Starting phenix.real_space_refine on Sat Dec 16 19:09:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cb8_7449/12_2023/6cb8_7449_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cb8_7449/12_2023/6cb8_7449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cb8_7449/12_2023/6cb8_7449.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cb8_7449/12_2023/6cb8_7449.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cb8_7449/12_2023/6cb8_7449_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cb8_7449/12_2023/6cb8_7449_neut_updated.pdb" } resolution = 3.8 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 54 5.49 5 S 216 5.16 5 C 31698 2.51 5 N 8478 2.21 5 O 9342 1.98 5 H 50436 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "0 PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "0 TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 100224 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO A 233 " pdbres="CDL A 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO B 233 " pdbres="CDL B 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO C 233 " pdbres="CDL C 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO D 233 " pdbres="CDL D 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO E 233 " pdbres="CDL E 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO F 233 " pdbres="CDL F 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO G 233 " pdbres="CDL G 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "H" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO H 233 " pdbres="CDL H 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "I" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO I 233 " pdbres="CDL I 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "J" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO J 233 " pdbres="CDL J 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "K" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO K 233 " pdbres="CDL K 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO L 233 " pdbres="CDL L 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "M" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO M 233 " pdbres="CDL M 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "N" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO N 233 " pdbres="CDL N 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "O" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO O 233 " pdbres="CDL O 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "P" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO P 233 " pdbres="CDL P 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "Q" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO Q 233 " pdbres="CDL Q 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO R 233 " pdbres="CDL R 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "S" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO S 233 " pdbres="CDL S 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "T" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO T 233 " pdbres="CDL T 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "U" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO U 233 " pdbres="CDL U 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "V" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO V 233 " pdbres="CDL V 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "W" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO W 233 " pdbres="CDL W 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "X" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO X 233 " pdbres="CDL X 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "Y" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO Y 233 " pdbres="CDL Y 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "Z" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO Z 233 " pdbres="CDL Z 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "0" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO 0 233 " pdbres="CDL 0 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Residues with excluded nonbonded symmetry interactions: 27 residue: pdb=" CB2 CDL A 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL A 301 " occ=0.00 residue: pdb=" CB2 CDL B 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL B 301 " occ=0.00 residue: pdb=" CB2 CDL C 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL C 301 " occ=0.00 residue: pdb=" CB2 CDL D 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL D 301 " occ=0.00 residue: pdb=" CB2 CDL E 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL E 301 " occ=0.00 residue: pdb=" CB2 CDL F 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL F 301 " occ=0.00 residue: pdb=" CB2 CDL G 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL G 301 " occ=0.00 residue: pdb=" CB2 CDL H 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL H 301 " occ=0.00 residue: pdb=" CB2 CDL I 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL I 301 " occ=0.00 residue: pdb=" CB2 CDL J 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL J 301 " occ=0.00 residue: pdb=" CB2 CDL K 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL K 301 " occ=0.00 residue: pdb=" CB2 CDL L 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL L 301 " occ=0.00 ... (remaining 15 not shown) Time building chain proxies: 31.79, per 1000 atoms: 0.32 Number of scatterers: 100224 At special positions: 0 Unit cell: (295.68, 295.68, 77.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 216 16.00 P 54 15.00 O 9342 8.00 N 8478 7.00 C 31698 6.00 H 50436 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 65.60 Conformation dependent library (CDL) restraints added in 8.9 seconds 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11880 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 135 helices and 81 sheets defined 22.2% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 19.60 Creating SS restraints... Processing helix chain 'A' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP A 6 " --> pdb=" O PRO A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 138 through 148 Processing helix chain 'B' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP B 6 " --> pdb=" O PRO B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 59 through 65 removed outlier: 5.387A pdb=" N GLU B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 138 through 148 Processing helix chain 'C' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP C 6 " --> pdb=" O PRO C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 132 Processing helix chain 'C' and resid 138 through 148 Processing helix chain 'D' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP D 6 " --> pdb=" O PRO D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 132 Processing helix chain 'D' and resid 138 through 148 Processing helix chain 'E' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP E 6 " --> pdb=" O PRO E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU E 65 " --> pdb=" O LEU E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 132 Processing helix chain 'E' and resid 138 through 148 Processing helix chain 'F' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP F 6 " --> pdb=" O PRO F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 34 Processing helix chain 'F' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU F 65 " --> pdb=" O LEU F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 132 Processing helix chain 'F' and resid 138 through 148 Processing helix chain 'G' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP G 6 " --> pdb=" O PRO G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU G 65 " --> pdb=" O