Starting phenix.real_space_refine (version: dev) on Sat Feb 25 06:01:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvi_27008/02_2023/8cvi_27008.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvi_27008/02_2023/8cvi_27008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvi_27008/02_2023/8cvi_27008.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvi_27008/02_2023/8cvi_27008.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvi_27008/02_2023/8cvi_27008.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvi_27008/02_2023/8cvi_27008.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.031 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 Process input model Symmetric amino acids flipped Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A ASP 114": "OD1" <-> "OD2" Residue "A ASP 121": "OD1" <-> "OD2" Residue "A ASP 124": "OD1" <-> "OD2" Residue "A ASP 159": "OD1" <-> "OD2" Residue "A GLU 455": "OE1" <-> "OE2" Residue "A ASP 459": "OD1" <-> "OD2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B ASP 121": "OD1" <-> "OD2" Residue "B PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 159": "OD1" <-> "OD2" Residue "B ASP 164": "OD1" <-> "OD2" Residue "B ASP 459": "OD1" <-> "OD2" Residue "B ASP 486": "OD1" <-> "OD2" Residue "B GLU 501": "OE1" <-> "OE2" Residue "B ASP 510": "OD1" <-> "OD2" Residue "C ASP 70": "OD1" <-> "OD2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C ASP 106": "OD1" <-> "OD2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C ASP 124": "OD1" <-> "OD2" Residue "C PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 166": "OD1" <-> "OD2" Residue "C ASP 459": "OD1" <-> "OD2" Residue "C ASP 472": "OD1" <-> "OD2" Residue "C PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 70": "OD1" <-> "OD2" Residue "D ASP 106": "OD1" <-> "OD2" Residue "D ASP 108": "OD1" <-> "OD2" Residue "D ASP 114": "OD1" <-> "OD2" Residue "D ASP 121": "OD1" <-> "OD2" Residue "D ASP 459": "OD1" <-> "OD2" Residue "D ASP 472": "OD1" <-> "OD2" Residue "D GLU 501": "OE1" <-> "OE2" Residue "D ASP 510": "OD1" <-> "OD2" Residue "N GLU 84": "OE1" <-> "OE2" Residue "N GLU 94": "OE1" <-> "OE2" Residue "N ASP 114": "OD1" <-> "OD2" Residue "N PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 159": "OD1" <-> "OD2" Residue "N ASP 486": "OD1" <-> "OD2" Residue "N GLU 501": "OE1" <-> "OE2" Residue "N ASP 510": "OD1" <-> "OD2" Residue "N TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 514": "OE1" <-> "OE2" Residue "X PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 70": "OD1" <-> "OD2" Residue "X GLU 84": "OE1" <-> "OE2" Residue "X GLU 94": "OE1" <-> "OE2" Residue "X ASP 106": "OD1" <-> "OD2" Residue "X ASP 108": "OD1" <-> "OD2" Residue "X ASP 121": "OD1" <-> "OD2" Residue "X GLU 122": "OE1" <-> "OE2" Residue "X ASP 124": "OD1" <-> "OD2" Residue "X ASP 459": "OD1" <-> "OD2" Residue "X ASP 472": "OD1" <-> "OD2" Residue "X TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 514": "OE1" <-> "OE2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E ASP 70": "OD1" <-> "OD2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "E PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 466": "OD1" <-> "OD2" Residue "E ASP 486": "OD1" <-> "OD2" Residue "O ASP 44": "OD1" <-> "OD2" Residue "O GLU 94": "OE1" <-> "OE2" Residue "O GLU 122": "OE1" <-> "OE2" Residue "O PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 486": "OD1" <-> "OD2" Residue "Y ASP 70": "OD1" <-> "OD2" Residue "Y ASP 121": "OD1" <-> "OD2" Residue "Y PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 459": "OD1" <-> "OD2" Residue "Y ASP 472": "OD1" <-> "OD2" Residue "Y GLU 501": "OE1" <-> "OE2" Residue "F ASP 70": "OD1" <-> "OD2" Residue "F ASP 106": "OD1" <-> "OD2" Residue "F ASP 114": "OD1" <-> "OD2" Residue "F GLU 115": "OE1" <-> "OE2" Residue "F ASP 121": "OD1" <-> "OD2" Residue "F GLU 122": "OE1" <-> "OE2" Residue "F PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 159": "OD1" <-> "OD2" Residue "F ASP 166": "OD1" <-> "OD2" Residue "P ASP 70": "OD1" <-> "OD2" Residue "P ASP 110": "OD1" <-> "OD2" Residue "P ASP 166": "OD1" <-> "OD2" Residue "P ASP 465": "OD1" <-> "OD2" Residue "P ASP 510": "OD1" <-> "OD2" Residue "P TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "Z ASP 110": "OD1" <-> "OD2" Residue "Z ASP 114": "OD1" <-> "OD2" Residue "Z ASP 159": "OD1" <-> "OD2" Residue "Z ASP 466": "OD1" <-> "OD2" Residue "Z GLU 501": "OE1" <-> "OE2" Residue "G ASP 44": "OD1" <-> "OD2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G ASP 108": "OD1" <-> "OD2" Residue "G ASP 110": "OD1" <-> "OD2" Residue "G PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 159": "OD1" <-> "OD2" Residue "G GLU 501": "OE1" <-> "OE2" Residue "Q GLU 30": "OE1" <-> "OE2" Residue "Q ASP 108": "OD1" <-> "OD2" Residue "Q ASP 110": "OD1" <-> "OD2" Residue "Q ASP 121": "OD1" <-> "OD2" Residue "Q ASP 159": "OD1" <-> "OD2" Residue "Q ASP 459": "OD1" <-> "OD2" Residue "Q GLU 514": "OE1" <-> "OE2" Residue "a GLU 94": "OE1" <-> "OE2" Residue "a ASP 110": "OD1" <-> "OD2" Residue "a ASP 121": "OD1" <-> "OD2" Residue "a ASP 486": "OD1" <-> "OD2" Residue "H ASP 106": "OD1" <-> "OD2" Residue "H ASP 114": "OD1" <-> "OD2" Residue "H GLU 115": "OE1" <-> "OE2" Residue "H PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 159": "OD1" <-> "OD2" Residue "H ASP 486": "OD1" <-> "OD2" Residue "H TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 514": "OE1" <-> "OE2" Residue "R ASP 70": "OD1" <-> "OD2" Residue "R GLU 79": "OE1" <-> "OE2" Residue "R ASP 108": "OD1" <-> "OD2" Residue "R ASP 121": "OD1" <-> "OD2" Residue "R PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 459": "OD1" <-> "OD2" Residue "R ASP 472": "OD1" <-> "OD2" Residue "R ASP 486": "OD1" <-> "OD2" Residue "R GLU 514": "OE1" <-> "OE2" Residue "b ASP 108": "OD1" <-> "OD2" Residue "b ASP 110": "OD1" <-> "OD2" Residue "b GLU 115": "OE1" <-> "OE2" Residue "b ASP 152": "OD1" <-> "OD2" Residue "b ASP 159": "OD1" <-> "OD2" Residue "b GLU 455": "OE1" <-> "OE2" Residue "b ASP 466": "OD1" <-> "OD2" Residue "b ASP 486": "OD1" <-> "OD2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I GLU 115": "OE1" <-> "OE2" Residue "I ASP 121": "OD1" <-> "OD2" Residue "I ASP 141": "OD1" <-> "OD2" Residue "I ASP 164": "OD1" <-> "OD2" Residue "I PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 472": "OD1" <-> "OD2" Residue "I GLU 501": "OE1" <-> "OE2" Residue "S GLU 30": "OE1" <-> "OE2" Residue "S ASP 43": "OD1" <-> "OD2" Residue "S ASP 70": "OD1" <-> "OD2" Residue "S GLU 79": "OE1" <-> "OE2" Residue "S ASP 108": "OD1" <-> "OD2" Residue "S ASP 114": "OD1" <-> "OD2" Residue "S ASP 121": "OD1" <-> "OD2" Residue "S ASP 159": "OD1" <-> "OD2" Residue "S ASP 465": "OD1" <-> "OD2" Residue "S ASP 466": "OD1" <-> "OD2" Residue "S ASP 486": "OD1" <-> "OD2" Residue "S GLU 501": "OE1" <-> "OE2" Residue "S TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 70": "OD1" <-> "OD2" Residue "c GLU 79": "OE1" <-> "OE2" Residue "c GLU 94": "OE1" <-> "OE2" Residue "c ASP 114": "OD1" <-> "OD2" Residue "c GLU 115": "OE1" <-> "OE2" Residue "c PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 508": "OD1" <-> "OD2" Residue "c TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 43": "OD1" <-> "OD2" Residue "J ASP 110": "OD1" <-> "OD2" Residue "J ASP 124": "OD1" <-> "OD2" Residue "J PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 459": "OD1" <-> "OD2" Residue "J ASP 466": "OD1" <-> "OD2" Residue "J ASP 486": "OD1" <-> "OD2" Residue "T ASP 44": "OD1" <-> "OD2" Residue "T ASP 70": "OD1" <-> "OD2" Residue "T GLU 94": "OE1" <-> "OE2" Residue "T PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 166": "OD1" <-> "OD2" Residue "T GLU 455": "OE1" <-> "OE2" Residue "T GLU 501": "OE1" <-> "OE2" Residue "d ASP 44": "OD1" <-> "OD2" Residue "d GLU 79": "OE1" <-> "OE2" Residue "d ASP 121": "OD1" <-> "OD2" Residue "d ASP 124": "OD1" <-> "OD2" Residue "d PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 152": "OD1" <-> "OD2" Residue "d ASP 159": "OD1" <-> "OD2" Residue "d ASP 164": "OD1" <-> "OD2" Residue "d ASP 486": "OD1" <-> "OD2" Residue "d GLU 501": "OE1" <-> "OE2" Residue "d TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 30": "OE1" <-> "OE2" Residue "K GLU 79": "OE1" <-> "OE2" Residue "K GLU 84": "OE1" <-> "OE2" Residue "K ASP 106": "OD1" <-> "OD2" Residue "K ASP 110": "OD1" <-> "OD2" Residue "K GLU 122": "OE1" <-> "OE2" Residue "K PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 159": "OD1" <-> "OD2" Residue "K ASP 465": "OD1" <-> "OD2" Residue "K ASP 486": "OD1" <-> "OD2" Residue "K ASP 510": "OD1" <-> "OD2" Residue "U ASP 43": "OD1" <-> "OD2" Residue "U ASP 70": "OD1" <-> "OD2" Residue "U GLU 79": "OE1" <-> "OE2" Residue "U GLU 94": "OE1" <-> "OE2" Residue "U ASP 106": "OD1" <-> "OD2" Residue "U ASP 110": "OD1" <-> "OD2" Residue "U GLU 115": "OE1" <-> "OE2" Residue "U ASP 121": "OD1" <-> "OD2" Residue "U PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 159": "OD1" <-> "OD2" Residue "U ASP 166": "OD1" <-> "OD2" Residue "U GLU 501": "OE1" <-> "OE2" Residue "U TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 514": "OE1" <-> "OE2" Residue "e ASP 108": "OD1" <-> "OD2" Residue "e ASP 124": "OD1" <-> "OD2" Residue "e ASP 152": "OD1" <-> "OD2" Residue "e ASP 159": "OD1" <-> "OD2" Residue "e ASP 472": "OD1" <-> "OD2" Residue "e GLU 501": "OE1" <-> "OE2" Residue "e ASP 510": "OD1" <-> "OD2" Residue "e GLU 514": "OE1" <-> "OE2" Residue "L GLU 79": "OE1" <-> "OE2" Residue "L GLU 84": "OE1" <-> "OE2" Residue "L GLU 94": "OE1" <-> "OE2" Residue "L ASP 108": "OD1" <-> "OD2" Residue "L ASP 121": "OD1" <-> "OD2" Residue "L ASP 159": "OD1" <-> "OD2" Residue "L ASP 166": "OD1" <-> "OD2" Residue "L ASP 459": "OD1" <-> "OD2" Residue "L ASP 472": "OD1" <-> "OD2" Residue "L GLU 501": "OE1" <-> "OE2" Residue "L ASP 508": "OD1" <-> "OD2" Residue "L ASP 510": "OD1" <-> "OD2" Residue "L GLU 514": "OE1" <-> "OE2" Residue "V GLU 30": "OE1" <-> "OE2" Residue "V ASP 70": "OD1" <-> "OD2" Residue "V ASP 108": "OD1" <-> "OD2" Residue "V GLU 115": "OE1" <-> "OE2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 166": "OD1" <-> "OD2" Residue "V PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 472": "OD1" <-> "OD2" Residue "V GLU 501": "OE1" <-> "OE2" Residue "f ASP 70": "OD1" <-> "OD2" Residue "f GLU 84": "OE1" <-> "OE2" Residue "f ASP 106": "OD1" <-> "OD2" Residue "f ASP 110": "OD1" <-> "OD2" Residue "f GLU 115": "OE1" <-> "OE2" Residue "f ASP 121": "OD1" <-> "OD2" Residue "f ASP 166": "OD1" <-> "OD2" Residue "f PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 466": "OD1" <-> "OD2" Residue "f ASP 472": "OD1" <-> "OD2" Residue "f ASP 508": "OD1" <-> "OD2" Residue "M GLU 30": "OE1" <-> "OE2" Residue "M ASP 70": "OD1" <-> "OD2" Residue "M GLU 84": "OE1" <-> "OE2" Residue "M GLU 94": "OE1" <-> "OE2" Residue "M ASP 108": "OD1" <-> "OD2" Residue "M ASP 114": "OD1" <-> "OD2" Residue "M ASP 121": "OD1" <-> "OD2" Residue "M PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 514": "OE1" <-> "OE2" Residue "W ASP 70": "OD1" <-> "OD2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W ASP 106": "OD1" <-> "OD2" Residue "W ASP 152": "OD1" <-> "OD2" Residue "W ASP 164": "OD1" <-> "OD2" Residue "W TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 30": "OE1" <-> "OE2" Residue "g GLU 94": "OE1" <-> "OE2" Residue "g ASP 466": "OD1" <-> "OD2" Residue "g GLU 501": "OE1" <-> "OE2" Residue "g ASP 508": "OD1" <-> "OD2" Residue "g GLU 514": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 66030 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 1985 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 264} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 1985 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 264} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 1985 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 264} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "N" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "X" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "E" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "O" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "Y" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "F" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "P" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "Z" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "G" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "Q" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "a" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "H" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "R" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "b" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1996 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 2, 'TRANS': 265} Chain breaks: 1 Chain: "I" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "S" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "c" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "J" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "T" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "d" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "K" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "U" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "e" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "L" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "V" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "f" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "M" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "W" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "g" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Residues with excluded nonbonded symmetry interactions: 15 residue: pdb=" N AILE I 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE I 38 " occ=0.50 residue: pdb=" N AILE S 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE S 38 " occ=0.50 residue: pdb=" N AILE c 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE c 38 " occ=0.50 residue: pdb=" N AILE J 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE J 38 " occ=0.50 residue: pdb=" N AILE T 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE T 38 " occ=0.50 residue: pdb=" N AILE d 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE d 38 " occ=0.50 residue: pdb=" N AILE K 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE K 38 " occ=0.50 residue: pdb=" N AILE U 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE U 38 " occ=0.50 residue: pdb=" N AILE e 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE e 38 " occ=0.50 residue: pdb=" N AILE L 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE L 38 " occ=0.50 residue: pdb=" N AILE V 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE V 38 " occ=0.50 residue: pdb=" N AILE f 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE f 38 " occ=0.50 ... (remaining 3 not shown) Time building chain proxies: 38.43, per 1000 atoms: 0.58 Number of scatterers: 66030 At special positions: 0 Unit cell: (145.8, 140.4, 319.68, 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 66 16.00 O 14310 8.00 N 12069 7.00 C 39585 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: 22.34 Conformation dependent library (CDL) restraints added in 10.8 seconds 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16686 Finding SS restraints... Secondary structure from input PDB file: 226 helices and 53 sheets defined 73.3% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 8 through 35 removed outlier: 3.571A pdb=" N LEU A 12 " --> pdb=" O ASN A 8 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 23 " --> pdb=" O ASN A 19 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 100 removed outlier: 3.655A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 129 removed outlier: 3.667A pdb=" N SER A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 459 through 508 removed outlier: 3.748A pdb=" N ALA A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 474 " --> pdb=" O GLN A 470 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 475 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 536 Processing helix chain 'A' and resid 540 through 546 Processing helix chain 'B' and resid 8 through 35 removed outlier: 3.703A pdb=" N LEU B 12 " --> pdb=" O ASN B 8 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE B 13 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR B 14 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B 23 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA B 24 " --> pdb=" O LYS B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 100 removed outlier: 3.687A pdb=" N ASN B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 129 removed outlier: 4.258A pdb=" N SER B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 459 through 508 removed outlier: 3.889A pdb=" N VAL B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN B 482 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN B 483 " --> pdb=" O GLY B 479 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 506 " --> pdb=" O ALA B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 537 removed outlier: 3.961A pdb=" N SER B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 546 removed outlier: 3.836A pdb=" N LEU B 543 " --> pdb=" O PRO B 539 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 546 " --> pdb=" O VAL B 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 35 removed outlier: 3.610A pdb=" N LEU C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER C 23 " --> pdb=" O ASN C 19 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 100 removed outlier: 3.642A pdb=" N ASN C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 130 removed outlier: 4.244A pdb=" N SER C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR C 130 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 459 through 508 removed outlier: 3.626A pdb=" N ALA C 480 " --> pdb=" O SER C 476 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL C 481 " --> pdb=" O SER C 477 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN C 482 " --> pdb=" O LEU C 478 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN C 483 " --> pdb=" O GLY C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 536 removed outlier: 3.718A pdb=" N GLU C 514 " --> pdb=" O ASP C 510 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS C 534 " --> pdb=" O SER C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 546 removed outlier: 3.768A pdb=" N LEU C 543 " --> pdb=" O PRO C 539 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU C 546 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 35 removed outlier: 3.860A pdb=" N ALA D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 100 Processing helix chain 'D' and resid 105 through 129 Processing helix chain 'D' and resid 164 through 169 Processing helix chain 'D' and resid 459 through 507 removed outlier: 3.942A pdb=" N VAL D 481 " --> pdb=" O SER D 477 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN D 482 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN D 483 " --> pdb=" O GLY D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 536 Processing helix chain 'D' and resid 539 through 547 removed outlier: 3.832A pdb=" N LEU D 543 " --> pdb=" O PRO D 539 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU D 546 " --> pdb=" O VAL D 542 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN D 547 " --> pdb=" O LEU D 543 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 35 removed outlier: 3.853A pdb=" N SER N 23 " --> pdb=" O ASN N 19 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA N 24 " --> pdb=" O LYS N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 101 removed outlier: 4.131A pdb=" N THR N 101 " --> pdb=" O VAL N 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 130 removed outlier: 3.618A pdb=" N THR N 130 " --> pdb=" O VAL N 126 " (cutoff:3.500A) Processing helix chain 'N' and resid 459 through 507 removed outlier: 4.365A pdb=" N VAL N 481 " --> pdb=" O SER N 477 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN N 482 " --> pdb=" O LEU N 478 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN N 483 " --> pdb=" O GLY N 479 " (cutoff:3.500A) Processing helix chain 'N' and resid 510 through 536 removed outlier: 3.832A pdb=" N SER N 516 " --> pdb=" O ALA N 512 " (cutoff:3.500A) Processing helix chain 'N' and resid 537 through 540 Processing helix chain 'N' and resid 541 through 547 removed outlier: 4.093A pdb=" N LEU N 545 " --> pdb=" O GLN N 541 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU N 546 " --> pdb=" O VAL N 542 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 35 removed outlier: 3.709A pdb=" N SER X 23 " --> pdb=" O ASN X 19 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA X 24 " --> pdb=" O LYS X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 100 removed outlier: 3.905A pdb=" N ASP X 44 " --> pdb=" O SER X 40 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ALA X 46 " --> pdb=" O LYS X 42 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N GLY X 47 " --> pdb=" O ASP X 43 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA X 49 " --> pdb=" O ALA X 45 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE X 50 " --> pdb=" O ALA X 46 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN X 88 " --> pdb=" O GLU X 84 " (cutoff:3.500A) Processing helix chain 'X' and resid 105 through 130 removed outlier: 4.036A pdb=" N THR X 130 " --> pdb=" O VAL X 126 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 169 Processing helix chain 'X' and resid 459 through 507 removed outlier: 3.800A pdb=" N VAL X 481 " --> pdb=" O SER X 477 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN X 482 " --> pdb=" O LEU X 478 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN X 483 " --> pdb=" O GLY X 479 " (cutoff:3.500A) Processing helix chain 'X' and resid 510 through 536 removed outlier: 3.509A pdb=" N GLU X 514 " --> pdb=" O ASP X 510 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER X 516 " --> pdb=" O ALA X 512 " (cutoff:3.500A) Processing helix chain 'X' and resid 537 through 540 Processing helix chain 'X' and resid 541 through 547 removed outlier: 3.600A pdb=" N LEU X 545 " --> pdb=" O GLN X 541 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU X 546 " --> pdb=" O VAL X 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 34 removed outlier: 3.650A pdb=" N LEU E 12 " --> pdb=" O ASN E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 100 removed outlier: 3.971A pdb=" N ASP E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N ALA E 46 " --> pdb=" O LYS E 42 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N GLY E 47 " --> pdb=" O ASP E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 129 Processing helix chain 'E' and resid 459 through 507 removed outlier: 4.241A pdb=" N VAL E 481 " --> pdb=" O SER E 477 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG E 484 " --> pdb=" O ALA E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 536 Processing helix chain 'E' and resid 537 through 540 Processing helix chain 'E' and resid 541 through 547 removed outlier: 4.123A pdb=" N LEU E 545 " --> pdb=" O GLN E 541 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU E 546 " --> pdb=" O VAL E 542 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN E 547 " --> pdb=" O LEU E 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 541 through 547' Processing helix chain 'O' and resid 8 through 34 removed outlier: 