) REVERT: E 474 MET cc_start: 0.9135 (mtp) cc_final: 0.8839 (mtp) REVERT: E 580 MET cc_start: 0.8653 (tpp) cc_final: 0.8435 (tpp) REVERT: E 630 MET cc_start: 0.8129 (mmm) cc_final: 0.7874 (mmm) REVERT: F 276 MET cc_start: 0.6552 (mmt) cc_final: 0.6235 (mmt) REVERT: F 408 ILE cc_start: 0.8610 (pt) cc_final: 0.8333 (mt) REVERT: F 580 MET cc_start: 0.8792 (tpp) cc_final: 0.8171 (mmt) REVERT: G 248 MET cc_start: 0.6924 (mtm) cc_final: 0.6705 (mtm) REVERT: G 276 MET cc_start: 0.6269 (mmt) cc_final: 0.6033 (mmt) REVERT: G 408 ILE cc_start: 0.8602 (pt) cc_final: 0.8229 (mt) REVERT: G 432 THR cc_start: 0.8951 (m) cc_final: 0.8621 (p) REVERT: G 451 ARG cc_start: 0.8372 (mtp180) cc_final: 0.8061 (mtp180) REVERT: H 225 MET cc_start: 0.6513 (mmp) cc_final: 0.6258 (mmp) REVERT: I 248 MET cc_start: 0.7151 (mtm) cc_final: 0.6898 (mtm) REVERT: I 276 MET cc_start: 0.6358 (mmt) cc_final: 0.6003 (mmt) REVERT: I 408 ILE cc_start: 0.8697 (pt) cc_final: 0.8406 (mt) REVERT: I 432 THR cc_start: 0.8978 (m) cc_final: 0.8731 (p) REVERT: I 451 ARG cc_start: 0.8509 (mtp180) cc_final: 0.8248 (mtp85) REVERT: I 464 MET cc_start: 0.8675 (mtp) cc_final: 0.8418 (mtm) REVERT: I 580 MET cc_start: 0.8731 (tpp) cc_final: 0.8493 (tpp) REVERT: I 630 MET cc_start: 0.8179 (mmm) cc_final: 0.7914 (mmm) REVERT: J 248 MET cc_start: 0.7179 (mtm) cc_final: 0.6881 (mtm) REVERT: J 276 MET cc_start: 0.6476 (mmt) cc_final: 0.6119 (mmt) REVERT: J 408 ILE cc_start: 0.8687 (pt) cc_final: 0.8381 (mt) REVERT: J 432 THR cc_start: 0.8941 (m) cc_final: 0.8638 (p) REVERT: J 464 MET cc_start: 0.8641 (mtp) cc_final: 0.8386 (mtm) REVERT: J 580 MET cc_start: 0.8739 (tpp) cc_final: 0.8116 (mmt) REVERT: K 580 MET cc_start: 0.8782 (tpp) cc_final: 0.8114 (mmt) REVERT: L 248 MET cc_start: 0.6972 (mtm) cc_final: 0.6761 (mtm) REVERT: L 276 MET cc_start: 0.6662 (mmt) cc_final: 0.6340 (mmt) REVERT: L 408 ILE cc_start: 0.8616 (pt) cc_final: 0.8329 (mt) REVERT: L 432 THR cc_start: 0.8963 (m) cc_final: 0.8623 (p) REVERT: L 464 MET cc_start: 0.8597 (mtp) cc_final: 0.8333 (mtm) REVERT: L 580 MET cc_start: 0.8763 (tpp) cc_final: 0.8140 (mmt) REVERT: M 248 MET cc_start: 0.6884 (mtm) cc_final: 0.6674 (mtm) REVERT: M 408 ILE cc_start: 0.8492 (pt) cc_final: 0.8034 (mt) REVERT: M 432 THR cc_start: 0.8952 (m) cc_final: 0.8621 (p) REVERT: M 451 ARG cc_start: 0.8358 (mtp180) cc_final: 0.8034 (mtp85) REVERT: M 626 ARG cc_start: 0.8233 (mtt90) cc_final: 0.7457 (mtt90) REVERT: N 225 MET cc_start: 0.6582 (mmp) cc_final: 0.6292 (mmp) REVERT: N 432 THR cc_start: 0.8931 (m) cc_final: 0.8648 (p) REVERT: N 451 ARG cc_start: 0.8447 (mtp180) cc_final: 0.8196 (mtp180) REVERT: N 464 MET cc_start: 0.8641 (mtp) cc_final: 0.8411 (mtm) REVERT: N 580 MET cc_start: 0.8709 (tpp) cc_final: 0.8485 (tpp) REVERT: O 248 MET cc_start: 0.7185 (mtm) cc_final: 0.6788 (mtm) REVERT: O 408 ILE cc_start: 0.8809 (pt) cc_final: 0.8292 (mm) REVERT: O 451 ARG cc_start: 0.8379 (mtp180) cc_final: 0.8167 (ttm170) REVERT: O 580 MET cc_start: 0.8682 (tpp) cc_final: 0.8381 (mmt) REVERT: O 626 ARG cc_start: 0.8109 (mtt90) cc_final: 0.7624 (mtt90) REVERT: P 276 MET cc_start: 0.6301 (mmt) cc_final: 0.6031 (mmt) REVERT: P 432 THR cc_start: 0.8962 (m) cc_final: 0.8670 (p) REVERT: Q 276 MET cc_start: 0.6540 (mmt) cc_final: 0.6293 (mmt) REVERT: Q 408 ILE cc_start: 0.8695 (pt) cc_final: 0.8446 (mt) REVERT: Q 432 THR cc_start: 0.8951 (m) cc_final: 0.8686 (p) REVERT: Q 451 ARG cc_start: 0.8403 (mtp180) cc_final: 0.8112 (mtp85) REVERT: Q 464 MET cc_start: 0.8730 (mtp) cc_final: 0.8403 (mtm) REVERT: Q 580 MET cc_start: 0.8758 (tpp) cc_final: 0.8530 (tpp) REVERT: R 248 MET cc_start: 0.7233 (mtm) cc_final: 0.6875 (mtm) REVERT: R 276 MET cc_start: 0.6459 (mmt) cc_final: 0.6120 (mmt) REVERT: R 408 ILE cc_start: 0.8675 (pt) cc_final: 0.8307 (mt) REVERT: R 432 THR cc_start: 0.8927 (m) cc_final: 0.8688 (p) REVERT: R 451 ARG cc_start: 0.8474 (mtp180) cc_final: 0.8220 (mtp85) REVERT: R 580 MET cc_start: 0.8715 (tpp) cc_final: 0.8109 (mmt) REVERT: S 248 MET cc_start: 0.7195 (mtm) cc_final: 0.6878 (mtm) REVERT: S 276 MET cc_start: 0.6714 (mmt) cc_final: 0.6407 (mmt) REVERT: S 408 ILE cc_start: 0.8605 (pt) cc_final: 0.8233 (mt) REVERT: S 432 THR cc_start: 0.8971 (m) cc_final: 0.8707 (p) REVERT: S 464 MET cc_start: 0.8604 (mtp) cc_final: 0.8332 (mtm) REVERT: S 626 ARG cc_start: 0.8202 (mtt90) cc_final: 0.7477 (mtt90) REVERT: T 432 THR cc_start: 0.8950 (m) cc_final: 0.8723 (p) REVERT: T 543 MET cc_start: 0.8687 (ptp) cc_final: 0.8474 (ptp) REVERT: T 580 MET cc_start: 0.8649 (tpp) cc_final: 0.8335 (mmt) REVERT: U 248 MET cc_start: 0.7106 (mtm) cc_final: 0.6700 (mtm) REVERT: U 276 MET cc_start: 0.6441 (mmt) cc_final: 0.6100 (mmt) REVERT: U 408 ILE cc_start: 0.8699 (pt) cc_final: 0.8377 (mt) REVERT: U 432 THR cc_start: 0.8963 (m) cc_final: 0.8664 (p) REVERT: U 451 ARG cc_start: 0.8492 (mtp180) cc_final: 0.8280 (ttm170) REVERT: U 580 MET cc_start: 0.8758 (tpp) cc_final: 0.8151 (mmt) REVERT: U 626 ARG cc_start: 0.8138 (mtt90) cc_final: 0.7581 (mtt90) REVERT: V 248 MET cc_start: 0.7226 (mtm) cc_final: 0.6895 (mtm) REVERT: V 276 MET cc_start: 0.6389 (mmt) cc_final: 0.6050 (mmt) REVERT: V 408 ILE cc_start: 0.8661 (pt) cc_final: 0.8245 (mt) REVERT: V 451 ARG cc_start: 0.8493 (mtp180) cc_final: 0.8244 (mtp85) REVERT: V 580 MET cc_start: 0.8700 (tpp) cc_final: 0.8459 (tpp) REVERT: W 276 MET cc_start: 0.6477 (mmt) cc_final: 0.6147 (mmt) REVERT: X 248 MET cc_start: 0.7189 (mtm) cc_final: 0.6932 (mtm) REVERT: X 276 MET cc_start: 0.6493 (mmt) cc_final: 0.6139 (mmt) REVERT: X 408 ILE cc_start: 0.8606 (pt) cc_final: 0.8247 (mt) REVERT: X 432 THR cc_start: 0.8952 (m) cc_final: 0.8681 (p) REVERT: X 464 MET cc_start: 0.8650 (mtp) cc_final: 0.8450 (mtm) REVERT: X 580 MET cc_start: 0.8745 (tpp) cc_final: 0.8134 (mmt) outliers start: 72 outliers final: 9 residues processed: 863 average time/residue: 0.5608 time to fit residues: 809.6753 Evaluate side-chains 584 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 575 time to evaluate : 4.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain M residue 213 ASP Chi-restraints excluded: chain O residue 399 GLU Chi-restraints excluded: chain P residue 213 ASP Chi-restraints excluded: chain P residue 399 GLU Chi-restraints excluded: chain R residue 213 ASP Chi-restraints excluded: chain S residue 213 ASP Chi-restraints excluded: chain V residue 213 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 648 optimal weight: 0.0370 chunk 582 optimal weight: 30.0000 chunk 322 optimal weight: 20.0000 chunk 198 optimal weight: 30.0000 chunk 392 optimal weight: 10.0000 chunk 310 optimal weight: 9.9990 chunk 601 optimal weight: 5.9990 chunk 232 optimal weight: 8.9990 chunk 366 optimal weight: 3.9990 chunk 448 optimal weight: 10.0000 chunk 697 optimal weight: 3.9990 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 544 GLN B 236 GLN B 544 GLN C 236 GLN C 544 GLN D 236 GLN E 236 GLN E 566 ASN F 236 GLN G 236 GLN G 544 GLN H 236 GLN H 544 GLN I 236 GLN I 544 GLN J 236 GLN J 544 GLN K 236 GLN K 544 GLN L 236 GLN L 544 GLN M 236 GLN M 486 GLN M 544 GLN N 236 GLN O 236 GLN P 236 GLN P 544 GLN Q 236 GLN Q 544 GLN R 236 GLN R 544 GLN S 236 GLN S 544 GLN T 236 GLN U 236 GLN V 236 GLN V 544 GLN W 236 GLN W 544 GLN X 236 GLN X 544 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 60072 Z= 0.488 Angle : 0.595 5.994 81072 Z= 0.315 Chirality : 0.047 0.142 9528 Planarity : 0.005 0.040 10368 Dihedral : 10.566 116.364 8228 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 1.03 % Allowed : 11.67 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -2.18 (0.09), residues: 7512 helix: 0.51 (0.11), residues: 2136 sheet: -1.01 (0.14), residues: 1128 loop : -2.77 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 584 HIS 0.005 0.002 HIS Q 603 PHE 0.018 0.002 PHE S 561 TYR 0.010 0.003 TYR E 493 ARG 0.004 0.000 ARG P 476 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15024 Ramachandran restraints generated. 7512 Oldfield, 0 Emsley, 7512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15024 Ramachandran restraints generated. 7512 Oldfield, 0 Emsley, 7512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 563 time to evaluate : 5.046 Fit side-chains REVERT: A 248 MET cc_start: 0.7345 (mtm) cc_final: 0.7067 (mtm) REVERT: A 408 ILE cc_start: 0.8529 (pt) cc_final: 0.8329 (mt) REVERT: A 580 MET cc_start: 0.8683 (tpp) cc_final: 0.8458 (tpp) REVERT: B 248 MET cc_start: 0.6667 (mtm) cc_final: 0.6460 (mtm) REVERT: B 580 MET cc_start: 0.8695 (tpp) cc_final: 0.8478 (tpp) REVERT: C 248 MET cc_start: 0.7284 (mtm) cc_final: 0.7008 (mtm) REVERT: C 580 MET cc_start: 0.8675 (tpp) cc_final: 0.8439 (tpp) REVERT: D 225 MET cc_start: 0.6313 (mmp) cc_final: 0.5747 (mmp) REVERT: D 422 MET cc_start: 0.8308 (mtt) cc_final: 0.8049 (mtt) REVERT: D 580 MET cc_start: 0.8667 (tpp) cc_final: 0.8423 (tpp) REVERT: D 630 MET cc_start: 0.8218 (mmm) cc_final: 0.7959 (mmm) REVERT: E 276 MET cc_start: 0.5895 (mmt) cc_final: 0.5691 (mmt) REVERT: E 408 ILE cc_start: 0.8435 (pt) cc_final: 0.8225 (mt) REVERT: E 630 MET cc_start: 0.8264 (mmm) cc_final: 0.8021 (mmm) REVERT: F 580 MET cc_start: 0.8698 (tpp) cc_final: 0.8483 (tpp) REVERT: G 248 MET cc_start: 0.7377 (mtm) cc_final: 0.7161 (mtm) REVERT: G 276 MET cc_start: 0.6364 (mmt) cc_final: 0.6110 (mmt) REVERT: G 408 ILE cc_start: 0.8555 (pt) cc_final: 0.8353 (mt) REVERT: G 451 ARG cc_start: 0.8458 (mtp180) cc_final: 0.8157 (ttm-80) REVERT: H 225 MET cc_start: 0.6671 (mmp) cc_final: 0.6393 (mmp) REVERT: I 248 MET cc_start: 0.7233 (mtm) cc_final: 0.6956 (mtm) REVERT: I 580 MET cc_start: 0.8688 (tpp) cc_final: 0.8460 (tpp) REVERT: J 248 MET cc_start: 0.7256 (mtm) cc_final: 0.6999 (mtm) REVERT: J 580 MET cc_start: 0.8681 (tpp) cc_final: 0.8455 (tpp) REVERT: K 580 MET cc_start: 0.8691 (tpp) cc_final: 0.8477 (tpp) REVERT: L 248 MET cc_start: 0.7389 (mtm) cc_final: 0.7143 (mtm) REVERT: L 580 MET cc_start: 0.8697 (tpp) cc_final: 0.8482 (tpp) REVERT: M 248 MET cc_start: 0.7371 (mtm) cc_final: 0.7143 (mtt) REVERT: M 408 ILE cc_start: 0.8569 (pt) cc_final: 0.8307 (mt) REVERT: M 422 MET cc_start: 0.8444 (mtt) cc_final: 0.8161 (mtt) REVERT: M 451 ARG cc_start: 0.8419 (mtp180) cc_final: 0.8087 (ttm-80) REVERT: N 225 MET cc_start: 0.6494 (mmp) cc_final: 0.6252 (mmp) REVERT: N 580 MET cc_start: 0.8682 (tpp) cc_final: 0.8458 (tpp) REVERT: O 248 MET cc_start: 0.7285 (mtm) cc_final: 0.6958 (mtt) REVERT: O 580 MET cc_start: 0.8648 (tpp) cc_final: 0.8412 (tpp) REVERT: P 225 MET cc_start: 0.6906 (mmt) cc_final: 0.6614 (mmt) REVERT: P 408 ILE cc_start: 0.8607 (pt) cc_final: 0.8361 (mt) REVERT: P 451 ARG cc_start: 0.8478 (mtp-110) cc_final: 0.8142 (mtm180) REVERT: Q 451 ARG cc_start: 0.8445 (mtp180) cc_final: 0.8138 (ttm-80) REVERT: Q 580 MET cc_start: 0.8707 (tpp) cc_final: 0.8486 (tpp) REVERT: R 248 MET cc_start: 0.7342 (mtm) cc_final: 0.7071 (mtm) REVERT: R 276 MET cc_start: 0.6424 (mmt) cc_final: 0.6089 (mmt) REVERT: R 408 ILE cc_start: 0.8576 (pt) cc_final: 0.8371 (mt) REVERT: R 580 MET cc_start: 0.8684 (tpp) cc_final: 0.8455 (tpp) REVERT: S 248 MET cc_start: 0.7391 (mtm) cc_final: 0.7150 (mtm) REVERT: S 276 MET cc_start: 0.6552 (mmt) cc_final: 0.6237 (mmt) REVERT: T 580 MET cc_start: 0.8651 (tpp) cc_final: 0.8402 (tpp) REVERT: U 248 MET cc_start: 0.7167 (mtm) cc_final: 0.6882 (mtm) REVERT: U 580 MET cc_start: 0.8672 (tpp) cc_final: 0.8445 (tpp) REVERT: V 248 MET cc_start: 0.7335 (mtm) cc_final: 0.7087 (mtm) REVERT: V 408 ILE cc_start: 0.8584 (pt) cc_final: 0.8357 (mt) REVERT: V 580 MET cc_start: 0.8675 (tpp) cc_final: 0.8441 (tpp) REVERT: X 248 MET cc_start: 0.7151 (mtm) cc_final: 0.6816 (mtm) REVERT: X 580 MET cc_start: 0.8681 (tpp) cc_final: 0.8456 (tpp) outliers start: 67 outliers final: 42 residues processed: 615 average time/residue: 0.5573 time to fit residues: 578.6001 Evaluate side-chains 576 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 534 time to evaluate : 5.