Starting phenix.real_space_refine on Sun Mar 24 00:50:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6u_33027/03_2024/7x6u_33027.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6u_33027/03_2024/7x6u_33027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6u_33027/03_2024/7x6u_33027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6u_33027/03_2024/7x6u_33027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6u_33027/03_2024/7x6u_33027.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6u_33027/03_2024/7x6u_33027.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 426 5.16 5 C 24384 2.51 5 N 6852 2.21 5 O 7662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A ASP 255": "OD1" <-> "OD2" Residue "A GLU 271": "OE1" <-> "OE2" Residue "A PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 220": "OE1" <-> "OE2" Residue "B ASP 266": "OD1" <-> "OD2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 320": "OD1" <-> "OD2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 86": "OE1" <-> "OE2" Residue "E PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 242": "OE1" <-> "OE2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "E ASP 255": "OD1" <-> "OD2" Residue "E GLU 271": "OE1" <-> "OE2" Residue "E PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 220": "OE1" <-> "OE2" Residue "F ASP 266": "OD1" <-> "OD2" Residue "F TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 320": "OD1" <-> "OD2" Residue "F PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 86": "OE1" <-> "OE2" Residue "I PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 242": "OE1" <-> "OE2" Residue "I GLU 250": "OE1" <-> "OE2" Residue "I ASP 255": "OD1" <-> "OD2" Residue "I GLU 271": "OE1" <-> "OE2" Residue "I PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 220": "OE1" <-> "OE2" Residue "J ASP 266": "OD1" <-> "OD2" Residue "J TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 320": "OD1" <-> "OD2" Residue "J PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 86": "OE1" <-> "OE2" Residue "M PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 242": "OE1" <-> "OE2" Residue "M GLU 250": "OE1" <-> "OE2" Residue "M ASP 255": "OD1" <-> "OD2" Residue "M GLU 271": "OE1" <-> "OE2" Residue "M PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 220": "OE1" <-> "OE2" Residue "N ASP 266": "OD1" <-> "OD2" Residue "N TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 320": "OD1" <-> "OD2" Residue "N PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 86": "OE1" <-> "OE2" Residue "Q PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 242": "OE1" <-> "OE2" Residue "Q GLU 250": "OE1" <-> "OE2" Residue "Q ASP 255": "OD1" <-> "OD2" Residue "Q GLU 271": "OE1" <-> "OE2" Residue "Q PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 220": "OE1" <-> "OE2" Residue "R ASP 266": "OD1" <-> "OD2" Residue "R TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 320": "OD1" <-> "OD2" Residue "R PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 86": "OE1" <-> "OE2" Residue "U PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 242": "OE1" <-> "OE2" Residue "U GLU 250": "OE1" <-> "OE2" Residue "U ASP 255": "OD1" <-> "OD2" Residue "U GLU 271": "OE1" <-> "OE2" Residue "U PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 220": "OE1" <-> "OE2" Residue "V ASP 266": "OD1" <-> "OD2" Residue "V TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 320": "OD1" <-> "OD2" Residue "V PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39324 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3342 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 23, 'TRANS': 431} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3145 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 20, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3342 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 23, 'TRANS': 431} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "F" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3145 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 20, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3342 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 23, 'TRANS': 431} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "J" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3145 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 20, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3342 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 23, 'TRANS': 431} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "N" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3145 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 20, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3342 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 23, 'TRANS': 431} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "R" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3145 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 20, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3342 Classifications: {'peptide': 455} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 23, 'TRANS': 431} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "V" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3145 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 20, 'TRANS': 412} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 19.95, per 1000 atoms: 0.51 Number of scatterers: 39324 At special positions: 0 Unit cell: (196.56, 201.96, 197.64, 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 426 16.00 O 7662 8.00 N 6852 7.00 C 24384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=126, symmetry=0 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 49 " distance=2.03 Simple disulfide: pdb=" SG CYS A 143 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 327 " distance=2.03 Simple disulfide: pdb=" SG CYS A 206 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 258 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 280 " distance=2.04 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 1 " - pdb=" SG CYS B 42 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 24 " distance=2.03 Simple disulfide: pdb=" SG CYS B 67 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 82 " - pdb=" SG CYS B 279 " distance=2.02 Simple disulfide: pdb=" SG CYS B 88 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 98 " - pdb=" SG CYS B 125 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.02 Simple disulfide: pdb=" SG CYS B 247 " - pdb=" SG CYS B 261 " distance=2.06 Simple disulfide: pdb=" SG CYS B 346 " - pdb=" SG CYS B 416 " distance=2.03 Simple disulfide: pdb=" SG CYS B 356 " - pdb=" SG CYS B 359 " distance=2.02 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS E 26 " - pdb=" SG CYS E 49 " distance=2.03 Simple disulfide: pdb=" SG CYS E 143 " - pdb=" SG CYS E 156 " distance=2.03 Simple disulfide: pdb=" SG CYS E 180 " - pdb=" SG CYS E 327 " distance=2.03 Simple disulfide: pdb=" SG CYS E 206 " - pdb=" SG CYS E 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 258 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 266 " - pdb=" SG CYS E 303 " distance=2.03 Simple disulfide: pdb=" SG CYS E 274 " - pdb=" SG CYS E 280 " distance=2.03 Simple disulfide: pdb=" SG CYS E 287 " - pdb=" SG CYS E 292 " distance=2.03 Simple disulfide: pdb=" SG CYS F 1 " - pdb=" SG CYS F 42 " distance=2.03 Simple disulfide: pdb=" SG CYS F 14 " - pdb=" SG CYS F 24 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 163 " distance=2.03 Simple disulfide: pdb=" SG CYS F 82 " - pdb=" SG CYS F 279 " distance=2.02 Simple disulfide: pdb=" SG CYS F 88 " - pdb=" SG CYS F 136 " distance=2.03 Simple disulfide: pdb=" SG CYS F 94 " - pdb=" SG CYS F 143 " distance=2.03 Simple disulfide: pdb=" SG CYS F 98 " - pdb=" SG CYS F 125 " distance=2.03 Simple disulfide: pdb=" SG CYS F 129 " - pdb=" SG CYS F 134 " distance=2.03 Simple disulfide: pdb=" SG CYS F 216 " - pdb=" SG CYS F 231 " distance=2.02 Simple disulfide: pdb=" SG CYS F 247 " - pdb=" SG CYS F 261 " distance=2.06 Simple disulfide: pdb=" SG CYS F 346 " - pdb=" SG CYS F 416 " distance=2.03 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F 359 " distance=2.02 Simple disulfide: pdb=" SG CYS F 381 " - pdb=" SG CYS F 412 " distance=2.03 Simple disulfide: pdb=" SG CYS I 26 " - pdb=" SG CYS I 49 " distance=2.03 Simple disulfide: pdb=" SG CYS I 143 " - pdb=" SG CYS I 156 " distance=2.03 Simple disulfide: pdb=" SG CYS I 180 " - pdb=" SG CYS I 327 " distance=2.03 Simple disulfide: pdb=" SG CYS I 206 " - pdb=" SG CYS I 216 " distance=2.03 Simple disulfide: pdb=" SG CYS I 258 " - pdb=" SG CYS I 305 " distance=2.03 Simple disulfide: pdb=" SG CYS I 266 " - pdb=" SG CYS I 303 " distance=2.03 Simple disulfide: pdb=" SG CYS I 274 " - pdb=" SG CYS I 280 " distance=2.04 Simple disulfide: pdb=" SG CYS I 287 " - pdb=" SG CYS I 292 " distance=2.03 Simple disulfide: pdb=" SG CYS J 1 " - pdb=" SG CYS J 42 " distance=2.03 Simple disulfide: pdb=" SG CYS J 14 " - pdb=" SG CYS J 24 " distance=2.03 Simple disulfide: pdb=" SG CYS J 67 " - pdb=" SG CYS J 163 " distance=2.03 Simple disulfide: pdb=" SG CYS J 82 " - pdb=" SG CYS J 279 " distance=2.02 Simple disulfide: pdb=" SG CYS J 88 " - pdb=" SG CYS J 136 " distance=2.03 Simple disulfide: pdb=" SG CYS J 94 " - pdb=" SG CYS J 143 " distance=2.03 Simple disulfide: pdb=" SG CYS J 98 " - pdb=" SG CYS J 125 " distance=2.03 Simple disulfide: pdb=" SG CYS J 129 " - pdb=" SG CYS J 134 " distance=2.03 Simple disulfide: pdb=" SG CYS J 216 " - pdb=" SG CYS J 231 " distance=2.02 Simple disulfide: pdb=" SG CYS J 247 " - pdb=" SG CYS J 261 " distance=2.06 Simple disulfide: pdb=" SG CYS J 346 " - pdb=" SG CYS J 416 " distance=2.03 Simple disulfide: pdb=" SG CYS J 356 " - pdb=" SG CYS J 359 " distance=2.02 Simple disulfide: pdb=" SG CYS J 381 " - pdb=" SG CYS J 412 " distance=2.03 Simple disulfide: pdb=" SG CYS M 26 " - pdb=" SG CYS M 49 " distance=2.03 Simple disulfide: pdb=" SG CYS M 143 " - pdb=" SG CYS M 156 " distance=2.03 Simple disulfide: pdb=" SG CYS M 180 " - pdb=" SG CYS M 327 " distance=2.03 Simple disulfide: pdb=" SG CYS M 206 " - pdb=" SG CYS M 216 " distance=2.03 Simple disulfide: pdb=" SG CYS M 258 " - pdb=" SG CYS M 305 " distance=2.03 Simple disulfide: pdb=" SG CYS M 266 " - pdb=" SG CYS M 303 " distance=2.03 Simple disulfide: pdb=" SG