3.842A pdb=" N ASN O 21 " --> pdb=" O ASN O 17 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER O 23 " --> pdb=" O ASN O 19 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA O 24 " --> pdb=" O LYS O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 100 removed outlier: 3.591A pdb=" N ALA O 49 " --> pdb=" O ALA O 45 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE O 72 " --> pdb=" O ALA O 68 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER O 73 " --> pdb=" O ASN O 69 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL O 74 " --> pdb=" O ASP O 70 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 129 Processing helix chain 'O' and resid 459 through 507 removed outlier: 4.199A pdb=" N VAL O 481 " --> pdb=" O SER O 477 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN O 482 " --> pdb=" O LEU O 478 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG O 505 " --> pdb=" O GLU O 501 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE O 506 " --> pdb=" O ALA O 502 " (cutoff:3.500A) Processing helix chain 'O' and resid 510 through 536 Processing helix chain 'O' and resid 537 through 542 removed outlier: 3.766A pdb=" N GLN O 541 " --> pdb=" O GLN O 537 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL O 542 " --> pdb=" O VAL O 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 537 through 542' Processing helix chain 'O' and resid 542 through 547 removed outlier: 4.202A pdb=" N LEU O 546 " --> pdb=" O VAL O 542 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN O 547 " --> pdb=" O LEU O 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 542 through 547' Processing helix chain 'Y' and resid 8 through 34 removed outlier: 4.430A pdb=" N SER Y 23 " --> pdb=" O ASN Y 19 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 101 removed outlier: 3.529A pdb=" N ALA Y 49 " --> pdb=" O ALA Y 45 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER Y 73 " --> pdb=" O ASN Y 69 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL Y 74 " --> pdb=" O ASP Y 70 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA Y 75 " --> pdb=" O GLY Y 71 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU Y 84 " --> pdb=" O GLY Y 80 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR Y 101 " --> pdb=" O VAL Y 97 " (cutoff:3.500A) Processing helix chain 'Y' and resid 105 through 129 Processing helix chain 'Y' and resid 459 through 507 removed outlier: 3.620A pdb=" N VAL Y 481 " --> pdb=" O SER Y 477 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN Y 482 " --> pdb=" O LEU Y 478 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE Y 506 " --> pdb=" O ALA Y 502 " (cutoff:3.500A) Processing helix chain 'Y' and resid 510 through 537 removed outlier: 3.771A pdb=" N GLN Y 537 " --> pdb=" O ALA Y 533 " (cutoff:3.500A) Processing helix chain 'Y' and resid 538 through 541 Processing helix chain 'Y' and resid 542 through 547 removed outlier: 3.646A pdb=" N LEU Y 546 " --> pdb=" O VAL Y 542 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN Y 547 " --> pdb=" O LEU Y 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 542 through 547' Processing helix chain 'F' and resid 8 through 35 removed outlier: 3.993A pdb=" N LEU F 12 " --> pdb=" O ASN F 8 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER F 34 " --> pdb=" O GLU F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 100 removed outlier: 3.612A pdb=" N ARG F 91 " --> pdb=" O ASN F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 129 Processing helix chain 'F' and resid 459 through 507 removed outlier: 3.656A pdb=" N VAL F 481 " --> pdb=" O SER F 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 536 Processing helix chain 'F' and resid 537 through 539 No H-bonds generated for 'chain 'F' and resid 537 through 539' Processing helix chain 'F' and resid 540 through 547 removed outlier: 3.726A pdb=" N SER F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) Processing helix chain 'P' and resid 8 through 35 removed outlier: 3.846A pdb=" N SER P 23 " --> pdb=" O ASN P 19 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA P 24 " --> pdb=" O LYS P 20 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER P 33 " --> pdb=" O ILE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 100 removed outlier: 3.661A pdb=" N VAL P 74 " --> pdb=" O ASP P 70 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA P 75 " --> pdb=" O GLY P 71 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN P 88 " --> pdb=" O GLU P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 129 Processing helix chain 'P' and resid 459 through 507 removed outlier: 3.771A pdb=" N VAL P 481 " --> pdb=" O SER P 477 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN P 482 " --> pdb=" O LEU P 478 " (cutoff:3.500A) Processing helix chain 'P' and resid 510 through 537 removed outlier: 3.941A pdb=" N GLN P 537 " --> pdb=" O ALA P 533 " (cutoff:3.500A) Processing helix chain 'P' and resid 540 through 547 removed outlier: 3.872A pdb=" N SER P 544 " --> pdb=" O GLN P 540 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 35 removed outlier: 3.566A pdb=" N ILE Z 13 " --> pdb=" O SER Z 9 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER Z 23 " --> pdb=" O ASN Z 19 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA Z 24 " --> pdb=" O LYS Z 20 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER Z 33 " --> pdb=" O ILE Z 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 44 through 100 removed outlier: 3.607A pdb=" N ARG Z 66 " --> pdb=" O THR Z 62 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU Z 84 " --> pdb=" O GLY Z 80 " (cutoff:3.500A) Processing helix chain 'Z' and resid 105 through 129 Processing helix chain 'Z' and resid 459 through 507 removed outlier: 3.887A pdb=" N VAL Z 481 " --> pdb=" O SER Z 477 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN Z 482 " --> pdb=" O LEU Z 478 " (cutoff:3.500A) Processing helix chain 'Z' and resid 510 through 537 removed outlier: 3.689A pdb=" N SER Z 516 " --> pdb=" O ALA Z 512 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN Z 537 " --> pdb=" O ALA Z 533 " (cutoff:3.500A) Processing helix chain 'Z' and resid 540 through 547 removed outlier: 3.776A pdb=" N SER Z 544 " --> pdb=" O GLN Z 540 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 35 removed outlier: 4.033A pdb=" N SER G 23 " --> pdb=" O ASN G 19 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 100 removed outlier: 3.857A pdb=" N ALA G 81 " --> pdb=" O THR G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 130 Processing helix chain 'G' and resid 164 through 169 Processing helix chain 'G' and resid 459 through 507 removed outlier: 3.570A pdb=" N ALA G 463 " --> pdb=" O ASP G 459 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL G 481 " --> pdb=" O SER G 477 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN G 482 " --> pdb=" O LEU G 478 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN G 483 " --> pdb=" O GLY G 479 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE G 506 " --> pdb=" O ALA G 502 " (cutoff:3.500A) Processing helix chain 'G' and resid 510 through 537 removed outlier: 3.739A pdb=" N GLN G 537 " --> pdb=" O ALA G 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 547 removed outlier: 3.990A pdb=" N SER G 544 " --> pdb=" O GLN G 540 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 35 removed outlier: 4.026A pdb=" N SER Q 23 " --> pdb=" O ASN Q 19 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA Q 24 " --> pdb=" O LYS Q 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 100 removed outlier: 3.782A pdb=" N ALA Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE Q 50 " --> pdb=" O ALA Q 46 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA Q 81 " --> pdb=" O THR Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 130 removed outlier: 3.638A pdb=" N THR Q 130 " --> pdb=" O VAL Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 169 Processing helix chain 'Q' and resid 459 through 507 removed outlier: 3.578A pdb=" N SER Q 477 " --> pdb=" O LYS Q 473 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU Q 478 " --> pdb=" O PHE Q 474 " (cutoff:3.500A) Processing helix chain 'Q' and resid 510 through 537 removed outlier: 3.954A pdb=" N SER Q 516 " --> pdb=" O ALA Q 512 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN Q 537 " --> pdb=" O ALA Q 533 " (cutoff:3.500A) Processing helix chain 'Q' and resid 540 through 547 removed outlier: 3.979A pdb=" N SER Q 544 " --> pdb=" O GLN Q 540 " (cutoff:3.500A) Processing helix chain 'a' and resid 10 through 35 removed outlier: 3.556A pdb=" N ASN a 21 " --> pdb=" O ASN a 17 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER a 23 " --> pdb=" O ASN a 19 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA a 24 " --> pdb=" O LYS a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 101 removed outlier: 3.547A pdb=" N ALA a 49 " --> pdb=" O ALA a 45 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN a 63 " --> pdb=" O LYS a 59 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN a 88 " --> pdb=" O GLU a 84 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR a 101 " --> pdb=" O VAL a 97 " (cutoff:3.500A) Processing helix chain 'a' and resid 105 through 130 removed outlier: 3.509A pdb=" N THR a 130 " --> pdb=" O VAL a 126 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 169 Processing helix chain 'a' and resid 459 through 507 removed outlier: 3.503A pdb=" N ALA a 463 " --> pdb=" O ASP a 459 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL a 481 " --> pdb=" O SER a 477 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE a 506 " --> pdb=" O ALA a 502 " (cutoff:3.500A) Processing helix chain 'a' and resid 510 through 537 removed outlier: 3.621A pdb=" N GLN a 537 " --> pdb=" O ALA a 533 " (cutoff:3.500A) Processing helix chain 'a' and resid 540 through 547 removed outlier: 4.028A pdb=" N SER a 544 " --> pdb=" O GLN a 540 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 35 removed outlier: 3.888A pdb=" N SER H 23 " --> pdb=" O ASN H 19 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA H 24 " --> pdb=" O LYS H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 100 removed outlier: 3.873A pdb=" N GLU H 84 " --> pdb=" O GLY H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 130 Processing helix chain 'H' and resid 459 through 507 removed outlier: 3.989A pdb=" N VAL H 481 " --> pdb=" O SER H 477 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN H 482 " --> pdb=" O LEU H 478 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER H 487 " --> pdb=" O ASN H 483 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG H 505 " --> pdb=" O GLU H 501 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE H 506 " --> pdb=" O ALA H 502 " (cutoff:3.500A) Processing helix chain 'H' and resid 510 through 537 removed outlier: 3.665A pdb=" N SER H 516 " --> pdb=" O ALA H 512 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN H 537 " --> pdb=" O ALA H 533 " (cutoff:3.500A) Processing helix chain 'H' and resid 540 through 547 removed outlier: 3.609A pdb=" N SER H 544 " --> pdb=" O GLN H 540 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN H 547 " --> pdb=" O LEU H 543 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 35 removed outlier: 3.512A pdb=" N ASN R 21 " --> pdb=" O ASN R 17 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER R 23 " --> pdb=" O ASN R 19 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA R 24 " --> pdb=" O LYS R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 100 removed outlier: 3.573A pdb=" N ARG R 53 " --> pdb=" O ALA R 49 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU R 84 " --> pdb=" O GLY R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 