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 539 THR Chi-restraints excluded: chain I residue 244 ASP Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 453 LEU Chi-restraints excluded: chain I residue 519 ILE Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain J residue 519 ILE Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain N residue 392 VAL Chi-restraints excluded: chain N residue 539 THR Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 403 VAL Chi-restraints excluded: chain O residue 519 ILE Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 519 ILE Chi-restraints excluded: chain R residue 244 ASP Chi-restraints excluded: chain R residue 403 VAL Chi-restraints excluded: chain R residue 519 ILE Chi-restraints excluded: chain S residue 244 ASP Chi-restraints excluded: chain S residue 519 ILE Chi-restraints excluded: chain T residue 244 ASP Chi-restraints excluded: chain T residue 392 VAL Chi-restraints excluded: chain U residue 244 ASP Chi-restraints excluded: chain U residue 403 VAL Chi-restraints excluded: chain U residue 519 ILE Chi-restraints excluded: chain V residue 244 ASP Chi-restraints excluded: chain V residue 403 VAL Chi-restraints excluded: chain V residue 453 LEU Chi-restraints excluded: chain V residue 519 ILE Chi-restraints excluded: chain W residue 244 ASP Chi-restraints excluded: chain X residue 244 ASP Chi-restraints excluded: chain X residue 519 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 387 optimal weight: 10.0000 chunk 216 optimal weight: 1.9990 chunk 580 optimal weight: 2.9990 chunk 474 optimal weight: 0.8980 chunk 192 optimal weight: 40.0000 chunk 698 optimal weight: 0.7980 chunk 754 optimal weight: 4.9990 chunk 622 optimal weight: 2.9990 chunk 692 optimal weight: 7.9990 chunk 238 optimal weight: 2.9990 chunk 560 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN C 236 GLN D 236 GLN E 236 GLN E 544 GLN F 236 GLN G 236 GLN H 236 GLN I 236 GLN J 236 GLN K 236 GLN L 236 GLN M 236 GLN M 486 GLN N 236 GLN O 236 GLN P 236 GLN Q 236 GLN Q 544 GLN R 236 GLN S 236 GLN U 236 GLN V 236 GLN W 236 GLN X 236 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 60072 Z= 0.221 Angle : 0.466 4.492 81072 Z= 0.248 Chirality : 0.043 0.132 9528 Planarity : 0.004 0.042 10368 Dihedral : 8.750 105.559 8208 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.45 % Allowed : 12.25 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.09), residues: 7512 helix: 1.44 (0.11), residues: 2136 sheet: -0.63 (0.14), residues: 1128 loop : -2.53 (0.08), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Q 584 HIS 0.004 0.001 HIS E 603 PHE 0.010 0.001 PHE W 561 TYR 0.005 0.002 TYR C 493 ARG 0.005 0.000 ARG X 451 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15024 Ramachandran restraints generated. 7512 Oldfield, 0 Emsley, 7512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15024 Ramachandran restraints generated. 7512 Oldfield, 0 Emsley, 7512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 604 time to evaluate : 5.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 THR cc_start: 0.9010 (m) cc_final: 0.8716 (p) REVERT: A 580 MET cc_start: 0.8697 (tpp) cc_final: 0.8172 (mmt) REVERT: A 616 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8821 (t) REVERT: B 580 MET cc_start: 0.8714 (tpp) cc_final: 0.8139 (mmt) REVERT: B 616 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8827 (t) REVERT: C 225 MET cc_start: 0.6446 (mmp) cc_final: 0.5907 (mmp) REVERT: C 432 THR cc_start: 0.9009 (m) cc_final: 0.8721 (p) REVERT: C 580 MET cc_start: 0.8690 (tpp) cc_final: 0.8158 (mmt) REVERT: C 616 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8811 (t) REVERT: D 422 MET cc_start: 0.8287 (mtt) cc_final: 0.8004 (mtt) REVERT: D 432 THR cc_start: 0.9000 (m) cc_final: 0.8716 (p) REVERT: D 580 MET cc_start: 0.8691 (tpp) cc_final: 0.8150 (mmt) REVERT: D 616 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8815 (t) REVERT: D 630 MET cc_start: 0.8165 (mmm) cc_final: 0.7892 (mmm) REVERT: E 474 MET cc_start: 0.9068 (mtp) cc_final: 0.8853 (mtp) REVERT: E 580 MET cc_start: 0.8649 (tpp) cc_final: 0.8349 (tpp) REVERT: E 616 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8814 (t) REVERT: F 580 MET cc_start: 0.8703 (tpp) cc_final: 0.8148 (mmt) REVERT: F 616 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8822 (t) REVERT: G 432 THR cc_start: 0.9005 (m) cc_final: 0.8718 (p) REVERT: G 451 ARG cc_start: 0.8381 (mtp180) cc_final: 0.8057 (ttm-80) REVERT: G 580 MET cc_start: 0.8690 (tpp) cc_final: 0.8190 (mmt) REVERT: G 616 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8840 (t) REVERT: H 580 MET cc_start: 0.8705 (tpp) cc_final: 0.8236 (mmt) REVERT: H 616 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8823 (t) REVERT: I 225 MET cc_start: 0.6466 (mmp) cc_final: 0.5970 (mmp) REVERT: I 432 THR cc_start: 0.9012 (m) cc_final: 0.8725 (p) REVERT: I 580 MET cc_start: 0.8697 (tpp) cc_final: 0.8160 (mmt) REVERT: I 616 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8803 (t) REVERT: J 432 THR cc_start: 0.9001 (m) cc_final: 0.8714 (p) REVERT: J 580 MET cc_start: 0.8695 (tpp) cc_final: 0.8131 (mmt) REVERT: J 616 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8822 (t) REVERT: K 580 MET cc_start: 0.8712 (tpp) cc_final: 0.8142 (mmt) REVERT: K 616 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8815 (t) REVERT: L 432 THR cc_start: 0.9008 (m) cc_final: 0.8714 (p) REVERT: L 580 MET cc_start: 0.8699 (tpp) cc_final: 0.8137 (mmt) REVERT: L 616 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8815 (t) REVERT: M 411 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8281 (mp) REVERT: M 422 MET cc_start: 0.8269 (mtt) cc_final: 0.8035 (mtt) REVERT: M 432 THR cc_start: 0.8998 (m) cc_final: 0.8708 (p) REVERT: M 451 ARG cc_start: 0.8356 (mtp180) cc_final: 0.8029 (ttm-80) REVERT: M 580 MET cc_start: 0.8705 (tpp) cc_final: 0.8193 (mmt) REVERT: M 616 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8823 (t) REVERT: N 432 THR cc_start: 0.9004 (m) cc_final: 0.8725 (p) REVERT: N 580 MET cc_start: 0.8702 (tpp) cc_final: 0.8169 (mmt) REVERT: N 616 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8813 (t) REVERT: O 223 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7406 (pm20) REVERT: O 248 MET cc_start: 0.7294 (mtm) cc_final: 0.7042 (mtm) REVERT: O 580 MET cc_start: 0.8674 (tpp) cc_final: 0.8144 (mmt) REVERT: O 616 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8808 (t) REVERT: P 432 THR cc_start: 0.9001 (m) cc_final: 0.8711 (p) REVERT: P 474 MET cc_start: 0.9056 (mtp) cc_final: 0.8814 (mtp) REVERT: P 580 MET cc_start: 0.8692 (tpp) cc_final: 0.8186 (mmt) REVERT: P 616 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8825 (t) REVERT: Q 432 THR cc_start: 0.9004 (m) cc_final: 0.8726 (p) REVERT: Q 451 ARG cc_start: 0.8366 (mtp180) cc_final: 0.8047 (ttm-80) REVERT: Q 580 MET cc_start: 0.8710 (tpp) cc_final: 0.8176 (mmt) REVERT: Q 616 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8820 (t) REVERT: R 225 MET cc_start: 0.6385 (mmp) cc_final: 0.5860 (mmp) REVERT: R 432 THR cc_start: 0.9001 (m) cc_final: 0.8711 (p) REVERT: R 580 MET cc_start: 0.8696 (tpp) cc_final: 0.8174 (mmt) REVERT: R 616 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8825 (t) REVERT: S 225 MET cc_start: 0.6474 (mmp) cc_final: 0.5962 (mmp) REVERT: S 432 THR cc_start: 0.9005 (m) cc_final: 0.8717 (p) REVERT: S 474 MET cc_start: 0.9026 (mtp) cc_final: 0.8787 (mtp) REVERT: S 580 MET cc_start: 0.8683 (tpp) cc_final: 0.8205 (mmt) REVERT: S 616 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8839 (t) REVERT: T 432 THR cc_start: 0.9005 (m) cc_final: 0.8726 (p) REVERT: T 580 MET cc_start: 0.8682 (tpp) cc_final: 0.8182 (mmt) REVERT: T 616 THR cc_start: 0.9058 (OUTLIER) cc_final: 0.8814 (t) REVERT: U 225 MET cc_start: 0.6479 (mmp) cc_final: 0.5963 (mmp) REVERT: U 432 THR cc_start: 0.9009 (m) cc_final: 0.8718 (p) REVERT: U 580 MET cc_start: 0.8679 (tpp) cc_final: 0.8133 (mmt) REVERT: U 616 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8823 (t) REVERT: V 225 MET cc_start: 0.6474 (mmp) cc_final: 0.5957 (mmp) REVERT: V 580 MET cc_start: 0.8677 (tpp) cc_final: 0.8114 (mmt) REVERT: V 616 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8809 (t) REVERT: W 580 MET cc_start: 0.8689 (tpp) cc_final: 0.8190 (mmt) REVERT: W 616 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8816 (t) REVERT: X 432 THR cc_start: 0.8999 (m) cc_final: 0.8716 (p) REVERT: X 580 MET cc_start: 0.8697 (tpp) cc_final: 0.8175 (mmt) REVERT: X 616 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8824 (t) outliers start: 94 outliers final: 33 residues processed: 686 average time/residue: 0.5731 time to fit residues: 662.1060 Evaluate side-chains 599 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 540 time to evaluate : 4.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain E residue 616 THR Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 616 THR Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 616 THR Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 435 THR Chi-restraints excluded: chain I residue 616 THR Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain J residue 453 LEU Chi-restraints excluded: chain J residue 616 THR Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 616 THR Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain L residue 616 THR Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 411 ILE Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 616 THR Chi-restraints excluded: chain N residue 244 ASP Chi-restraints excluded: chain N residue 616 THR Chi-restraints excluded: chain O residue 223 GLU Chi-restraints excluded: chain O residue 399 GLU Chi-restraints excluded: chain O residue 403 VAL Chi-restraints excluded: chain O residue 435 THR Chi-restraints excluded: chain O residue 519 ILE Chi-restraints excluded: chain O residue 616 THR Chi-restraints excluded: chain P residue 519 ILE Chi-restraints excluded: chain P residue 616 THR Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 616 THR Chi-restraints excluded: chain R residue 403 VAL Chi-restraints excluded: chain R residue 435 THR Chi-restraints excluded: chain R residue 616 THR Chi-restraints excluded: chain S residue 519 ILE Chi-restraints excluded: chain S residue 616 THR Chi-restraints excluded: chain T residue 616 THR Chi-restraints excluded: chain U residue 403 VAL Chi-restraints excluded: chain U residue 519 ILE Chi-restraints excluded: chain U residue 616 THR Chi-restraints excluded: chain V residue 519 ILE Chi-restraints excluded: chain V residue 616 THR Chi-restraints excluded: chain W residue 435 THR Chi-restraints excluded: chain W residue 616 THR Chi-restraints excluded: chain X residue 519 ILE Chi-restraints excluded: chain X residue 616 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 690 optimal weight: 5.9990 chunk 525 optimal weight: 8.9990 chunk 362 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 333 optimal weight: 1.9990 chunk 469 optimal weight: 2.9990 chunk 701 optimal weight: 0.6980 chunk 742 optimal weight: 40.0000 chunk 366 optimal weight: 10.0000 chunk 664 optimal weight: 2.9990 chunk 200 optimal weight: 8.