CYS M 274 " - pdb=" SG CYS M 280 " distance=2.04 Simple disulfide: pdb=" SG CYS M 287 " - pdb=" SG CYS M 292 " distance=2.03 Simple disulfide: pdb=" SG CYS N 1 " - pdb=" SG CYS N 42 " distance=2.03 Simple disulfide: pdb=" SG CYS N 14 " - pdb=" SG CYS N 24 " distance=2.03 Simple disulfide: pdb=" SG CYS N 67 " - pdb=" SG CYS N 163 " distance=2.03 Simple disulfide: pdb=" SG CYS N 82 " - pdb=" SG CYS N 279 " distance=2.02 Simple disulfide: pdb=" SG CYS N 88 " - pdb=" SG CYS N 136 " distance=2.03 Simple disulfide: pdb=" SG CYS N 94 " - pdb=" SG CYS N 143 " distance=2.03 Simple disulfide: pdb=" SG CYS N 98 " - pdb=" SG CYS N 125 " distance=2.03 Simple disulfide: pdb=" SG CYS N 129 " - pdb=" SG CYS N 134 " distance=2.03 Simple disulfide: pdb=" SG CYS N 216 " - pdb=" SG CYS N 231 " distance=2.02 Simple disulfide: pdb=" SG CYS N 247 " - pdb=" SG CYS N 261 " distance=2.06 Simple disulfide: pdb=" SG CYS N 346 " - pdb=" SG CYS N 416 " distance=2.03 Simple disulfide: pdb=" SG CYS N 356 " - pdb=" SG CYS N 359 " distance=2.02 Simple disulfide: pdb=" SG CYS N 381 " - pdb=" SG CYS N 412 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 26 " - pdb=" SG CYS Q 49 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 143 " - pdb=" SG CYS Q 156 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 180 " - pdb=" SG CYS Q 327 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 206 " - pdb=" SG CYS Q 216 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 258 " - pdb=" SG CYS Q 305 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 266 " - pdb=" SG CYS Q 303 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 274 " - pdb=" SG CYS Q 280 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 287 " - pdb=" SG CYS Q 292 " distance=2.03 Simple disulfide: pdb=" SG CYS R 1 " - pdb=" SG CYS R 42 " distance=2.03 Simple disulfide: pdb=" SG CYS R 14 " - pdb=" SG CYS R 24 " distance=2.03 Simple disulfide: pdb=" SG CYS R 67 " - pdb=" SG CYS R 163 " distance=2.03 Simple disulfide: pdb=" SG CYS R 82 " - pdb=" SG CYS R 279 " distance=2.02 Simple disulfide: pdb=" SG CYS R 88 " - pdb=" SG CYS R 136 " distance=2.03 Simple disulfide: pdb=" SG CYS R 94 " - pdb=" SG CYS R 143 " distance=2.03 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 125 " distance=2.03 Simple disulfide: pdb=" SG CYS R 129 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 216 " - pdb=" SG CYS R 231 " distance=2.02 Simple disulfide: pdb=" SG CYS R 247 " - pdb=" SG CYS R 261 " distance=2.06 Simple disulfide: pdb=" SG CYS R 346 " - pdb=" SG CYS R 416 " distance=2.03 Simple disulfide: pdb=" SG CYS R 356 " - pdb=" SG CYS R 359 " distance=2.02 Simple disulfide: pdb=" SG CYS R 381 " - pdb=" SG CYS R 412 " distance=2.03 Simple disulfide: pdb=" SG CYS U 26 " - pdb=" SG CYS U 49 " distance=2.03 Simple disulfide: pdb=" SG CYS U 143 " - pdb=" SG CYS U 156 " distance=2.03 Simple disulfide: pdb=" SG CYS U 180 " - pdb=" SG CYS U 327 " distance=2.03 Simple disulfide: pdb=" SG CYS U 206 " - pdb=" SG CYS U 216 " distance=2.03 Simple disulfide: pdb=" SG CYS U 258 " - pdb=" SG CYS U 305 " distance=2.03 Simple disulfide: pdb=" SG CYS U 266 " - pdb=" SG CYS U 303 " distance=2.03 Simple disulfide: pdb=" SG CYS U 274 " - pdb=" SG CYS U 280 " distance=2.04 Simple disulfide: pdb=" SG CYS U 287 " - pdb=" SG CYS U 292 " distance=2.03 Simple disulfide: pdb=" SG CYS V 1 " - pdb=" SG CYS V 42 " distance=2.03 Simple disulfide: pdb=" SG CYS V 14 " - pdb=" SG CYS V 24 " distance=2.03 Simple disulfide: pdb=" SG CYS V 67 " - pdb=" SG CYS V 163 " distance=2.03 Simple disulfide: pdb=" SG CYS V 82 " - pdb=" SG CYS V 279 " distance=2.02 Simple disulfide: pdb=" SG CYS V 88 " - pdb=" SG CYS V 136 " distance=2.03 Simple disulfide: pdb=" SG CYS V 94 " - pdb=" SG CYS V 143 " distance=2.03 Simple disulfide: pdb=" SG CYS V 98 " - pdb=" SG CYS V 125 " distance=2.03 Simple disulfide: pdb=" SG CYS V 129 " - pdb=" SG CYS V 134 " distance=2.03 Simple disulfide: pdb=" SG CYS V 216 " - pdb=" SG CYS V 231 " distance=2.02 Simple disulfide: pdb=" SG CYS V 247 " - pdb=" SG CYS V 261 " distance=2.06 Simple disulfide: pdb=" SG CYS V 346 " - pdb=" SG CYS V 416 " distance=2.03 Simple disulfide: pdb=" SG CYS V 356 " - pdb=" SG CYS V 359 " distance=2.02 Simple disulfide: pdb=" SG CYS V 381 " - pdb=" SG CYS V 412 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Links applied ALPHA1-4 " NAG D 2 " - " MAN D 3 " " NAG H 2 " - " MAN H 3 " " NAG L 2 " - " MAN L 3 " " NAG P 2 " - " MAN P 3 " " NAG T 2 " - " MAN T 3 " " NAG X 2 " - " MAN X 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG D 1 " - " ASN A 63 " " NAG H 1 " - " ASN E 63 " " NAG L 1 " - " ASN I 63 " " NAG P 1 " - " ASN M 63 " " NAG T 1 " - " ASN Q 63 " " NAG X 1 " - " ASN U 63 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.38 Conformation dependent library (CDL) restraints added in 7.7 seconds 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9624 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 96 sheets defined 13.6% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.52 Creating SS restraints... Processing helix chain 'A' and resid 43 through 53 removed outlier: 3.986A pdb=" N LYS A 47 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 48 " --> pdb=" O TYR A 44 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N CYS A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 50 " --> pdb=" O GLU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 64 removed outlier: 3.858A pdb=" N SER A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 97 through 102 removed outlier: 3.583A pdb=" N ASP A 102 " --> pdb=" O CYS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.521A pdb=" N PHE A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 Processing helix chain 'A' and resid 451 through 457 removed outlier: 3.981A pdb=" N PHE A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 476 removed outlier: 3.534A pdb=" N TYR A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 438 through 448 removed outlier: 3.982A pdb=" N TYR B 442 " --> pdb=" O VAL B 438 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET B 443 " --> pdb=" O ASP B 439 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER B 448 " --> pdb=" O GLN B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 456 removed outlier: 3.965A pdb=" N ASN B 455 " --> pdb=" O PRO B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 467 removed outlier: 3.569A pdb=" N THR B 460 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN B 464 " --> pdb=" O THR B 460 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 467 " --> pdb=" O LEU B 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 53 removed outlier: 3.987A pdb=" N LYS E 47 " --> pdb=" O GLY E 43 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE E 48 " --> pdb=" O TYR E 44 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N CYS E 49 " --> pdb=" O SER E 45 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN E 50 " --> pdb=" O GLU E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 64 removed outlier: 3.858A pdb=" N SER E 58 " --> pdb=" O LEU E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 92 Processing helix chain 'E' and resid 97 through 102 removed outlier: 3.582A pdb=" N ASP E 102 " --> pdb=" O CYS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 187 through 202 removed outlier: 3.521A pdb=" N PHE E 202 " --> pdb=" O SER E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 274 Processing helix chain 'E' and resid 451 through 457 removed outlier: 3.980A pdb=" N PHE E 455 " --> pdb=" O LYS E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 476 removed outlier: 3.534A pdb=" N TYR E 464 " --> pdb=" O ILE E 460 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU E 467 " --> pdb=" O GLY E 463 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU E 470 " --> pdb=" O GLY E 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 253 Processing helix chain 'F' and resid 438 through 448 removed outlier: 3.981A pdb=" N TYR F 442 " --> pdb=" O VAL F 438 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET F 443 " --> pdb=" O ASP F 439 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER F 448 " --> pdb=" O GLN F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 456 removed outlier: 3.965A pdb=" N ASN F 455 " --> pdb=" O PRO F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 467 removed outlier: 3.569A pdb=" N THR F 460 " --> pdb=" O ILE F 456 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN F 464 " --> pdb=" O THR F 460 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE F 467 " --> pdb=" O LEU F 463 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 53 removed outlier: 3.986A pdb=" N LYS I 47 " --> pdb=" O GLY I 43 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE I 48 " --> pdb=" O TYR I 44 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N CYS I 49 " --> pdb=" O SER I 45 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN I 50 " --> pdb=" O GLU I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 64 removed outlier: 3.858A pdb=" N SER I 58 " --> pdb=" O LEU I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 92 Processing helix chain 'I' and resid 97 through 102 removed outlier: 3.583A pdb=" N ASP I 102 " --> pdb=" O CYS I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 163 Processing helix chain 'I' and resid 187 through 202 removed outlier: 3.521A pdb=" N PHE I 202 " --> pdb=" O SER I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 274 Processing helix chain 'I' and resid 451 through 457 removed outlier: 3.981A pdb=" N PHE I 455 " --> pdb=" O LYS I 451 " (cutoff:3.500A) Processing helix chain 'I' and resid 460 through 476 removed outlier: 3.533A pdb=" N TYR I 464 " --> pdb=" O ILE I 460 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU I 467 " --> pdb=" O GLY I 463 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU I 470 " --> pdb=" O GLY I 466 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 253 Processing helix chain 'J' and resid 438 through 448 removed outlier: 3.982A pdb=" N TYR J 442 " --> pdb=" O VAL J 438 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET J 443 " --> pdb=" O ASP J 439 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER J 448 " --> pdb=" O GLN J 444 " (cutoff:3.500A) Processing helix chain 'J' and resid 