Starting phenix.real_space_refine on Fri Dec 8 18:18:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9k_12104/12_2023/7b9k_12104_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9k_12104/12_2023/7b9k_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_12104/12_2023/7b9k_12104.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9k_12104/12_2023/7b9k_12104.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9k_12104/12_2023/7b9k_12104_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b9k_12104/12_2023/7b9k_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-1.21rc1-5172/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: 22.19, 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: 17.08 Conformation dependent library (CDL) restraints added in 7.7 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: 7.94 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: 19.43 Time building geometry restraints manager: 19.00 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 7.740 Check model and map are aligned: 0.650 Set scattering table: 0.410 Process input model: 117.080 Find NCS groups from input model: 3.520 Set up NCS constraints: 0.480 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: 0.020 Load rotamer database and sin/cos tables:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.140 ------------------------------------------------------------------------------- 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 : 5.037 Fit side-chains outliers start: 72 outliers final: 9 residues processed: 863 average time/residue: 0.5670 time to fit residues: 818.5170 Evaluate side-chains 563 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 554 time to evaluate : 4.986 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4067 time to fit residues: 13.8331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 40.0000 chunk 322 optimal weight: 20.0000 chunk 198 optimal weight: 40.0000 chunk 392 optimal weight: 10.0000 chunk 310 optimal weight: 10.0000 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 I 236 GLN I 544 GLN J 236 GLN J 544 GLN K 236 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: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 60072 Z= 0.492 Angle : 0.601 5.709 81072 Z= 0.318 Chirality : 0.047 0.143 9528 Planarity : 0.005 0.041 10368 Dihedral : 10.403 115.124 8208 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.09 % Allowed : 11.85 % Favored : 87.05 % 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: 0.53 (0.11), residues: 2136 sheet: -1.07 (0.13), residues: 1128 loop : -2.76 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP M 584 HIS 0.005 0.002 HIS G 603 PHE 0.018 0.002 PHE E 561 TYR 0.011 0.003 TYR N 493 ARG 0.004 0.000 ARG M 626 *********************** 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 634 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 563 time to evaluate : 5.056 Fit side-chains outliers start: 71 outliers final: 43 residues processed: 620 average time/residue: 0.5730 time to fit residues: 603.4031 Evaluate side-chains 575 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 532 time to evaluate : 4.970 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.4079 time to fit residues: 40.7387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 580 optimal weight: 30.0000 chunk 474 optimal weight: 0.9980 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: 0.9980 chunk 238 optimal weight: 2.9990 chunk 560 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 F 236 GLN G 236 GLN H 236 GLN I 236 GLN J 236 GLN K 236 GLN K 544 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: 0.8015 moved from start: 0.1748 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= 0.198 Angle : 0.465 4.561 81072 Z= 0.248 Chirality : 0.043 0.128 9528 Planarity : 0.004 0.041 10368 Dihedral : 8.821 105.948 8208 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.95 % Allowed : 12.64 % Favored : 86.41 % 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: -1.50 (0.09), residues: 7512 helix: 1.46 (0.11), residues: 2136 sheet: -0.67 (0.14), residues: 1128 loop : -2.56 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 584 HIS 0.004 0.001 HIS E 603 PHE 0.009 0.001 PHE H 561 TYR 0.005 0.001 TYR E 493 ARG 0.004 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 644 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 582 time to evaluate : 5.061 Fit side-chains outliers start: 62 outliers final: 19 residues processed: 642 average time/residue: 0.5812 time to fit residues: 627.2808 Evaluate side-chains 542 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 523 time to evaluate : 5.000 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.4370 time to fit residues: 22.9061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 690 optimal weight: 0.9990 chunk 525 optimal weight: 8.9990 chunk 362 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 333 optimal weight: 4.9990 chunk 469 optimal weight: 6.9990 chunk 701 optimal weight: 0.7980 chunk 742 optimal weight: 40.0000 chunk 366 optimal weight: 0.2980 chunk 664 optimal weight: 0.9990 chunk 200 optimal weight: 8.