LEU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 132 Processing helix chain 'G' and resid 138 through 148 Processing helix chain 'H' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP H 6 " --> pdb=" O PRO H 2 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU H 65 " --> pdb=" O LEU H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 132 Processing helix chain 'H' and resid 138 through 148 Processing helix chain 'I' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP I 6 " --> pdb=" O PRO I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 34 Processing helix chain 'I' and resid 59 through 65 removed outlier: 3.500A pdb=" N LEU I 63 " --> pdb=" O THR I 59 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLU I 65 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 132 Processing helix chain 'I' and resid 138 through 148 Processing helix chain 'J' and resid 2 through 16 removed outlier: 3.624A pdb=" N ASP J 6 " --> pdb=" O PRO J 2 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 34 Processing helix chain 'J' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU J 65 " --> pdb=" O LEU J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 132 Processing helix chain 'J' and resid 138 through 148 Processing helix chain 'K' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP K 6 " --> pdb=" O PRO K 2 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 34 Processing helix chain 'K' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU K 65 " --> pdb=" O LEU K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 132 Processing helix chain 'K' and resid 138 through 148 Processing helix chain 'L' and resid 2 through 16 removed outlier: 3.624A pdb=" N ASP L 6 " --> pdb=" O PRO L 2 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 34 Processing helix chain 'L' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU L 65 " --> pdb=" O LEU L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 132 Processing helix chain 'L' and resid 138 through 148 Processing helix chain 'M' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP M 6 " --> pdb=" O PRO M 2 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 34 Processing helix chain 'M' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU M 65 " --> pdb=" O LEU M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 132 Processing helix chain 'M' and resid 138 through 148 Processing helix chain 'N' and resid 2 through 16 removed outlier: 3.624A pdb=" N ASP N 6 " --> pdb=" O PRO N 2 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 34 Processing helix chain 'N' and resid 59 through 65 removed outlier: 3.500A pdb=" N LEU N 63 " --> pdb=" O THR N 59 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLU N 65 " --> pdb=" O LEU N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 132 Processing helix chain 'N' and resid 138 through 148 Processing helix chain 'O' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP O 6 " --> pdb=" O PRO O 2 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 34 Processing helix chain 'O' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU O 65 " --> pdb=" O LEU O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 132 Processing helix chain 'O' and resid 138 through 148 Processing helix chain 'P' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP P 6 " --> pdb=" O PRO P 2 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 34 Processing helix chain 'P' and resid 59 through 65 removed outlier: 3.500A pdb=" N LEU P 63 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLU P 65 " --> pdb=" O LEU P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 132 Processing helix chain 'P' and resid 138 through 148 Processing helix chain 'Q' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP Q 6 " --> pdb=" O PRO Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 34 Processing helix chain 'Q' and resid 59 through 65 removed outlier: 3.500A pdb=" N LEU Q 63 " --> pdb=" O THR Q 59 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLU Q 65 " --> pdb=" O LEU Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 121 through 132 Processing helix chain 'Q' and resid 138 through 148 Processing helix chain 'R' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP R 6 " --> pdb=" O PRO R 2 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 34 Processing helix chain 'R' and resid 59 through 65 removed outlier: 3.500A pdb=" N LEU R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLU R 65 " --> pdb=" O LEU R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 132 Processing helix chain 'R' and resid 138 through 148 Processing helix chain 'S' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP S 6 " --> pdb=" O PRO S 2 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 34 Processing helix chain 'S' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU S 65 " --> pdb=" O LEU S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 121 through 132 Processing helix chain 'S' and resid 138 through 148 Processing helix chain 'T' and resid 2 through 16 removed outlier: 3.624A pdb=" N ASP T 6 " --> pdb=" O PRO T 2 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 34 Processing helix chain 'T' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU T 65 " --> pdb=" O LEU T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 121 through 132 Processing helix chain 'T' and resid 138 through 148 Processing helix chain 'U' and resid 2 through 16 removed outlier: 3.624A pdb=" N ASP U 6 " --> pdb=" O PRO U 2 " (cutoff:3.500A) Processing helix chain 'U' and resid 29 through 34 Processing helix chain 'U' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU U 65 " --> pdb=" O LEU U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 121 through 132 Processing helix chain 'U' and resid 138 through 148 Processing helix chain 'V' and resid 2 through 16 removed outlier: 3.622A pdb=" N ASP V 6 " --> pdb=" O PRO V 2 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 34 Processing helix chain 'V' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU V 65 " --> pdb=" O LEU V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 121 through 132 Processing helix chain 'V' and resid 138 through 148 Processing helix chain 'W' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP W 6 " --> pdb=" O PRO W 2 " (cutoff:3.500A) Processing helix chain 'W' and resid 29 through 34 Processing helix chain 'W' and resid 59 through 65 removed outlier: 5.387A pdb=" N GLU W 65 " --> pdb=" O LEU W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 132 Processing helix chain 'W' and resid 138 through 148 Processing helix chain 'X' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP X 6 " --> pdb=" O PRO X 2 " (cutoff:3.500A) Processing helix chain 'X' and resid 29 through 34 Processing helix chain 'X' and resid 59 through 65 removed outlier: 3.500A pdb=" N LEU X 63 " --> pdb=" O THR X 59 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLU X 65 " --> pdb=" O LEU X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 121 through 132 Processing helix chain 'X' and resid 138 through 148 Processing helix chain 'Y' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP Y 6 " --> pdb=" O PRO Y 2 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 34 Processing helix chain 'Y' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU Y 65 " --> pdb=" O LEU Y 61 " (cutoff:3.500A) Processing helix chain 'Y' and resid 121 through 132 Processing helix chain 'Y' and resid 138 through 148 Processing helix chain 'Z' and resid 2 through 16 removed outlier: 3.624A pdb=" N ASP Z 6 " --> pdb=" O PRO Z 2 " (cutoff:3.500A) Processing helix chain 'Z' and resid 29 through 34 Processing helix chain 'Z' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU Z 65 " --> pdb=" O LEU Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 121 through 132 Processing helix chain 'Z' and resid 138 through 148 Processing helix chain '0' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP 0 6 " --> pdb=" O PRO 0 2 " (cutoff:3.500A) Processing helix chain '0' and resid 29 through 34 Processing helix chain '0' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU 0 65 " --> pdb=" O LEU 0 61 " (cutoff:3.500A) Processing helix chain '0' and resid 121 through 132 Processing helix chain '0' and resid 138 through 148 Processing sheet with id= 1, first strand: chain 'A' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU A 204 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG A 207 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET A 155 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS A 37 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR A 112 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR A 165 " --> pdb=" O THR A 112 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU A 156 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 205 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU B 204 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG B 207 " --> pdb=" O MET B 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET B 155 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N CYS B 37 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL B 99 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR B 112 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR B 165 " --> pdb=" O THR B 112 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU B 156 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA B 205 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU C 204 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG C 207 " --> pdb=" O MET C 155 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET C 155 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS C 37 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 81 through 95 removed outlier: 3.728A pdb=" N VAL C 99 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR C 112 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR C 165 " --> pdb=" O THR C 112 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU C 156 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA C 205 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU D 204 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG D 207 " --> pdb=" O MET D 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET D 155 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS D 37 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL D 99 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR D 112 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR D 165 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU D 156 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA D 205 " --> pdb=" O VAL D 158 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU E 204 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG E 207 " --> pdb=" O MET E 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET E 155 " --> pdb=" O ARG E 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS E 37 " --> pdb=" O VAL E 154 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL E 99 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR E 112 " --> pdb=" O THR E 165 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR E 165 " --> pdb=" O THR E 112 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'E' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU E 156 " --> pdb=" O ARG E 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA E 205 " --> pdb=" O VAL E 158 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU F 204 " --> pdb=" O LEU F 24 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG F 207 " --> pdb=" O MET F 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET F 155 " --> pdb=" O ARG F 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS F 37 " --> pdb=" O VAL F 154 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL F 99 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR F 112 " --> pdb=" O THR F 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR F 165 " --> pdb=" O THR F 112 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'F' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU F 156 " --> pdb=" O ARG F 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA F 205 " --> pdb=" O VAL F 158 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU G 204 " --> pdb=" O LEU G 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG G 207 " --> pdb=" O MET G 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET G 155 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS G 37 " --> pdb=" O VAL G 154 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL G 99 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR G 112 " --> pdb=" O THR G 165 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR G 165 " --> pdb=" O THR G 112 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'G' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU G 156 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA G 205 " --> pdb=" O VAL G 158 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'H' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU H 204 " --> pdb=" O LEU H 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG H 207 " --> pdb=" O MET H 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET H 155 " --> pdb=" O ARG H 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS H 37 " --> pdb=" O VAL H 154 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'H' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL H 99 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR H 112 " --> pdb=" O THR H 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR H 165 " --> pdb=" O THR H 112 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'H' and resid 156 through 159 removed outlier: 4.621A pdb=" N GLU H 156 " --> pdb=" O ARG H 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA H 205 " --> pdb=" O VAL H 158 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'I' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU I 204 " --> pdb=" O LEU I 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG I 207 " --> pdb=" O MET I 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET I 155 " --> pdb=" O ARG I 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS I 37 " --> pdb=" O VAL I 154 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'I' and resid 81 through 95 removed outlier: 3.728A pdb=" N VAL I 99 " --> pdb=" O VAL I 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR I 112 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR I 165 " --> pdb=" O THR I 112 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'I' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU I 156 " --> pdb=" O ARG I 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA I 205 " --> pdb=" O VAL I 158 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'J' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU J 204 " --> pdb=" O LEU J 24 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG J 207 " --> pdb=" O MET J 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET J 155 " --> pdb=" O ARG J 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS J 37 " --> pdb=" O VAL J 154 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'J' and resid 81 through 