130 removed outlier: 3.662A pdb=" N THR R 130 " --> pdb=" O VAL R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 459 through 507 removed outlier: 4.063A pdb=" N VAL R 481 " --> pdb=" O SER R 477 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN R 482 " --> pdb=" O LEU R 478 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER R 487 " --> pdb=" O ASN R 483 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG R 505 " --> pdb=" O GLU R 501 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE R 506 " --> pdb=" O ALA R 502 " (cutoff:3.500A) Processing helix chain 'R' and resid 510 through 537 removed outlier: 3.822A pdb=" N SER R 516 " --> pdb=" O ALA R 512 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN R 537 " --> pdb=" O ALA R 533 " (cutoff:3.500A) Processing helix chain 'R' and resid 540 through 547 removed outlier: 3.565A pdb=" N SER R 544 " --> pdb=" O GLN R 540 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN R 547 " --> pdb=" O LEU R 543 " (cutoff:3.500A) Processing helix chain 'b' and resid 10 through 35 removed outlier: 3.686A pdb=" N SER b 23 " --> pdb=" O ASN b 19 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA b 24 " --> pdb=" O LYS b 20 " (cutoff:3.500A) Processing helix chain 'b' and resid 45 through 101 removed outlier: 3.697A pdb=" N GLU b 84 " --> pdb=" O GLY b 80 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR b 101 " --> pdb=" O VAL b 97 " (cutoff:3.500A) Processing helix chain 'b' and resid 105 through 130 removed outlier: 3.622A pdb=" N THR b 130 " --> pdb=" O VAL b 126 " (cutoff:3.500A) Processing helix chain 'b' and resid 459 through 507 removed outlier: 3.539A pdb=" N ALA b 463 " --> pdb=" O ASP b 459 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL b 481 " --> pdb=" O SER b 477 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN b 482 " --> pdb=" O LEU b 478 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER b 487 " --> pdb=" O ASN b 483 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG b 505 " --> pdb=" O GLU b 501 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE b 506 " --> pdb=" O ALA b 502 " (cutoff:3.500A) Processing helix chain 'b' and resid 510 through 536 removed outlier: 3.597A pdb=" N SER b 516 " --> pdb=" O ALA b 512 " (cutoff:3.500A) Processing helix chain 'b' and resid 537 through 539 No H-bonds generated for 'chain 'b' and resid 537 through 539' Processing helix chain 'b' and resid 540 through 547 removed outlier: 3.947A pdb=" N SER b 544 " --> pdb=" O GLN b 540 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN b 547 " --> pdb=" O LEU b 543 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 34 removed outlier: 3.821A pdb=" N SER I 23 " --> pdb=" O ASN I 19 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA I 24 " --> pdb=" O LYS I 20 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER I 34 " --> pdb=" O GLU I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 100 removed outlier: 4.379A pdb=" N GLU I 84 " --> pdb=" O GLY I 80 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE I 85 " --> pdb=" O ALA I 81 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU I 94 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 129 Processing helix chain 'I' and resid 459 through 508 removed outlier: 3.622A pdb=" N PHE I 474 " --> pdb=" O GLN I 470 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG I 505 " --> pdb=" O GLU I 501 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE I 506 " --> pdb=" O ALA I 502 " (cutoff:3.500A) Processing helix chain 'I' and resid 510 through 537 removed outlier: 3.726A pdb=" N SER I 516 " --> pdb=" O ALA I 512 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLN I 537 " --> pdb=" O ALA I 533 " (cutoff:3.500A) Processing helix chain 'I' and resid 540 through 547 removed outlier: 3.550A pdb=" N GLN I 547 " --> pdb=" O LEU I 543 " (cutoff:3.500A) Processing helix chain 'S' and resid 8 through 34 removed outlier: 3.510A pdb=" N ASN S 16 " --> pdb=" O LEU S 12 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER S 23 " --> pdb=" O ASN S 19 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA S 24 " --> pdb=" O LYS S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 100 removed outlier: 3.515A pdb=" N GLN S 48 " --> pdb=" O ASP S 44 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG S 66 " --> pdb=" O THR S 62 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY S 71 " --> pdb=" O ASN S 67 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU S 84 " --> pdb=" O GLY S 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 129 Processing helix chain 'S' and resid 459 through 508 removed outlier: 3.846A pdb=" N ALA S 463 " --> pdb=" O ASP S 459 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG S 505 " --> pdb=" O GLU S 501 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE S 506 " --> pdb=" O ALA S 502 " (cutoff:3.500A) Processing helix chain 'S' and resid 510 through 537 removed outlier: 3.707A pdb=" N VAL S 515 " --> pdb=" O TYR S 511 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER S 516 " --> pdb=" O ALA S 512 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN S 537 " --> pdb=" O ALA S 533 " (cutoff:3.500A) Processing helix chain 'S' and resid 540 through 547 removed outlier: 3.628A pdb=" N GLN S 547 " --> pdb=" O LEU S 543 " (cutoff:3.500A) Processing helix chain 'c' and resid 8 through 34 removed outlier: 3.896A pdb=" N ASN c 16 " --> pdb=" O LEU c 12 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER c 23 " --> pdb=" O ASN c 19 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA c 24 " --> pdb=" O LYS c 20 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER c 34 " --> pdb=" O GLU c 30 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 100 removed outlier: 3.675A pdb=" N SER c 73 " --> pdb=" O ASN c 69 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE c 85 " --> pdb=" O ALA c 81 " (cutoff:3.500A) Processing helix chain 'c' and resid 106 through 129 Processing helix chain 'c' and resid 459 through 508 removed outlier: 3.631A pdb=" N ALA c 463 " --> pdb=" O ASP c 459 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG c 505 " --> pdb=" O GLU c 501 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE c 506 " --> pdb=" O ALA c 502 " (cutoff:3.500A) Processing helix chain 'c' and resid 510 through 535 Processing helix chain 'c' and resid 540 through 547 removed outlier: 3.705A pdb=" N SER c 544 " --> pdb=" O GLN c 540 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN c 547 " --> pdb=" O LEU c 543 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 34 removed outlier: 3.547A pdb=" N LEU J 12 " --> pdb=" O ASN J 8 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA J 24 " --> pdb=" O LYS J 20 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER J 34 " --> pdb=" O GLU J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 100 removed outlier: 4.335A pdb=" N GLN J 48 " --> pdb=" O ASP J 44 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE J 72 " --> pdb=" O ALA J 68 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER J 73 " --> pdb=" O ASN J 69 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL J 74 " --> pdb=" O ASP J 70 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU J 84 " --> pdb=" O GLY J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 129 Processing helix chain 'J' and resid 459 through 505 removed outlier: 3.554A pdb=" N THR J 497 " --> pdb=" O ASN J 493 " (cutoff:3.500A) Processing helix chain 'J' and resid 512 through 536 Processing helix chain 'J' and resid 539 through 546 removed outlier: 4.285A pdb=" N LEU J 543 " --> pdb=" O PRO J 539 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER J 544 " --> pdb=" O GLN J 540 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 34 removed outlier: 3.650A pdb=" N SER T 23 " --> pdb=" O ASN T 19 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA T 24 " --> pdb=" O LYS T 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 100 removed outlier: 4.253A pdb=" N SER T 73 " --> pdb=" O ASN T 69 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL T 74 " --> pdb=" O ASP T 70 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA T 75 " --> pdb=" O GLY T 71 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU T 84 " --> pdb=" O GLY T 80 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE T 85 " --> pdb=" O ALA T 81 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 129 Processing helix chain 'T' and resid 459 through 483 removed outlier: 3.876A pdb=" N ALA T 463 " --> pdb=" O ASP T 459 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU T 464 " --> pdb=" O PRO T 460 " (cutoff:3.500A) Processing helix chain 'T' and resid 484 through 505 Processing helix chain 'T' and resid 510 through 536 Processing helix chain 'T' and resid 537 through 539 No H-bonds generated for 'chain 'T' and resid 537 through 539' Processing helix chain 'T' and resid 540 through 547 removed outlier: 3.567A pdb=" N SER T 544 " --> pdb=" O GLN T 540 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN T 547 " --> pdb=" O LEU T 543 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 34 removed outlier: 3.791A pdb=" N SER d 23 " --> pdb=" O ASN d 19 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA d 24 " --> pdb=" O LYS d 20 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER d 34 " --> pdb=" O GLU d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 100 removed outlier: 3.570A pdb=" N ILE d 72 " --> pdb=" O ALA d 68 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER d 73 " --> pdb=" O ASN d 69 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL d 74 " --> pdb=" O ASP d 70 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN d 98 " --> pdb=" O GLU d 94 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 129 Processing helix chain 'd' and resid 459 through 507 removed outlier: 4.154A pdb=" N ALA d 467 " --> pdb=" O ALA d 463 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE d 506 " --> pdb=" O ALA d 502 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN d 507 " --> pdb=" O GLN d 503 " (cutoff:3.500A) Processing helix chain 'd' and resid 512 through 537 removed outlier: 3.923A pdb=" N GLN d 537 " --> pdb=" O ALA d 533 " (cutoff:3.500A) Processing helix chain 'd' and resid 539 through 547 removed outlier: 4.123A pdb=" N LEU d 543 " --> pdb=" O PRO d 539 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER d 544 " --> pdb=" O GLN d 540 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 34 removed outlier: 3.590A pdb=" N LEU K 12 " --> pdb=" O ASN K 8 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER K 23 " --> pdb=" O ASN K 19 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA K 24 " --> pdb=" O LYS K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 100 removed outlier: 3.719A pdb=" N GLN K 48 " --> pdb=" O ASP K 44 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER K 73 " --> pdb=" O ASN K 69 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 129 removed outlier: 3.583A pdb=" N GLU K 115 " --> pdb=" O SER K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 169 Processing helix chain 'K' and resid 459 through 507 removed outlier: 3.760A pdb=" N ASP K 466 " --> pdb=" O ALA K 462 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA K 467 " --> pdb=" O ALA K 463 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE K 506 " --> pdb=" O ALA K 502 " (cutoff:3.500A) Processing helix chain 'K' and resid 512 through 536 Processing helix chain 'K' and resid 537 through 539 No H-bonds generated for 'chain 'K' and resid 537 through 539' Processing helix chain 'K' and resid 540 through 547 removed outlier: 3.805A pdb=" N SER K 544 " --> pdb=" O GLN K 540 