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 544 GLN C 236 GLN D 236 GLN E 236 GLN F 236 GLN G 236 GLN H 236 GLN I 236 GLN I 544 GLN J 236 GLN K 236 GLN L 236 GLN M 236 GLN N 236 GLN O 236 GLN Q 236 GLN Q 544 GLN R 236 GLN S 236 GLN U 236 GLN U 544 GLN V 236 GLN W 236 GLN X 236 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 60072 Z= 0.278 Angle : 0.487 7.069 81072 Z= 0.259 Chirality : 0.044 0.131 9528 Planarity : 0.004 0.039 10368 Dihedral : 7.730 89.997 8208 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.32 % Allowed : 13.88 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.19 (0.10), residues: 7512 helix: 1.68 (0.11), residues: 2136 sheet: -0.44 (0.15), residues: 1128 loop : -2.35 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Q 584 HIS 0.004 0.001 HIS E 603 PHE 0.012 0.001 PHE H 561 TYR 0.005 0.002 TYR H 493 ARG 0.005 0.000 ARG P 451 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15024 Ramachandran restraints generated. 7512 Oldfield, 0 Emsley, 7512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15024 Ramachandran restraints generated. 7512 Oldfield, 0 Emsley, 7512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 567 time to evaluate : 5.160 Fit side-chains revert: symmetry clash REVERT: A 432 THR cc_start: 0.9029 (m) cc_final: 0.8686 (p) REVERT: A 580 MET cc_start: 0.8666 (tpp) cc_final: 0.8138 (mmt) REVERT: A 616 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8824 (t) REVERT: B 580 MET cc_start: 0.8669 (tpp) cc_final: 0.8147 (mmt) REVERT: B 616 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8831 (t) REVERT: C 248 MET cc_start: 0.7361 (mtm) cc_final: 0.7159 (mtm) REVERT: C 432 THR cc_start: 0.9034 (m) cc_final: 0.8698 (p) REVERT: C 580 MET cc_start: 0.8661 (tpp) cc_final: 0.8132 (mmt) REVERT: C 616 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8817 (t) REVERT: D 422 MET cc_start: 0.8319 (mtt) cc_final: 0.8031 (mtt) REVERT: D 432 THR cc_start: 0.9020 (m) cc_final: 0.8692 (p) REVERT: D 580 MET cc_start: 0.8660 (tpp) cc_final: 0.8136 (mmt) REVERT: D 616 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8811 (t) REVERT: D 630 MET cc_start: 0.8177 (mmm) cc_final: 0.7890 (mmm) REVERT: E 225 MET cc_start: 0.6498 (mmp) cc_final: 0.5944 (mmp) REVERT: E 411 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8290 (mp) REVERT: E 616 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8763 (t) REVERT: F 580 MET cc_start: 0.8672 (tpp) cc_final: 0.8147 (mmt) REVERT: F 616 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8827 (t) REVERT: G 225 MET cc_start: 0.6326 (mmp) cc_final: 0.5829 (mmp) REVERT: G 276 MET cc_start: 0.6705 (mmt) cc_final: 0.6403 (mmt) REVERT: G 432 THR cc_start: 0.9027 (m) cc_final: 0.8697 (p) REVERT: G 451 ARG cc_start: 0.8416 (mtp180) cc_final: 0.8079 (ttm-80) REVERT: G 616 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8826 (t) REVERT: H 451 ARG cc_start: 0.8558 (mtp180) cc_final: 0.8355 (mtp85) REVERT: H 616 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8814 (t) REVERT: I 432 THR cc_start: 0.9033 (m) cc_final: 0.8698 (p) REVERT: I 580 MET cc_start: 0.8659 (tpp) cc_final: 0.8131 (mmt) REVERT: I 616 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8796 (t) REVERT: J 225 MET cc_start: 0.6467 (mmp) cc_final: 0.5966 (mmp) REVERT: J 432 THR cc_start: 0.9021 (m) cc_final: 0.8696 (p) REVERT: J 580 MET cc_start: 0.8658 (tpp) cc_final: 0.8129 (mmt) REVERT: J 616 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8825 (t) REVERT: K 580 MET cc_start: 0.8665 (tpp) cc_final: 0.8136 (mmt) REVERT: K 616 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8818 (t) REVERT: L 432 THR cc_start: 0.9022 (m) cc_final: 0.8689 (p) REVERT: L 580 MET cc_start: 0.8662 (tpp) cc_final: 0.8134 (mmt) REVERT: L 616 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8803 (t) REVERT: M 276 MET cc_start: 0.6085 (mmt) cc_final: 0.5855 (mmt) REVERT: M 411 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8291 (mp) REVERT: M 422 MET cc_start: 0.8288 (mtt) cc_final: 0.8020 (mtt) REVERT: M 432 THR cc_start: 0.9019 (m) cc_final: 0.8691 (p) REVERT: M 451 ARG cc_start: 0.8374 (mtp180) cc_final: 0.8042 (ttm-80) REVERT: M 580 MET cc_start: 0.8680 (tpp) cc_final: 0.8132 (mmt) REVERT: M 616 THR cc_start: 0.9072 (OUTLIER) cc_final: 0.8818 (t) REVERT: N 432 THR cc_start: 0.9026 (m) cc_final: 0.8701 (p) REVERT: N 580 MET cc_start: 0.8666 (tpp) cc_final: 0.8143 (mmt) REVERT: N 616 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8803 (t) REVERT: O 248 MET cc_start: 0.7300 (mtm) cc_final: 0.6981 (mtm) REVERT: O 580 MET cc_start: 0.8628 (tpp) cc_final: 0.8140 (mmt) REVERT: O 616 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8809 (t) REVERT: P 432 THR cc_start: 0.9029 (m) cc_final: 0.8696 (p) REVERT: P 580 MET cc_start: 0.8673 (tpp) cc_final: 0.8127 (mmt) REVERT: P 616 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8763 (t) REVERT: Q 432 THR cc_start: 0.9028 (m) cc_final: 0.8700 (p) REVERT: Q 616 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8812 (t) REVERT: R 432 THR cc_start: 0.9022 (m) cc_final: 0.8686 (p) REVERT: R 580 MET cc_start: 0.8660 (tpp) cc_final: 0.8136 (mmt) REVERT: R 616 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8819 (t) REVERT: S 432 THR cc_start: 0.9026 (m) cc_final: 0.8693 (p) REVERT: S 616 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8779 (t) REVERT: T 432 THR cc_start: 0.9029 (m) cc_final: 0.8704 (p) REVERT: T 580 MET cc_start: 0.8659 (tpp) cc_final: 0.8145 (mmt) REVERT: T 616 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8819 (t) REVERT: U 225 MET cc_start: 0.6583 (mmp) cc_final: 0.6374 (mmp) REVERT: U 432 THR cc_start: 0.9031 (m) cc_final: 0.8691 (p) REVERT: U 580 MET cc_start: 0.8657 (tpp) cc_final: 0.8399 (mmt) REVERT: U 616 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8809 (t) REVERT: V 616 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8810 (t) REVERT: W 616 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8821 (t) REVERT: X 432 THR cc_start: 0.9021 (m) cc_final: 0.8689 (p) REVERT: X 580 MET cc_start: 0.8666 (tpp) cc_final: 0.8141 (mmt) REVERT: X 616 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8814 (t) outliers start: 86 outliers final: 47 residues processed: 645 average time/residue: 0.5676 time to fit residues: 632.2366 Evaluate side-chains 619 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 546 time to evaluate : 5.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 616 THR Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 616 THR Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 616 THR Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 435 THR Chi-restraints excluded: chain I residue 519 ILE Chi-restraints excluded: chain I residue 616 THR Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain J residue 519 ILE Chi-restraints excluded: chain J residue 616 THR Chi-restraints excluded: chain K residue 616 THR Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain L residue 616 THR Chi-restraints excluded: chain M residue 239 ILE Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 411 ILE Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 616 THR Chi-restraints excluded: chain N residue 616 THR Chi-restraints excluded: chain O residue 239 ILE Chi-restraints excluded: chain O residue 403 VAL Chi-restraints excluded: chain O residue 435 THR Chi-restraints excluded: chain O residue 519 ILE Chi-restraints excluded: chain O residue 616 THR Chi-restraints excluded: chain P residue 519 ILE Chi-restraints excluded: chain P residue 616 THR Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 616 THR Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 403 VAL Chi-restraints excluded: chain R residue 435 THR Chi-restraints excluded: chain R residue 519 ILE Chi-restraints excluded: chain R residue 616 THR Chi-restraints excluded: chain S residue 239 ILE Chi-restraints excluded: chain S residue 519 ILE Chi-restraints excluded: chain S residue 616 THR Chi-restraints excluded: chain T residue 616 THR Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 403 VAL Chi-restraints excluded: chain U residue 519 ILE Chi-restraints excluded: chain U residue 616 THR Chi-restraints excluded: chain V residue 239 ILE Chi-restraints excluded: chain V residue 519 ILE Chi-restraints excluded: chain V residue 616 THR Chi-restraints excluded: chain W residue 244 ASP Chi-restraints excluded: chain W residue 435 THR Chi-restraints excluded: chain W residue 616 THR Chi-restraints excluded: chain X residue 239 ILE Chi-restraints excluded: chain X residue 519 ILE Chi-restraints excluded: chain X residue 616 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 618 optimal weight: 8.9990 chunk 421 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 552 optimal weight: 0.0980 chunk 306 optimal weight: 1.9990 chunk 633 optimal weight: 0.8980 chunk 513 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 379 optimal weight: 1.9990 chunk 666 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN C 236 GLN E 236 GLN F 236 GLN G 236 GLN J 236 GLN K 544 GLN M 236 GLN N 236 GLN O 544 GLN Q 236 GLN R 236 GLN S 236 GLN V 236 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 60072 Z= 0.207 Angle : 0.449 4.850 81072 Z= 0.239 Chirality : 0.043 0.132 9528 Planarity : 0.004 0.039 10368 Dihedral : 6.545 68.240 8208 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.37 % Allowed : 14.30 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.89 (0.10), residues: 7512 helix: 1.97 (0.12), residues: 2136 sheet: -0.18 (0.15), residues: 1128 loop : -2.22 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP V 389 HIS 0.004 0.001 HIS E 603 PHE 0.009 0.001 PHE E 394 TYR 0.004 0.001 TYR U 493 ARG 0.005 0.000 ARG P 451 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15024 Ramachandran restraints generated. 7512 Oldfield, 0 Emsley, 7512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15024 Ramachandran restraints generated. 