95 removed outlier: 3.728A pdb=" N VAL J 99 " --> pdb=" O VAL J 95 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N THR J 112 " --> pdb=" O THR J 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR J 165 " --> pdb=" O THR J 112 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'J' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU J 156 " --> pdb=" O ARG J 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA J 205 " --> pdb=" O VAL J 158 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'K' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU K 204 " --> pdb=" O LEU K 24 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG K 207 " --> pdb=" O MET K 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET K 155 " --> pdb=" O ARG K 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS K 37 " --> pdb=" O VAL K 154 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'K' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL K 99 " --> pdb=" O VAL K 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR K 112 " --> pdb=" O THR K 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR K 165 " --> pdb=" O THR K 112 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'K' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU K 156 " --> pdb=" O ARG K 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA K 205 " --> pdb=" O VAL K 158 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'L' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU L 204 " --> pdb=" O LEU L 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG L 207 " --> pdb=" O MET L 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET L 155 " --> pdb=" O ARG L 207 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N CYS L 37 " --> pdb=" O VAL L 154 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'L' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL L 99 " --> pdb=" O VAL L 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR L 112 " --> pdb=" O THR L 165 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR L 165 " --> pdb=" O THR L 112 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'L' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU L 156 " --> pdb=" O ARG L 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA L 205 " --> pdb=" O VAL L 158 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'M' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU M 204 " --> pdb=" O LEU M 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG M 207 " --> pdb=" O MET M 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET M 155 " --> pdb=" O ARG M 207 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS M 37 " --> pdb=" O VAL M 154 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'M' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL M 99 " --> pdb=" O VAL M 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR M 112 " --> pdb=" O THR M 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR M 165 " --> pdb=" O THR M 112 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'M' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU M 156 " --> pdb=" O ARG M 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA M 205 " --> pdb=" O VAL M 158 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'N' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU N 204 " --> pdb=" O LEU N 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG N 207 " --> pdb=" O MET N 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET N 155 " --> pdb=" O ARG N 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS N 37 " --> pdb=" O VAL N 154 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'N' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL N 99 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR N 112 " --> pdb=" O THR N 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR N 165 " --> pdb=" O THR N 112 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'N' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU N 156 " --> pdb=" O ARG N 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA N 205 " --> pdb=" O VAL N 158 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'O' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU O 204 " --> pdb=" O LEU O 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG O 207 " --> pdb=" O MET O 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET O 155 " --> pdb=" O ARG O 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS O 37 " --> pdb=" O VAL O 154 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'O' and resid 81 through 95 removed outlier: 3.726A pdb=" N VAL O 99 " --> pdb=" O VAL O 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR O 112 " --> pdb=" O THR O 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR O 165 " --> pdb=" O THR O 112 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'O' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU O 156 " --> pdb=" O ARG O 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA O 205 " --> pdb=" O VAL O 158 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'P' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU P 204 " --> pdb=" O LEU P 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG P 207 " --> pdb=" O MET P 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET P 155 " --> pdb=" O ARG P 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS P 37 " --> pdb=" O VAL P 154 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'P' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL P 99 " --> pdb=" O VAL P 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR P 112 " --> pdb=" O THR P 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR P 165 " --> pdb=" O THR P 112 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'P' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU P 156 " --> pdb=" O ARG P 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA P 205 " --> pdb=" O VAL P 158 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'Q' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU Q 204 " --> pdb=" O LEU Q 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG Q 207 " --> pdb=" O MET Q 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET Q 155 " --> pdb=" O ARG Q 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS Q 37 " --> pdb=" O VAL Q 154 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'Q' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL Q 99 " --> pdb=" O VAL Q 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR Q 112 " --> pdb=" O THR Q 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR Q 165 " --> pdb=" O THR Q 112 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'Q' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU Q 156 " --> pdb=" O ARG Q 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA Q 205 " --> pdb=" O VAL Q 158 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'R' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU R 204 " --> pdb=" O LEU R 24 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG R 207 " --> pdb=" O MET R 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET R 155 " --> pdb=" O ARG R 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS R 37 " --> pdb=" O VAL R 154 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'R' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL R 99 " --> pdb=" O VAL R 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR R 112 " --> pdb=" O THR R 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR R 165 " --> pdb=" O THR R 112 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'R' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU R 156 " --> pdb=" O ARG R 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA R 205 " --> pdb=" O VAL R 158 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'S' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU S 204 " --> pdb=" O LEU S 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG S 207 " --> pdb=" O MET S 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET S 155 " --> pdb=" O ARG S 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS S 37 " --> pdb=" O VAL S 154 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'S' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL S 99 " --> pdb=" O VAL S 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR S 112 " --> pdb=" O THR S 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR S 165 " --> pdb=" O THR S 112 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'S' and resid 156 through 159 removed outlier: 4.621A pdb=" N GLU S 156 " --> pdb=" O ARG S 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA S 205 " --> pdb=" O VAL S 158 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'T' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU T 204 " --> pdb=" O LEU T 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG T 207 " --> pdb=" O MET T 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET T 155 " --> pdb=" O ARG T 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS T 37 " --> pdb=" O VAL T 154 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'T' and resid 81 through 95 removed outlier: 3.726A pdb=" N VAL T 99 " --> pdb=" O VAL T 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR T 112 " --> pdb=" O THR T 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR T 165 " --> pdb=" O THR T 112 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'T' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU T 156 " --> pdb=" O ARG T 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA T 205 " --> pdb=" O VAL T 158 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'U' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU U 204 " --> pdb=" O LEU U 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG U 207 " --> pdb=" O MET U 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET U 155 " --> pdb=" O ARG U 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS U 37 " --> pdb=" O VAL U 154 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'U' and resid 81 through 95 removed outlier: 3.728A pdb=" N VAL U 99 " --> pdb=" O VAL U 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR U 112 " --> pdb=" O THR U 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR U 165 " --> pdb=" O THR U 112 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'U' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU U 156 " --> pdb=" O ARG U 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA U 205 " --> pdb=" O VAL U 158 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'V' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU V 204 " --> pdb=" O LEU V 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG V 207 " --> pdb=" O MET V 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET V 155 " --> pdb=" O ARG V 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS V 37 " --> pdb=" O VAL V 154 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'V' and resid 81 through 95 removed outlier: 3.728A pdb=" N VAL V 99 " --> pdb=" O VAL V 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR V 112 " --> pdb=" O THR V 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR V 165 " --> pdb=" O THR V 112 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'V' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU V 156 " --> pdb=" O ARG V 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA V 205 " --> pdb=" O VAL V 158 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'W' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU W 204 " --> pdb=" O LEU W 24 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG W 207 " --> pdb=" O MET W 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET W 155 " --> pdb=" O ARG W 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS W 37 " --> pdb=" O VAL W 154 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'W' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL W 99 " --> pdb=" O VAL W 95 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR W 112 " --> pdb=" O THR W 165 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR W 165 " --> pdb=" O THR W 112 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'W' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU W 156 " --> pdb=" O ARG W 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA W 205 " --> pdb=" O VAL W 158 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'X' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU X 204 " --> pdb=" O LEU X 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG X 207 " --> pdb=" O MET X 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET X 155 " --> pdb=" O ARG X 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS X 37 " --> pdb=" O VAL X 154 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'X' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL X 99 " --> pdb=" O VAL X 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR X 112 " --> pdb=" O THR X 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR X 165 " --> pdb=" O THR X 112 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'X' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU X 156 " --> pdb=" O ARG X 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA X 205 " --> pdb=" O VAL X 158 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'Y' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU Y 204 " --> pdb=" O LEU Y 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG Y 207 " --> pdb=" O MET Y 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET Y 155 " --> pdb=" O ARG Y 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS Y 37 " --> pdb=" O VAL Y 154 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'Y' and resid 81 through 95 removed outlier: 3.728A pdb=" N VAL Y 99 " --> pdb=" O VAL Y 95 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR Y 112 " --> pdb=" O THR Y 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR Y 165 " --> pdb=" O THR Y 112 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'Y' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU Y 156 " --> pdb=" O ARG Y 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA Y 205 " --> pdb=" O VAL Y 158 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'Z' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU Z 204 " --> pdb=" O LEU Z 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG Z 207 " --> pdb=" O MET Z 155 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET Z 155 " --> pdb=" O ARG Z 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS Z 37 " --> pdb=" O VAL Z 154 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'Z' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL Z 99 " --> pdb=" O VAL Z 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR Z 112 " --> pdb=" O THR Z 165 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR Z 165 " --> pdb=" O THR Z 112 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'Z' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU Z 156 " --> pdb=" O ARG Z 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA Z 205 " --> pdb=" O VAL Z 158 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain '0' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU 0 204 " --> pdb=" O LEU 0 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG 0 207 " --> pdb=" O MET 0 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET 0 155 " --> pdb=" O ARG 0 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS 0 37 " --> pdb=" O VAL 0 154 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain '0' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL 0 99 " --> pdb=" O VAL 0 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR 0 112 " --> pdb=" O THR 0 165 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR 0 165 " --> pdb=" O THR 0 112 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain '0' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU 0 156 " --> pdb=" O ARG 0 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA 0 205 " --> pdb=" O VAL 0 158 " (cutoff:3.500A) 2208 hydrogen bonds defined for protein. 