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 34 removed outlier: 3.924A pdb=" N SER U 23 " --> pdb=" O ASN U 19 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA U 24 " --> pdb=" O LYS U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 100 removed outlier: 3.730A pdb=" N GLN U 48 " --> pdb=" O ASP U 44 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA U 49 " --> pdb=" O ALA U 45 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE U 50 " --> pdb=" O ALA U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 105 through 129 Processing helix chain 'U' and resid 459 through 505 Processing helix chain 'U' and resid 512 through 537 removed outlier: 3.924A pdb=" N GLN U 537 " --> pdb=" O ALA U 533 " (cutoff:3.500A) Processing helix chain 'U' and resid 540 through 547 removed outlier: 4.115A pdb=" N SER U 544 " --> pdb=" O GLN U 540 " (cutoff:3.500A) Processing helix chain 'e' and resid 8 through 34 removed outlier: 3.837A pdb=" N SER e 23 " --> pdb=" O ASN e 19 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA e 24 " --> pdb=" O LYS e 20 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 100 removed outlier: 4.492A pdb=" N ALA e 49 " --> pdb=" O ALA e 45 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE e 50 " --> pdb=" O ALA e 46 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER e 73 " --> pdb=" O ASN e 69 " (cutoff:3.500A) Processing helix chain 'e' and resid 105 through 129 Processing helix chain 'e' and resid 164 through 169 Processing helix chain 'e' and resid 459 through 507 removed outlier: 3.647A pdb=" N ALA e 467 " --> pdb=" O ALA e 463 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE e 506 " --> pdb=" O ALA e 502 " (cutoff:3.500A) Processing helix chain 'e' and resid 513 through 537 removed outlier: 4.103A pdb=" N GLN e 537 " --> pdb=" O ALA e 533 " (cutoff:3.500A) Processing helix chain 'e' and resid 540 through 547 removed outlier: 4.275A pdb=" N SER e 544 " --> pdb=" O GLN e 540 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 34 removed outlier: 3.954A pdb=" N THR L 14 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER L 23 " --> pdb=" O ASN L 19 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA L 24 " --> pdb=" O LYS L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 100 removed outlier: 3.916A pdb=" N GLN L 48 " --> pdb=" O ASP L 44 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR L 77 " --> pdb=" O SER L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 130 Processing helix chain 'L' and resid 459 through 507 removed outlier: 3.602A pdb=" N ALA L 463 " --> pdb=" O ASP L 459 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG L 505 " --> pdb=" O GLU L 501 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE L 506 " --> pdb=" O ALA L 502 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN L 507 " --> pdb=" O GLN L 503 " (cutoff:3.500A) Processing helix chain 'L' and resid 510 through 536 removed outlier: 3.733A pdb=" N SER L 516 " --> pdb=" O ALA L 512 " (cutoff:3.500A) Processing helix chain 'L' and resid 537 through 539 No H-bonds generated for 'chain 'L' and resid 537 through 539' Processing helix chain 'L' and resid 540 through 547 removed outlier: 3.942A pdb=" N SER L 544 " --> pdb=" O GLN L 540 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN L 547 " --> pdb=" O LEU L 543 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 34 Processing helix chain 'V' and resid 44 through 101 removed outlier: 4.345A pdb=" N GLN V 48 " --> pdb=" O ASP V 44 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG V 53 " --> pdb=" O ALA V 49 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN V 88 " --> pdb=" O GLU V 84 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N THR V 101 " --> pdb=" O VAL V 97 " (cutoff:3.500A) Processing helix chain 'V' and resid 105 through 130 removed outlier: 3.617A pdb=" N THR V 130 " --> pdb=" O VAL V 126 " (cutoff:3.500A) Processing helix chain 'V' and resid 459 through 507 removed outlier: 3.554A pdb=" N ALA V 463 " --> pdb=" O ASP V 459 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG V 505 " --> pdb=" O GLU V 501 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE V 506 " --> pdb=" O ALA V 502 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN V 507 " --> pdb=" O GLN V 503 " (cutoff:3.500A) Processing helix chain 'V' and resid 510 through 536 removed outlier: 3.853A pdb=" N SER V 516 " --> pdb=" O ALA V 512 " (cutoff:3.500A) Processing helix chain 'V' and resid 537 through 540 Processing helix chain 'V' and resid 541 through 547 removed outlier: 3.828A pdb=" N LEU V 545 " --> pdb=" O GLN V 541 " (cutoff:3.500A) Processing helix chain 'f' and resid 8 through 34 removed outlier: 3.643A pdb=" N SER f 23 " --> pdb=" O ASN f 19 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA f 24 " --> pdb=" O LYS f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 45 through 100 removed outlier: 3.659A pdb=" N ASN f 88 " --> pdb=" O GLU f 84 " (cutoff:3.500A) Processing helix chain 'f' and resid 105 through 130 Processing helix chain 'f' and resid 164 through 169 Processing helix chain 'f' and resid 459 through 505 removed outlier: 3.776A pdb=" N ALA f 463 " --> pdb=" O ASP f 459 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG f 505 " --> pdb=" O GLU f 501 " (cutoff:3.500A) Processing helix chain 'f' and resid 510 through 537 removed outlier: 3.818A pdb=" N SER f 516 " --> pdb=" O ALA f 512 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN f 537 " --> pdb=" O ALA f 533 " (cutoff:3.500A) Processing helix chain 'f' and resid 540 through 547 removed outlier: 4.037A pdb=" N SER f 544 " --> pdb=" O GLN f 540 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 34 removed outlier: 3.757A pdb=" N SER M 23 " --> pdb=" O ASN M 19 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA M 24 " --> pdb=" O LYS M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 100 removed outlier: 3.518A pdb=" N SER M 56 " --> pdb=" O ASN M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 129 removed outlier: 3.569A pdb=" N SER M 111 " --> pdb=" O SER M 107 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE M 112 " --> pdb=" O ASP M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 459 through 508 removed outlier: 3.909A pdb=" N THR M 497 " --> pdb=" O ASN M 493 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN M 498 " --> pdb=" O ASN M 494 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG M 505 " --> pdb=" O GLU M 501 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE M 506 " --> pdb=" O ALA M 502 " (cutoff:3.500A) Processing helix chain 'M' and resid 510 through 536 Processing helix chain 'M' and resid 537 through 541 removed outlier: 3.763A pdb=" N GLN M 541 " --> pdb=" O VAL M 538 " (cutoff:3.500A) Processing helix chain 'M' and resid 542 through 547 removed outlier: 4.227A pdb=" N LEU M 546 " --> pdb=" O VAL M 542 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN M 547 " --> pdb=" O LEU M 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 542 through 547' Processing helix chain 'W' and resid 8 through 34 removed outlier: 3.633A pdb=" N SER W 23 " --> pdb=" O ASN W 19 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA W 24 " --> pdb=" O LYS W 20 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 101 removed outlier: 3.933A pdb=" N ALA W 49 " --> pdb=" O ALA W 45 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR W 101 " --> pdb=" O VAL W 97 " (cutoff:3.500A) Processing helix chain 'W' and resid 105 through 129 removed outlier: 4.139A pdb=" N SER W 111 " --> pdb=" O SER W 107 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE W 112 " --> pdb=" O ASP W 108 " (cutoff:3.500A) Processing helix chain 'W' and resid 459 through 508 removed outlier: 3.556A pdb=" N ALA W 463 " --> pdb=" O ASP W 459 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR W 497 " --> pdb=" O ASN W 493 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN W 498 " --> pdb=" O ASN W 494 " (cutoff:3.500A) Processing helix chain 'W' and resid 510 through 537 removed outlier: 3.661A pdb=" N GLU W 514 " --> pdb=" O ASP W 510 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER W 516 " --> pdb=" O ALA W 512 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN W 537 " --> pdb=" O ALA W 533 " (cutoff:3.500A) Processing helix chain 'W' and resid 538 through 541 Processing helix chain 'W' and resid 542 through 547 removed outlier: 4.127A pdb=" N LEU W 546 " --> pdb=" O VAL W 542 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN W 547 " --> pdb=" O LEU W 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 542 through 547' Processing helix chain 'g' and resid 8 through 34 removed outlier: 3.676A pdb=" N SER g 23 " --> pdb=" O ASN g 19 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA g 24 " --> pdb=" O LYS g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 38 through 42 removed outlier: 4.129A pdb=" N LYS g 42 " --> pdb=" O ASN g 39 " (cutoff:3.500A) Processing helix chain 'g' and resid 46 through 101 removed outlier: 3.599A pdb=" N ILE g 50 " --> pdb=" O ALA g 46 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR g 101 " --> pdb=" O VAL g 97 " (cutoff:3.500A) Processing helix chain 'g' and resid 105 through 129 Processing helix chain 'g' and resid 164 through 169 removed outlier: 3.500A pdb=" N GLY g 169 " --> pdb=" O SER g 165 " (cutoff:3.500A) Processing helix chain 'g' and resid 459 through 508 removed outlier: 3.529A pdb=" N ALA g 463 " --> pdb=" O ASP g 459 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR g 497 " --> pdb=" O ASN g 493 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN g 498 " --> pdb=" O ASN g 494 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE g 506 " --> pdb=" O ALA g 502 " (cutoff:3.500A) Processing helix chain 'g' and resid 510 through 536 Processing helix chain 'g' and resid 537 through 539 No H-bonds generated for 'chain 'g' and resid 537 through 539' Processing helix chain 'g' and resid 540 through 547 removed outlier: 4.012A pdb=" N SER g 544 " --> pdb=" O GLN g 540 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 146 Processing sheet with id=AA3, first strand: chain 'B' and resid 131 through 132 Processing sheet with id=AA4, first strand: chain 'B' and resid 144 through 147 Processing sheet with id=AA5, first strand: chain 'C' and resid 131 through 132 Processing sheet with id=AA6, first strand: chain 'C' and resid 143 through 147 Processing sheet with id=AA7, first strand: chain 'D' and resid 131 through 132 Processing sheet with id=AA8, first strand: chain 'D' and resid 143 through 146 Processing sheet with id=AA9, first strand: chain 'N' and resid 131 through 132 Processing sheet with id=AB1, first strand: chain 'N' and resid 143 through 146 Processing sheet with id=AB2, first strand: chain 'X' and resid 131 through 132 Processing sheet with id=AB3, first strand: chain 'X' and resid 143 through 147 Processing sheet with id=AB4, first strand: chain 'E' and resid 131 through 132 Processing sheet with id=AB5, first strand: chain 'E' and resid 144 through 146 Processing sheet with id=AB6, first strand: chain 'O' and resid 131 through 132 Processing sheet with id=AB7, first strand: chain 'O' and resid 143 through 147 Processing sheet with id=AB8, first strand: chain 'Y' and resid 131 through 132 Processing sheet with id=AB9, first strand: chain 'Y' and resid 143 through 146 Processing sheet with id=AC1, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AC2, first strand: chain 'F' and resid 144 through 147 Processing sheet with id=AC3, first strand: chain 'P' and resid 131 through 132 Processing sheet with id=AC4, first strand: chain 'P' and resid 144 through 147 Processing sheet with id=AC5, first strand: chain 'Z' and resid 