450 through 456 removed outlier: 3.965A pdb=" N ASN J 455 " --> pdb=" O PRO J 451 " (cutoff:3.500A) Processing helix chain 'J' and resid 456 through 467 removed outlier: 3.568A pdb=" N THR J 460 " --> pdb=" O ILE J 456 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN J 464 " --> pdb=" O THR J 460 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE J 467 " --> pdb=" O LEU J 463 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 53 removed outlier: 3.987A pdb=" N LYS M 47 " --> pdb=" O GLY M 43 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE M 48 " --> pdb=" O TYR M 44 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N CYS M 49 " --> pdb=" O SER M 45 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN M 50 " --> pdb=" O GLU M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 64 removed outlier: 3.857A pdb=" N SER M 58 " --> pdb=" O LEU M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 92 Processing helix chain 'M' and resid 97 through 102 removed outlier: 3.583A pdb=" N ASP M 102 " --> pdb=" O CYS M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 163 Processing helix chain 'M' and resid 187 through 202 removed outlier: 3.521A pdb=" N PHE M 202 " --> pdb=" O SER M 198 " (cutoff:3.500A) Processing helix chain 'M' and resid 267 through 274 Processing helix chain 'M' and resid 451 through 457 removed outlier: 3.980A pdb=" N PHE M 455 " --> pdb=" O LYS M 451 " (cutoff:3.500A) Processing helix chain 'M' and resid 460 through 476 removed outlier: 3.535A pdb=" N TYR M 464 " --> pdb=" O ILE M 460 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU M 467 " --> pdb=" O GLY M 463 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU M 470 " --> pdb=" O GLY M 466 " (cutoff:3.500A) Processing helix chain 'N' and resid 249 through 253 Processing helix chain 'N' and resid 438 through 448 removed outlier: 3.982A pdb=" N TYR N 442 " --> pdb=" O VAL N 438 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET N 443 " --> pdb=" O ASP N 439 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER N 448 " --> pdb=" O GLN N 444 " (cutoff:3.500A) Processing helix chain 'N' and resid 450 through 456 removed outlier: 3.965A pdb=" N ASN N 455 " --> pdb=" O PRO N 451 " (cutoff:3.500A) Processing helix chain 'N' and resid 456 through 467 removed outlier: 3.568A pdb=" N THR N 460 " --> pdb=" O ILE N 456 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN N 464 " --> pdb=" O THR N 460 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE N 467 " --> pdb=" O LEU N 463 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 53 removed outlier: 3.987A pdb=" N LYS Q 47 " --> pdb=" O GLY Q 43 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE Q 48 " --> pdb=" O TYR Q 44 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N CYS Q 49 " --> pdb=" O SER Q 45 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN Q 50 " --> pdb=" O GLU Q 46 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 64 removed outlier: 3.858A pdb=" N SER Q 58 " --> pdb=" O LEU Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 92 Processing helix chain 'Q' and resid 97 through 102 removed outlier: 3.583A pdb=" N ASP Q 102 " --> pdb=" O CYS Q 99 " (cutoff:3.500A) Processing helix chain 'Q' and resid 160 through 163 Processing helix chain 'Q' and resid 187 through 202 removed outlier: 3.521A pdb=" N PHE Q 202 " --> pdb=" O SER Q 198 " (cutoff:3.500A) Processing helix chain 'Q' and resid 267 through 274 Processing helix chain 'Q' and resid 451 through 457 removed outlier: 3.981A pdb=" N PHE Q 455 " --> pdb=" O LYS Q 451 " (cutoff:3.500A) Processing helix chain 'Q' and resid 460 through 476 removed outlier: 3.534A pdb=" N TYR Q 464 " --> pdb=" O ILE Q 460 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU Q 467 " --> pdb=" O GLY Q 463 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU Q 470 " --> pdb=" O GLY Q 466 " (cutoff:3.500A) Processing helix chain 'R' and resid 249 through 253 Processing helix chain 'R' and resid 438 through 448 removed outlier: 3.983A pdb=" N TYR R 442 " --> pdb=" O VAL R 438 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET R 443 " --> pdb=" O ASP R 439 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER R 448 " --> pdb=" O GLN R 444 " (cutoff:3.500A) Processing helix chain 'R' and resid 450 through 456 removed outlier: 3.965A pdb=" N ASN R 455 " --> pdb=" O PRO R 451 " (cutoff:3.500A) Processing helix chain 'R' and resid 456 through 467 removed outlier: 3.569A pdb=" N THR R 460 " --> pdb=" O ILE R 456 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN R 464 " --> pdb=" O THR R 460 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE R 467 " --> pdb=" O LEU R 463 " (cutoff:3.500A) Processing helix chain 'U' and resid 43 through 53 removed outlier: 3.986A pdb=" N LYS U 47 " --> pdb=" O GLY U 43 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE U 48 " --> pdb=" O TYR U 44 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N CYS U 49 " --> pdb=" O SER U 45 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN U 50 " --> pdb=" O GLU U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 64 removed outlier: 3.858A pdb=" N SER U 58 " --> pdb=" O LEU U 54 " (cutoff:3.500A) Processing helix chain 'U' and resid 87 through 92 Processing helix chain 'U' and resid 97 through 102 removed outlier: 3.584A pdb=" N ASP U 102 " --> pdb=" O CYS U 99 " (cutoff:3.500A) Processing helix chain 'U' and resid 160 through 163 Processing helix chain 'U' and resid 187 through 202 removed outlier: 3.520A pdb=" N PHE U 202 " --> pdb=" O SER U 198 " (cutoff:3.500A) Processing helix chain 'U' and resid 267 through 274 Processing helix chain 'U' and resid 451 through 457 removed outlier: 3.981A pdb=" N PHE U 455 " --> pdb=" O LYS U 451 " (cutoff:3.500A) Processing helix chain 'U' and resid 460 through 476 removed outlier: 3.534A pdb=" N TYR U 464 " --> pdb=" O ILE U 460 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU U 467 " --> pdb=" O GLY U 463 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU U 470 " --> pdb=" O GLY U 466 " (cutoff:3.500A) Processing helix chain 'V' and resid 249 through 253 Processing helix chain 'V' and resid 438 through 448 removed outlier: 3.981A pdb=" N TYR V 442 " --> pdb=" O VAL V 438 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET V 443 " --> pdb=" O ASP V 439 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER V 448 " --> pdb=" O GLN V 444 " (cutoff:3.500A) Processing helix chain 'V' and resid 450 through 456 removed outlier: 3.965A pdb=" N ASN V 455 " --> pdb=" O PRO V 451 " (cutoff:3.500A) Processing helix chain 'V' and resid 456 through 467 removed outlier: 3.569A pdb=" N THR V 460 " --> pdb=" O ILE V 456 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN V 464 " --> pdb=" O THR V 460 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE V 467 " --> pdb=" O LEU V 463 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 109 through 110 removed outlier: 3.665A pdb=" N TRP A 141 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE A 130 " --> pdb=" O TRP A 141 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 129 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 147 through 148 Processing sheet with id= 3, first strand: chain 'A' and resid 177 through 180 removed outlier: 3.886A pdb=" N CYS A 327 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER A 331 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL A 227 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA A 228 " --> pdb=" O MET A 240 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET A 240 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 238 " --> pdb=" O MET A 230 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 207 through 208 Processing sheet with id= 5, first strand: chain 'A' and resid 244 through 248 Processing sheet with id= 6, first strand: chain 'A' and resid 257 through 259 removed outlier: 3.644A pdb=" N TYR A 259 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 304 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 352 through 353 Processing sheet with id= 8, first strand: chain 'B' and resid 28 through 29 removed outlier: 3.792A pdb=" N GLY B 28 " --> pdb=" O ARG B 325 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 322 " --> pdb=" O TYR B 202 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 40 through 41 removed outlier: 6.382A pdb=" N VAL B 171 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE B 63 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER B 169 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU B 65 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL B 167 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE B 172 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE B 184 " --> pdb=" O ILE B 172 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 73 through 75 removed outlier: 3.546A pdb=" N TRP B 158 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU B 219 " --> pdb=" O LYS B 159 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 229 " --> pdb=" O CYS B 216 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'B' and resid 79 through 81 Processing sheet with id= 12, first strand: chain 'B' and resid 84 through 85 Processing sheet with id= 13, first strand: chain 'B' and resid 268 through 271 Processing sheet with id= 14, first strand: chain 'B' and resid 346 through 347 removed outlier: 3.541A pdb=" N THR B 347 " --> pdb=" O HIS B 370 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS B 370 " --> pdb=" O THR B 347 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N SER B 366 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'B' and resid 346 through 347 removed outlier: 3.541A pdb=" N THR B 347 " --> pdb=" O HIS B 370 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS B 370 " --> pdb=" O THR B 347 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE B 367 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'B' and resid 375 through 376 removed outlier: 3.857A pdb=" N SER B 375 " --> pdb=" O GLU B 392 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'E' and resid 109 through 110 removed outlier: 3.665A pdb=" N TRP E 141 " --> pdb=" O PHE E 130 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE E 130 " --> pdb=" O TRP E 141 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU E 129 " --> pdb=" O LEU E 173 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'E' and resid 147 through 148 Processing sheet with id= 19, first strand: chain 'E' and resid 177 through 180 removed outlier: 3.886A pdb=" N CYS E 327 " --> pdb=" O ASP E 231 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER E 331 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL E 227 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA E 228 " --> pdb=" O MET E 240 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET E 240 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE E 238 " --> pdb=" O MET E 230 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'E' and resid 207 through 208 Processing sheet with id= 21, first strand: chain 'E' and resid 244 through 248 Processing sheet with id= 22, first strand: chain 'E' and resid 257 through 259 removed outlier: 3.645A pdb=" N TYR E 259 " --> pdb=" O ARG E 304 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG E 304 " --> pdb=" O TYR E 259 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'E' and resid 352 through 353 Processing sheet with id= 24, first strand: chain 'F' and resid 28 through 29 removed outlier: 3.793A pdb=" N GLY F 28 " --> pdb=" O ARG F 325 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR F 322 " --> pdb=" O TYR F 202 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'F' and resid 40 through 41 removed outlier: 6.382A pdb=" N VAL F 171 " --> pdb=" O LYS F 61 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE F 63 " --> pdb=" O SER F 169 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER F 169 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU F 65 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL F 167 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE F 172 " --> pdb=" O PHE F 184 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE F 184 " --> pdb=" O ILE F 172 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'F' and resid 73 through 75 removed outlier: 3.546A pdb=" N TRP F 158 " --> pdb=" O VAL F 75 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU F 219 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA F 229 " --> pdb=" O CYS F 216 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'F' and resid 79 through 81 Processing sheet with id= 28, first strand: chain 'F' and resid 84 through 85 Processing sheet with id= 29, first strand: chain 'F' and resid 268 through 271 Processing sheet with id= 30, first strand: chain 'F' and resid 346 through 347 removed outlier: 3.542A pdb=" N THR F 347 " --> pdb=" O HIS F 370 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS F 370 " --> pdb=" O THR F 347 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N SER F 366 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'F' and resid 346 through 347 removed outlier: 3.542A pdb=" N THR F 347 " --> pdb=" O HIS F 370 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS F 370 " --> pdb=" O THR F 347 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE F 367 " --> pdb=" O VAL F 399 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'F' and resid 375 through 376 removed outlier: 3.858A pdb=" N SER F 375 " --> pdb=" O GLU F 392 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'I' and resid 109 through 110 removed outlier: 3.665A pdb=" N TRP I 141 " --> pdb=" O PHE I 130 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE I 130 " --> pdb=" O TRP I 141 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU I 129 " --> pdb=" O LEU I 173 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'I' and resid 147 through 148 Processing sheet with id= 35, first strand: chain 'I' and resid 177 through 180 removed outlier: 3.885A pdb=" N CYS I 327 " --> pdb=" O ASP I 231 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER I 331 " --> pdb=" O VAL I 227 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL I 227 " --> pdb=" O SER I 331 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA I 228 " --> pdb=" O MET I 240 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET I 240 " --> pdb=" O ALA I 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE I 238 " --> pdb=" O MET I 230 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'I' and resid 207 through 208 Processing sheet with id= 37, first strand: chain 'I' and resid 244 through 248 Processing sheet with id= 38, first strand: chain 'I' and resid 257 through 259 removed outlier: 3.644A pdb=" N TYR I 259 " --> pdb=" O ARG I 304 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG I 304 " --> pdb=" O TYR I 259 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'I' and resid 352 through 353 Processing sheet with id= 40, first strand: chain 'J' and resid 28 through 29 removed outlier: 3.793A pdb=" N GLY J 28 " --> pdb=" O ARG J 325 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR J 322 " --> pdb=" O TYR J 202 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'J' and resid 40 through 41 removed outlier: 6.382A pdb=" N VAL J 171 " --> pdb=" O LYS J 61 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE J 63 " --> pdb=" O SER J 169 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N SER J 169 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU J 65 " --> pdb=" O VAL J 167 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL J 167 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE J 172 " --> pdb=" O PHE J 184 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE J 184 " --> pdb=" O ILE J 172 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'J' and resid 73 through 75 removed outlier: 3.545A pdb=" N TRP J 158 " --> pdb=" O VAL J 75 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU J 219 " --> pdb=" O LYS J 159 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA J 229 " --> pdb=" O CYS J 216 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'J' and resid 79 through 81 Processing sheet with id= 44, first strand: chain 'J' and resid 84 through 85 Processing sheet with id= 45, first strand: chain 'J' and resid 268 through 271 Processing sheet with id= 46, first strand: chain 'J' and resid 346 through 347 removed outlier: 3.541A pdb=" N THR J 347 " --> pdb=" O HIS J 370 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS J 370 " --> pdb=" O THR J 347 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N SER J 366 " --> pdb=" O THR J 351 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'J' and resid 346 through 347 removed outlier: 3.541A pdb=" N THR J 347 " --> pdb=" O HIS J 370 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS J 370 " --> pdb=" O THR J 347 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE J 367 " --> pdb=" O VAL J 399 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'J' and resid 375 through 376 removed outlier: 3.857A pdb=" N SER J 375 " --> pdb=" O GLU J 392 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'M' and resid 109 through 110 removed outlier: 3.665A pdb=" N TRP M 141 " --> pdb=" O PHE M 130 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE M 130 " --> pdb=" O TRP M 141 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU M 129 " --> pdb=" O LEU M 173 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'M' and resid 147 through 148 Processing sheet with id= 51, first strand: chain 'M' and resid 177 through 180 removed outlier: 3.886A pdb=" N CYS M 327 " --> pdb=" O ASP M 231 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER M 331 " --> pdb=" O VAL M 227 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL M 227 " --> pdb=" O SER M 331 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA M 228 " --> pdb=" O MET M 240 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET M 240 " --> pdb=" O ALA M 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE M 238 " --> pdb=" O MET M 230 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'M' and resid 207 through 208 Processing sheet with id= 53, first strand: chain 'M' and resid 244 through 248 Processing sheet with id= 54, first strand: chain 'M' and resid 257 through 259 removed outlier: 3.644A pdb=" N TYR M 259 " --> pdb=" O ARG M 304 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG M 304 " --> pdb=" O TYR M 259 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'M' and resid 352 through 353 Processing sheet with id= 56, first strand: chain 'N' and resid 28 through 29 removed outlier: 3.793A pdb=" N GLY N 28 " --> pdb=" O ARG N 325 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR N 322 " --> pdb=" O TYR N 202 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'N' and resid 40 through 41 removed outlier: 6.382A pdb=" N VAL N 171 " --> pdb=" O LYS N 61 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE N 63 " --> pdb=" O SER N 169 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER N 169 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU N 65 " --> pdb=" O VAL N 167 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL N 167 " --> pdb=" O LEU N 65 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE N 172 " --> pdb=" O PHE N 184 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE N 184 " --> pdb=" O ILE N 172 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'N' and resid 73 through 75 removed outlier: 3.545A pdb=" N TRP N 158 " --> pdb=" O VAL N 75 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU N 219 " --> pdb=" O LYS N 159 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA N 229 " --> pdb=" O CYS N 216 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'N' and resid 79 through 81 Processing sheet with id= 60, first strand: chain 'N' and resid 84 through 85 Processing sheet with id= 61, first strand: chain 'N' and resid 268 through 271 Processing sheet with id= 62, first strand: chain 'N' and resid 346 through 347 removed outlier: 3.542A pdb=" N THR N 347 " --> pdb=" O HIS N 370 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS N 370 " --> pdb=" O THR N 347 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N SER N 366 " --> pdb=" O THR N 351 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'N' and resid 346 through 347 removed outlier: 3.542A pdb=" N THR N 347 " --> pdb=" O HIS N 370 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS N 370 " --> pdb=" O THR N 347 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE N 367 " --> pdb=" O VAL N 399 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'N' and resid 375 through 376 removed outlier: 3.856A pdb=" N SER N 375 " --> pdb=" O GLU N 392 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'Q' and resid 109 through 110 removed outlier: 3.665A pdb=" N TRP Q 141 " --> pdb=" O PHE Q 130 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE Q 130 " --> pdb=" O TRP Q 141 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU Q 129 " --> pdb=" O LEU Q 173 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'Q' and resid 147 through 148 Processing sheet with id= 67, first strand: chain 'Q' and resid 177 through 180 removed outlier: 3.886A pdb=" N CYS Q 327 " --> pdb=" O ASP Q 231 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER Q 331 " --> pdb=" O VAL Q 227 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL Q 227 " --> pdb=" O SER Q 331 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA Q 228 " --> pdb=" O MET Q 240 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET Q 240 " --> pdb=" O ALA Q 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE Q 238 " --> pdb=" O MET Q 230 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'Q' and resid 207 through 208 Processing sheet with id= 69, first strand: chain 'Q' and resid 244 through 248 Processing sheet with id= 70, first strand: chain 'Q' and resid 257 through 259 removed outlier: 3.643A pdb=" N TYR Q 259 " --> pdb=" O ARG Q 304 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG Q 304 " --> pdb=" O TYR Q 259 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'Q' and resid 352 through 353 Processing sheet with id= 72, first strand: chain 'R' and resid 28 through 29 removed outlier: 3.792A pdb=" N GLY R 28 " --> pdb=" O ARG R 325 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR R 322 " --> pdb=" O TYR R 202 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'R' and resid 40 through 41 removed outlier: 6.382A pdb=" N VAL R 171 " --> pdb=" O LYS R 61 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE R 63 " --> pdb=" O SER R 169 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER R 169 " --> pdb=" O ILE R 63 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU R 65 " --> pdb=" O VAL R 167 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL R 167 " --> pdb=" O LEU R 65 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE R 172 " --> pdb=" O PHE R 184 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE R 184 " --> pdb=" O ILE R 172 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'R' and resid 73 through 75 removed outlier: 3.545A pdb=" N TRP R 158 " --> pdb=" O VAL R 75 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU R 219 " --> pdb=" O LYS R 159 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA R 229 " --> pdb=" O CYS R 216 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'R' and resid 79 through 81 Processing sheet with id= 76, first strand: chain 'R' and resid 84 through 85 Processing sheet with id= 77, first strand: chain 'R' and resid 268 through 271 Processing sheet with id= 78, first strand: chain 'R' and resid 346 through 347 removed outlier: 3.542A pdb=" N THR R 347 " --> pdb=" O HIS R 370 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS R 370 " --> pdb=" O THR R 347 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N SER R 366 " --> pdb=" O THR R 351 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'R' and resid 346 through 347 removed outlier: 3.542A pdb=" N THR R 347 " --> pdb=" O HIS R 370 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS R 370 " --> pdb=" O THR R 347 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE R 367 " --> pdb=" O VAL R 399 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'R' and resid 375 through 376 removed outlier: 3.857A pdb=" N SER R 375 " --> pdb=" O GLU R 392 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'U' and resid 109 through 110 removed outlier: 3.665A pdb=" N TRP U 141 " --> pdb=" O PHE U 130 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE U 130 " --> pdb=" O TRP U 141 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU U 129 " --> pdb=" O LEU U 173 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'U' and resid 147 through 148 Processing sheet with id= 83, first strand: chain 'U' and resid 177 through 180 removed outlier: 3.886A pdb=" N CYS U 327 " --> pdb=" O ASP U 231 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER U 331 " --> pdb=" O VAL U 227 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL U 227 " --> pdb=" O SER U 331 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA U 228 " --> pdb=" O MET U 240 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET U 240 " --> pdb=" O ALA U 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE U 238 " --> pdb=" O MET U 230 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'U' and resid 207 through 208 Processing sheet with id= 85, first strand: chain 'U' and resid 244 through 248 Processing sheet with id= 86, first strand: chain 'U' and resid 257 through 259 removed outlier: 3.644A pdb=" N TYR U 259 " --> pdb=" O ARG U 304 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG U 304 " --> pdb=" O TYR U 259 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'U' and resid 352 through 353 Processing sheet with id= 88, first strand: chain 'V' and resid 28 through 29 removed outlier: 3.792A pdb=" N GLY V 28 " --> pdb=" O ARG V 325 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR V 322 " --> pdb=" O TYR V 202 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'V' and resid 40 through 41 removed outlier: 6.382A pdb=" N VAL V 171 " --> pdb=" O LYS V 61 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE V 63 " --> pdb=" O SER V 169 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER V 169 " --> pdb=" O ILE V 63 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU V 65 " --> pdb=" O VAL V 167 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL V 167 " --> pdb=" O LEU V 65 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE V 172 " --> pdb=" O PHE V 184 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE V 184 " --> pdb=" O ILE V 172 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'V' and resid 73 through 75 removed outlier: 3.546A pdb=" N TRP V 158 " --> pdb=" O VAL V 75 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU V 219 " --> pdb=" O LYS V 159 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA V 229 " --> pdb=" O CYS V 216 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'V' and resid 79 through 81 Processing sheet with id= 92, first strand: chain 'V' and resid 84 through 85 Processing sheet with id= 93, first strand: chain 'V' and resid 268 through 271 Processing sheet with id= 94, first strand: chain 'V' and resid 346 through 347 removed outlier: 3.540A pdb=" N THR V 347 " --> pdb=" O HIS V 370 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS V 370 " --> pdb=" O THR V 347 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N SER V 366 " --> pdb=" O THR V 351 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'V' and resid 346 through 347 removed outlier: 3.540A pdb=" N THR V 347 " --> pdb=" O HIS V 370 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS V 370 " --> pdb=" O THR V 347 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE V 367 " --> pdb=" O VAL V 399 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'V' and resid 375 through 376 removed outlier: 3.857A pdb=" N SER V 375 " --> pdb=" O GLU V 392 " (cutoff:3.500A) 702 hydrogen bonds defined for protein. 1728 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: 12.84 Time building geometry restraints manager: 19.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 13062 1.35 - 1.47: 9509 1.47 - 1.59: 17011 1.59 - 1.72: 0 1.72 - 1.84: 540 Bond restraints: 40122 Sorted by residual: bond pdb=" C1 MAN T 3 " pdb=" C2 MAN T 3 " ideal model delta sigma weight residual 1.526 1.578 -0.052 2.00e-02 2.50e+03 6.73e+00 bond pdb=" C1 MAN D 3 " pdb=" C2 MAN D 3 " ideal model delta sigma weight residual 1.526 1.577 -0.051 2.00e-02 2.50e+03 6.58e+00 bond pdb=" C1 MAN X 3 " pdb=" C2 MAN X 3 " ideal model delta sigma weight residual 1.526 1.577 -0.051 2.00e-02 2.50e+03 6.56e+00 bond pdb=" C1 MAN P 3 " pdb=" C2 MAN P 3 " ideal model delta sigma weight residual 1.526 1.577 -0.051 2.00e-02 2.50e+03 6.48e+00 bond pdb=" C1 MAN H 3 " pdb=" C2 MAN H 3 " ideal model delta sigma weight residual 1.526 1.577 -0.051 2.00e-02 2.50e+03 6.47e+00 ... (remaining 40117 not shown) Histogram of bond angle deviations from ideal: 98.22 - 105.41: 863 105.41 - 112.59: 21083 112.59 - 119.78: 12532 119.78 - 126.97: 19199 126.97 - 134.15: 593 Bond angle restraints: 54270 Sorted by residual: angle pdb=" N PRO U 445 " pdb=" CA PRO U 445 " pdb=" CB PRO U 445 " ideal model delta sigma weight residual 103.36 110.40 -7.04 8.80e-01 1.29e+00 6.40e+01 angle pdb=" N PRO M 445 " pdb=" CA PRO M 445 " pdb=" CB PRO M 445 " ideal model delta sigma weight residual 103.36 110.39 -7.03 8.80e-01 1.29e+00 6.38e+01 angle pdb=" N PRO A 445 " pdb=" CA PRO A 445 " pdb=" CB PRO A 445 " ideal model delta sigma weight residual 103.36 110.37 -7.01 8.80e-01 1.29e+00 6.34e+01 angle pdb=" N PRO Q 445 " pdb=" CA PRO Q 445 " pdb=" CB PRO Q 445 " ideal model delta sigma weight residual 103.36 110.35 -6.99 8.80e-01 1.29e+00 6.31e+01 angle pdb=" N PRO I 445 " pdb=" CA PRO I 445 " pdb=" CB PRO I 445 " ideal model delta sigma weight residual 103.36 110.34 -6.98 8.80e-01 1.29e+00 6.30e+01 ... (remaining 54265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 22019 16.94 - 33.88: 2142 33.88 - 50.82: 433 50.82 - 67.76: 90 67.76 - 84.69: 36 Dihedral angle restraints: 24720 sinusoidal: 9690 harmonic: 15030 Sorted by residual: dihedral pdb=" CB CYS R 88 " pdb=" SG CYS R 88 " pdb=" SG CYS R 136 " pdb=" CB CYS R 136 " ideal model delta sinusoidal sigma weight residual 93.00 177.69 -84.69 1 1.00e+01 1.00e-02 8.71e+01 dihedral pdb=" CB CYS J 88 " pdb=" SG CYS J 88 " pdb=" SG CYS J 136 " pdb=" CB CYS J 136 " ideal model delta sinusoidal sigma weight residual 93.00 177.68 -84.68 1 1.00e+01 1.00e-02 8.71e+01 dihedral pdb=" CB CYS F 88 " pdb=" SG CYS F 88 " pdb=" SG CYS F 136 " pdb=" CB CYS F 136 " ideal model delta sinusoidal sigma weight residual 93.00 177.68 -84.68 1 1.00e+01 1.00e-02 8.71e+01 ... (remaining 24717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4633 0.053 - 0.105: 1137 0.105 - 0.158: 242 0.158 - 0.211: 30 0.211 - 0.264: 36 Chirality restraints: 6078 Sorted by residual: chirality pdb=" CA CYS F 261 " pdb=" N CYS F 261 " pdb=" C CYS F 261 " pdb=" CB CYS F 261 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA CYS B 261 " pdb=" N CYS B 261 " pdb=" C CYS B 261 " pdb=" CB CYS B 261 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA CYS R 261 " pdb=" N CYS R 261 " pdb=" C CYS R 261 " pdb=" CB CYS R 261 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 6075 not shown) Planarity restraints: 7032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU Q 167 " 0.048 5.00e-02 4.00e+02 7.35e-02 8.64e+00 pdb=" N PRO Q 168 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO Q 168 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO Q 168 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 167 " -0.048 5.00e-02 4.00e+02 7.35e-02 8.63e+00 pdb=" N PRO A 168 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU I 167 " -0.048 5.00e-02 4.00e+02 7.35e-02 8.63e+00 pdb=" N PRO I 168 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO I 168 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO I 168 " -0.040 5.00e-02 4.00e+02 ... (remaining 7029 not shown) Histogram of nonbonded interaction distances: 0.51 - 1.39: 86 1.39 - 2.26: 413 2.26 - 3.14: 33722 3.14 - 4.02: 96021 4.02 - 4.90: 157486 Warning: very small nonbonded interaction distances. Nonbonded interactions: 287728 Sorted by model distance: nonbonded pdb=" O CYS A 156 " pdb=" OG SER E 299 " model vdw 0.507 2.440 nonbonded pdb=" O CYS Q 156 " pdb=" OG SER U 299 " model vdw 0.517 2.440 nonbonded pdb=" O CYS I 156 " pdb=" OG SER M 299 " model vdw 0.582 2.440 nonbonded pdb=" C GLU A 154 " pdb=" N ALA E 298 " model vdw 0.602 3.350 nonbonded pdb=" C GLU Q 154 " pdb=" N ALA U 298 " model vdw 0.612 3.350 ... (remaining 287723 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' selection = chain 'M' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'N' selection = chain 'R' selection = chain 'V' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'S' selection = chain 'W' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' selection = chain 'T' selection = chain 'X' } Set up NCS constraints Number of NCS constrained groups: 4 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' selection = chain 'M' selection = chain 'Q' selection = chain 'U' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'N' selection = chain 'R' selection = chain 'V' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'S' selection = chain 'W' } pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' selection = chain 'T' selection = chain 'X' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.860 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: 15.460 Check model and map are aligned: 0.600 Set scattering table: 0.330 Process input model: 100.300 Find NCS groups from input model: 2.860 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5868 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 : 0.004 0.052 40122 Z= 0.274 Angle : 0.945 14.686 54270 Z= 0.553 Chirality : 0.052 0.264 6078 Planarity : 0.006 0.073 7026 Dihedral : 13.225 78.106 14718 Min Nonbonded Distance : 0.507 Molprobity Statistics. All-atom Clashscore : 29.62 Ramachandran Plot: Outliers : 0.57 % Allowed : 10.09 % Favored : 89.34 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.10), residues: 5280 helix: -0.61 (0.21), residues: 612 sheet: -2.16 (0.14), residues: 1194 loop : -2.84 (0.09), residues: 3474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP E 174 HIS 0.007 0.002 HIS V 44 PHE 0.031 0.002 PHE E 330 TYR 0.028 0.002 TYR J 280 ARG 0.009 0.001 ARG N 380 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 TRP cc_start: 0.8644 (m100) cc_final: 0.8392 (m-10) REVERT: A 96 LEU cc_start: 0.8195 (tt) cc_final: 0.6987 (mp) REVERT: A 103 TRP cc_start: 0.7855 (t-100) cc_final: 0.6537 (t-100) REVERT: A 166 LEU cc_start: 0.6599 (tp) cc_final: 0.6287 (tp) REVERT: A 230 MET cc_start: 0.7901 (ppp) cc_final: 0.7490 (ppp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1540 time to fit residues: 13.5508 Evaluate side-chains 52 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.371 Evaluate side-chains 75 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.385 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: B 87 ARG cc_start: 0.7873 (mmt90) cc_final: 0.7615 (mmt-90) REVERT: B 270 ILE cc_start: 0.8673 (tp) cc_final: 0.8408 (tp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1441 time to fit residues: 13.2435 Evaluate side-chains 59 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.356 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0021 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0026 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 445 optimal weight: 8.9990 chunk 400 optimal weight: 9.9990 chunk 222 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 269 optimal weight: 0.8980 chunk 213 optimal weight: 20.0000 chunk 413 optimal weight: 10.0000 chunk 160 optimal weight: 0.4980 chunk 251 optimal weight: 0.0170 chunk 308 optimal weight: 30.0000 chunk 479 optimal weight: 0.3980 overall best weight: 1.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 HIS B 370 HIS B 411 GLN ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5877 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 40122 Z= 0.233 Angle : 0.766 9.524 54270 Z= 0.400 Chirality : 0.048 0.216 6078 Planarity : 0.005 0.047 7026 Dihedral : 7.139 40.656 6210 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.91 % Favored : 88.75 % Rotamer: Outliers : 0.29 % Allowed : 5.83 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.10), residues: 5280 helix: -0.30 (0.20), residues: 666 sheet: -1.76 (0.14), residues: 1200 loop : -2.94 (0.08), residues: 3414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 149 HIS 0.006 0.001 HIS M 56 PHE 0.028 0.003 PHE N 195 TYR 0.019 0.002 TYR M 328 ARG 0.008 0.001 ARG M 149 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 TRP cc_start: 0.8574 (m100) cc_final: 0.8257 (m-90) REVERT: A 96 LEU cc_start: 0.7986 (tt) cc_final: 0.7034 (mp) REVERT: A 166 LEU cc_start: 0.6387 (tp) cc_final: 0.6122 (tp) REVERT: A 183 MET cc_start: 0.8290 (ppp) cc_final: 0.7912 (ppp) REVERT: A 230 MET cc_start: 0.8243 (ppp) cc_final: 0.7677 (ppp) REVERT: A 240 MET cc_start: 0.7791 (pmm) cc_final: 0.7564 (pmm) REVERT: A 333 MET cc_start: 0.7436 (mmm) cc_final: 0.6872 (mmm) REVERT: A 369 GLU cc_start: 0.7163 (mp0) cc_final: 0.6273 (mp0) outliers start: 1 outliers final: 1 residues processed: 73 average time/residue: 0.1837 time to fit residues: 16.0058 Evaluate side-chains 54 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.386 Evaluate side-chains 77 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 ARG cc_start: 0.8018 (mmt90) cc_final: 0.7578 (mmt180) REVERT: B 225 LYS cc_start: 0.5275 (mmtm) cc_final: 0.4786 (tppt) REVERT: B 245 ILE cc_start: 0.8981 (mm) cc_final: 0.8335 (mm) REVERT: B 246 GLN cc_start: 0.7639 (pm20) cc_final: 0.6573 (pt0) REVERT: B 295 ILE cc_start: 0.8432 (mp) cc_final: 0.8069 (tp) REVERT: B 328 PHE cc_start: 0.8233 (m-80) cc_final: 0.7937 (m-80) outliers start: 1 outliers final: 0 residues processed: 77 average time/residue: 0.1443 time to fit residues: 13.6208 Evaluate side-chains 61 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.548 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0025 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0031 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 266 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 399 optimal weight: 10.0000 chunk 326 optimal weight: 0.0020 chunk 132 optimal weight: 9.9990 chunk 480 optimal weight: 1.9990 chunk 518 optimal weight: 0.0000 chunk 427 optimal weight: 9.9990 chunk 476 optimal weight: 0.2980 chunk 163 optimal weight: 0.3980 chunk 385 optimal weight: 8.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 HIS B 370 HIS B 374 ASN ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5828 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 40122 Z= 0.313 Angle : 0.848 13.312 54270 Z= 0.448 Chirality : 0.051 0.337 6078 Planarity : 0.007 0.087 7026 Dihedral : 7.098 39.983 6210 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.02 % Favored : 88.64 % Rotamer: Outliers : 0.15 % Allowed : 4.37 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.10), residues: 5280 helix: -0.20 (0.20), residues: 666 sheet: -1.85 (0.14), residues: 1110 loop : -2.96 (0.08), residues: 3504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP A 247 HIS 0.013 0.002 HIS E 40 PHE 0.085 0.006 PHE I 330 TYR 0.028 0.003 TYR A 328 ARG 0.048 0.003 ARG I 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 TRP cc_start: 0.8486 (m100) cc_final: 0.8256 (m-90) REVERT: A 96 LEU cc_start: 0.8132 (tt) cc_final: 0.7015 (mp) REVERT: A 166 LEU cc_start: 0.6272 (tp) cc_final: 0.6034 (tp) REVERT: A 183 MET cc_start: 0.8192 (ppp) cc_final: 0.7772 (ppp) REVERT: A 230 MET cc_start: 0.8242 (ppp) cc_final: 0.7668 (ppp) REVERT: A 369 GLU cc_start: 0.7184 (mp0) cc_final: 0.6354 (mp0) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1558 time to fit residues: 13.2518 Evaluate side-chains 49 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.371 Evaluate side-chains 79 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.6366 (tmt170) cc_final: 0.4711 (pmt-80) REVERT: B 87 ARG cc_start: 0.8556 (mmt90) cc_final: 0.7816 (mmt180) REVERT: B 225 LYS cc_start: 0.5226 (mmtm) cc_final: 0.4742 (tppt) REVERT: B 246 GLN cc_start: 0.7768 (pm20) cc_final: 0.6795 (pt0) REVERT: B 295 ILE cc_start: 0.8359 (mp) cc_final: 0.7999 (tp) REVERT: B 328 PHE cc_start: 0.8186 (m-80) cc_final: 0.7867 (m-80) outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 0.1691 time to fit residues: 15.9430 Evaluate side-chains 63 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.389 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0021 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0031 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 0.0870 chunk 361 optimal weight: 0.2980 chunk 249 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 229 optimal weight: 10.0000 