6543 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: 41.01 Time building geometry restraints manager: 69.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 50355 1.03 - 1.23: 218 1.23 - 1.42: 20383 1.42 - 1.62: 29781 1.62 - 1.81: 405 Bond restraints: 101142 Sorted by residual: bond pdb=" OB2 CDL K 301 " pdb=" PB2 CDL K 301 " ideal model delta sigma weight residual 1.579 1.651 -0.072 1.50e-02 4.44e+03 2.27e+01 bond pdb=" OB2 CDL R 301 " pdb=" PB2 CDL R 301 " ideal model delta sigma weight residual 1.579 1.650 -0.071 1.50e-02 4.44e+03 2.23e+01 bond pdb=" OA2 CDL U 301 " pdb=" PA1 CDL U 301 " ideal model delta sigma weight residual 1.579 1.650 -0.071 1.50e-02 4.44e+03 2.23e+01 bond pdb=" OB2 CDL D 301 " pdb=" PB2 CDL D 301 " ideal model delta sigma weight residual 1.579 1.650 -0.071 1.50e-02 4.44e+03 2.22e+01 bond pdb=" OA2 CDL S 301 " pdb=" PA1 CDL S 301 " ideal model delta sigma weight residual 1.579 1.650 -0.071 1.50e-02 4.44e+03 2.22e+01 ... (remaining 101137 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.17: 1549 106.17 - 113.12: 121472 113.12 - 120.08: 28878 120.08 - 127.03: 30891 127.03 - 133.99: 459 Bond angle restraints: 183249 Sorted by residual: angle pdb=" CB2 CDL Z 301 " pdb=" OB2 CDL Z 301 " pdb=" PB2 CDL Z 301 " ideal model delta sigma weight residual 121.27 118.40 2.87 1.00e+00 1.00e+00 8.26e+00 angle pdb=" CB2 CDL I 301 " pdb=" OB2 CDL I 301 " pdb=" PB2 CDL I 301 " ideal model delta sigma weight residual 121.27 118.40 2.87 1.00e+00 1.00e+00 8.24e+00 angle pdb=" CB2 CDL W 301 " pdb=" OB2 CDL W 301 " pdb=" PB2 CDL W 301 " ideal model delta sigma weight residual 121.27 118.40 2.87 1.00e+00 1.00e+00 8.23e+00 angle pdb=" CB2 CDL S 301 " pdb=" OB2 CDL S 301 " pdb=" PB2 CDL S 301 " ideal model delta sigma weight residual 121.27 118.40 2.87 1.00e+00 1.00e+00 8.21e+00 angle pdb=" CB2 CDL C 301 " pdb=" OB2 CDL C 301 " pdb=" PB2 CDL C 301 " ideal model delta sigma weight residual 121.27 118.41 2.86 1.00e+00 1.00e+00 8.21e+00 ... (remaining 183244 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.26: 42884 14.26 - 28.52: 2611 28.52 - 42.78: 756 42.78 - 57.03: 135 57.03 - 71.29: 54 Dihedral angle restraints: 46440 sinusoidal: 25326 harmonic: 21114 Sorted by residual: dihedral pdb=" CA GLY Y 19 " pdb=" C GLY Y 19 " pdb=" N ASP Y 20 " pdb=" CA ASP Y 20 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA GLY C 19 " pdb=" C GLY C 19 " pdb=" N ASP C 20 " pdb=" CA ASP C 20 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA GLY S 19 " pdb=" C GLY S 19 " pdb=" N ASP S 20 " pdb=" CA ASP S 20 " ideal model delta harmonic sigma weight residual 180.00 -154.44 -25.56 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 46437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 4397 0.032 - 0.064: 2246 0.064 - 0.096: 937 0.096 - 0.129: 328 0.129 - 0.161: 57 Chirality restraints: 7965 Sorted by residual: chirality pdb=" CA VAL B 39 " pdb=" N VAL B 39 " pdb=" C VAL B 39 " pdb=" CB VAL B 39 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.45e-01 chirality pdb=" CA VAL M 39 " pdb=" N VAL M 39 " pdb=" C VAL M 39 " pdb=" CB VAL M 39 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" CA VAL U 39 " pdb=" N VAL U 39 " pdb=" C VAL U 39 " pdb=" CB VAL U 39 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.38e-01 ... (remaining 7962 not shown) Planarity restraints: 14553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 178 " 0.045 5.00e-02 4.00e+02 6.97e-02 7.78e+00 pdb=" N PRO H 179 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO H 179 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 179 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 178 " -0.045 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO C 179 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 179 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 179 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU L 178 " 0.045 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO L 179 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO L 179 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO L 179 " 0.038 5.00e-02 4.00e+02 ... (remaining 14550 not shown) Histogram of nonbonded interaction distances: 0.43 - 1.26: 270 1.26 - 2.10: 5536 2.10 - 2.93: 280253 2.93 - 3.77: 409455 3.77 - 4.60: 710838 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1406352 Sorted by model distance: nonbonded pdb="HD21 LEU G 27 " pdb=" HE1 PHE H 79 " model vdw 0.429 2.270 nonbonded pdb="HD21 LEU O 27 " pdb=" HE1 PHE P 79 " model vdw 0.429 2.270 nonbonded pdb="HD21 LEU F 27 " pdb=" HE1 PHE G 79 " model vdw 0.429 2.270 nonbonded pdb="HD21 LEU V 27 " pdb=" HE1 PHE W 79 " model vdw 0.429 2.270 nonbonded pdb="HD21 LEU K 27 " pdb=" HE1 PHE L 79 " model vdw 0.429 2.270 ... (remaining 1406347 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 '0' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 5.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.070 Extract box with map and model: 16.160 Check model and map are aligned: 1.090 Set scattering table: 0.710 Process input model: 267.120 Find NCS groups from input model: 3.860 Set up NCS constraints: 0.670 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 298.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2825 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 : 0.006 0.072 50706 Z= 0.384 Angle : 0.842 8.453 68715 Z= 0.442 Chirality : 0.046 0.161 7965 Planarity : 0.006 0.070 8667 Dihedral : 11.709 71.294 18981 Min Nonbonded Distance : 1.542 Molprobity Statistics. All-atom Clashscore : 37.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.58 % Favored : 81.42 % Rotamer: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -5.72 (0.09), residues: 6102 helix: -2.46 (0.12), residues: 1269 sheet: -3.41 (0.08), residues: 2592 loop : -4.85 (0.09), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP Z 219 HIS 0.008 0.002 HIS U 147 PHE 0.020 0.002 PHE C 30 TYR 0.012 0.002 TYR O 206 ARG 0.009 0.002 ARG U 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1391 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1391 time to evaluate : 5.