131 through 132 Processing sheet with id=AC6, first strand: chain 'Z' and resid 144 through 146 Processing sheet with id=AC7, first strand: chain 'G' and resid 143 through 146 Processing sheet with id=AC8, first strand: chain 'Q' and resid 131 through 132 Processing sheet with id=AC9, first strand: chain 'Q' and resid 143 through 147 Processing sheet with id=AD1, first strand: chain 'a' and resid 143 through 146 Processing sheet with id=AD2, first strand: chain 'H' and resid 131 through 132 Processing sheet with id=AD3, first strand: chain 'H' and resid 143 through 146 Processing sheet with id=AD4, first strand: chain 'R' and resid 143 through 147 Processing sheet with id=AD5, first strand: chain 'b' and resid 143 through 146 Processing sheet with id=AD6, first strand: chain 'I' and resid 131 through 132 Processing sheet with id=AD7, first strand: chain 'I' and resid 143 through 147 Processing sheet with id=AD8, first strand: chain 'S' and resid 131 through 132 Processing sheet with id=AD9, first strand: chain 'S' and resid 144 through 147 removed outlier: 3.564A pdb=" N MET S 144 " --> pdb=" O ILE S 158 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'c' and resid 131 through 132 Processing sheet with id=AE2, first strand: chain 'c' and resid 143 through 147 removed outlier: 3.533A pdb=" N ILE c 146 " --> pdb=" O ILE c 156 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 144 through 147 Processing sheet with id=AE4, first strand: chain 'T' and resid 131 through 132 Processing sheet with id=AE5, first strand: chain 'T' and resid 143 through 147 Processing sheet with id=AE6, first strand: chain 'd' and resid 131 through 132 Processing sheet with id=AE7, first strand: chain 'd' and resid 144 through 147 Processing sheet with id=AE8, first strand: chain 'K' and resid 143 through 147 Processing sheet with id=AE9, first strand: chain 'U' and resid 131 through 132 Processing sheet with id=AF1, first strand: chain 'U' and resid 143 through 147 Processing sheet with id=AF2, first strand: chain 'e' and resid 143 through 147 removed outlier: 3.681A pdb=" N ILE e 156 " --> pdb=" O ILE e 146 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 142 through 147 Processing sheet with id=AF4, first strand: chain 'V' and resid 142 through 147 Processing sheet with id=AF5, first strand: chain 'f' and resid 142 through 146 Processing sheet with id=AF6, first strand: chain 'M' and resid 143 through 147 Processing sheet with id=AF7, first strand: chain 'W' and resid 143 through 147 Processing sheet with id=AF8, first strand: chain 'g' and resid 143 through 147 5390 hydrogen bonds defined for protein. 16017 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: 24.32 Time building geometry restraints manager: 24.27 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: 24213 1.34 - 1.45: 3631 1.45 - 1.57: 38234 1.57 - 1.69: 0 1.69 - 1.80: 132 Bond restraints: 66210 Sorted by residual: bond pdb=" C VAL F 538 " pdb=" N PRO F 539 " ideal model delta sigma weight residual 1.334 1.364 -0.030 8.40e-03 1.42e+04 1.30e+01 bond pdb=" C VAL J 538 " pdb=" N PRO J 539 " ideal model delta sigma weight residual 1.337 1.352 -0.015 9.80e-03 1.04e+04 2.36e+00 bond pdb=" C VAL a 538 " pdb=" N PRO a 539 " ideal model delta sigma weight residual 1.334 1.346 -0.013 8.40e-03 1.42e+04 2.30e+00 bond pdb=" CA VAL A 148 " pdb=" CB VAL A 148 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.08e-02 8.57e+03 1.57e+00 bond pdb=" CA ASP J 508 " pdb=" CB ASP J 508 " ideal model delta sigma weight residual 1.527 1.547 -0.020 1.61e-02 3.86e+03 1.56e+00 ... (remaining 66205 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.07: 315 106.07 - 112.50: 35935 112.50 - 118.93: 19461 118.93 - 125.36: 33758 125.36 - 131.79: 99 Bond angle restraints: 89568 Sorted by residual: angle pdb=" N ILE d 5 " pdb=" CA ILE d 5 " pdb=" C ILE d 5 " ideal model delta sigma weight residual 113.71 109.47 4.24 9.50e-01 1.11e+00 1.99e+01 angle pdb=" N ILE I 5 " pdb=" CA ILE I 5 " pdb=" C ILE I 5 " ideal model delta sigma weight residual 112.96 109.53 3.43 1.00e+00 1.00e+00 1.17e+01 angle pdb=" C TYR e 511 " pdb=" N ALA e 512 " pdb=" CA ALA e 512 " ideal model delta sigma weight residual 121.54 128.07 -6.53 1.91e+00 2.74e-01 1.17e+01 angle pdb=" N ILE U 5 " pdb=" CA ILE U 5 " pdb=" C ILE U 5 " ideal model delta sigma weight residual 113.42 109.43 3.99 1.17e+00 7.31e-01 1.16e+01 angle pdb=" C GLU V 94 " pdb=" N LEU V 95 " pdb=" CA LEU V 95 " ideal model delta sigma weight residual 121.58 114.96 6.62 1.95e+00 2.63e-01 1.15e+01 ... (remaining 89563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 37985 17.99 - 35.99: 2761 35.99 - 53.98: 445 53.98 - 71.97: 103 71.97 - 89.97: 70 Dihedral angle restraints: 41364 sinusoidal: 15825 harmonic: 25539 Sorted by residual: dihedral pdb=" CA SER V 40 " pdb=" C SER V 40 " pdb=" N ALA V 41 " pdb=" CA ALA V 41 " ideal model delta harmonic sigma weight residual 180.00 -146.42 -33.58 0 5.00e+00 4.00e-02 4.51e+01 dihedral pdb=" CA VAL S 538 " pdb=" C VAL S 538 " pdb=" N PRO S 539 " pdb=" CA PRO S 539 " ideal model delta harmonic sigma weight residual 180.00 147.08 32.92 0 5.00e+00 4.00e-02 4.34e+01 dihedral pdb=" CA ALA V 41 " pdb=" C ALA V 41 " pdb=" N LYS V 42 " pdb=" CA LYS V 42 " ideal model delta harmonic sigma weight residual 180.00 147.64 32.36 0 5.00e+00 4.00e-02 4.19e+01 ... (remaining 41361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 8729 0.038 - 0.076: 1815 0.076 - 0.113: 369 0.113 - 0.151: 74 0.151 - 0.189: 8 Chirality restraints: 10995 Sorted by residual: chirality pdb=" CG LEU g 170 " pdb=" CB LEU g 170 " pdb=" CD1 LEU g 170 " pdb=" CD2 LEU g 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CA ASP U 508 " pdb=" N ASP U 508 " pdb=" C ASP U 508 " pdb=" CB ASP U 508 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CA ASP T 508 " pdb=" N ASP T 508 " pdb=" C ASP T 508 " pdb=" CB ASP T 508 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.06e-01 ... (remaining 10992 not shown) Planarity restraints: 12150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA d 512 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C ALA d 512 " -0.055 2.00e-02 2.50e+03 pdb=" O ALA d 512 " 0.021 2.00e-02 2.50e+03 pdb=" N THR d 513 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA U 512 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.96e+00 pdb=" C ALA U 512 " -0.055 2.00e-02 2.50e+03 pdb=" O ALA U 512 " 0.020 2.00e-02 2.50e+03 pdb=" N THR U 513 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA K 512 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C ALA K 512 " -0.048 2.00e-02 2.50e+03 pdb=" O ALA K 512 " 0.018 2.00e-02 2.50e+03 pdb=" N THR K 513 " 0.016 2.00e-02 2.50e+03 ... (remaining 12147 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 1211 2.64 - 3.20: 67952 3.20 - 3.77: 107811 3.77 - 4.33: 136764 4.33 - 4.90: 232456 Nonbonded interactions: 546194 Sorted by model distance: nonbonded pdb=" OG1 THR I 497 " pdb=" OD1 ASN S 16 " model vdw 2.073 2.440 nonbonded pdb=" OG SER Y 127 " pdb=" O ILE Y 163 " model vdw 2.106 2.440 nonbonded pdb=" OG SER T 34 " pdb=" ND2 ASN T 39 " model vdw 2.116 2.520 nonbonded pdb=" OG SER W 127 " pdb=" O ILE W 163 " model vdw 2.116 2.440 nonbonded pdb=" O PHE H 173 " pdb=" OG1 THR H 457 " model vdw 2.128 2.440 ... (remaining 546189 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 37 or resid 39 through 546)) selection = (chain 'B' and (resid 3 through 37 or resid 39 through 546)) selection = (chain 'C' and (resid 3 through 37 or resid 39 through 546)) selection = (chain 'D' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'E' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'F' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'G' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'H' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'I' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'J' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'K' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'L' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'M' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'N' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'O' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'P' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'Q' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'R' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'S' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'T' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'U' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'V' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'W' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'X' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'Y' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'Z' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'a' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'b' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'c' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'd' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'e' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'f' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) selection = (chain 'g' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 37 or resid 39 through 546)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 39585 2.51 5 N 12069 2.21 5 O 14310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 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: 15.240 Check model and map are aligned: 0.730 Process input model: 148.610 Find NCS groups from input model: 4.510 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Set scattering table: 0.500 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 174.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 66210 Z= 0.171 Angle : 0.490 10.145 89568 Z= 0.299 Chirality : 0.034 0.189 10995 Planarity : 0.002 0.064 12150 Dihedral : 13.535 89.969 24678 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.05 % Favored : 95.90 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.09), residues: 8769 helix: 1.98 (0.06), residues: 6288 sheet: 0.01 (0.23), residues: 462 loop : -2.08 (0.13), residues: 2019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1899 residues out of total 7440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1899 time to evaluate : 6.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1899 average time/residue: 0.6293 time to fit residues: 2005.7570 Evaluate side-chains 1308 residues out of total 7440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1308 time to evaluate : 6.027 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.0268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 724 optimal weight: 6.9990 chunk 650 optimal weight: 0.6980 chunk 360 optimal weight: 3.9990 chunk 222 optimal weight: 0.0870 chunk 438 optimal weight: 6.9990 chunk 347 optimal weight: 3.9990 chunk 672 optimal weight: 3.9990 chunk 260 optimal weight: 0.7980 chunk 408 optimal weight: 6.9990 chunk 500 optimal weight: 5.9990 chunk 779 optimal weight: 6.9990 overall best weight: 1.