7512 Oldfield, 0 Emsley, 7512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 566 time to evaluate : 5.010 Fit side-chains REVERT: A 225 MET cc_start: 0.6440 (mmp) cc_final: 0.5922 (mmp) REVERT: A 432 THR cc_start: 0.8943 (m) cc_final: 0.8663 (p) REVERT: A 580 MET cc_start: 0.8638 (tpp) cc_final: 0.8109 (mmt) REVERT: A 616 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8763 (t) REVERT: B 580 MET cc_start: 0.8646 (tpp) cc_final: 0.8123 (mmt) REVERT: B 616 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8800 (t) REVERT: C 225 MET cc_start: 0.6397 (mmp) cc_final: 0.5913 (mmp) REVERT: C 432 THR cc_start: 0.8945 (m) cc_final: 0.8656 (p) REVERT: C 580 MET cc_start: 0.8630 (tpp) cc_final: 0.8107 (mmt) REVERT: C 616 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8759 (t) REVERT: D 422 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7956 (mtt) REVERT: D 432 THR cc_start: 0.8933 (m) cc_final: 0.8657 (p) REVERT: D 580 MET cc_start: 0.8637 (tpp) cc_final: 0.8119 (mmt) REVERT: D 616 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8762 (t) REVERT: D 630 MET cc_start: 0.8083 (mmm) cc_final: 0.7779 (mmm) REVERT: E 248 MET cc_start: 0.6377 (mtm) cc_final: 0.6084 (mtm) REVERT: E 411 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8293 (mp) REVERT: E 580 MET cc_start: 0.8565 (tpp) cc_final: 0.8247 (tpp) REVERT: E 616 THR cc_start: 0.9041 (OUTLIER) cc_final: 0.8783 (t) REVERT: F 580 MET cc_start: 0.8644 (tpp) cc_final: 0.8124 (mmt) REVERT: F 616 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8773 (t) REVERT: G 432 THR cc_start: 0.8936 (m) cc_final: 0.8661 (p) REVERT: G 580 MET cc_start: 0.8567 (tpp) cc_final: 0.8065 (mmt) REVERT: G 616 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8767 (t) REVERT: H 580 MET cc_start: 0.8583 (tpp) cc_final: 0.8080 (mmt) REVERT: H 616 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8771 (t) REVERT: I 432 THR cc_start: 0.8944 (m) cc_final: 0.8656 (p) REVERT: I 580 MET cc_start: 0.8633 (tpp) cc_final: 0.8111 (mmt) REVERT: I 616 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8800 (t) REVERT: J 432 THR cc_start: 0.8932 (m) cc_final: 0.8656 (p) REVERT: J 580 MET cc_start: 0.8632 (tpp) cc_final: 0.8118 (mmt) REVERT: J 616 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8767 (t) REVERT: K 580 MET cc_start: 0.8637 (tpp) cc_final: 0.8113 (mmt) REVERT: K 616 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8788 (t) REVERT: L 432 THR cc_start: 0.8936 (m) cc_final: 0.8646 (p) REVERT: L 580 MET cc_start: 0.8635 (tpp) cc_final: 0.8120 (mmt) REVERT: L 616 THR cc_start: 0.9031 (OUTLIER) cc_final: 0.8766 (t) REVERT: M 411 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8256 (mp) REVERT: M 422 MET cc_start: 0.8231 (mtt) cc_final: 0.7968 (mtt) REVERT: M 432 THR cc_start: 0.8927 (m) cc_final: 0.8647 (p) REVERT: M 580 MET cc_start: 0.8660 (tpp) cc_final: 0.8149 (mmt) REVERT: M 616 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8790 (t) REVERT: N 432 THR cc_start: 0.8966 (m) cc_final: 0.8687 (p) REVERT: N 580 MET cc_start: 0.8642 (tpp) cc_final: 0.8128 (mmt) REVERT: N 616 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8812 (t) REVERT: O 248 MET cc_start: 0.7279 (mtm) cc_final: 0.7073 (mtm) REVERT: O 580 MET cc_start: 0.8604 (tpp) cc_final: 0.8363 (mmt) REVERT: O 616 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8779 (t) REVERT: P 276 MET cc_start: 0.6145 (mmt) cc_final: 0.5851 (mmt) REVERT: P 432 THR cc_start: 0.8937 (m) cc_final: 0.8649 (p) REVERT: P 580 MET cc_start: 0.8660 (tpp) cc_final: 0.8150 (mmt) REVERT: P 616 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8781 (t) REVERT: Q 432 THR cc_start: 0.8968 (m) cc_final: 0.8700 (p) REVERT: Q 580 MET cc_start: 0.8572 (tpp) cc_final: 0.8115 (mmt) REVERT: Q 616 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8820 (t) REVERT: R 225 MET cc_start: 0.6225 (mmp) cc_final: 0.5742 (mmp) REVERT: R 432 THR cc_start: 0.8929 (m) cc_final: 0.8640 (p) REVERT: R 580 MET cc_start: 0.8638 (tpp) cc_final: 0.8117 (mmt) REVERT: R 616 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8789 (t) REVERT: S 225 MET cc_start: 0.6296 (mmp) cc_final: 0.5819 (mmp) REVERT: S 276 MET cc_start: 0.6556 (mmt) cc_final: 0.6252 (mmt) REVERT: S 432 THR cc_start: 0.8933 (m) cc_final: 0.8656 (p) REVERT: S 580 MET cc_start: 0.8585 (tpp) cc_final: 0.8070 (mmt) REVERT: S 616 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8798 (t) REVERT: T 432 THR cc_start: 0.8966 (m) cc_final: 0.8698 (p) REVERT: T 580 MET cc_start: 0.8630 (tpp) cc_final: 0.8110 (mmt) REVERT: T 616 THR cc_start: 0.9058 (OUTLIER) cc_final: 0.8790 (t) REVERT: U 432 THR cc_start: 0.8939 (m) cc_final: 0.8662 (p) REVERT: U 580 MET cc_start: 0.8629 (tpp) cc_final: 0.8138 (mmt) REVERT: U 616 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8754 (t) REVERT: U 626 ARG cc_start: 0.8109 (mtt90) cc_final: 0.7627 (mtt90) REVERT: V 225 MET cc_start: 0.6260 (mmp) cc_final: 0.5796 (mmp) REVERT: V 276 MET cc_start: 0.6317 (mmt) cc_final: 0.6025 (mmt) REVERT: V 580 MET cc_start: 0.8554 (tpp) cc_final: 0.8247 (tpp) REVERT: V 616 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8781 (t) REVERT: W 580 MET cc_start: 0.8584 (tpp) cc_final: 0.8260 (tpp) REVERT: W 616 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8765 (t) REVERT: X 225 MET cc_start: 0.6392 (mmp) cc_final: 0.5897 (mmp) REVERT: X 432 THR cc_start: 0.8934 (m) cc_final: 0.8651 (p) REVERT: X 580 MET cc_start: 0.8639 (tpp) cc_final: 0.8130 (mmt) REVERT: X 616 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8768 (t) outliers start: 89 outliers final: 54 residues processed: 648 average time/residue: 0.5236 time to fit residues: 584.1576 Evaluate side-chains 619 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 538 time to evaluate : 4.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 616 THR Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 616 THR Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 560 HIS Chi-restraints excluded: chain H residue 616 THR Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 244 ASP Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 435 THR Chi-restraints excluded: chain I residue 519 ILE Chi-restraints excluded: chain I residue 616 THR Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 519 ILE Chi-restraints excluded: chain J residue 616 THR Chi-restraints excluded: chain K residue 239 ILE Chi-restraints excluded: chain K residue 616 THR Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 616 THR Chi-restraints excluded: chain M residue 411 ILE Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 616 THR Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 244 ASP Chi-restraints excluded: chain N residue 392 VAL Chi-restraints excluded: chain N residue 616 THR Chi-restraints excluded: chain O residue 223 GLU Chi-restraints excluded: chain O residue 239 ILE Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 399 GLU Chi-restraints excluded: chain O residue 403 VAL Chi-restraints excluded: chain O residue 435 THR Chi-restraints excluded: chain O residue 519 ILE Chi-restraints excluded: chain O residue 616 THR Chi-restraints excluded: chain P residue 239 ILE Chi-restraints excluded: chain P residue 519 ILE Chi-restraints excluded: chain P residue 616 THR Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 616 THR Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 403 VAL Chi-restraints excluded: chain R residue 519 ILE Chi-restraints excluded: chain R residue 616 THR Chi-restraints excluded: chain S residue 239 ILE Chi-restraints excluded: chain S residue 244 ASP Chi-restraints excluded: chain S residue 519 ILE Chi-restraints excluded: chain S residue 616 THR Chi-restraints excluded: chain T residue 239 ILE Chi-restraints excluded: chain T residue 244 ASP Chi-restraints excluded: chain T residue 616 THR Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 403 VAL Chi-restraints excluded: chain U residue 519 ILE Chi-restraints excluded: chain U residue 616 THR Chi-restraints excluded: chain V residue 519 ILE Chi-restraints excluded: chain V residue 616 THR Chi-restraints excluded: chain W residue 239 ILE Chi-restraints excluded: chain W residue 616 THR Chi-restraints excluded: chain X residue 239 ILE Chi-restraints excluded: chain X residue 519 ILE Chi-restraints excluded: chain X residue 616 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 249 optimal weight: 1.9990 chunk 668 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 435 optimal weight: 3.9990 chunk 183 optimal weight: 0.0870 chunk 743 optimal weight: 9.9990 chunk 616 optimal weight: 1.9990 chunk 344 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 245 optimal weight: 5.9990 chunk 390 optimal weight: 0.8980 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 544 GLN D 236 GLN F 236 GLN G 236 GLN I 236 GLN J 236 GLN L 236 GLN N 236 GLN O 236 GLN P 486 GLN R 236 GLN S 236 GLN U 236 GLN W 236 GLN X 236 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 60072 Z= 0.158 Angle : 0.423 5.231 81072 Z= 0.225 Chirality : 0.042 0.129 9528 Planarity : 0.004 0.041 10368 Dihedral : 5.872 53.360 8208 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.61 % Allowed : 13.91 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.10), residues: 7512 helix: 2.20 (0.12), residues: 2136 sheet: 0.13 (0.15), residues: 1128 loop : -2.06 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 389 HIS 0.004 0.001 HIS N 603 PHE 0.008 0.001 PHE F 394 TYR 0.004 0.001 TYR D 493 ARG 0.003 0.000 ARG P 451 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15024 Ramachandran restraints generated. 7512 Oldfield, 0 Emsley, 7512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15024 Ramachandran restraints generated. 7512 Oldfield, 0 Emsley, 7512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 549 time to evaluate : 5.089 Fit side-chains REVERT: A 248 MET cc_start: 0.6507 (mtm) cc_final: 0.6278 (mtt) REVERT: A 432 THR cc_start: 0.8923 (m) cc_final: 0.8716 (p) REVERT: A 580 MET cc_start: 0.8617 (tpp) cc_final: 0.8118 (mmt) REVERT: A 616 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8776 (t) REVERT: B 225 MET cc_start: 0.6700 (mmp) cc_final: 0.6494 (mmp) REVERT: B 580 MET cc_start: 0.8643 (tpp) cc_final: 0.8102 (mmt) REVERT: B 616 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8785 (t) REVERT: C 432 THR cc_start: 0.8916 (m) cc_final: 0.8713 (p) REVERT: C 580 MET cc_start: 0.8642 (tpp) cc_final: 0.8119 (mmt) REVERT: C 616 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8774 (t) REVERT: D 422 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7931 (mtt) REVERT: D 580 MET cc_start: 0.8645 (tpp) cc_final: 0.8117 (mmt) REVERT: D 616 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8773 (t) REVERT: D 630 MET cc_start: 0.8051 (mmm) cc_final: 0.7720 (mmm) REVERT: E 225 MET cc_start: 0.6389 (mmp) cc_final: 0.5868 (mmp) REVERT: E 248 MET cc_start: 0.6324 (mtm) cc_final: 0.5783 (mtm) REVERT: E 411 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8232 (mp) REVERT: E 543 MET cc_start: 0.8385 (ptp) cc_final: 0.7945 (mtp) REVERT: E 580 MET cc_start: 0.8589 (tpp) cc_final: 0.8285 (tpp) REVERT: E 616 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8759 (t) REVERT: F 580 MET cc_start: 0.8641 (tpp) cc_final: 0.8119 (mmt) REVERT: F 616 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8789 (t) REVERT: G 225 MET cc_start: 0.6567 (mmp) cc_final: 0.6054 (mmp) REVERT: G 248 MET cc_start: 0.6375 (mtm) cc_final: 0.6138 (mtt) REVERT: G 580 MET cc_start: 0.8596 (tpp) cc_final: 0.8284 (tpp) REVERT: G 616 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8782 (t) REVERT: G 626 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7727 (mtm-85) REVERT: H 248 MET cc_start: 0.6302 (mtm) cc_final: 0.6038 (mtt) REVERT: H 580 MET cc_start: 0.8605 (tpp) cc_final: 0.8300 (tpp) REVERT: H 616 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8780 (t) REVERT: H 626 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7728 (mtm-85) REVERT: I 248 MET cc_start: 0.6530 (mtm) cc_final: 0.6305 (mtt) REVERT: I 580 MET cc_start: 0.8626 (tpp) cc_final: 0.8111 (mmt) REVERT: I 616 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8764 (t) REVERT: I 626 ARG cc_start: 0.8065 (mtt90) cc_final: 0.7691 (mtm-85) REVERT: J 248 MET cc_start: 0.6498 (mtm) cc_final: 0.6286 (mtt) REVERT: J 580 MET cc_start: 0.8632 (tpp) cc_final: 0.8113 (mmt) REVERT: J 616 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8777 (t) REVERT: J 626 ARG cc_start: 0.8115 (mtt90) cc_final: 0.7739 (mtm-85) REVERT: K 580 MET cc_start: 0.8624 (tpp) cc_final: 0.8102 (mmt) REVERT: K 616 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8772 (t) REVERT: L 432 THR cc_start: 0.8918 (m) cc_final: 0.8717 (p) REVERT: L 580 MET cc_start: 0.8635 (tpp) cc_final: 0.8116 (mmt) REVERT: L 616 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8780 (t) REVERT: M 411 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8276 (mp) REVERT: M 422 MET cc_start: 0.8183 (mtt) cc_final: 0.7920 (mtt) REVERT: M 580 MET cc_start: 0.8683 (tpp) cc_final: 0.8252 (mmt) REVERT: M 616 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8773 (t) REVERT: N 580 MET cc_start: 0.8656 (tpp) cc_final: 0.8119 (mmt) REVERT: N 616 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8774 (t) REVERT: N 626 ARG cc_start: 0.8081 (mtt90) cc_final: 0.7679 (mtm-85) REVERT: O 225 MET cc_start: 0.6636 (mmp) cc_final: 0.6347 (mmt) REVERT: O 580 MET cc_start: 0.8627 (tpp) cc_final: 0.8109 (mmt) REVERT: O 616 THR cc_start: 0.9031 (OUTLIER) cc_final: 0.8763 (t) REVERT: O 626 ARG cc_start: 0.8094 (mtt90) cc_final: 0.7633 (mtt90) REVERT: P 225 MET cc_start: 0.6441 (mmp) cc_final: 0.6177 (mmt) REVERT: P 248 MET cc_start: 0.6494 (mtm) cc_final: 0.6285 (mtm) REVERT: P 276 MET cc_start: 0.6088 (mmt) cc_final: 0.5881 (mmt) REVERT: P 580 MET cc_start: 0.8681 (tpp) cc_final: 0.8243 (mmt) REVERT: P 616 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8768 (t) REVERT: Q 248 MET cc_start: 0.6495 (mtm) cc_final: 0.6293 (mtt) REVERT: Q 432 THR cc_start: 0.8918 (m) cc_final: 0.8715 (p) REVERT: Q 580 MET cc_start: 0.8599 (tpp) cc_final: 0.8282 (tpp) REVERT: Q 616 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8780 (t) REVERT: R 248 MET cc_start: 0.6517 (mtm) cc_final: 0.6253 (mtt) REVERT: R 432 THR cc_start: 0.8911 (m) cc_final: 0.8711 (p) REVERT: R 580 MET cc_start: 0.8629 (tpp) cc_final: 0.8119 (mmt) REVERT: R 616 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8775 (t) REVERT: R 626 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7731 (mtm-85) REVERT: S 248 MET cc_start: 0.6503 (mtm) cc_final: 0.6267 (mtt) REVERT: S 432 THR cc_start: 0.8954 (m) cc_final: 0.8715 (p) REVERT: S 580 MET cc_start: 0.8610 (tpp) cc_final: 0.8297 (tpp) REVERT: S 616 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8784 (t) REVERT: T 580 MET cc_start: 0.8636 (tpp) cc_final: 0.8137 (mmt) REVERT: T 616 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8775 (t) REVERT: T 626 ARG cc_start: 0.8021 (mtt90) cc_final: 0.7647 (mtt90) REVERT: U 580 MET cc_start: 0.8621 (tpp) cc_final: 0.8118 (mmt) REVERT: U 616 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8763 (t) REVERT: U 626 ARG cc_start: 0.8059 (mtt90) cc_final: 0.7638 (mtt90) REVERT: V 248 MET cc_start: 0.6510 (mtm) cc_final: 0.6247 (mtt) REVERT: V 580 MET cc_start: 0.8572 (tpp) cc_final: 0.8243 (tpp) REVERT: V 616 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8767 (t) REVERT: W 580 MET cc_start: 0.8612 (tpp) cc_final: 0.8298 (tpp) REVERT: W 616 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8782 (t) REVERT: X 580 MET cc_start: 0.8636 (tpp) cc_final: 0.8123 (mmt) REVERT: X 616 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8778 (t) outliers start: 105 outliers final: 58 residues processed: 647 average time/residue: 0.5303 time to fit residues: 596.2671 Evaluate side-chains 594 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 509 time to evaluate : 5.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 560 HIS Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 560 HIS Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 560 HIS Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 560 HIS Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 560 HIS Chi-restraints excluded: chain E residue 616 THR Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 560 HIS Chi-restraints excluded: chain F residue 616 THR Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain G residue 560 HIS Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 560 HIS Chi-restraints excluded: chain H residue 616 THR Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 519 ILE Chi-restraints excluded: chain I residue 560 HIS Chi-restraints excluded: chain I residue 616 THR Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 519 ILE Chi-restraints excluded: chain J residue 560 HIS Chi-restraints excluded: chain J residue 616 THR Chi-restraints excluded: chain K residue 239 ILE Chi-restraints excluded: chain K residue 560 HIS Chi-restraints excluded: chain K residue 616 THR Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 560 HIS Chi-restraints excluded: chain L residue 616 THR Chi-restraints excluded: chain M residue 239 ILE Chi-restraints excluded: chain M residue 411 ILE Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 560 HIS Chi-restraints excluded: chain M residue 616 THR Chi-restraints excluded: chain N residue 560 HIS Chi-restraints excluded: chain N residue 616 THR Chi-restraints excluded: chain O residue 223 GLU Chi-restraints excluded: chain O residue 519 ILE Chi-restraints excluded: chain O residue 560 HIS Chi-restraints excluded: chain O residue 616 THR Chi-restraints excluded: chain P residue 239 ILE Chi-restraints excluded: chain P residue 519 ILE Chi-restraints excluded: chain P residue 560 HIS Chi-restraints excluded: chain P residue 616 THR Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 560 HIS Chi-restraints excluded: chain Q residue 616 THR Chi-restraints excluded: chain R residue 519 ILE Chi-restraints excluded: chain R residue 560 HIS Chi-restraints excluded: chain R residue 616 THR Chi-restraints excluded: chain S residue 519 ILE Chi-restraints excluded: chain S residue 560 HIS Chi-restraints excluded: chain S residue 616 THR Chi-restraints excluded: chain T residue 560 HIS Chi-restraints excluded: chain T residue 616 THR Chi-restraints excluded: chain U residue 519 ILE Chi-restraints excluded: chain U residue 560 HIS Chi-restraints excluded: chain U residue 616 THR Chi-restraints excluded: chain V residue 239 ILE Chi-restraints excluded: chain V residue 519 ILE Chi-restraints excluded: chain V residue 616 THR Chi-restraints excluded: chain W residue 239 ILE Chi-restraints excluded: chain W residue 560 HIS Chi-restraints excluded: chain W residue 616 THR Chi-restraints excluded: chain X residue 519 ILE Chi-restraints excluded: chain X residue 560 HIS Chi-restraints excluded: chain X residue 616 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 716 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 423 optimal weight: 9.9990 chunk 542 optimal weight: 2.9990 chunk 420 optimal weight: 10.0000 chunk 625 optimal weight: 0.9980 chunk 414 optimal weight: 3.9990 chunk 740 optimal weight: 30.0000 chunk 463 optimal weight: 3.9990 chunk 451 optimal weight: 20.0000 chunk 341 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 GLN C 236 GLN D 236 GLN E 236 GLN F 544 GLN I 236 GLN L 236 GLN M 236 GLN O 236 GLN P 236 GLN P 486 GLN Q 236 GLN S 236 GLN U 236 GLN U 486 GLN V 236 GLN V 486 GLN W 236 GLN X 236 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 60072 Z= 0.315 Angle : 0.488 7.272 81072 Z= 0.258 Chirality : 0.044 0.126 9528 Planarity : 0.004 0.036 10368 Dihedral : 6.045 52.777 8208 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.69 % Allowed : 14.84 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.62 (0.10), residues: 7512 helix: 2.02 (0.11), residues: 2136 sheet: 0.19 (0.15), residues: 1128 loop : -2.01 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 584 HIS 0.004 0.001 HIS N 603 PHE 0.013 0.002 PHE Q 561 TYR 0.006 0.002 TYR B 493 ARG 0.003 0.000 ARG B 451 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15024 Ramachandran restraints generated. 7512 Oldfield, 0 Emsley, 7512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15024 Ramachandran restraints generated. 7512 Oldfield, 0 Emsley, 7512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 519 time to evaluate : 5.159 Fit side-chains REVERT: A 580 MET cc_start: 0.8643 (tpp) cc_final: 0.8364 (mmt) REVERT: A 616 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8778 (t) REVERT: B 248 MET cc_start: 0.4953 (mtt) cc_final: 0.4271 (mtt) REVERT: B 580 MET cc_start: 0.8617 (tpp) cc_final: 0.8355 (mmt) REVERT: B 616 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8770 (t) REVERT: C 580 MET cc_start: 0.8646 (tpp) cc_final: 0.8115 (mmt) REVERT: C 616 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8774 (t) REVERT: D 248 MET cc_start: 0.6112 (mmm) cc_final: 0.5598 (mtt) REVERT: D 422 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8082 (mtt) REVERT: D 580 MET cc_start: 0.8635 (tpp) cc_final: 0.8103 (mmt) REVERT: D 616 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8765 (t) REVERT: D 630 MET cc_start: 0.8194 (mmm) cc_final: 0.7891 (mmm) REVERT: E 257 VAL cc_start: 0.6792 (OUTLIER) cc_final: 0.6546 (p) REVERT: E 411 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8261 (mp) REVERT: E 580 MET cc_start: 0.8594 (tpp) cc_final: 0.8083 (mmt) REVERT: E 616 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8749 (t) REVERT: F 580 MET cc_start: 0.8655 (tpp) cc_final: 0.8150 (mmt) REVERT: F 616 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8768 (t) REVERT: G 580 MET cc_start: 0.8595 (tpp) cc_final: 0.8097 (mmt) REVERT: G 616 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8771 (t) REVERT: H 453 LEU cc_start: 0.8114 (mt) cc_final: 0.7912 (mt) REVERT: H 580 MET cc_start: 0.8610 (tpp) cc_final: 0.8108 (mmt) REVERT: H 616 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8770 (t) REVERT: I 616 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8752 (t) REVERT: J 580 MET cc_start: 0.8622 (tpp) cc_final: 0.8346 (mmt) REVERT: J 616 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8767 (t) REVERT: K 248 MET cc_start: 0.6152 (mmm) cc_final: 0.5570 (mtt) REVERT: K 580 MET cc_start: 0.8643 (tpp) cc_final: 0.8096 (mmt) REVERT: K 616 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8757 (t) REVERT: L 580 MET cc_start: 0.8649 (tpp) cc_final: 0.8145 (mmt) REVERT: L 616 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8830 (t) REVERT: L 626 ARG cc_start: 0.7950 (mtm-85) cc_final: 0.7618 (mtt90) REVERT: M 411 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8294 (mp) REVERT: M 422 MET cc_start: 0.8321 (mtt) cc_final: 0.8066 (mtt) REVERT: M 616 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8760 (t) REVERT: N 453 LEU cc_start: 0.8169 (mt) cc_final: 0.7931 (mt) REVERT: N 580 MET cc_start: 0.8633 (tpp) cc_final: 0.8370 (mmt) REVERT: N 616 THR cc_start: 0.9008 (OUTLIER) cc_final: 0.8758 (t) REVERT: O 580 MET cc_start: 0.8622 (tpp) cc_final: 0.8071 (mmt) REVERT: O 616 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8753 (t) REVERT: P 225 MET cc_start: 0.6427 (mmp) cc_final: 0.6104 (mmt) REVERT: P 276 MET cc_start: 0.6212 (mmt) cc_final: 0.5948 (mmt) REVERT: P 616 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8758 (t) REVERT: Q 580 MET cc_start: 0.8602 (tpp) cc_final: 0.8098 (mmt) REVERT: Q 616 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8829 (t) REVERT: R 225 MET cc_start: 0.6594 (mmp) cc_final: 0.6057 (mmp) REVERT: R 580 MET cc_start: 0.8640 (tpp) cc_final: 0.8373 (mmt) REVERT: R 616 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8777 (t) REVERT: S 616 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8781 (t) REVERT: T 248 MET cc_start: 0.6077 (mmm) cc_final: 0.5611 (mtt) REVERT: T 580 MET cc_start: 0.8616 (tpp) cc_final: 0.8329 (mmt) REVERT: T 616 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8765 (t) REVERT: U 248 MET cc_start: 0.6491 (mtm) cc_final: 0.6288 (mtt) REVERT: U 580 MET cc_start: 0.8632 (tpp) cc_final: 0.8122 (mmt) REVERT: U 616 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8753 (t) REVERT: V 580 MET cc_start: 0.8598 (tpp) cc_final: 0.8100 (mmt) REVERT: V 616 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8750 (t) REVERT: W 451 ARG cc_start: 0.8392 (mtp180) cc_final: 0.8143 (mtp85) REVERT: W 580 MET cc_start: 0.8609 (tpp) cc_final: 0.8101 (mmt) REVERT: W 616 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8764 (t) REVERT: X 616 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8770 (t) outliers start: 110 outliers final: 62 residues processed: 623 average time/residue: 0.5240 time to fit residues: 567.0490 Evaluate side-chains 586 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 496 time to evaluate : 5.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 616 THR Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 616 THR Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 616 THR Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 244 ASP Chi-restraints excluded: chain I residue 435 THR Chi-restraints excluded: chain I residue 519 ILE Chi-restraints excluded: chain I residue 616 THR Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 519 ILE Chi-restraints excluded: chain J residue 616 THR Chi-restraints excluded: chain K residue 239 ILE Chi-restraints excluded: chain K residue 616 THR Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 616 THR Chi-restraints excluded: chain M residue 239 ILE Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 411 ILE Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 616 THR Chi-restraints excluded: chain N residue 244 ASP Chi-restraints excluded: chain N residue 392 VAL Chi-restraints excluded: chain N residue 616 THR Chi-restraints excluded: chain O residue 223 GLU Chi-restraints excluded: chain O residue 239 ILE Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 435 THR Chi-restraints excluded: chain O residue 519 ILE Chi-restraints excluded: chain O residue 616 THR Chi-restraints excluded: chain P residue 519 ILE Chi-restraints excluded: chain P residue 616 THR Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 616 THR Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 244 ASP Chi-restraints excluded: chain R residue 519 ILE Chi-restraints excluded: chain R residue 616 THR Chi-restraints excluded: chain S residue 239 ILE Chi-restraints excluded: chain S residue 244 ASP Chi-restraints excluded: chain S residue 519 ILE Chi-restraints excluded: chain S residue 616 THR Chi-restraints excluded: chain T residue 244 ASP Chi-restraints excluded: chain T residue 392 VAL Chi-restraints excluded: chain T residue 616 THR Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 244 ASP Chi-restraints excluded: chain U residue 519 ILE Chi-restraints excluded: chain U residue 616 THR Chi-restraints excluded: chain V residue 239 ILE Chi-restraints excluded: chain V residue 244 ASP Chi-restraints excluded: chain V residue 519 ILE Chi-restraints excluded: chain V residue 616 THR Chi-restraints excluded: chain W residue 239 ILE Chi-restraints excluded: chain W residue 616 THR Chi-restraints excluded: chain X residue 239 ILE Chi-restraints excluded: chain X residue 244 ASP Chi-restraints excluded: chain X residue 519 ILE Chi-restraints excluded: chain X residue 616 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 457 optimal weight: 10.0000 chunk 295 optimal weight: 8.9990 chunk 442 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 470 optimal weight: 6.9990 chunk 504 optimal weight: 1.9990 chunk 365 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 581 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 GLN B 544 GLN E 544 GLN G 544 GLN M 236 GLN M 544 GLN P 236 GLN P 486 GLN P 544 GLN R 544 GLN S 236 GLN S 544 GLN U 486 GLN U 544 GLN V 544 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 60072 Z= 0.333 Angle : 0.499 6.561 81072 Z= 0.264 Chirality : 0.044 0.125 9528 Planarity : 0.004 0.036 10368 Dihedral : 6.085 49.445 8208 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.75 % Allowed : 15.05 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.64 (0.10), residues: 7512 helix: 1.89 (0.11), residues: 2136 sheet: 0.12 (0.15), residues: 1128 loop : -1.94 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 584 HIS 0.005 0.001 HIS N 603 PHE 0.013 0.002 PHE J 561 TYR 0.006 0.002 TYR T 493 ARG 0.003 0.000 ARG B 451 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15024 Ramachandran restraints generated. 7512 Oldfield, 0 Emsley, 7512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15024 Ramachandran restraints generated. 7512 Oldfield, 0 Emsley, 7512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 510 time to evaluate : 5.197 Fit side-chains REVERT: A 580 MET cc_start: 0.8660 (tpp) cc_final: 0.8424 (tpp) REVERT: A 616 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8783 (t) REVERT: B 248 MET cc_start: 0.5057 (mtt) cc_final: 0.4524 (mtt) REVERT: B 580 MET cc_start: 0.8640 (tpp) cc_final: 0.8390 (tpp) REVERT: B 616 THR cc_start: 0.9075 (OUTLIER) cc_final: 0.8826 (t) REVERT: C 580 MET cc_start: 0.8655 (tpp) cc_final: 0.8426 (tpp) REVERT: C 616 THR cc_start: 0.9074 (OUTLIER) cc_final: 0.8825 (t) REVERT: D 248 MET cc_start: 0.6100 (mmm) cc_final: 0.5508 (mtt) REVERT: D 422 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8087 (mtt) REVERT: D 580 MET cc_start: 0.8649 (tpp) cc_final: 0.8419 (tpp) REVERT: D 616 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8824 (t) REVERT: D 630 MET cc_start: 0.8189 (mmm) cc_final: 0.7871 (mmm) REVERT: E 225 MET cc_start: 0.6425 (mmp) cc_final: 0.6018 (mmp) REVERT: E 248 MET cc_start: 0.6137 (mtm) cc_final: 0.5830 (mtt) REVERT: E 411 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8296 (mp) REVERT: E 616 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8819 (t) REVERT: F 225 MET cc_start: 0.6715 (mmp) cc_final: 0.6501 (mmp) REVERT: F 580 MET cc_start: 0.8661 (tpp) cc_final: 0.8114 (mmt) REVERT: F 616 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8817 (t) REVERT: G 248 MET cc_start: 0.6650 (mtm) cc_final: 0.6390 (mtt) REVERT: G 616 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8829 (t) REVERT: H 616 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8832 (t) REVERT: I 248 MET cc_start: 0.6658 (mtm) cc_final: 0.6420 (mtt) REVERT: I 616 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8797 (t) REVERT: J 248 MET cc_start: 0.6648 (mtm) cc_final: 0.6396 (mtt) REVERT: J 580 MET cc_start: 0.8639 (tpp) cc_final: 0.8407 (tpp) REVERT: J 616 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8810 (t) REVERT: K 248 MET cc_start: 0.6030 (mmm) cc_final: 0.5781 (mtt) REVERT: K 580 MET cc_start: 0.8653 (tpp) cc_final: 0.8422 (tpp) REVERT: K 616 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8822 (t) REVERT: L 225 MET cc_start: 0.6510 (mmp) cc_final: 0.6004 (mmp) REVERT: L 451 ARG cc_start: 0.8422 (mtp180) cc_final: 0.8179 (mtp85) REVERT: L 580 MET cc_start: 0.8662 (tpp) cc_final: 0.8112 (mmt) REVERT: L 616 THR cc_start: 0.9079 (OUTLIER) cc_final: 0.8831 (t) REVERT: M 411 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8278 (mp) REVERT: M 422 MET cc_start: 0.8343 (mtt) cc_final: 0.8088 (mtt) REVERT: M 616 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8766 (t) REVERT: N 453 LEU cc_start: 0.8005 (mt) cc_final: 0.7798 (mt) REVERT: N 543 MET cc_start: 0.8766 (ptp) cc_final: 0.8480 (ptp) REVERT: N 580 MET cc_start: 0.8645 (tpp) cc_final: 0.8416 (tpp) REVERT: N 616 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8804 (t) REVERT: O 225 MET cc_start: 0.6557 (mmp) cc_final: 0.6350 (mmt) REVERT: O 580 MET cc_start: 0.8643 (tpp) cc_final: 0.8411 (tpp) REVERT: O 616 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8814 (t) REVERT: P 225 MET cc_start: 0.6377 (mmp) cc_final: 0.6023 (mmt) REVERT: P 616 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8815 (t) REVERT: Q 616 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8834 (t) REVERT: R 225 MET cc_start: 0.6556 (mmp) cc_final: 0.6015 (mmp) REVERT: R 580 MET cc_start: 0.8657 (tpp) cc_final: 0.8423 (tpp) REVERT: R 616 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8782 (t) REVERT: S 616 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8781 (t) REVERT: T 248 MET cc_start: 0.6070 (mmm) cc_final: 0.5798 (mtt) REVERT: T 580 MET cc_start: 0.8646 (tpp) cc_final: 0.8410 (tpp) REVERT: T 616 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8759 (t) REVERT: U 534 ARG cc_start: 0.8339 (mtm180) cc_final: 0.8109 (mtm110) REVERT: U 580 MET cc_start: 0.8647 (tpp) cc_final: 0.8412 (tpp) REVERT: U 616 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8813 (t) REVERT: V 616 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8806 (t) REVERT: W 248 MET cc_start: 0.6151 (mmm) cc_final: 0.5430 (mtt) REVERT: W 616 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8826 (t) REVERT: X 616 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8817 (t) outliers start: 114 outliers final: 68 residues processed: 618 average time/residue: 0.5321 time to fit residues: 571.5339 Evaluate side-chains 596 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 501 time to evaluate : 5.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 616 THR Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 616 THR Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 616 THR Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 244 ASP Chi-restraints excluded: chain I residue 435 THR Chi-restraints excluded: chain I residue 519 ILE Chi-restraints excluded: chain I residue 616 THR Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 519 ILE Chi-restraints excluded: chain J residue 616 THR Chi-restraints excluded: chain K residue 239 ILE Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 616 THR Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 616 THR Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 411 ILE Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 616 THR Chi-restraints excluded: chain N residue 244 ASP Chi-restraints excluded: chain N residue 616 THR Chi-restraints excluded: chain O residue 223 GLU Chi-restraints excluded: chain O residue 239 ILE Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 435 THR Chi-restraints excluded: chain O residue 519 ILE Chi-restraints excluded: chain O residue 616 THR Chi-restraints excluded: chain P residue 223 GLU Chi-restraints excluded: chain P residue 239 ILE Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 519 ILE Chi-restraints excluded: chain P residue 616 THR Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 616 THR Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 244 ASP Chi-restraints excluded: chain R residue 519 ILE Chi-restraints excluded: chain R residue 616 THR Chi-restraints excluded: chain S residue 239 ILE Chi-restraints excluded: chain S residue 244 ASP Chi-restraints excluded: chain S residue 519 ILE Chi-restraints excluded: chain S residue 616 THR Chi-restraints excluded: chain T residue 244 ASP Chi-restraints excluded: chain T residue 392 VAL Chi-restraints excluded: chain T residue 616 THR Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 244 ASP Chi-restraints excluded: chain U residue 519 ILE Chi-restraints excluded: chain U residue 616 THR Chi-restraints excluded: chain V residue 239 ILE Chi-restraints excluded: chain V residue 244 ASP Chi-restraints excluded: chain V residue 519 ILE Chi-restraints excluded: chain V residue 616 THR Chi-restraints excluded: chain W residue 239 ILE Chi-restraints excluded: chain W residue 244 ASP Chi-restraints excluded: chain W residue 392 VAL Chi-restraints excluded: chain W residue 616 THR Chi-restraints excluded: chain X residue 239 ILE Chi-restraints excluded: chain X residue 244 ASP Chi-restraints excluded: chain X residue 519 ILE Chi-restraints excluded: chain X residue 616 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 673 optimal weight: 6.9990 chunk 709 optimal weight: 40.0000 chunk 647 optimal weight: 5.9990 chunk 689 optimal weight: 1.9990 chunk 708 optimal weight: 30.0000 chunk 415 optimal weight: 2.9990 chunk 300 optimal weight: 0.8980 chunk 541 optimal weight: 5.9990 chunk 211 optimal weight: 0.0670 chunk 623 optimal weight: 2.9990 chunk 652 optimal weight: 6.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 236 GLN D 544 GLN E 236 GLN ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 544 GLN G 236 GLN ** I 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 544 GLN P 236 GLN P 486 GLN P 544 GLN Q 544 GLN R 236 GLN R 544 GLN S 236 GLN S 544 GLN U 486 GLN V 236 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 60072 Z= 0.224 Angle : 0.457 6.618 81072 Z= 0.242 Chirality : 0.043 0.144 9528 Planarity : 0.004 0.035 10368 Dihedral : 5.821 49.193 8208 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.49 % Allowed : 15.28 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.10), residues: 7512 helix: 2.12 (0.11), residues: 2136 sheet: 0.29 (0.15), residues: 1128 loop : -1.89 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 584 HIS 0.004 0.001 HIS F 603 PHE 0.011 0.001 PHE S 394 TYR 0.005 0.001 TYR B 493 ARG 0.003 0.000 ARG W 451 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15024 Ramachandran restraints generated. 7512 Oldfield, 0 Emsley, 7512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15024 Ramachandran restraints generated. 7512 Oldfield, 0 Emsley, 7512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 521 time to evaluate : 5.103 Fit side-chains REVERT: A 248 MET cc_start: 0.6307 (mtm) cc_final: 0.6095 (mtt) REVERT: A 580 MET cc_start: 0.8621 (tpp) cc_final: 0.8124 (mmt) REVERT: A 616 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8774 (t) REVERT: B 248 MET cc_start: 0.5083 (mtt) cc_final: 0.4555 (mtt) REVERT: B 580 MET cc_start: 0.8620 (tpp) cc_final: 0.8123 (mmt) REVERT: B 616 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8781 (t) REVERT: C 543 MET cc_start: 0.8569 (ptp) cc_final: 0.8368 (mtm) REVERT: C 580 MET cc_start: 0.8618 (tpp) cc_final: 0.8094 (mmt) REVERT: C 616 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8768 (t) REVERT: D 248 MET cc_start: 0.6117 (mmm) cc_final: 0.5827 (mtt) REVERT: D 580 MET cc_start: 0.8613 (tpp) cc_final: 0.8091 (mmt) REVERT: D 616 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8765 (t) REVERT: D 630 MET cc_start: 0.8121 (mmm) cc_final: 0.7825 (mmm) REVERT: E 411 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8311 (mp) REVERT: E 580 MET cc_start: 0.8516 (tpp) cc_final: 0.8093 (mmt) REVERT: E 616 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8758 (t) REVERT: F 225 MET cc_start: 0.6759 (mmp) cc_final: 0.6554 (mmp) REVERT: F 248 MET cc_start: 0.6227 (mmm) cc_final: 0.5886 (mmm) REVERT: F 580 MET cc_start: 0.8620 (tpp) cc_final: 0.8125 (mmt) REVERT: F 616 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8775 (t) REVERT: G 225 MET cc_start: 0.6572 (mmp) cc_final: 0.6086 (mmp) REVERT: G 248 MET cc_start: 0.6572 (mtm) cc_final: 0.6340 (mtt) REVERT: G 580 MET cc_start: 0.8529 (tpp) cc_final: 0.8070 (mmt) REVERT: G 616 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8772 (t) REVERT: G 626 ARG cc_start: 0.8138 (mtt90) cc_final: 0.7708 (mtm-85) REVERT: H 248 MET cc_start: 0.6417 (mtm) cc_final: 0.6153 (mtt) REVERT: H 580 MET cc_start: 0.8542 (tpp) cc_final: 0.8121 (mmt) REVERT: H 616 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8778 (t) REVERT: I 580 MET cc_start: 0.8503 (tpp) cc_final: 0.8044 (mmt) REVERT: I 616 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8756 (t) REVERT: I 626 ARG cc_start: 0.8135 (mtt90) cc_final: 0.7692 (mtm-85) REVERT: J 248 MET cc_start: 0.6550 (mtm) cc_final: 0.6346 (mtt) REVERT: J 580 MET cc_start: 0.8606 (tpp) cc_final: 0.8083 (mmt) REVERT: J 616 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8770 (t) REVERT: K 248 MET cc_start: 0.6051 (mmm) cc_final: 0.5646 (mtt) REVERT: K 580 MET cc_start: 0.8627 (tpp) cc_final: 0.8134 (mmt) REVERT: K 616 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8765 (t) REVERT: L 451 ARG cc_start: 0.8416 (mtp180) cc_final: 0.8177 (mtp85) REVERT: L 580 MET cc_start: 0.8616 (tpp) cc_final: 0.8126 (mmt) REVERT: L 616 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8777 (t) REVERT: L 626 ARG cc_start: 0.7944 (mtm-85) cc_final: 0.7620 (mtt90) REVERT: M 248 MET cc_start: 0.6225 (mtm) cc_final: 0.6024 (mtt) REVERT: M 411 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8244 (mp) REVERT: M 422 MET cc_start: 0.8258 (mtt) cc_final: 0.8023 (mtt) REVERT: M 580 MET cc_start: 0.8527 (tpp) cc_final: 0.8053 (mmt) REVERT: M 616 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8790 (t) REVERT: N 248 MET cc_start: 0.6417 (mmm) cc_final: 0.6193 (mtt) REVERT: N 580 MET cc_start: 0.8610 (tpp) cc_final: 0.8086 (mmt) REVERT: N 616 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8764 (t) REVERT: O 225 MET cc_start: 0.6484 (mmp) cc_final: 0.6282 (mmt) REVERT: O 580 MET cc_start: 0.8608 (tpp) cc_final: 0.8112 (mmt) REVERT: O 616 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8759 (t) REVERT: O 626 ARG cc_start: 0.8087 (mtm-85) cc_final: 0.7785 (mtm-85) REVERT: P 248 MET cc_start: 0.6263 (mtm) cc_final: 0.6015 (mtt) REVERT: P 580 MET cc_start: 0.8528 (tpp) cc_final: 0.8043 (mmt) REVERT: P 616 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8759 (t) REVERT: Q 580 MET cc_start: 0.8535 (tpp) cc_final: 0.8113 (mmt) REVERT: Q 616 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8781 (t) REVERT: R 225 MET cc_start: 0.6484 (mmp) cc_final: 0.5964 (mmp) REVERT: R 580 MET cc_start: 0.8617 (tpp) cc_final: 0.8099 (mmt) REVERT: R 616 THR cc_start: 0.9031 (OUTLIER) cc_final: 0.8779 (t) REVERT: S 225 MET cc_start: 0.6519 (mmp) cc_final: 0.6027 (mmp) REVERT: S 580 MET cc_start: 0.8535 (tpp) cc_final: 0.8077 (mmt) REVERT: S 616 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8777 (t) REVERT: T 248 MET cc_start: 0.6154 (mmm) cc_final: 0.5733 (mtt) REVERT: T 580 MET cc_start: 0.8605 (tpp) cc_final: 0.8075 (mmt) REVERT: T 616 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8768 (t) REVERT: U 580 MET cc_start: 0.8610 (tpp) cc_final: 0.8082 (mmt) REVERT: U 616 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8757 (t) REVERT: U 626 ARG cc_start: 0.8102 (mtt90) cc_final: 0.7584 (mtt90) REVERT: V 580 MET cc_start: 0.8565 (tpp) cc_final: 0.8061 (mmt) REVERT: V 616 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8758 (t) REVERT: W 248 MET cc_start: 0.6151 (mmm) cc_final: 0.5147 (mtt) REVERT: W 580 MET cc_start: 0.8540 (tpp) cc_final: 0.8116 (mmt) REVERT: W 616 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8772 (t) REVERT: X 580 MET cc_start: 0.8513 (tpp) cc_final: 0.8055 (mmt) REVERT: X 616 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8772 (t) outliers start: 97 outliers final: 54 residues processed: 615 average time/residue: 0.5283 time to fit residues: 563.3905 Evaluate side-chains 581 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 501 time to evaluate : 5.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 616 THR Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 616 THR Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 616 THR Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 244 ASP Chi-restraints excluded: chain I residue 519 ILE Chi-restraints excluded: chain I residue 616 THR Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 519 ILE Chi-restraints excluded: chain J residue 616 THR Chi-restraints excluded: chain K residue 239 ILE Chi-restraints excluded: chain K residue 616 THR Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 616 THR Chi-restraints excluded: chain M residue 239 ILE Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 411 ILE Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 616 THR Chi-restraints excluded: chain N residue 392 VAL Chi-restraints excluded: chain N residue 616 THR Chi-restraints excluded: chain O residue 223 GLU Chi-restraints excluded: chain O residue 239 ILE Chi-restraints excluded: chain O residue 435 THR Chi-restraints excluded: chain O residue 519 ILE Chi-restraints excluded: chain O residue 616 THR Chi-restraints excluded: chain P residue 239 ILE Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 519 ILE Chi-restraints excluded: chain P residue 616 THR Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 616 THR Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 519 ILE Chi-restraints excluded: chain R residue 616 THR Chi-restraints excluded: chain S residue 239 ILE Chi-restraints excluded: chain S residue 519 ILE Chi-restraints excluded: chain S residue 616 THR Chi-restraints excluded: chain T residue 616 THR Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 244 ASP Chi-restraints excluded: chain U residue 519 ILE Chi-restraints excluded: chain U residue 616 THR Chi-restraints excluded: chain V residue 239 ILE Chi-restraints excluded: chain V residue 519 ILE Chi-restraints excluded: chain V residue 616 THR Chi-restraints excluded: chain W residue 239 ILE Chi-restraints excluded: chain W residue 392 VAL Chi-restraints excluded: chain W residue 616 THR Chi-restraints excluded: chain X residue 239 ILE Chi-restraints excluded: chain X residue 244 ASP Chi-restraints excluded: chain X residue 519 ILE Chi-restraints excluded: chain X residue 616 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 687 optimal weight: 2.9990 chunk 452 optimal weight: 7.9990 chunk 729 optimal weight: 6.9990 chunk 445 optimal weight: 6.9990 chunk 346 optimal weight: 4.9990 chunk 507 optimal weight: 6.9990 chunk 765 optimal weight: 2.9990 chunk 704 optimal weight: 0.7980 chunk 609 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 470 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 GLN C 236 GLN E 236 GLN G 236 GLN H 544 GLN ** I 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 544 GLN M 236 GLN P 236 GLN P 486 GLN P 544 GLN Q 544 GLN R 236 GLN R 544 GLN S 236 GLN S 544 GLN U 486 GLN U 544 GLN V 236 GLN V 486 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 60072 Z= 0.334 Angle : 0.508 5.939 81072 Z= 0.268 Chirality : 0.044 0.151 9528 Planarity : 0.004 0.045 10368 Dihedral : 5.966 48.887 8208 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.46 % Allowed : 15.56 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.56 (0.10), residues: 7512 helix: 1.96 (0.11), residues: 2136 sheet: 0.40 (0.16), residues: 1080 loop : -1.94 (0.09), residues: 4296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 584 HIS 0.005 0.001 HIS N 603 PHE 0.014 0.002 PHE E 394 TYR 0.006 0.002 TYR N 493 ARG 0.004 0.000 ARG M 626 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15024 Ramachandran restraints generated. 7512 Oldfield, 0 Emsley, 7512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15024 Ramachandran restraints generated. 7512 Oldfield, 0 Emsley, 7512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 500 time to evaluate : 5.133 Fit side-chains REVERT: A 248 MET cc_start: 0.6435 (mtm) cc_final: 0.6200 (mtt) REVERT: A 580 MET cc_start: 0.8652 (tpp) cc_final: 0.8420 (tpp) REVERT: A 616 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8788 (t) REVERT: B 580 MET cc_start: 0.8642 (tpp) cc_final: 0.8413 (tpp) REVERT: B 616 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8833 (t) REVERT: C 580 MET cc_start: 0.8644 (tpp) cc_final: 0.8417 (tpp) REVERT: C 616 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8793 (t) REVERT: D 580 MET cc_start: 0.8642 (tpp) cc_final: 0.8415 (tpp) REVERT: D 616 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8810 (t) REVERT: D 630 MET cc_start: 0.8226 (mmm) cc_final: 0.7906 (mmm) REVERT: E 411 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8279 (mp) REVERT: E 616 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8815 (t) REVERT: F 543 MET cc_start: 0.8844 (ptp) cc_final: 0.8640 (mtp) REVERT: F 580 MET cc_start: 0.8654 (tpp) cc_final: 0.8416 (tpp) REVERT: F 616 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8824 (t) REVERT: G 225 MET cc_start: 0.6613 (mmp) cc_final: 0.6108 (mmp) REVERT: G 248 MET cc_start: 0.6642 (mtm) cc_final: 0.6373 (mtm) REVERT: G 616 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8831 (t) REVERT: H 616 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8831 (t) REVERT: I 248 MET cc_start: 0.5609 (mtt) cc_final: 0.5368 (mtt) REVERT: I 616 THR cc_start: 0.9031 (OUTLIER) cc_final: 0.8799 (t) REVERT: J 248 MET cc_start: 0.6632 (mtm) cc_final: 0.6384 (mtm) REVERT: J 580 MET cc_start: 0.8637 (tpp) cc_final: 0.8412 (tpp) REVERT: J 616 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8813 (t) REVERT: K 580 MET cc_start: 0.8644 (tpp) cc_final: 0.8103 (mmt) REVERT: K 616 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8820 (t) REVERT: L 580 MET cc_start: 0.8652 (tpp) cc_final: 0.8413 (tpp) REVERT: L 616 THR cc_start: 0.9079 (OUTLIER) cc_final: 0.8845 (t) REVERT: M 411 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8288 (mp) REVERT: M 422 MET cc_start: 0.8320 (mtt) cc_final: 0.8101 (mtt) REVERT: M 616 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8778 (t) REVERT: N 248 MET cc_start: 0.5990 (mmm) cc_final: 0.5599 (mtt) REVERT: N 580 MET cc_start: 0.8640 (tpp) cc_final: 0.8413 (tpp) REVERT: N 616 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8819 (t) REVERT: O 580 MET cc_start: 0.8635 (tpp) cc_final: 0.8408 (tpp) REVERT: O 616 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8801 (t) REVERT: O 626 ARG cc_start: 0.8160 (mtm-85) cc_final: 0.7824 (mtm-85) REVERT: P 225 MET cc_start: 0.6442 (mmt) cc_final: 0.6172 (mmp) REVERT: P 616 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8815 (t) REVERT: Q 616 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8841 (t) REVERT: R 580 MET cc_start: 0.8649 (tpp) cc_final: 0.8419 (tpp) REVERT: R 616 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8798 (t) REVERT: S 225 MET cc_start: 0.6607 (mmp) cc_final: 0.6106 (mmp) REVERT: S 616 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8800 (t) REVERT: T 580 MET cc_start: 0.8642 (tpp) cc_final: 0.8408 (tpp) REVERT: T 616 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8757 (t) REVERT: U 580 MET cc_start: 0.8625 (tpp) cc_final: 0.8394 (tpp) REVERT: U 616 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8827 (t) REVERT: V 616 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8812 (t) REVERT: W 616 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8821 (t) REVERT: X 616 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8814 (t) outliers start: 95 outliers final: 65 residues processed: 593 average time/residue: 0.5203 time to fit residues: 537.2693 Evaluate side-chains 581 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 490 time to evaluate : 5.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 616 THR Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 616 THR Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 616 THR Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 244 ASP Chi-restraints excluded: chain I residue 435 THR Chi-restraints excluded: chain I residue 519 ILE Chi-restraints excluded: chain I residue 616 THR Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 519 ILE Chi-restraints excluded: chain J residue 616 THR Chi-restraints excluded: chain K residue 239 ILE Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 616 THR Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 616 THR Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 411 ILE Chi-restraints excluded: chain M residue 519 ILE Chi-restraints excluded: chain M residue 616 THR Chi-restraints excluded: chain N residue 392 VAL Chi-restraints excluded: chain N residue 435 THR Chi-restraints excluded: chain N residue 616 THR Chi-restraints excluded: chain O residue 223 GLU Chi-restraints excluded: chain O residue 239 ILE Chi-restraints excluded: chain O residue 244 ASP Chi-restraints excluded: chain O residue 435 THR Chi-restraints excluded: chain O residue 519 ILE Chi-restraints excluded: chain O residue 616 THR Chi-restraints excluded: chain P residue 239 ILE Chi-restraints excluded: chain P residue 244 ASP Chi-restraints excluded: chain P residue 519 ILE Chi-restraints excluded: chain P residue 616 THR Chi-restraints excluded: chain Q residue 239 ILE Chi-restraints excluded: chain Q residue 244 ASP Chi-restraints excluded: chain Q residue 616 THR Chi-restraints excluded: chain R residue 239 ILE Chi-restraints excluded: chain R residue 244 ASP Chi-restraints excluded: chain R residue 519 ILE Chi-restraints excluded: chain R residue 616 THR Chi-restraints excluded: chain S residue 239 ILE Chi-restraints excluded: chain S residue 519 ILE Chi-restraints excluded: chain S residue 616 THR Chi-restraints excluded: chain T residue 244 ASP Chi-restraints excluded: chain T residue 616 THR Chi-restraints excluded: chain U residue 239 ILE Chi-restraints excluded: chain U residue 244 ASP Chi-restraints excluded: chain U residue 519 ILE Chi-restraints excluded: chain U residue 616 THR Chi-restraints excluded: chain V residue 244 ASP Chi-restraints excluded: chain V residue 519 ILE Chi-restraints excluded: chain V residue 616 THR Chi-restraints excluded: chain W residue 239 ILE Chi-restraints excluded: chain W residue 244 ASP Chi-restraints excluded: chain W residue 392 VAL Chi-restraints excluded: chain W residue 616 THR Chi-restraints excluded: chain X residue 239 ILE Chi-restraints excluded: chain X residue 244 ASP Chi-restraints excluded: chain X residue 519 ILE Chi-restraints excluded: chain X residue 616 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 373 optimal weight: 0.8980 chunk 483 optimal weight: 10.0000 chunk 649 optimal weight: 0.9980 chunk 186 optimal weight: 0.9980 chunk 561 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 610 optimal weight: 30.0000 chunk 255 optimal weight: 3.9990 chunk 626 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 GLN C 236 GLN E 236 GLN ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 544 GLN G 236 GLN ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 544 GLN ** I 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 544 GLN ** K 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 236 GLN ** O 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 236 GLN P 486 GLN Q 544 GLN R 236 GLN R 544 GLN S 236 GLN S 544 GLN U 486 GLN ** U 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 236 GLN ** V 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.155133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.098566 restraints weight = 70894.210| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.21 r_work: 0.2981 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 60072 Z= 0.178 Angle : 0.445 7.471 81072 Z= 0.236 Chirality : 0.043 0.150 9528 Planarity : 0.004 0.037 10368 Dihedral : 5.616 49.105 8208 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.37 % Allowed : 15.39 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.35 (0.10), residues: 7512 helix: 2.30 (0.11), residues: 2136 sheet: 0.36 (0.16), residues: 1128 loop : -1.88 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 420 HIS 0.003 0.001 HIS N 603 PHE 0.011 0.001 PHE G 394 TYR 0.004 0.001 TYR K 493 ARG 0.003 0.000 ARG M 626 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11986.58 seconds wall clock time: 212 minutes 17.64 seconds (12737.64 seconds total)