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1391 average time/residue: 1.4375 time to fit residues: 3125.3320 Evaluate side-chains 851 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 851 time to evaluate : 5.862 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.6290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 524 optimal weight: 3.9990 chunk 470 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 160 optimal weight: 8.9990 chunk 317 optimal weight: 2.9990 chunk 251 optimal weight: 5.9990 chunk 486 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 295 optimal weight: 0.8980 chunk 362 optimal weight: 2.9990 chunk 563 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 GLN F 88 GLN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 HIS K 116 GLN L 187 GLN M 187 GLN N 187 GLN ** O 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN ** P 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 187 GLN ** Q 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 187 GLN R 187 GLN S 187 GLN ** U 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 83 ASN V 168 GLN W 138 HIS ** X 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 217 ASN Y 217 ASN Y 230 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4553 moved from start: 0.6835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 50706 Z= 0.391 Angle : 0.927 13.546 68715 Z= 0.484 Chirality : 0.052 0.216 7965 Planarity : 0.008 0.087 8667 Dihedral : 8.321 59.764 6831 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 23.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 14.77 % Favored : 85.19 % Rotamer: Outliers : 2.70 % Allowed : 12.08 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -4.45 (0.10), residues: 6102 helix: -1.01 (0.14), residues: 1269 sheet: -2.79 (0.09), residues: 2538 loop : -4.11 (0.10), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 219 HIS 0.010 0.002 HIS E 0 PHE 0.027 0.003 PHE S 140 TYR 0.024 0.003 TYR R 152 ARG 0.028 0.002 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1183 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1032 time to evaluate : 5.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 151 outliers final: 93 residues processed: 1133 average time/residue: 1.3428 time to fit residues: 2433.7179 Evaluate side-chains 885 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 792 time to evaluate : 6.173 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 8 residues processed: 93 average time/residue: 1.0454 time to fit residues: 186.8526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 313 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 469 optimal weight: 1.9990 chunk 384 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 564 optimal weight: 2.9990 chunk 610 optimal weight: 3.9990 chunk 503 optimal weight: 1.9990 chunk 560 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 453 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN B 88 GLN C 230 GLN D 32 HIS ** E 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 226 ASN M 83 ASN N 83 ASN ** O 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 217 ASN Z 230 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5604 moved from start: 1.0683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 50706 Z= 0.371 Angle : 0.853 14.096 68715 Z= 0.444 Chirality : 0.049 0.291 7965 Planarity : 0.007 0.099 8667 Dihedral : 7.464 58.952 6831 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 26.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.75 % Favored : 87.25 % Rotamer: Outliers : 3.99 % Allowed : 15.57 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.10), residues: 6102 helix: -0.81 (0.14), residues: 1296 sheet: -2.65 (0.09), residues: 2538 loop : -3.81 (0.11), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 219 HIS 0.012 0.002 HIS X 138 PHE 0.040 0.002 PHE J 48 TYR 0.025 0.002 TYR J 206 ARG 0.013 0.001 ARG Q 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1135 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 912 time to evaluate : 5.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 223 outliers final: 115 residues processed: 1088 average time/residue: 1.2752 time to fit residues: 2226.8050 Evaluate side-chains 774 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 659 time to evaluate : 5.836 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 9 residues processed: 115 average time/residue: 1.1180 time to fit residues: 233.6673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 558 optimal weight: 4.9990 chunk 424 optimal weight: 0.9990 chunk 293 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 269 optimal weight: 3.9990 chunk 379 optimal weight: 3.9990 chunk 566 optimal weight: 5.9990 chunk 600 optimal weight: 0.9990 chunk 296 optimal weight: 2.9990 chunk 537 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 HIS ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 ASN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 226 ASN N 78 ASN O 78 ASN O 138 HIS O 226 ASN ** P 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 116 GLN ** T 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 147 HIS V 150 ASN V 230 GLN Y 217 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6193 moved from start: 1.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 50706 Z= 0.318 Angle : 0.791 12.177 68715 Z= 0.410 Chirality : 0.048 0.189 7965 Planarity : 0.007 0.078 8667 Dihedral : 7.107 59.989 6831 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.57 % Favored : 86.43 % Rotamer: Outliers : 3.36 % Allowed : 19.20 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -3.82 (0.10), residues: 6102 helix: -0.49 (0.15), residues: 1295 sheet: -2.69 (0.10), residues: 2504 loop : -3.38 (0.11), residues: 2303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 219 HIS 0.006 0.001 HIS J 32 PHE 0.028 0.002 PHE S 79 TYR 0.041 0.002 TYR L 206 ARG 0.012 0.001 ARG H 145 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 757 time to evaluate : 5.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 188 outliers final: 103 residues processed: 910 average time/residue: 1.2756 time to fit residues: 1892.6084 Evaluate side-chains 721 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 618 time to evaluate : 5.962 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 4 residues processed: 103 average time/residue: 0.9673 time to fit residues: 187.8704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 499 optimal weight: 0.8980 chunk 340 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 446 optimal weight: 1.9990 chunk 247 optimal weight: 0.7980 chunk 512 optimal weight: 4.9990 chunk 414 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 306 optimal weight: 3.9990 chunk 538 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 GLN I 78 ASN L 109 GLN L 226 ASN O 109 GLN P 191 ASN Q 78 ASN ** Q 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 230 GLN ** T 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 230 GLN W 168 GLN X 150 ASN Y 217 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 moved from start: 1.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 50706 Z= 0.196 Angle : 0.625 11.227 68715 Z= 0.323 Chirality : 0.043 0.154 7965 Planarity : 0.005 0.074 8667 Dihedral : 6.635 59.881 6831 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 1.70 % Allowed : 21.69 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -3.49 (0.10), residues: 6102 helix: -0.00 (0.15), residues: 1295 sheet: -2.58 (0.10), residues: 2530 loop : -3.20 (0.12), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 219 HIS 0.004 0.001 HIS H 32 PHE 0.019 0.001 PHE C 33 TYR 0.025 0.001 TYR R 152 ARG 0.020 0.001 ARG T 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 665 time to evaluate : 6.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 55 residues processed: 740 average time/residue: 1.3144 time to fit residues: 1563.9406 Evaluate side-chains 614 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 559 time to evaluate : 5.916 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 6 residues processed: 55 average time/residue: 0.9789 time to fit residues: 105.6206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 201 optimal weight: 1.9990 chunk 540 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 352 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 600 optimal weight: 0.9990 chunk 498 optimal weight: 3.9990 chunk 278 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 315 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 GLN ** E 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 78 ASN K 109 GLN L 226 ASN ** M 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 16 ASN ** Q 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 217 ASN ** 0 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 1.