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN B 22 GLN ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 GLN B 482 GLN C 3 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN C 86 ASN C 88 ASN C 525 GLN ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN D 21 ASN D 63 GLN D 67 ASN D 86 ASN D 129 GLN D 507 GLN ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 GLN N 536 ASN N 537 GLN N 541 GLN X 48 GLN X 67 ASN X 86 ASN X 503 GLN X 522 GLN E 6 ASN E 22 GLN E 136 ASN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 525 GLN ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 491 ASN Y 522 GLN F 21 ASN F 22 GLN F 39 ASN F 129 GLN F 482 GLN F 537 GLN P 6 ASN P 17 ASN P 129 GLN P 136 ASN ** P 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 536 ASN Z 6 ASN Z 129 GLN Z 154 GLN Z 494 ASN G 63 GLN G 98 GLN G 517 ASN Q 498 ASN Q 540 GLN a 3 GLN ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 ASN ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 GLN H 537 GLN ** R 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN b 21 ASN b 86 ASN b 174 ASN b 537 GLN I 22 GLN ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 ASN I 525 GLN S 3 GLN ** S 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 ASN ** S 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN S 507 GLN S 547 GLN c 39 ASN ** c 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 86 ASN c 147 GLN c 540 GLN ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 ASN J 76 GLN J 154 GLN T 16 ASN T 17 ASN T 22 GLN ** T 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 491 ASN d 17 ASN ** d 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 ASN ** d 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 522 GLN d 526 GLN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 547 GLN ** U 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 6 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN ** U 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 498 ASN U 525 GLN U 540 GLN e 16 ASN ** e 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 63 GLN e 67 ASN e 86 ASN e 503 GLN e 547 GLN L 76 GLN L 133 ASN ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 525 GLN L 526 GLN ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 498 ASN V 503 GLN V 507 GLN V 526 GLN f 171 ASN f 470 GLN f 540 GLN M 76 GLN M 171 ASN M 483 ASN M 529 ASN W 131 GLN W 136 ASN W 526 GLN ** g 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 86 ASN g 147 GLN g 507 GLN g 536 ASN Total number of N/Q/H flips: 118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 66210 Z= 0.243 Angle : 0.543 9.730 89568 Z= 0.297 Chirality : 0.038 0.273 10995 Planarity : 0.003 0.064 12150 Dihedral : 3.829 35.048 9216 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.15 % Favored : 95.84 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.81 (0.09), residues: 8769 helix: 3.09 (0.06), residues: 6315 sheet: 0.43 (0.23), residues: 462 loop : -2.15 (0.14), residues: 1992 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1527 residues out of total 7440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1384 time to evaluate : 6.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 143 outliers final: 82 residues processed: 1459 average time/residue: 0.6225 time to fit residues: 1556.5206 Evaluate side-chains 1335 residues out of total 7440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1253 time to evaluate : 6.006 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 0 residues processed: 82 average time/residue: 0.4973 time to fit residues: 85.0931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 433 optimal weight: 9.9990 chunk 241 optimal weight: 2.9990 chunk 648 optimal weight: 5.9990 chunk 530 optimal weight: 6.9990 chunk 214 optimal weight: 7.9990 chunk 780 optimal weight: 5.9990 chunk 843 optimal weight: 2.9990 chunk 695 optimal weight: 0.0970 chunk 774 optimal weight: 0.9980 chunk 266 optimal weight: 7.9990 chunk 626 optimal weight: 0.9980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN C 69 ASN ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 GLN N 537 GLN N 541 GLN X 48 GLN X 171 ASN ** X 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 537 GLN X 547 GLN E 22 GLN E 537 GLN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 525 GLN Y 22 GLN Y 154 GLN F 22 GLN F 491 ASN P 6 ASN P 129 GLN ** P 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 6 ASN Z 17 ASN Z 129 GLN ** Z 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 ASN G 498 ASN a 3 GLN ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 491 ASN a 525 GLN a 529 ASN H 8 ASN ** H 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 ASN R 154 GLN I 22 GLN ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 ASN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 540 GLN S 547 GLN ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 517 ASN d 15 GLN ** d 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 6 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 86 ASN e 547 GLN ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 498 ASN M 76 GLN M 131 GLN W 498 ASN ** g 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 67 ASN g 86 ASN g 147 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 66210 Z= 0.220 Angle : 0.521 9.002 89568 Z= 0.286 Chirality : 0.037 0.359 10995 Planarity : 0.003 0.062 12150 Dihedral : 3.832 35.274 9216 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.91 % Favored : 96.07 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 3.23 (0.09), residues: 8769 helix: 3.39 (0.06), residues: 6330 sheet: 0.61 (0.22), residues: 462 loop : -2.07 (0.14), residues: 1977 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1458 residues out of total 7440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1364 time to evaluate : 6.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 44 residues processed: 1418 average time/residue: 0.6184 time to fit residues: 1497.3942 Evaluate side-chains 1293 residues out of total 7440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1249 time to evaluate : 6.115 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.5101 time to fit residues: 49.7550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 771 optimal weight: 0.9990 chunk 586 optimal weight: 0.9980 chunk 405 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 372 optimal weight: 4.9990 chunk 524 optimal weight: 0.9990 chunk 783 optimal weight: 0.8980 chunk 829 optimal weight: 4.9990 chunk 409 optimal weight: 1.9990 chunk 742 optimal weight: 6.9990 chunk 223 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN B 57 ASN B 76 GLN ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 537 GLN X 48 GLN ** X 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 537 GLN E 21 ASN E 22 GLN O 57 ASN ** O 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 22 GLN ** Y 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN F 147 GLN ** F 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 ASN ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 536 ASN Z 6 ASN Z 17 ASN Z 129 GLN G 98 GLN Q 6 ASN Q 498 ASN ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 517 ASN H 537 GLN ** R 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 ASN R 147 GLN b 174 ASN b 537 GLN ** S 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 507 GLN S 536 ASN S 540 GLN ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 15 GLN ** d 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 522 GLN d 526 GLN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 3 GLN U 21 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 547 GLN ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 507 GLN W 17 ASN W 171 ASN W 498 ASN ** g 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 147 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 66210 Z= 0.180 Angle : 0.507 10.702 89568 Z= 0.278 Chirality : 0.036 0.334 10995 Planarity : 0.003 0.063 12150 Dihedral : 3.753 34.807 9216 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.98 % Favored : 96.00 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 3.49 (0.09), residues: 8769 helix: 3.59 (0.06), residues: 6330 sheet: 0.75 (0.22), residues: 462 loop : -2.01 (0.14), residues: 1977 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1463 residues out of total 7440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1370 time to evaluate : 6.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 50 residues processed: 1416 average time/residue: 0.6151 time to fit residues: 1498.2356 Evaluate side-chains 1301 residues out of total 7440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1251 time to evaluate : 5.999 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.4862 time to fit residues: 53.7910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 690 optimal weight: 9.9990 chunk 470 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 617 optimal weight: 5.9990 chunk 342 optimal weight: 0.9980 chunk 707 optimal weight: 5.9990 chunk 573 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 423 optimal weight: 0.9980 chunk 744 optimal weight: 0.0050 chunk 209 optimal weight: 0.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN C 525 GLN ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 48 GLN ** X 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 537 GLN E 21 ASN O 540 GLN ** O 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 22 GLN ** Y 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 ASN ** F 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 ASN ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 6 ASN Z 129 GLN Q 6 ASN Q 498 ASN Q 507 GLN ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 525 GLN H 154 GLN ** R 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 ASN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 536 ASN S 540 GLN ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 6 ASN ** d 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 86 ASN ** d 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 522 GLN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 17 ASN U 21 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 17 ASN e 547 GLN ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 536 ASN M 131 GLN M 494 ASN W 131 GLN W 171 ASN ** g 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 529 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 66210 Z= 0.181 Angle : 0.513 10.796 89568 Z= 0.280 Chirality : 0.036 0.359 10995 Planarity : 0.003 0.062 12150 Dihedral : 3.713 34.589 9216 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.00 % Favored : 95.98 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 3.63 (0.09), residues: 8769 helix: 3.69 (0.06), residues: 6315 sheet: 0.84 (0.22), residues: 462 loop : -1.90 (0.14), residues: 1992 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1447 residues out of total 7440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1358 time to evaluate : 6.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 41 residues processed: 1405 average time/residue: 0.6235 time to fit residues: 1501.5154 Evaluate side-chains 1305 residues out of total 7440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1264 time to evaluate : 6.026 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.4846 time to fit residues: 45.7133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 279 optimal weight: 3.9990 chunk 746 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 486 optimal weight: 0.8980 chunk 204 optimal weight: 6.9990 chunk 830 optimal weight: 0.8980 chunk 689 optimal weight: 7.9990 chunk 384 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 274 optimal weight: 0.9980 chunk 435 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 526 GLN ** X 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 547 GLN E 21 ASN ** O 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 ASN ** F 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 ASN ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 536 ASN Z 6 ASN Z 129 GLN G 16 ASN Q 6 ASN ** Q 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 39 ASN Q 498 ASN ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 525 GLN ** R 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 537 GLN I 86 ASN ** S 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 ASN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 536 ASN S 540 GLN ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 ASN U 21 ASN U 113 GLN e 17 ASN ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 171 ASN W 498 ASN ** g 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 66210 Z= 0.179 Angle : 0.515 10.748 89568 Z= 0.281 Chirality : 0.036 0.265 10995 Planarity : 0.003 0.061 12150 Dihedral : 3.695 34.211 9216 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.89 % Favored : 96.09 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 3.71 (0.09), residues: 8769 helix: 3.74 (0.06), residues: 6315 sheet: 0.94 (0.22), residues: 462 loop : -1.86 (0.14), residues: 1992 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1416 residues out of total 7440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1345 time to evaluate : 6.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 33 residues processed: 1386 average time/residue: 0.6287 time to fit residues: 1488.4806 Evaluate side-chains 1275 residues out of total 7440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1242 time to evaluate : 6.004 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.4855 time to fit residues: 38.5017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 800 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 472 optimal weight: 5.9990 chunk 606 optimal weight: 4.9990 chunk 469 optimal weight: 0.7980 chunk 698 optimal weight: 7.9990 chunk 463 optimal weight: 1.9990 chunk 826 optimal weight: 3.9990 chunk 517 optimal weight: 0.9980 chunk 504 optimal weight: 0.4980 chunk 381 optimal weight: 0.0070 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN C 537 GLN ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 537 GLN X 547 GLN E 21 ASN ** O 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 ASN ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 6 ASN Z 16 ASN Z 129 GLN Q 6 ASN Q 17 ASN Q 498 ASN a 3 GLN ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 ASN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 536 ASN ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 86 ASN e 17 ASN e 526 GLN e 540 GLN ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 503 GLN ** V 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 GLN M 171 ASN W 498 ASN ** g 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 66210 Z= 0.168 Angle : 0.514 10.984 89568 Z= 0.282 Chirality : 0.036 0.306 10995 Planarity : 0.003 0.061 12150 Dihedral : 3.652 34.195 9216 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.92 % Favored : 96.07 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 3.76 (0.09), residues: 8769 helix: 3.77 (0.06), residues: 6330 sheet: 1.06 (0.22), residues: 462 loop : -1.88 (0.14), residues: 1977 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1394 residues out of total 7440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1340 time to evaluate : 6.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 24 residues processed: 1370 average time/residue: 0.6386 time to fit residues: 1491.8779 Evaluate side-chains 1287 residues out of total 7440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1263 time to evaluate : 6.066 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.5016 time to fit residues: 30.8431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 511 optimal weight: 0.0020 chunk 330 optimal weight: 0.9990 chunk 493 optimal weight: 9.9990 chunk 249 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 160 optimal weight: 5.9990 chunk 525 optimal weight: 1.9990 chunk 563 optimal weight: 4.9990 chunk 408 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 650 optimal weight: 7.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 8 ASN ** N 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 526 GLN ** X 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 540 GLN Y 22 GLN P 6 ASN P 536 ASN Z 129 GLN G 16 ASN ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 ASN Q 76 GLN ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 ASN ** R 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 21 ASN ** S 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 536 ASN ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 15 GLN ** d 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 21 ASN ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 17 ASN ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 129 GLN ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 GLN ** g 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 66210 Z= 0.238 Angle : 0.557 10.916 89568 Z= 0.304 Chirality : 0.038 0.385 10995 Planarity : 0.003 0.062 12150 Dihedral : 3.755 34.502 9216 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.15 % Favored : 95.84 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.09), residues: 8769 helix: 3.66 (0.06), residues: 6330 sheet: 0.98 (0.22), residues: 462 loop : -1.90 (0.14), residues: 1977 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1342 residues out of total 7440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1285 time to evaluate : 6.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 33 residues processed: 1318 average time/residue: 0.6323 time to fit residues: 1421.5974 Evaluate side-chains 1270 residues out of total 7440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1237 time to evaluate : 6.075 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.5004 time to fit residues: 38.9922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 752 optimal weight: 1.9990 chunk 792 optimal weight: 8.9990 chunk 722 optimal weight: 0.8980 chunk 770 optimal weight: 7.9990 chunk 463 optimal weight: 0.5980 chunk 335 optimal weight: 0.9990 chunk 605 optimal weight: 0.8980 chunk 236 optimal weight: 5.9990 chunk 696 optimal weight: 1.9990 chunk 728 optimal weight: 0.7980 chunk 767 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 547 GLN E 22 GLN E 537 GLN ** O 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 540 GLN Y 22 GLN ** Y 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 ASN Z 6 ASN Z 129 GLN ** Z 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 ASN ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 ASN Q 39 ASN Q 498 ASN ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 ASN ** R 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 537 GLN I 491 ASN ** S 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 ASN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 536 ASN ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 15 GLN ** d 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 ASN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 17 ASN ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 GLN W 131 GLN ** g 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 66210 Z= 0.184 Angle : 0.542 11.084 89568 Z= 0.296 Chirality : 0.036 0.331 10995 Planarity : 0.003 0.060 12150 Dihedral : 3.700 34.253 9216 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.83 % Favored : 96.15 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 3.73 (0.09), residues: 8769 helix: 3.78 (0.06), residues: 6300 sheet: 1.06 (0.22), residues: 462 loop : -1.91 (0.14), residues: 2007 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1343 residues out of total 7440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1304 time to evaluate : 6.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 13 residues processed: 1323 average time/residue: 0.6366 time to fit residues: 1441.2179 Evaluate side-chains 1284 residues out of total 7440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1271 time to evaluate : 6.056 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.4883 time to fit residues: 20.1560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 506 optimal weight: 2.9990 chunk 814 optimal weight: 1.9990 chunk 497 optimal weight: 0.6980 chunk 386 optimal weight: 0.6980 chunk 566 optimal weight: 2.9990 chunk 854 optimal weight: 1.9990 chunk 786 optimal weight: 2.9990 chunk 680 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 525 optimal weight: 0.8980 chunk 417 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 540 GLN Y 22 GLN ** Y 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 ASN P 536 ASN Z 129 GLN G 16 ASN ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 ASN Q 39 ASN Q 498 ASN ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 129 GLN H 8 ASN ** R 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 536 ASN ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 ASN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 17 ASN ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 3 GLN ** g 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.082 66210 Z= 0.209 Angle : 0.555 13.805 89568 Z= 0.302 Chirality : 0.037 0.346 10995 Planarity : 0.003 0.060 12150 Dihedral : 3.716 34.377 9216 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.10 % Favored : 95.88 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 3.69 (0.09), residues: 8769 helix: 3.74 (0.06), residues: 6285 sheet: 1.04 (0.22), residues: 462 loop : -1.86 (0.14), residues: 2022 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1297 residues out of total 7440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1268 time to evaluate : 7.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 1281 average time/residue: 0.6482 time to fit residues: 1421.2778 Evaluate side-chains 1256 residues out of total 7440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1239 time to evaluate : 6.087 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.5113 time to fit residues: 24.4356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 540 optimal weight: 0.9980 chunk 725 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 627 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 189 optimal weight: 0.8980 chunk 681 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 700 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** C 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 547 GLN ** O 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 540 GLN Y 22 GLN ** Y 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 ASN Z 6 ASN Z 129 GLN ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 ASN Q 498 ASN ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 ASN ** R 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 537 GLN ** S 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 ASN ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 536 ASN ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 133 ASN ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 GLN g 39 ASN ** g 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 88 ASN ** g 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.118471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.100505 restraints weight = 365066.710| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 4.32 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3664 r_free = 0.3664 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3664 r_free = 0.3664 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.091 66210 Z= 0.203 Angle : 0.553 11.099 89568 Z= 0.302 Chirality : 0.037 0.382 10995 Planarity : 0.003 0.060 12150 Dihedral : 3.711 34.185 9216 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.98 % Favored : 96.00 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.09), residues: 8769 helix: 3.76 (0.06), residues: 6285 sheet: 1.07 (0.22), residues: 462 loop : -1.86 (0.14), residues: 2022 =============================================================================== Job complete usr+sys time: 20244.95 seconds wall clock time: 353 minutes 27.50 seconds (21207.50 seconds total)