chunk 322 optimal weight: 20.0000 chunk 482 optimal weight: 3.9990 chunk 510 optimal weight: 0.0030 chunk 251 optimal weight: 3.9990 chunk 456 optimal weight: 40.0000 chunk 137 optimal weight: 0.0020 overall best weight: 0.2376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 64 HIS A 294 HIS Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 HIS B 370 HIS ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5819 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 40122 Z= 0.313 Angle : 0.848 13.312 54270 Z= 0.448 Chirality : 0.051 0.337 6078 Planarity : 0.007 0.087 7026 Dihedral : 7.098 39.983 6210 Min Nonbonded Distance : 0.726 Molprobity Statistics. All-atom Clashscore : 30.10 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.02 % Favored : 88.64 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.10), residues: 5280 helix: -0.20 (0.20), residues: 666 sheet: -1.85 (0.14), residues: 1110 loop : -2.96 (0.08), residues: 3504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP M 247 HIS 0.013 0.002 HIS I 40 PHE 0.085 0.006 PHE I 330 TYR 0.028 0.003 TYR E 328 ARG 0.048 0.003 ARG I 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 TRP cc_start: 0.8497 (m100) cc_final: 0.8260 (m-90) REVERT: A 96 LEU cc_start: 0.8019 (tt) cc_final: 0.6999 (mp) REVERT: A 166 LEU cc_start: 0.6286 (tp) cc_final: 0.6034 (tp) REVERT: A 183 MET cc_start: 0.8238 (ppp) cc_final: 0.7772 (ppp) REVERT: A 230 MET cc_start: 0.8264 (ppp) cc_final: 0.7628 (ppp) REVERT: A 232 VAL cc_start: 0.8371 (p) cc_final: 0.8170 (p) REVERT: A 369 GLU cc_start: 0.7185 (mp0) cc_final: 0.6363 (mp0) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1483 time to fit residues: 12.1968 Evaluate side-chains 50 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.409 Evaluate side-chains 76 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.6363 (tmt170) cc_final: 0.4709 (pmt-80) REVERT: B 87 ARG cc_start: 0.8563 (mmt90) cc_final: 0.7822 (mmt180) REVERT: B 225 LYS cc_start: 0.5190 (mmtm) cc_final: 0.4720 (tppt) REVERT: B 246 GLN cc_start: 0.7696 (pm20) cc_final: 0.6852 (pt0) REVERT: B 328 PHE cc_start: 0.8174 (m-80) cc_final: 0.7866 (m-80) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1631 time to fit residues: 14.9156 Evaluate side-chains 63 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.335 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0023 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0032 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 425 optimal weight: 3.9990 chunk 289 optimal weight: 0.6980 chunk 7 optimal weight: 0.0170 chunk 380 optimal weight: 0.0370 chunk 210 optimal weight: 0.0270 chunk 435 optimal weight: 6.9990 chunk 352 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 260 optimal weight: 7.9990 chunk 458 optimal weight: 6.9990 chunk 128 optimal weight: 0.0470 overall best weight: 0.1652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 64 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 HIS B 370 HIS ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5817 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 40122 Z= 0.313 Angle : 0.847 13.315 54270 Z= 0.448 Chirality : 0.051 0.337 6078 Planarity : 0.007 0.087 7026 Dihedral : 7.098 39.983 6210 Min Nonbonded Distance : 0.728 Molprobity Statistics. All-atom Clashscore : 30.53 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.02 % Favored : 88.64 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.10), residues: 5280 helix: -0.20 (0.20), residues: 666 sheet: -1.85 (0.14), residues: 1110 loop : -2.96 (0.08), residues: 3504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP M 247 HIS 0.013 0.002 HIS M 40 PHE 0.085 0.006 PHE I 330 TYR 0.027 0.003 TYR U 328 ARG 0.048 0.003 ARG I 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 TRP cc_start: 0.8499 (m100) cc_final: 0.8260 (m-90) REVERT: A 96 LEU cc_start: 0.8012 (tt) cc_final: 0.6999 (mp) REVERT: A 166 LEU cc_start: 0.6288 (tp) cc_final: 0.6034 (tp) REVERT: A 183 MET cc_start: 0.8240 (ppp) cc_final: 0.7771 (ppp) REVERT: A 230 MET cc_start: 0.8256 (ppp) cc_final: 0.7628 (ppp) REVERT: A 369 GLU cc_start: 0.7190 (mp0) cc_final: 0.6357 (mp0) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1497 time to fit residues: 11.8736 Evaluate side-chains 50 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.430 Evaluate side-chains 75 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.6356 (tmt170) cc_final: 0.4709 (pmt-80) REVERT: B 87 ARG cc_start: 0.8559 (mmt90) cc_final: 0.7822 (mmt180) REVERT: B 225 LYS cc_start: 0.5190 (mmtm) cc_final: 0.4715 (tppt) REVERT: B 246 GLN cc_start: 0.7637 (pm20) cc_final: 0.6839 (pt0) REVERT: B 328 PHE cc_start: 0.8173 (m-80) cc_final: 0.7866 (m-80) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1763 time to fit residues: 15.8919 Evaluate side-chains 63 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.363 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0024 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0029 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 0.1980 chunk 459 optimal weight: 20.0000 chunk 100 optimal weight: 4.9990 chunk 299 optimal weight: 0.1980 chunk 125 optimal weight: 2.9990 chunk 510 optimal weight: 4.9990 chunk 424 optimal weight: 0.5980 chunk 236 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 168 optimal weight: 0.0020 chunk 268 optimal weight: 3.9990 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 64 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 HIS B 370 HIS ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5817 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 40122 Z= 0.313 Angle : 0.847 13.315 54270 Z= 0.448 Chirality : 0.051 0.337 6078 Planarity : 0.007 0.087 7026 Dihedral : 7.098 39.983 6210 Min Nonbonded Distance : 0.728 Molprobity Statistics. All-atom Clashscore : 30.53 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.02 % Favored : 88.64 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.10), residues: 5280 helix: -0.20 (0.20), residues: 666 sheet: -1.85 (0.14), residues: 1110 loop : -2.96 (0.08), residues: 3504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP M 247 HIS 0.013 0.002 HIS E 40 PHE 0.085 0.006 PHE I 330 TYR 0.027 0.003 TYR E 328 ARG 0.048 0.003 ARG U 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 TRP cc_start: 0.8499 (m100) cc_final: 0.8260 (m-90) REVERT: A 96 LEU cc_start: 0.8012 (tt) cc_final: 0.6999 (mp) REVERT: A 166 LEU cc_start: 0.6288 (tp) cc_final: 0.6034 (tp) REVERT: A 183 MET cc_start: 0.8240 (ppp) cc_final: 0.7771 (ppp) REVERT: A 230 MET cc_start: 0.8256 (ppp) cc_final: 0.7628 (ppp) REVERT: A 369 GLU cc_start: 0.7190 (mp0) cc_final: 0.6357 (mp0) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1454 time to fit residues: 11.5562 Evaluate side-chains 50 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.395 Evaluate side-chains 75 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.6357 (tmt170) cc_final: 0.4709 (pmt-80) REVERT: B 87 ARG cc_start: 0.8560 (mmt90) cc_final: 0.7822 (mmt180) REVERT: B 225 LYS cc_start: 0.5190 (mmtm) cc_final: 0.4715 (tppt) REVERT: B 246 GLN cc_start: 0.7637 (pm20) cc_final: 0.6839 (pt0) REVERT: B 328 PHE cc_start: 0.8172 (m-80) cc_final: 0.7866 (m-80) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1665 time to fit residues: 14.9945 Evaluate side-chains 63 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.375 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0026 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0026 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 8.9990 chunk 57 optimal weight: 0.0020 chunk 291 optimal weight: 0.0040 chunk 373 optimal weight: 0.9980 chunk 289 optimal weight: 0.0020 chunk 430 optimal weight: 10.0000 chunk 285 optimal weight: 6.9990 chunk 508 optimal weight: 0.3980 chunk 318 optimal weight: 0.0870 chunk 310 optimal weight: 9.9990 chunk 234 optimal weight: 3.9990 overall best weight: 0.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 HIS B 370 HIS ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 ASN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5810 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 40122 Z= 0.284 Angle : 0.853 15.839 54270 Z= 0.440 Chirality : 0.051 0.209 6078 Planarity : 0.010 0.274 7026 Dihedral : 7.157 38.731 6210 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.82 % Favored : 87.84 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.10), residues: 5280 helix: -0.01 (0.21), residues: 648 sheet: -1.80 (0.14), residues: 1200 loop : -3.00 (0.08), residues: 3432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP M 247 HIS 0.014 0.002 HIS M 40 PHE 0.046 0.005 PHE I 418 TYR 0.049 0.003 TYR Q 124 ARG 0.043 0.003 ARG I 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 92 TRP cc_start: 0.8485 (m100) cc_final: 0.8210 (m-90) REVERT: A 96 LEU cc_start: 0.7970 (tt) cc_final: 0.7055 (mp) REVERT: A 166 LEU cc_start: 0.6281 (tp) cc_final: 0.6037 (tp) REVERT: A 183 MET cc_start: 0.8277 (ppp) cc_final: 0.7801 (ppp) REVERT: A 230 MET cc_start: 0.8289 (ppp) cc_final: 0.7574 (ppp) REVERT: A 369 GLU cc_start: 0.7145 (mp0) cc_final: 0.6297 (mp0) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1427 time to fit residues: 12.1785 Evaluate side-chains 49 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.391 Evaluate side-chains 72 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.6235 (tmt170) cc_final: 0.4618 (pmt-80) REVERT: B 87 ARG cc_start: 0.8260 (mmt90) cc_final: 0.7739 (mmt180) REVERT: B 225 LYS cc_start: 0.5133 (mmtm) cc_final: 0.4660 (tppt) REVERT: B 246 GLN cc_start: 0.7560 (pm20) cc_final: 0.7004 (pt0) REVERT: B 263 TRP cc_start: 0.5893 (t60) cc_final: 0.5405 (t60) REVERT: B 295 ILE cc_start: 0.8225 (mp) cc_final: 0.7888 (tp) REVERT: B 328 PHE cc_start: 0.8253 (m-80) cc_final: 0.7966 (m-80) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1505 time to fit residues: 13.2089 Evaluate side-chains 56 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.363 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0023 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0034 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 0.0170 chunk 203 optimal weight: 50.0000 chunk 303 optimal weight: 9.9990 chunk 153 optimal weight: 20.0000 chunk 99 optimal weight: 0.0170 chunk 98 optimal weight: 4.9990 chunk 323 optimal weight: 9.9990 chunk 346 optimal weight: 9.9990 chunk 251 optimal weight: 0.0970 chunk 47 optimal weight: 20.0000 chunk 400 optimal weight: 0.0670 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 HIS B 370 HIS ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5804 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 40122 Z= 0.294 Angle : 0.849 15.417 54270 Z= 0.438 Chirality : 0.050 0.204 6078 Planarity : 0.010 0.272 7026 Dihedral : 7.163 38.727 6210 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 25.21 Ramachandran Plot: Outliers : 0.34 % Allowed : 12.05 % Favored : 87.61 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.10), residues: 5280 helix: -0.00 (0.21), residues: 648 sheet: -1.80 (0.14), residues: 1200 loop : -3.00 (0.08), residues: 3432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP I 247 HIS 0.014 0.002 HIS M 40 PHE 0.038 0.004 PHE I 418 TYR 0.040 0.003 TYR Q 124 ARG 0.041 0.003 ARG I 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 92 TRP cc_start: 0.8487 (m100) cc_final: 0.8210 (m-90) REVERT: A 96 LEU cc_start: 0.8062 (tt) cc_final: 0.7061 (mp) REVERT: A 131 GLU cc_start: 0.7324 (pt0) cc_final: 0.6740 (pt0) REVERT: A 166 LEU cc_start: 0.6311 (tp) cc_final: 0.6033 (tp) REVERT: A 183 MET cc_start: 0.8248 (ppp) cc_final: 0.7793 (ppp) REVERT: A 230 MET cc_start: 0.8265 (ppp) cc_final: 0.7565 (ppp) REVERT: A 369 GLU cc_start: 0.7151 (mp0) cc_final: 0.5928 (mp0) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1511 time to fit residues: 12.4999 Evaluate side-chains 49 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.439 Evaluate side-chains 70 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.6244 (tmt170) cc_final: 0.4629 (pmt-80) REVERT: B 87 ARG cc_start: 0.8260 (mmt90) cc_final: 0.7741 (mmt180) REVERT: B 225 LYS cc_start: 0.5132 (mmtm) cc_final: 0.4663 (tppt) REVERT: B 246 GLN cc_start: 0.7548 (pm20) cc_final: 0.7001 (pt0) REVERT: B 295 ILE cc_start: 0.8221 (mp) cc_final: 0.7889 (tp) REVERT: B 328 PHE cc_start: 0.8258 (m-80) cc_final: 0.7970 (m-80) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1603 time to fit residues: 13.6173 Evaluate side-chains 56 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.340 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0024 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0027 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 462 optimal weight: 0.9990 chunk 487 optimal weight: 0.0170 chunk 444 optimal weight: 0.0770 chunk 474 optimal weight: 6.9990 chunk 285 optimal weight: 4.9990 chunk 206 optimal weight: 6.9990 chunk 372 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 428 optimal weight: 0.0870 chunk 448 optimal weight: 20.0000 chunk 472 optimal weight: 0.8980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 HIS B 370 HIS Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5805 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 40122 Z= 0.301 Angle : 0.851 15.302 54270 Z= 0.441 Chirality : 0.051 0.235 6078 Planarity : 0.011 0.277 7026 Dihedral : 7.151 38.281 6210 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 21.25 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.82 % Favored : 87.84 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.10), residues: 5280 helix: 0.08 (0.21), residues: 648 sheet: -1.87 (0.14), residues: 1110 loop : -3.00 (0.08), residues: 3522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP I 247 HIS 0.021 0.003 HIS Q 294 PHE 0.074 0.004 PHE J 107 TYR 0.025 0.003 TYR E 138 ARG 0.039 0.002 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 TRP cc_start: 0.8479 (m100) cc_final: 0.8200 (m-90) REVERT: A 96 LEU cc_start: 0.8110 (tt) cc_final: 0.7138 (mp) REVERT: A 131 GLU cc_start: 0.7213 (pt0) cc_final: 0.6676 (pt0) REVERT: A 166 LEU cc_start: 0.6304 (tp) cc_final: 0.6044 (tp) REVERT: A 183 MET cc_start: 0.8259 (ppp) cc_final: 0.7807 (ppp) REVERT: A 230 MET cc_start: 0.8277 (ppp) cc_final: 0.7610 (ppp) REVERT: A 369 GLU cc_start: 0.7130 (mp0) cc_final: 0.5911 (mp0) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1479 time to fit residues: 12.6325 Evaluate side-chains 50 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.400 Evaluate side-chains 72 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.6181 (tmt170) cc_final: 0.4576 (pmt-80) REVERT: B 87 ARG cc_start: 0.8323 (mmt90) cc_final: 0.7790 (mmt180) REVERT: B 225 LYS cc_start: 0.5107 (mmtm) cc_final: 0.4649 (tppt) REVERT: B 246 GLN cc_start: 0.7482 (pm20) cc_final: 0.7049 (pt0) REVERT: B 263 TRP cc_start: 0.5741 (t60) cc_final: 0.5234 (t60) REVERT: B 295 ILE cc_start: 0.8260 (mp) cc_final: 0.7945 (tp) REVERT: B 328 PHE cc_start: 0.8259 (m-80) cc_final: 0.7980 (m-80) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1591 time to fit residues: 13.9095 Evaluate side-chains 56 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.364 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0023 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0028 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 0.0770 chunk 501 optimal weight: 2.9990 chunk 306 optimal weight: 0.2980 chunk 237 optimal weight: 4.9990 chunk 348 optimal weight: 0.0010 chunk 526 optimal weight: 50.0000 chunk 484 optimal weight: 5.9990 chunk 418 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 323 optimal weight: 10.0000 chunk 256 optimal weight: 9.9990 overall best weight: 1.6748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5808 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 40122 Z= 0.338 Angle : 0.842 14.486 54270 Z= 0.438 Chirality : 0.051 0.230 6078 Planarity : 0.011 0.274 7026 Dihedral : 7.118 38.186 6210 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 21.33 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.93 % Favored : 87.73 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.10), residues: 5280 helix: 0.09 (0.21), residues: 648 sheet: -1.74 (0.15), residues: 1044 loop : -3.05 (0.08), residues: 3588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP I 247 HIS 0.021 0.003 HIS Q 294 PHE 0.058 0.004 PHE J 107 TYR 0.035 0.003 TYR Q 124 ARG 0.041 0.003 ARG M 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 92 TRP cc_start: 0.8488 (m100) cc_final: 0.8199 (m-90) REVERT: A 96 LEU cc_start: 0.8103 (tt) cc_final: 0.7148 (mp) REVERT: A 131 GLU cc_start: 0.7144 (pt0) cc_final: 0.6653 (pt0) REVERT: A 166 LEU cc_start: 0.6316 (tp) cc_final: 0.6030 (tp) REVERT: A 183 MET cc_start: 0.8263 (ppp) cc_final: 0.7803 (ppp) REVERT: A 230 MET cc_start: 0.8295 (ppp) cc_final: 0.7696 (ppp) REVERT: A 333 MET cc_start: 0.7251 (mmm) cc_final: 0.6525 (mmm) REVERT: A 369 GLU cc_start: 0.7127 (mp0) cc_final: 0.5915 (mp0) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1379 time to fit residues: 11.5913 Evaluate side-chains 49 residues out of total 385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.343 Evaluate side-chains 70 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.6178 (tmt170) cc_final: 0.4573 (pmt-80) REVERT: B 87 ARG cc_start: 0.8332 (mmt90) cc_final: 0.7791 (mmt180) REVERT: B 225 LYS cc_start: 0.5102 (mmtm) cc_final: 0.4641 (tppt) REVERT: B 246 GLN cc_start: 0.7468 (pm20) cc_final: 0.7035 (pt0) REVERT: B 328 PHE cc_start: 0.8285 (m-80) cc_final: 0.8009 (m-80) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1595 time to fit residues: 13.5606 Evaluate side-chains 55 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.317 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0020 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0027 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 7.9990 chunk 446 optimal weight: 3.9990 chunk 128 optimal weight: 0.0050 chunk 386 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 419 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 430 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 77 optimal weight: 40.0000 overall best weight: 5.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.143581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.129798 restraints weight = 13760.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.131567 restraints weight = 9240.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.132816 restraints weight = 6770.391| |-----------------------------------------------------------------------------| r_work (final): 0.3973 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.174738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.167554 restraints weight = 11636.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.168382 restraints weight = 8450.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.168857 restraints weight = 6617.739| |-----------------------------------------------------------------------------| r_work (final): 0.4056 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.188223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.180695 restraints weight = 991.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.183971 restraints weight = 434.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.185213 restraints weight = 296.182| |-----------------------------------------------------------------------------| r_work (final): 0.4310 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.134036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.131101 restraints weight = 124.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.132588 restraints weight = 67.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.133339 restraints weight = 34.947| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5743 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 40122 Z= 0.334 Angle : 0.837 13.910 54270 Z= 0.435 Chirality : 0.051 0.239 6078 Planarity : 0.011 0.271 7026 Dihedral : 7.113 38.113 6210 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.34 % Allowed : 12.16 % Favored : 87.50 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.10), residues: 5280 helix: 0.11 (0.21), residues: 648 sheet: -1.86 (0.15), residues: 1062 loop : -3.00 (0.08), residues: 3570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP I 247 HIS 0.017 0.003 HIS Q 294 PHE 0.053 0.004 PHE J 107 TYR 0.025 0.003 TYR Q 138 ARG 0.039 0.003 ARG E 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4838.03 seconds wall clock time: 95 minutes 2.78 seconds (5702.78 seconds total)