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN B 544 GLN C 236 GLN D 236 GLN F 236 GLN G 236 GLN H 236 GLN I 236 GLN J 236 GLN K 236 GLN L 236 GLN N 236 GLN O 236 GLN O 544 GLN Q 236 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: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 60072 Z= 0.174 Angle : 0.457 6.690 81072 Z= 0.244 Chirality : 0.043 0.130 9528 Planarity : 0.004 0.040 10368 Dihedral : 7.576 90.920 8208 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.15 % Allowed : 14.19 % Favored : 85.65 % 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: -1.06 (0.10), residues: 7512 helix: 1.93 (0.12), residues: 2136 sheet: -0.36 (0.15), residues: 1128 loop : -2.37 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 584 HIS 0.004 0.001 HIS E 603 PHE 0.008 0.001 PHE T 614 TYR 0.003 0.001 TYR F 493 ARG 0.006 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 562 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 552 time to evaluate : 5.101 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 558 average time/residue: 0.5813 time to fit residues: 546.7784 Evaluate side-chains 519 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 516 time to evaluate : 5.039 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4723 time to fit residues: 9.4272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 618 optimal weight: 10.0000 chunk 421 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 552 optimal weight: 6.9990 chunk 306 optimal weight: 5.9990 chunk 633 optimal weight: 5.9990 chunk 513 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 379 optimal weight: 2.9990 chunk 666 optimal weight: 10.0000 chunk 187 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 GLN C 544 GLN D 544 GLN E 236 GLN G 486 GLN G 544 GLN I 544 GLN J 544 GLN L 544 GLN M 236 GLN M 544 GLN P 236 GLN P 544 GLN Q 544 GLN R 544 GLN S 544 GLN T 544 GLN U 486 GLN V 486 GLN V 544 GLN W 544 GLN X 486 GLN X 544 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 60072 Z= 0.505 Angle : 0.588 5.681 81072 Z= 0.310 Chirality : 0.047 0.128 9528 Planarity : 0.004 0.036 10368 Dihedral : 7.354 75.450 8208 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.83 % Allowed : 15.19 % Favored : 83.98 % 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: -1.21 (0.09), residues: 7512 helix: 1.48 (0.11), residues: 2136 sheet: -0.49 (0.14), residues: 1128 loop : -2.24 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP W 584 HIS 0.005 0.001 HIS M 603 PHE 0.017 0.002 PHE H 561 TYR 0.009 0.003 TYR T 493 ARG 0.005 0.000 ARG S 626 *********************** 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 587 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 533 time to evaluate : 5.043 Fit side-chains outliers start: 54 outliers final: 36 residues processed: 582 average time/residue: 0.5735 time to fit residues: 575.4893 Evaluate side-chains 545 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 509 time to evaluate : 5.009 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.4133 time to fit residues: 35.6709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 249 optimal weight: 0.9980 chunk 668 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 435 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 743 optimal weight: 3.9990 chunk 616 optimal weight: 0.3980 chunk 344 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 245 optimal weight: 0.5980 chunk 390 optimal weight: 50.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 C 544 GLN D 236 GLN E 236 GLN F 236 GLN G 236 GLN H 236 GLN I 236 GLN J 236 GLN L 236 GLN L 544 GLN M 236 GLN N 236 GLN O 236 GLN P 236 GLN P 486 GLN P 544 GLN Q 236 GLN Q 544 GLN R 236 GLN R 544 GLN S 236 GLN S 544 GLN U 236 GLN V 236 GLN V 544 GLN W 236 GLN X 236 GLN X 544 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 60072 Z= 0.146 Angle : 0.439 5.045 81072 Z= 0.234 Chirality : 0.043 0.130 9528 Planarity : 0.004 0.040 10368 Dihedral : 6.140 57.111 8208 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.34 % Allowed : 14.73 % Favored : 84.93 % 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: -0.70 (0.10), residues: 7512 helix: 2.14 (0.12), residues: 2136 sheet: -0.05 (0.15), residues: 1128 loop : -2.11 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 389 HIS 0.004 0.001 HIS N 603 PHE 0.009 0.001 PHE A 614 TYR 0.004 0.001 TYR K 493 ARG 0.006 0.000 ARG C 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 567 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 545 time to evaluate : 5.016 Fit side-chains outliers start: 22 outliers final: 7 residues processed: 563 average time/residue: 0.5779 time to fit residues: 549.1109 Evaluate side-chains 514 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 507 time to evaluate : 4.986 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4059 time to fit residues: 12.3963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 423 optimal weight: 0.8980 chunk 542 optimal weight: 4.9990 chunk 420 optimal weight: 5.9990 chunk 625 optimal weight: 6.9990 chunk 414 optimal weight: 4.9990 chunk 740 optimal weight: 30.0000 chunk 463 optimal weight: 4.9990 chunk 451 optimal weight: 20.0000 chunk 341 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 C 486 GLN D 236 GLN E 236 GLN F 236 GLN G 236 GLN H 236 GLN I 236 GLN J 236 GLN K 544 GLN L 236 GLN M 236 GLN N 236 GLN O 236 GLN O 544 GLN P 236 GLN P 486 GLN P 544 GLN Q 236 GLN R 236 GLN R 486 GLN S 236 GLN T 544 GLN U 236 GLN U 486 GLN U 544 GLN V 236 GLN W 236 GLN X 236 GLN X 486 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2384 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= 0.298 Angle : 0.493 6.198 81072 Z= 0.260 Chirality : 0.044 0.126 9528 Planarity : 0.004 0.037 10368 Dihedral : 6.183 54.650 8208 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.60 % Allowed : 15.48 % Favored : 83.92 % 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: -0.70 (0.10), residues: 7512 helix: 2.02 (0.11), residues: 2136 sheet: -0.03 (0.15), residues: 1128 loop : -2.05 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP V 584 HIS 0.004 0.001 HIS F 603 PHE 0.013 0.001 PHE G 561 TYR 0.005 0.002 TYR F 493 ARG 0.005 0.000 ARG P 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 546 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 507 time to evaluate : 5.416 Fit side-chains outliers start: 39 outliers final: 16 residues processed: 541 average time/residue: 0.5380 time to fit residues: 507.1708 Evaluate side-chains 511 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 495 time to evaluate : 4.979 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.4132 time to fit residues: 19.5315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 457 optimal weight: 0.2980 chunk 295 optimal weight: 7.9990 chunk 442 optimal weight: 3.9990 chunk 222 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 470 optimal weight: 7.9990 chunk 504 optimal weight: 2.9990 chunk 365 optimal weight: 1.9990 chunk 68 optimal weight: 0.0670 chunk 581 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 F 236 GLN G 236 GLN H 236 GLN I 236 GLN I 544 GLN J 236 GLN J 544 GLN L 236 GLN M 236 GLN P 236 GLN P 486 GLN Q 236 GLN R 236 GLN S 236 GLN U 236 GLN U 486 GLN U 544 GLN V 236 GLN X 236 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 60072 Z= 0.138 Angle : 0.430 6.564 81072 Z= 0.228 Chirality : 0.043 0.125 9528 Planarity : 0.004 0.039 10368 Dihedral : 5.655 49.949 8208 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.38 % Allowed : 15.51 % Favored : 84.10 % 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: -0.39 (0.10), residues: 7512 helix: 2.39 (0.12), residues: 2136 sheet: 0.23 (0.15), residues: 1128 loop : -1.95 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 389 HIS 0.003 0.001 HIS F 603 PHE 0.010 0.001 PHE C 614 TYR 0.003 0.001 TYR M 493 ARG 0.005 0.000 ARG L 524 *********************** 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 544 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 519 time to evaluate : 4.983 Fit side-chains outliers start: 25 outliers final: 8 residues processed: 541 average time/residue: 0.5464 time to fit residues: 513.1353 Evaluate side-chains 478 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 470 time to evaluate : 4.958 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4722 time to fit residues: 13.6455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 673 optimal weight: 20.0000 chunk 709 optimal weight: 0.7980 chunk 647 optimal weight: 0.5980 chunk 689 optimal weight: 4.9990 chunk 708 optimal weight: 9.9990 chunk 415 optimal weight: 2.9990 chunk 300 optimal weight: 5.9990 chunk 541 optimal weight: 4.9990 chunk 211 optimal weight: 0.0870 chunk 623 optimal weight: 4.9990 chunk 652 optimal weight: 5.9990 overall best weight: 1.8962 ------------------------------------------------------------------------------- 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 F 236 GLN G 236 GLN H 236 GLN I 236 GLN J 236 GLN L 236 GLN M 236 GLN P 236 GLN P 486 GLN Q 236 GLN R 236 GLN R 486 GLN S 236 GLN U 236 GLN U 486 GLN V 236 GLN X 236 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 60072 Z= 0.240 Angle : 0.477 9.501 81072 Z= 0.250 Chirality : 0.043 0.124 9528 Planarity : 0.004 0.035 10368 Dihedral : 5.719 49.071 8208 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.29 % Allowed : 16.07 % Favored : 83.64 % 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: -0.40 (0.10), residues: 7512 helix: 2.32 (0.11), residues: 2136 sheet: 0.25 (0.15), residues: 1128 loop : -1.92 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 584 HIS 0.004 0.001 HIS N 603 PHE 0.012 0.001 PHE E 394 TYR 0.004 0.001 TYR K 493 ARG 0.004 0.000 ARG P 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 492 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 473 time to evaluate : 5.061 Fit side-chains outliers start: 19 outliers final: 2 residues processed: 491 average time/residue: 0.5389 time to fit residues: 460.0360 Evaluate side-chains 462 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 460 time to evaluate : 5.001 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4468 time to fit residues: 8.6442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 729 optimal weight: 2.9990 chunk 445 optimal weight: 1.9990 chunk 346 optimal weight: 4.9990 chunk 507 optimal weight: 1.9990 chunk 765 optimal weight: 5.9990 chunk 704 optimal weight: 0.2980 chunk 609 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 470 optimal weight: 5.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 544 GLN ** F 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 236 GLN P 236 GLN P 486 GLN R 236 GLN R 544 GLN S 236 GLN T 544 GLN U 486 GLN V 236 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 60072 Z= 0.234 Angle : 0.477 8.608 81072 Z= 0.250 Chirality : 0.044 0.124 9528 Planarity : 0.004 0.039 10368 Dihedral : 5.708 48.781 8208 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.22 % Allowed : 16.13 % Favored : 83.66 % 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: 2.35 (0.11), residues: 2136 sheet: 0.33 (0.15), residues: 1128 loop : -1.90 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 584 HIS 0.004 0.001 HIS N 603 PHE 0.011 0.001 PHE S 394 TYR 0.004 0.001 TYR N 493 ARG 0.004 0.000 ARG P 451 ********************** 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 482 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 468 time to evaluate : 5.051 Fit side-chains outliers start: 14 outliers final: 1 residues processed: 482 average time/residue: 0.5555 time to fit residues: 462.7072 Evaluate side-chains 457 residues out of total 6504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 456 time to evaluate : 4.993 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4085 time to fit residues: 7.7152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 768 random chunks: chunk 373 optimal weight: 4.9990 chunk 483 optimal weight: 9.9990 chunk 649 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 561 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 169 optimal weight: 0.7980 chunk 610 optimal weight: 30.0000 chunk 255 optimal weight: 0.8980 chunk 626 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 236 GLN O 544 GLN P 236 GLN P 486 GLN R 236 GLN S 236 GLN S 544 GLN T 544 GLN U 486 GLN V 236 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.156428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.100366 restraints weight = 70808.529| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.21 r_work: 0.2995 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 60072 Z= 0.161 Angle : 0.454 8.441 81072 Z= 0.238 Chirality : 0.043 0.124 9528 Planarity : 0.004 0.043 10368 Dihedral : 5.457 48.899 8208 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.17 % Allowed : 16.42 % Favored : 83.41 % 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: -0.22 (0.10), residues: 7512 helix: 2.57 (0.11), residues: 2136 sheet: 0.45 (0.16), residues: 1128 loop : -1.90 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X 584 HIS 0.003 0.001 HIS N 603 PHE 0.010 0.001 PHE X 394 TYR 0.003 0.001 TYR D 493 ARG 0.005 0.000 ARG A 534 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11220.10 seconds wall clock time: 199 minutes 8.94 seconds (11948.94 seconds total)