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 50706 Z= 0.237 Angle : 0.659 12.648 68715 Z= 0.342 Chirality : 0.045 0.338 7965 Planarity : 0.006 0.070 8667 Dihedral : 6.368 55.780 6831 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.16 % Favored : 87.84 % Rotamer: Outliers : 2.22 % Allowed : 22.49 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -3.47 (0.10), residues: 6102 helix: 0.06 (0.15), residues: 1293 sheet: -2.63 (0.10), residues: 2526 loop : -3.12 (0.12), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 219 HIS 0.005 0.001 HIS H 147 PHE 0.029 0.002 PHE E 140 TYR 0.020 0.001 TYR U 58 ARG 0.010 0.001 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 630 time to evaluate : 6.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 124 outliers final: 79 residues processed: 729 average time/residue: 1.3221 time to fit residues: 1537.5272 Evaluate side-chains 609 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 530 time to evaluate : 5.928 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 8 residues processed: 79 average time/residue: 0.9754 time to fit residues: 144.7491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 579 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 342 optimal weight: 1.9990 chunk 438 optimal weight: 1.9990 chunk 339 optimal weight: 0.9980 chunk 505 optimal weight: 5.9990 chunk 335 optimal weight: 0.0870 chunk 598 optimal weight: 2.9990 chunk 374 optimal weight: 2.9990 chunk 364 optimal weight: 1.9990 chunk 276 optimal weight: 5.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 GLN D 192 ASN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 226 ASN ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 16 ASN R 16 ASN ** T 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 217 ASN ** 0 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 1.6293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 50706 Z= 0.254 Angle : 0.673 11.588 68715 Z= 0.348 Chirality : 0.045 0.210 7965 Planarity : 0.006 0.073 8667 Dihedral : 6.512 53.537 6831 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.27 % Favored : 87.73 % Rotamer: Outliers : 1.93 % Allowed : 23.28 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -3.50 (0.10), residues: 6102 helix: -0.01 (0.15), residues: 1292 sheet: -2.66 (0.10), residues: 2508 loop : -3.11 (0.12), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Q 219 HIS 0.012 0.001 HIS G 147 PHE 0.023 0.002 PHE E 140 TYR 0.040 0.001 TYR J 152 ARG 0.012 0.001 ARG J 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 601 time to evaluate : 6.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 56 residues processed: 681 average time/residue: 1.3480 time to fit residues: 1463.8783 Evaluate side-chains 587 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 531 time to evaluate : 6.007 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 9 residues processed: 56 average time/residue: 1.0040 time to fit residues: 107.5160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 370 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 357 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 380 optimal weight: 3.9990 chunk 407 optimal weight: 1.9990 chunk 295 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 470 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN D 109 GLN E 109 GLN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 ASN ** K 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 226 ASN ** M 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 GLN ** V 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 217 ASN 0 32 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 1.7420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 50706 Z= 0.260 Angle : 0.683 11.109 68715 Z= 0.353 Chirality : 0.045 0.215 7965 Planarity : 0.006 0.076 8667 Dihedral : 6.462 50.013 6831 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.31 % Favored : 86.69 % Rotamer: Outliers : 1.52 % Allowed : 23.42 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: -3.47 (0.10), residues: 6102 helix: -0.05 (0.15), residues: 1295 sheet: -2.52 (0.10), residues: 2338 loop : -3.22 (0.11), residues: 2469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 49 HIS 0.005 0.001 HIS I 0 PHE 0.045 0.002 PHE P 79 TYR 0.021 0.001 TYR R 152 ARG 0.012 0.001 ARG N 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 591 time to evaluate : 5.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 51 residues processed: 652 average time/residue: 1.3308 time to fit residues: 1387.7204 Evaluate side-chains 585 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 534 time to evaluate : 7.037 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 9 residues processed: 51 average time/residue: 1.0179 time to fit residues: 99.5897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 544 optimal weight: 0.9980 chunk 573 optimal weight: 1.9990 chunk 523 optimal weight: 2.9990 chunk 557 optimal weight: 0.9990 chunk 335 optimal weight: 6.9990 chunk 242 optimal weight: 0.7980 chunk 437 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 504 optimal weight: 0.6980 chunk 527 optimal weight: 1.9990 chunk 555 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 HIS D 109 GLN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 226 ASN ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 78 ASN V 147 HIS ** V 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 217 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 1.7838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 50706 Z= 0.210 Angle : 0.630 9.206 68715 Z= 0.324 Chirality : 0.044 0.201 7965 Planarity : 0.005 0.081 8667 Dihedral : 6.281 49.847 6831 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.09 % Favored : 88.91 % Rotamer: Outliers : 0.95 % Allowed : 24.26 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: 6102 helix: 0.10 (0.15), residues: 1296 sheet: -2.42 (0.10), residues: 2338 loop : -3.15 (0.11), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 49 HIS 0.007 0.001 HIS S 0 PHE 0.040 0.001 PHE Q 81 TYR 0.021 0.001 TYR R 152 ARG 0.010 0.001 ARG V 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12204 Ramachandran restraints generated. 6102 Oldfield, 0 Emsley, 6102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 565 time to evaluate : 5.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 35 residues processed: 603 average time/residue: 1.3075 time to fit residues: 1257.1773 Evaluate side-chains 557 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 522 time to evaluate : 6.040 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 10 residues processed: 35 average time/residue: 1.0766 time to fit residues: 71.3889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 621 random chunks: chunk 366 optimal weight: 3.9990 chunk 589 optimal weight: 4.9990 chunk 359 optimal weight: 3.9990 chunk 279 optimal weight: 0.6980 chunk 410 optimal weight: 0.5980 chunk 618 optimal weight: 0.9980 chunk 569 optimal weight: 0.9980 chunk 492 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 380 optimal weight: 0.9980 chunk 302 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: