Starting phenix.real_space_refine (version: dev) on Wed Apr 6 19:22:12 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qzf_4685/04_2022/6qzf_4685.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qzf_4685/04_2022/6qzf_4685.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/6qzf_4685/04_2022/6qzf_4685.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qzf_4685/04_2022/6qzf_4685.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qzf_4685/04_2022/6qzf_4685.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qzf_4685/04_2022/6qzf_4685.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.233 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 71628 Number of models: 1 Model: "" Number of chains: 60 Chain: "0a" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2240 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "0b" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2240 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "0c" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2240 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "0d" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2240 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "0e" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2240 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "0f" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2240 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "0g" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2240 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "0h" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2240 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "0i" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2240 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "0j" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2240 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "0k" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2240 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "0l" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2240 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "0A" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2300 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 286} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 36 Chain: "0B" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2300 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 286} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 36 Chain: "0C" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2300 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 286} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 36 Chain: "0D" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2300 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 286} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 36 Chain: "0E" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2300 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 286} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 36 Chain: "0F" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2300 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 286} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 36 Chain: "0G" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2300 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 286} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 36 Chain: "0H" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2300 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 286} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 36 Chain: "0I" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2300 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 286} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 36 Chain: "0J" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2300 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 286} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 36 Chain: "0K" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2300 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 286} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 36 Chain: "0L" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2300 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 286} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 433 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "B" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 482 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 514 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "D" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 433 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "E" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 482 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 514 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "G" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 433 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "H" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 482 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 514 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "J" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 433 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "K" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 482 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "L" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 514 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "M" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 433 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "N" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 482 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "O" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 514 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "P" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 433 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "Q" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 482 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "R" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 514 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "S" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 433 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "T" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 482 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "U" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 514 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "V" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 433 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "W" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 482 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "X" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 514 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "Y" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 433 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "Z" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 482 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "a" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 514 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "b" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 433 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "c" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 482 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "d" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 514 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "e" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 433 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "f" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 482 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "g" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 514 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "h" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 433 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "i" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 482 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "j" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 514 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Time building chain proxies: 29.17, per 1000 atoms: 0.41 Number of scatterers: 71628 At special positions: 0 Unit cell: (239.36, 239.36, 323.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 300 16.00 O 14160 8.00 N 11904 7.00 C 45264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 22.36 Conformation dependent library (CDL) restraints added in 7.5 seconds 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16992 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 0 sheets defined 45.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain '0a' and resid 11 through 36 removed outlier: 3.509A pdb=" N ARG0a 22 " --> pdb=" O GLN0a 18 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0a 25 " --> pdb=" O ASN0a 21 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS0a 26 " --> pdb=" O ARG0a 22 " (cutoff:3.500A) Processing helix chain '0a' and resid 49 through 60 removed outlier: 3.825A pdb=" N SER0a 56 " --> pdb=" O PHE0a 52 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS0a 58 " --> pdb=" O GLU0a 54 " (cutoff:3.500A) Processing helix chain '0a' and resid 130 through 154 removed outlier: 3.540A pdb=" N GLU0a 135 " --> pdb=" O THR0a 131 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU0a 136 " --> pdb=" O PRO0a 132 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE0a 137 " --> pdb=" O THR0a 133 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU0a 140 " --> pdb=" O LEU0a 136 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA0a 142 " --> pdb=" O ALA0a 138 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU0a 143 " --> pdb=" O ALA0a 139 " (cutoff:3.500A) Processing helix chain '0a' and resid 164 through 166 No H-bonds generated for 'chain '0a' and resid 164 through 166' Processing helix chain '0a' and resid 167 through 180 Processing helix chain '0a' and resid 192 through 194 No H-bonds generated for 'chain '0a' and resid 192 through 194' Processing helix chain '0a' and resid 206 through 226 removed outlier: 3.628A pdb=" N ASN0a 211 " --> pdb=" O VAL0a 207 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA0a 212 " --> pdb=" O ASP0a 208 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN0a 213 " --> pdb=" O LYS0a 209 " (cutoff:3.500A) Processing helix chain '0a' and resid 247 through 269 removed outlier: 3.652A pdb=" N GLU0a 251 " --> pdb=" O ASP0a 247 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL0a 256 " --> pdb=" O SER0a 252 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N PHE0a 257 " --> pdb=" O SER0a 253 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU0a 258 " --> pdb=" O GLY0a 254 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS0a 259 " --> pdb=" O THR0a 255 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER0a 260 " --> pdb=" O VAL0a 256 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA0a 264 " --> pdb=" O SER0a 260 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS0a 267 " --> pdb=" O GLU0a 263 " (cutoff:3.500A) Processing helix chain '0a' and resid 284 through 297 removed outlier: 4.097A pdb=" N ILE0a 295 " --> pdb=" O GLU0a 291 " (cutoff:3.500A) Processing helix chain '0b' and resid 11 through 36 removed outlier: 3.509A pdb=" N ARG0b 22 " --> pdb=" O GLN0b 18 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE0b 25 " --> pdb=" O ASN0b 21 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS0b 26 " --> pdb=" O ARG0b 22 " (cutoff:3.500A) Processing helix chain '0b' and resid 49 through 60 removed outlier: 3.825A pdb=" N SER0b 56 " --> pdb=" O PHE0b 52 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS0b 58 " --> pdb=" O GLU0b 54 " (cutoff:3.500A) Processing helix chain '0b' and resid 130 through 154 removed outlier: 3.541A pdb=" N GLU0b 135 " --> pdb=" O THR0b 131 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU0b 136 " --> pdb=" O PRO0b 132 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE0b 137 " --> pdb=" O THR0b 133 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU0b 140 " --> pdb=" O LEU0b 136 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA0b 142 " --> pdb=" O ALA0b 138 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU0b 143 " --> pdb=" O ALA0b 139 " (cutoff:3.500A) Processing helix chain '0b' and resid 164 through 166 No H-bonds generated for 'chain '0b' and resid 164 through 166' Processing helix chain '0b' and resid 167 through 180 Processing helix chain '0b' and resid 192 through 194 No H-bonds generated for 'chain '0b' and resid 192 through 194' Processing helix chain '0b' and resid 206 through 226 removed outlier: 3.626A pdb=" N ASN0b 211 " --> pdb=" O VAL0b 207 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA0b 212 " --> pdb=" O ASP0b 208 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN0b 213 " --> pdb=" O LYS0b 209 " (cutoff:3.500A) Processing helix chain '0b' and resid 247 through 269 removed outlier: 3.653A pdb=" N GLU0b 251 " --> pdb=" O ASP0b 247 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL0b 256 " --> pdb=" O SER0b 252 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE0b 257 " --> pdb=" O SER0b 253 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU0b 258 " --> pdb=" O GLY0b 254 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS0b 259 " --> pdb=" O THR0b 255 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER0b 260 " --> pdb=" O VAL0b 256 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA0b 264 " --> pdb=" O SER0b 260 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS0b 267 " --> pdb=" O GLU0b 263 " (cutoff:3.500A) Processing helix chain '0b' and resid 284 through 297 removed outlier: 4.097A pdb=" N ILE0b 295 " --> pdb=" O GLU0b 291 " (cutoff:3.500A) Processing helix chain '0c' and resid 11 through 36 removed outlier: 3.510A pdb=" N ARG0c 22 " --> pdb=" O GLN0c 18 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0c 25 " --> pdb=" O ASN0c 21 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS0c 26 " --> pdb=" O ARG0c 22 " (cutoff:3.500A) Processing helix chain '0c' and resid 49 through 60 removed outlier: 3.825A pdb=" N SER0c 56 " --> pdb=" O PHE0c 52 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS0c 58 " --> pdb=" O GLU0c 54 " (cutoff:3.500A) Processing helix chain '0c' and resid 130 through 154 removed outlier: 3.541A pdb=" N GLU0c 135 " --> pdb=" O THR0c 131 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU0c 136 " --> pdb=" O PRO0c 132 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE0c 137 " --> pdb=" O THR0c 133 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU0c 140 " --> pdb=" O LEU0c 136 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA0c 142 " --> pdb=" O ALA0c 138 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU0c 143 " --> pdb=" O ALA0c 139 " (cutoff:3.500A) Processing helix chain '0c' and resid 164 through 166 No H-bonds generated for 'chain '0c' and resid 164 through 166' Processing helix chain '0c' and resid 167 through 180 Processing helix chain '0c' and resid 192 through 194 No H-bonds generated for 'chain '0c' and resid 192 through 194' Processing helix chain '0c' and resid 206 through 226 removed outlier: 3.627A pdb=" N ASN0c 211 " --> pdb=" O VAL0c 207 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA0c 212 " --> pdb=" O ASP0c 208 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN0c 213 " --> pdb=" O LYS0c 209 " (cutoff:3.500A) Processing helix chain '0c' and resid 247 through 269 removed outlier: 3.653A pdb=" N GLU0c 251 " --> pdb=" O ASP0c 247 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL0c 256 " --> pdb=" O SER0c 252 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE0c 257 " --> pdb=" O SER0c 253 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU0c 258 " --> pdb=" O GLY0c 254 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS0c 259 " --> pdb=" O THR0c 255 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER0c 260 " --> pdb=" O VAL0c 256 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA0c 264 " --> pdb=" O SER0c 260 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS0c 267 " --> pdb=" O GLU0c 263 " (cutoff:3.500A) Processing helix chain '0c' and resid 284 through 297 removed outlier: 4.097A pdb=" N ILE0c 295 " --> pdb=" O GLU0c 291 " (cutoff:3.500A) Processing helix chain '0d' and resid 11 through 36 removed outlier: 3.509A pdb=" N ARG0d 22 " --> pdb=" O GLN0d 18 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0d 25 " --> pdb=" O ASN0d 21 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS0d 26 " --> pdb=" O ARG0d 22 " (cutoff:3.500A) Processing helix chain '0d' and resid 49 through 60 removed outlier: 3.826A pdb=" N SER0d 56 " --> pdb=" O PHE0d 52 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS0d 58 " --> pdb=" O GLU0d 54 " (cutoff:3.500A) Processing helix chain '0d' and resid 130 through 154 removed outlier: 3.540A pdb=" N GLU0d 135 " --> pdb=" O THR0d 131 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU0d 136 " --> pdb=" O PRO0d 132 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE0d 137 " --> pdb=" O THR0d 133 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU0d 140 " --> pdb=" O LEU0d 136 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA0d 142 " --> pdb=" O ALA0d 138 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU0d 143 " --> pdb=" O ALA0d 139 " (cutoff:3.500A) Processing helix chain '0d' and resid 164 through 166 No H-bonds generated for 'chain '0d' and resid 164 through 166' Processing helix chain '0d' and resid 167 through 180 Processing helix chain '0d' and resid 192 through 194 No H-bonds generated for 'chain '0d' and resid 192 through 194' Processing helix chain '0d' and resid 206 through 226 removed outlier: 3.627A pdb=" N ASN0d 211 " --> pdb=" O VAL0d 207 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA0d 212 " --> pdb=" O ASP0d 208 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN0d 213 " --> pdb=" O LYS0d 209 " (cutoff:3.500A) Processing helix chain '0d' and resid 247 through 269 removed outlier: 3.654A pdb=" N GLU0d 251 " --> pdb=" O ASP0d 247 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL0d 256 " --> pdb=" O SER0d 252 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE0d 257 " --> pdb=" O SER0d 253 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU0d 258 " --> pdb=" O GLY0d 254 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS0d 259 " --> pdb=" O THR0d 255 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER0d 260 " --> pdb=" O VAL0d 256 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA0d 264 " --> pdb=" O SER0d 260 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS0d 267 " --> pdb=" O GLU0d 263 " (cutoff:3.500A) Processing helix chain '0d' and resid 284 through 297 removed outlier: 4.097A pdb=" N ILE0d 295 " --> pdb=" O GLU0d 291 " (cutoff:3.500A) Processing helix chain '0e' and resid 11 through 36 removed outlier: 3.509A pdb=" N ARG0e 22 " --> pdb=" O GLN0e 18 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE0e 25 " --> pdb=" O ASN0e 21 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS0e 26 " --> pdb=" O ARG0e 22 " (cutoff:3.500A) Processing helix chain '0e' and resid 49 through 60 removed outlier: 3.826A pdb=" N SER0e 56 " --> pdb=" O PHE0e 52 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS0e 58 " --> pdb=" O GLU0e 54 " (cutoff:3.500A) Processing helix chain '0e' and resid 130 through 154 removed outlier: 3.540A pdb=" N GLU0e 135 " --> pdb=" O THR0e 131 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU0e 136 " --> pdb=" O PRO0e 132 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE0e 137 " --> pdb=" O THR0e 133 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU0e 140 " --> pdb=" O LEU0e 136 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA0e 142 " --> pdb=" O ALA0e 138 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU0e 143 " --> pdb=" O ALA0e 139 " (cutoff:3.500A) Processing helix chain '0e' and resid 164 through 166 No H-bonds generated for 'chain '0e' and resid 164 through 166' Processing helix chain '0e' and resid 167 through 180 Processing helix chain '0e' and resid 192 through 194 No H-bonds generated for 'chain '0e' and resid 192 through 194' Processing helix chain '0e' and resid 206 through 226 removed outlier: 3.627A pdb=" N ASN0e 211 " --> pdb=" O VAL0e 207 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA0e 212 " --> pdb=" O ASP0e 208 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN0e 213 " --> pdb=" O LYS0e 209 " (cutoff:3.500A) Processing helix chain '0e' and resid 247 through 269 removed outlier: 3.652A pdb=" N GLU0e 251 " --> pdb=" O ASP0e 247 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL0e 256 " --> pdb=" O SER0e 252 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE0e 257 " --> pdb=" O SER0e 253 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU0e 258 " --> pdb=" O GLY0e 254 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS0e 259 " --> pdb=" O THR0e 255 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER0e 260 " --> pdb=" O VAL0e 256 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA0e 264 " --> pdb=" O SER0e 260 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS0e 267 " --> pdb=" O GLU0e 263 " (cutoff:3.500A) Processing helix chain '0e' and resid 284 through 297 removed outlier: 4.097A pdb=" N ILE0e 295 " --> pdb=" O GLU0e 291 " (cutoff:3.500A) Processing helix chain '0f' and resid 11 through 36 removed outlier: 3.510A pdb=" N ARG0f 22 " --> pdb=" O GLN0f 18 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0f 25 " --> pdb=" O ASN0f 21 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS0f 26 " --> pdb=" O ARG0f 22 " (cutoff:3.500A) Processing helix chain '0f' and resid 49 through 60 removed outlier: 3.826A pdb=" N SER0f 56 " --> pdb=" O PHE0f 52 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS0f 58 " --> pdb=" O GLU0f 54 " (cutoff:3.500A) Processing helix chain '0f' and resid 130 through 154 removed outlier: 3.539A pdb=" N GLU0f 135 " --> pdb=" O THR0f 131 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU0f 136 " --> pdb=" O PRO0f 132 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE0f 137 " --> pdb=" O THR0f 133 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU0f 140 " --> pdb=" O LEU0f 136 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA0f 142 " --> pdb=" O ALA0f 138 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU0f 143 " --> pdb=" O ALA0f 139 " (cutoff:3.500A) Processing helix chain '0f' and resid 164 through 166 No H-bonds generated for 'chain '0f' and resid 164 through 166' Processing helix chain '0f' and resid 167 through 180 Processing helix chain '0f' and resid 192 through 194 No H-bonds generated for 'chain '0f' and resid 192 through 194' Processing helix chain '0f' and resid 206 through 226 removed outlier: 3.627A pdb=" N ASN0f 211 " --> pdb=" O VAL0f 207 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA0f 212 " --> pdb=" O ASP0f 208 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN0f 213 " --> pdb=" O LYS0f 209 " (cutoff:3.500A) Processing helix chain '0f' and resid 247 through 269 removed outlier: 3.653A pdb=" N GLU0f 251 " --> pdb=" O ASP0f 247 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL0f 256 " --> pdb=" O SER0f 252 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE0f 257 " --> pdb=" O SER0f 253 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU0f 258 " --> pdb=" O GLY0f 254 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS0f 259 " --> pdb=" O THR0f 255 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER0f 260 " --> pdb=" O VAL0f 256 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA0f 264 " --> pdb=" O SER0f 260 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS0f 267 " --> pdb=" O GLU0f 263 " (cutoff:3.500A) Processing helix chain '0f' and resid 284 through 297 removed outlier: 4.096A pdb=" N ILE0f 295 " --> pdb=" O GLU0f 291 " (cutoff:3.500A) Processing helix chain '0g' and resid 11 through 36 removed outlier: 3.509A pdb=" N ARG0g 22 " --> pdb=" O GLN0g 18 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE0g 25 " --> pdb=" O ASN0g 21 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS0g 26 " --> pdb=" O ARG0g 22 " (cutoff:3.500A) Processing helix chain '0g' and resid 49 through 60 removed outlier: 3.825A pdb=" N SER0g 56 " --> pdb=" O PHE0g 52 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS0g 58 " --> pdb=" O GLU0g 54 " (cutoff:3.500A) Processing helix chain '0g' and resid 130 through 154 removed outlier: 3.540A pdb=" N GLU0g 135 " --> pdb=" O THR0g 131 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU0g 136 " --> pdb=" O PRO0g 132 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE0g 137 " --> pdb=" O THR0g 133 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU0g 140 " --> pdb=" O LEU0g 136 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA0g 142 " --> pdb=" O ALA0g 138 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU0g 143 " --> pdb=" O ALA0g 139 " (cutoff:3.500A) Processing helix chain '0g' and resid 164 through 166 No H-bonds generated for 'chain '0g' and resid 164 through 166' Processing helix chain '0g' and resid 167 through 180 Processing helix chain '0g' and resid 192 through 194 No H-bonds generated for 'chain '0g' and resid 192 through 194' Processing helix chain '0g' and resid 206 through 226 removed outlier: 3.627A pdb=" N ASN0g 211 " --> pdb=" O VAL0g 207 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA0g 212 " --> pdb=" O ASP0g 208 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN0g 213 " --> pdb=" O LYS0g 209 " (cutoff:3.500A) Processing helix chain '0g' and resid 247 through 269 removed outlier: 3.653A pdb=" N GLU0g 251 " --> pdb=" O ASP0g 247 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL0g 256 " --> pdb=" O SER0g 252 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE0g 257 " --> pdb=" O SER0g 253 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU0g 258 " --> pdb=" O GLY0g 254 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS0g 259 " --> pdb=" O THR0g 255 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER0g 260 " --> pdb=" O VAL0g 256 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA0g 264 " --> pdb=" O SER0g 260 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS0g 267 " --> pdb=" O GLU0g 263 " (cutoff:3.500A) Processing helix chain '0g' and resid 284 through 297 removed outlier: 4.096A pdb=" N ILE0g 295 " --> pdb=" O GLU0g 291 " (cutoff:3.500A) Processing helix chain '0h' and resid 11 through 36 removed outlier: 3.511A pdb=" N ARG0h 22 " --> pdb=" O GLN0h 18 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0h 25 " --> pdb=" O ASN0h 21 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS0h 26 " --> pdb=" O ARG0h 22 " (cutoff:3.500A) Processing helix chain '0h' and resid 49 through 60 removed outlier: 3.825A pdb=" N SER0h 56 " --> pdb=" O PHE0h 52 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS0h 58 " --> pdb=" O GLU0h 54 " (cutoff:3.500A) Processing helix chain '0h' and resid 130 through 154 removed outlier: 3.540A pdb=" N GLU0h 135 " --> pdb=" O THR0h 131 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU0h 136 " --> pdb=" O PRO0h 132 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE0h 137 " --> pdb=" O THR0h 133 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU0h 140 " --> pdb=" O LEU0h 136 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA0h 142 " --> pdb=" O ALA0h 138 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU0h 143 " --> pdb=" O ALA0h 139 " (cutoff:3.500A) Processing helix chain '0h' and resid 164 through 166 No H-bonds generated for 'chain '0h' and resid 164 through 166' Processing helix chain '0h' and resid 167 through 180 Processing helix chain '0h' and resid 192 through 194 No H-bonds generated for 'chain '0h' and resid 192 through 194' Processing helix chain '0h' and resid 206 through 226 removed outlier: 3.627A pdb=" N ASN0h 211 " --> pdb=" O VAL0h 207 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA0h 212 " --> pdb=" O ASP0h 208 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN0h 213 " --> pdb=" O LYS0h 209 " (cutoff:3.500A) Processing helix chain '0h' and resid 247 through 269 removed outlier: 3.652A pdb=" N GLU0h 251 " --> pdb=" O ASP0h 247 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL0h 256 " --> pdb=" O SER0h 252 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE0h 257 " --> pdb=" O SER0h 253 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU0h 258 " --> pdb=" O GLY0h 254 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS0h 259 " --> pdb=" O THR0h 255 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER0h 260 " --> pdb=" O VAL0h 256 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA0h 264 " --> pdb=" O SER0h 260 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS0h 267 " --> pdb=" O GLU0h 263 " (cutoff:3.500A) Processing helix chain '0h' and resid 284 through 297 removed outlier: 4.096A pdb=" N ILE0h 295 " --> pdb=" O GLU0h 291 " (cutoff:3.500A) Processing helix chain '0i' and resid 11 through 36 removed outlier: 3.509A pdb=" N ARG0i 22 " --> pdb=" O GLN0i 18 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0i 25 " --> pdb=" O ASN0i 21 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS0i 26 " --> pdb=" O ARG0i 22 " (cutoff:3.500A) Processing helix chain '0i' and resid 49 through 60 removed outlier: 3.824A pdb=" N SER0i 56 " --> pdb=" O PHE0i 52 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS0i 58 " --> pdb=" O GLU0i 54 " (cutoff:3.500A) Processing helix chain '0i' and resid 130 through 154 removed outlier: 3.540A pdb=" N GLU0i 135 " --> pdb=" O THR0i 131 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU0i 136 " --> pdb=" O PRO0i 132 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE0i 137 " --> pdb=" O THR0i 133 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU0i 140 " --> pdb=" O LEU0i 136 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA0i 142 " --> pdb=" O ALA0i 138 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU0i 143 " --> pdb=" O ALA0i 139 " (cutoff:3.500A) Processing helix chain '0i' and resid 164 through 166 No H-bonds generated for 'chain '0i' and resid 164 through 166' Processing helix chain '0i' and resid 167 through 180 Processing helix chain '0i' and resid 192 through 194 No H-bonds generated for 'chain '0i' and resid 192 through 194' Processing helix chain '0i' and resid 206 through 226 removed outlier: 3.627A pdb=" N ASN0i 211 " --> pdb=" O VAL0i 207 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA0i 212 " --> pdb=" O ASP0i 208 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN0i 213 " --> pdb=" O LYS0i 209 " (cutoff:3.500A) Processing helix chain '0i' and resid 247 through 269 removed outlier: 3.651A pdb=" N GLU0i 251 " --> pdb=" O ASP0i 247 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL0i 256 " --> pdb=" O SER0i 252 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE0i 257 " --> pdb=" O SER0i 253 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU0i 258 " --> pdb=" O GLY0i 254 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS0i 259 " --> pdb=" O THR0i 255 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER0i 260 " --> pdb=" O VAL0i 256 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA0i 264 " --> pdb=" O SER0i 260 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS0i 267 " --> pdb=" O GLU0i 263 " (cutoff:3.500A) Processing helix chain '0i' and resid 284 through 297 removed outlier: 4.097A pdb=" N ILE0i 295 " --> pdb=" O GLU0i 291 " (cutoff:3.500A) Processing helix chain '0j' and resid 11 through 36 removed outlier: 3.509A pdb=" N ARG0j 22 " --> pdb=" O GLN0j 18 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0j 25 " --> pdb=" O ASN0j 21 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS0j 26 " --> pdb=" O ARG0j 22 " (cutoff:3.500A) Processing helix chain '0j' and resid 49 through 60 removed outlier: 3.825A pdb=" N SER0j 56 " --> pdb=" O PHE0j 52 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS0j 58 " --> pdb=" O GLU0j 54 " (cutoff:3.500A) Processing helix chain '0j' and resid 130 through 154 removed outlier: 3.540A pdb=" N GLU0j 135 " --> pdb=" O THR0j 131 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU0j 136 " --> pdb=" O PRO0j 132 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE0j 137 " --> pdb=" O THR0j 133 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU0j 140 " --> pdb=" O LEU0j 136 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA0j 142 " --> pdb=" O ALA0j 138 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU0j 143 " --> pdb=" O ALA0j 139 " (cutoff:3.500A) Processing helix chain '0j' and resid 164 through 166 No H-bonds generated for 'chain '0j' and resid 164 through 166' Processing helix chain '0j' and resid 167 through 180 Processing helix chain '0j' and resid 192 through 194 No H-bonds generated for 'chain '0j' and resid 192 through 194' Processing helix chain '0j' and resid 206 through 226 removed outlier: 3.627A pdb=" N ASN0j 211 " --> pdb=" O VAL0j 207 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA0j 212 " --> pdb=" O ASP0j 208 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN0j 213 " --> pdb=" O LYS0j 209 " (cutoff:3.500A) Processing helix chain '0j' and resid 247 through 269 removed outlier: 3.653A pdb=" N GLU0j 251 " --> pdb=" O ASP0j 247 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL0j 256 " --> pdb=" O SER0j 252 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE0j 257 " --> pdb=" O SER0j 253 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU0j 258 " --> pdb=" O GLY0j 254 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS0j 259 " --> pdb=" O THR0j 255 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER0j 260 " --> pdb=" O VAL0j 256 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA0j 264 " --> pdb=" O SER0j 260 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS0j 267 " --> pdb=" O GLU0j 263 " (cutoff:3.500A) Processing helix chain '0j' and resid 284 through 297 removed outlier: 4.097A pdb=" N ILE0j 295 " --> pdb=" O GLU0j 291 " (cutoff:3.500A) Processing helix chain '0k' and resid 11 through 36 removed outlier: 3.510A pdb=" N ARG0k 22 " --> pdb=" O GLN0k 18 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0k 25 " --> pdb=" O ASN0k 21 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS0k 26 " --> pdb=" O ARG0k 22 " (cutoff:3.500A) Processing helix chain '0k' and resid 49 through 60 removed outlier: 3.826A pdb=" N SER0k 56 " --> pdb=" O PHE0k 52 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS0k 58 " --> pdb=" O GLU0k 54 " (cutoff:3.500A) Processing helix chain '0k' and resid 130 through 154 removed outlier: 3.539A pdb=" N GLU0k 135 " --> pdb=" O THR0k 131 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU0k 136 " --> pdb=" O PRO0k 132 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE0k 137 " --> pdb=" O THR0k 133 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU0k 140 " --> pdb=" O LEU0k 136 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA0k 142 " --> pdb=" O ALA0k 138 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU0k 143 " --> pdb=" O ALA0k 139 " (cutoff:3.500A) Processing helix chain '0k' and resid 164 through 166 No H-bonds generated for 'chain '0k' and resid 164 through 166' Processing helix chain '0k' and resid 167 through 180 Processing helix chain '0k' and resid 192 through 194 No H-bonds generated for 'chain '0k' and resid 192 through 194' Processing helix chain '0k' and resid 206 through 226 removed outlier: 3.627A pdb=" N ASN0k 211 " --> pdb=" O VAL0k 207 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA0k 212 " --> pdb=" O ASP0k 208 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN0k 213 " --> pdb=" O LYS0k 209 " (cutoff:3.500A) Processing helix chain '0k' and resid 247 through 269 removed outlier: 3.653A pdb=" N GLU0k 251 " --> pdb=" O ASP0k 247 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL0k 256 " --> pdb=" O SER0k 252 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE0k 257 " --> pdb=" O SER0k 253 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU0k 258 " --> pdb=" O GLY0k 254 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS0k 259 " --> pdb=" O THR0k 255 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER0k 260 " --> pdb=" O VAL0k 256 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA0k 264 " --> pdb=" O SER0k 260 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS0k 267 " --> pdb=" O GLU0k 263 " (cutoff:3.500A) Processing helix chain '0k' and resid 284 through 297 removed outlier: 4.096A pdb=" N ILE0k 295 " --> pdb=" O GLU0k 291 " (cutoff:3.500A) Processing helix chain '0l' and resid 11 through 36 removed outlier: 3.509A pdb=" N ARG0l 22 " --> pdb=" O GLN0l 18 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0l 25 " --> pdb=" O ASN0l 21 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS0l 26 " --> pdb=" O ARG0l 22 " (cutoff:3.500A) Processing helix chain '0l' and resid 49 through 60 removed outlier: 3.826A pdb=" N SER0l 56 " --> pdb=" O PHE0l 52 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS0l 58 " --> pdb=" O GLU0l 54 " (cutoff:3.500A) Processing helix chain '0l' and resid 130 through 154 removed outlier: 3.540A pdb=" N GLU0l 135 " --> pdb=" O THR0l 131 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU0l 136 " --> pdb=" O PRO0l 132 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE0l 137 " --> pdb=" O THR0l 133 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU0l 140 " --> pdb=" O LEU0l 136 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA0l 142 " --> pdb=" O ALA0l 138 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU0l 143 " --> pdb=" O ALA0l 139 " (cutoff:3.500A) Processing helix chain '0l' and resid 164 through 166 No H-bonds generated for 'chain '0l' and resid 164 through 166' Processing helix chain '0l' and resid 167 through 180 Processing helix chain '0l' and resid 192 through 194 No H-bonds generated for 'chain '0l' and resid 192 through 194' Processing helix chain '0l' and resid 206 through 226 removed outlier: 3.628A pdb=" N ASN0l 211 " --> pdb=" O VAL0l 207 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA0l 212 " --> pdb=" O ASP0l 208 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN0l 213 " --> pdb=" O LYS0l 209 " (cutoff:3.500A) Processing helix chain '0l' and resid 247 through 269 removed outlier: 3.654A pdb=" N GLU0l 251 " --> pdb=" O ASP0l 247 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL0l 256 " --> pdb=" O SER0l 252 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE0l 257 " --> pdb=" O SER0l 253 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU0l 258 " --> pdb=" O GLY0l 254 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS0l 259 " --> pdb=" O THR0l 255 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER0l 260 " --> pdb=" O VAL0l 256 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA0l 264 " --> pdb=" O SER0l 260 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS0l 267 " --> pdb=" O GLU0l 263 " (cutoff:3.500A) Processing helix chain '0l' and resid 284 through 297 removed outlier: 4.097A pdb=" N ILE0l 295 " --> pdb=" O GLU0l 291 " (cutoff:3.500A) Processing helix chain '0A' and resid 8 through 16 removed outlier: 4.194A pdb=" N TRP0A 15 " --> pdb=" O TYR0A 11 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER0A 16 " --> pdb=" O ILE0A 12 " (cutoff:3.500A) Processing helix chain '0A' and resid 23 through 36 removed outlier: 3.693A pdb=" N GLY0A 31 " --> pdb=" O LYS0A 27 " (cutoff:3.500A) Proline residue: 0A 33 - end of helix Processing helix chain '0A' and resid 47 through 59 removed outlier: 3.776A pdb=" N ILE0A 56 " --> pdb=" O GLU0A 52 " (cutoff:3.500A) Processing helix chain '0A' and resid 68 through 96 removed outlier: 3.920A pdb=" N PHE0A 72 " --> pdb=" O THR0A 68 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS0A 73 " --> pdb=" O GLU0A 69 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE0A 74 " --> pdb=" O GLY0A 70 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU0A 77 " --> pdb=" O LYS0A 73 " (cutoff:3.500A) Proline residue: 0A 85 - end of helix removed outlier: 3.787A pdb=" N LYS0A 89 " --> pdb=" O PRO0A 85 " (cutoff:3.500A) Processing helix chain '0A' and resid 263 through 273 Processing helix chain '0A' and resid 276 through 284 Processing helix chain '0B' and resid 8 through 16 removed outlier: 4.194A pdb=" N TRP0B 15 " --> pdb=" O TYR0B 11 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER0B 16 " --> pdb=" O ILE0B 12 " (cutoff:3.500A) Processing helix chain '0B' and resid 23 through 36 removed outlier: 3.692A pdb=" N GLY0B 31 " --> pdb=" O LYS0B 27 " (cutoff:3.500A) Proline residue: 0B 33 - end of helix Processing helix chain '0B' and resid 47 through 59 removed outlier: 3.776A pdb=" N ILE0B 56 " --> pdb=" O GLU0B 52 " (cutoff:3.500A) Processing helix chain '0B' and resid 68 through 96 removed outlier: 3.920A pdb=" N PHE0B 72 " --> pdb=" O THR0B 68 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS0B 73 " --> pdb=" O GLU0B 69 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE0B 74 " --> pdb=" O GLY0B 70 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU0B 77 " --> pdb=" O LYS0B 73 " (cutoff:3.500A) Proline residue: 0B 85 - end of helix removed outlier: 3.786A pdb=" N LYS0B 89 " --> pdb=" O PRO0B 85 " (cutoff:3.500A) Processing helix chain '0B' and resid 263 through 273 Processing helix chain '0B' and resid 276 through 284 Processing helix chain '0C' and resid 8 through 16 removed outlier: 4.194A pdb=" N TRP0C 15 " --> pdb=" O TYR0C 11 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER0C 16 " --> pdb=" O ILE0C 12 " (cutoff:3.500A) Processing helix chain '0C' and resid 23 through 36 removed outlier: 3.693A pdb=" N GLY0C 31 " --> pdb=" O LYS0C 27 " (cutoff:3.500A) Proline residue: 0C 33 - end of helix Processing helix chain '0C' and resid 47 through 59 removed outlier: 3.777A pdb=" N ILE0C 56 " --> pdb=" O GLU0C 52 " (cutoff:3.500A) Processing helix chain '0C' and resid 68 through 96 removed outlier: 3.920A pdb=" N PHE0C 72 " --> pdb=" O THR0C 68 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS0C 73 " --> pdb=" O GLU0C 69 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE0C 74 " --> pdb=" O GLY0C 70 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU0C 77 " --> pdb=" O LYS0C 73 " (cutoff:3.500A) Proline residue: 0C 85 - end of helix removed outlier: 3.786A pdb=" N LYS0C 89 " --> pdb=" O PRO0C 85 " (cutoff:3.500A) Processing helix chain '0C' and resid 263 through 273 Processing helix chain '0C' and resid 276 through 284 Processing helix chain '0D' and resid 8 through 16 removed outlier: 4.193A pdb=" N TRP0D 15 " --> pdb=" O TYR0D 11 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER0D 16 " --> pdb=" O ILE0D 12 " (cutoff:3.500A) Processing helix chain '0D' and resid 23 through 36 removed outlier: 3.693A pdb=" N GLY0D 31 " --> pdb=" O LYS0D 27 " (cutoff:3.500A) Proline residue: 0D 33 - end of helix Processing helix chain '0D' and resid 47 through 59 removed outlier: 3.776A pdb=" N ILE0D 56 " --> pdb=" O GLU0D 52 " (cutoff:3.500A) Processing helix chain '0D' and resid 68 through 96 removed outlier: 3.920A pdb=" N PHE0D 72 " --> pdb=" O THR0D 68 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS0D 73 " --> pdb=" O GLU0D 69 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE0D 74 " --> pdb=" O GLY0D 70 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU0D 77 " --> pdb=" O LYS0D 73 " (cutoff:3.500A) Proline residue: 0D 85 - end of helix removed outlier: 3.786A pdb=" N LYS0D 89 " --> pdb=" O PRO0D 85 " (cutoff:3.500A) Processing helix chain '0D' and resid 263 through 273 Processing helix chain '0D' and resid 276 through 284 Processing helix chain '0E' and resid 8 through 16 removed outlier: 4.193A pdb=" N TRP0E 15 " --> pdb=" O TYR0E 11 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER0E 16 " --> pdb=" O ILE0E 12 " (cutoff:3.500A) Processing helix chain '0E' and resid 23 through 36 removed outlier: 3.693A pdb=" N GLY0E 31 " --> pdb=" O LYS0E 27 " (cutoff:3.500A) Proline residue: 0E 33 - end of helix Processing helix chain '0E' and resid 47 through 59 removed outlier: 3.776A pdb=" N ILE0E 56 " --> pdb=" O GLU0E 52 " (cutoff:3.500A) Processing helix chain '0E' and resid 68 through 96 removed outlier: 3.919A pdb=" N PHE0E 72 " --> pdb=" O THR0E 68 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS0E 73 " --> pdb=" O GLU0E 69 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE0E 74 " --> pdb=" O GLY0E 70 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU0E 77 " --> pdb=" O LYS0E 73 " (cutoff:3.500A) Proline residue: 0E 85 - end of helix removed outlier: 3.786A pdb=" N LYS0E 89 " --> pdb=" O PRO0E 85 " (cutoff:3.500A) Processing helix chain '0E' and resid 263 through 273 Processing helix chain '0E' and resid 276 through 284 Processing helix chain '0F' and resid 8 through 16 removed outlier: 4.194A pdb=" N TRP0F 15 " --> pdb=" O TYR0F 11 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER0F 16 " --> pdb=" O ILE0F 12 " (cutoff:3.500A) Processing helix chain '0F' and resid 23 through 36 removed outlier: 3.693A pdb=" N GLY0F 31 " --> pdb=" O LYS0F 27 " (cutoff:3.500A) Proline residue: 0F 33 - end of helix Processing helix chain '0F' and resid 47 through 59 removed outlier: 3.777A pdb=" N ILE0F 56 " --> pdb=" O GLU0F 52 " (cutoff:3.500A) Processing helix chain '0F' and resid 68 through 96 removed outlier: 3.920A pdb=" N PHE0F 72 " --> pdb=" O THR0F 68 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS0F 73 " --> pdb=" O GLU0F 69 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE0F 74 " --> pdb=" O GLY0F 70 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU0F 77 " --> pdb=" O LYS0F 73 " (cutoff:3.500A) Proline residue: 0F 85 - end of helix removed outlier: 3.786A pdb=" N LYS0F 89 " --> pdb=" O PRO0F 85 " (cutoff:3.500A) Processing helix chain '0F' and resid 263 through 273 Processing helix chain '0F' and resid 276 through 284 Processing helix chain '0G' and resid 8 through 16 removed outlier: 4.193A pdb=" N TRP0G 15 " --> pdb=" O TYR0G 11 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER0G 16 " --> pdb=" O ILE0G 12 " (cutoff:3.500A) Processing helix chain '0G' and resid 23 through 36 removed outlier: 3.693A pdb=" N GLY0G 31 " --> pdb=" O LYS0G 27 " (cutoff:3.500A) Proline residue: 0G 33 - end of helix Processing helix chain '0G' and resid 47 through 59 removed outlier: 3.776A pdb=" N ILE0G 56 " --> pdb=" O GLU0G 52 " (cutoff:3.500A) Processing helix chain '0G' and resid 68 through 96 removed outlier: 3.919A pdb=" N PHE0G 72 " --> pdb=" O THR0G 68 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS0G 73 " --> pdb=" O GLU0G 69 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE0G 74 " --> pdb=" O GLY0G 70 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU0G 77 " --> pdb=" O LYS0G 73 " (cutoff:3.500A) Proline residue: 0G 85 - end of helix removed outlier: 3.787A pdb=" N LYS0G 89 " --> pdb=" O PRO0G 85 " (cutoff:3.500A) Processing helix chain '0G' and resid 263 through 273 Processing helix chain '0G' and resid 276 through 284 Processing helix chain '0H' and resid 8 through 16 removed outlier: 4.194A pdb=" N TRP0H 15 " --> pdb=" O TYR0H 11 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER0H 16 " --> pdb=" O ILE0H 12 " (cutoff:3.500A) Processing helix chain '0H' and resid 23 through 36 removed outlier: 3.693A pdb=" N GLY0H 31 " --> pdb=" O LYS0H 27 " (cutoff:3.500A) Proline residue: 0H 33 - end of helix Processing helix chain '0H' and resid 47 through 59 removed outlier: 3.776A pdb=" N ILE0H 56 " --> pdb=" O GLU0H 52 " (cutoff:3.500A) Processing helix chain '0H' and resid 68 through 96 removed outlier: 3.919A pdb=" N PHE0H 72 " --> pdb=" O THR0H 68 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS0H 73 " --> pdb=" O GLU0H 69 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE0H 74 " --> pdb=" O GLY0H 70 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU0H 77 " --> pdb=" O LYS0H 73 " (cutoff:3.500A) Proline residue: 0H 85 - end of helix removed outlier: 3.787A pdb=" N LYS0H 89 " --> pdb=" O PRO0H 85 " (cutoff:3.500A) Processing helix chain '0H' and resid 263 through 273 Processing helix chain '0H' and resid 276 through 284 Processing helix chain '0I' and resid 8 through 16 removed outlier: 4.194A pdb=" N TRP0I 15 " --> pdb=" O TYR0I 11 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER0I 16 " --> pdb=" O ILE0I 12 " (cutoff:3.500A) Processing helix chain '0I' and resid 23 through 36 removed outlier: 3.693A pdb=" N GLY0I 31 " --> pdb=" O LYS0I 27 " (cutoff:3.500A) Proline residue: 0I 33 - end of helix Processing helix chain '0I' and resid 47 through 59 removed outlier: 3.776A pdb=" N ILE0I 56 " --> pdb=" O GLU0I 52 " (cutoff:3.500A) Processing helix chain '0I' and resid 68 through 96 removed outlier: 3.919A pdb=" N PHE0I 72 " --> pdb=" O THR0I 68 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS0I 73 " --> pdb=" O GLU0I 69 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE0I 74 " --> pdb=" O GLY0I 70 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU0I 77 " --> pdb=" O LYS0I 73 " (cutoff:3.500A) Proline residue: 0I 85 - end of helix removed outlier: 3.787A pdb=" N LYS0I 89 " --> pdb=" O PRO0I 85 " (cutoff:3.500A) Processing helix chain '0I' and resid 263 through 273 Processing helix chain '0I' and resid 276 through 284 Processing helix chain '0J' and resid 8 through 16 removed outlier: 4.194A pdb=" N TRP0J 15 " --> pdb=" O TYR0J 11 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER0J 16 " --> pdb=" O ILE0J 12 " (cutoff:3.500A) Processing helix chain '0J' and resid 23 through 36 removed outlier: 3.693A pdb=" N GLY0J 31 " --> pdb=" O LYS0J 27 " (cutoff:3.500A) Proline residue: 0J 33 - end of helix Processing helix chain '0J' and resid 47 through 59 removed outlier: 3.776A pdb=" N ILE0J 56 " --> pdb=" O GLU0J 52 " (cutoff:3.500A) Processing helix chain '0J' and resid 68 through 96 removed outlier: 3.919A pdb=" N PHE0J 72 " --> pdb=" O THR0J 68 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS0J 73 " --> pdb=" O GLU0J 69 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE0J 74 " --> pdb=" O GLY0J 70 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU0J 77 " --> pdb=" O LYS0J 73 " (cutoff:3.500A) Proline residue: 0J 85 - end of helix removed outlier: 3.786A pdb=" N LYS0J 89 " --> pdb=" O PRO0J 85 " (cutoff:3.500A) Processing helix chain '0J' and resid 263 through 273 Processing helix chain '0J' and resid 276 through 284 Processing helix chain '0K' and resid 8 through 16 removed outlier: 4.194A pdb=" N TRP0K 15 " --> pdb=" O TYR0K 11 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER0K 16 " --> pdb=" O ILE0K 12 " (cutoff:3.500A) Processing helix chain '0K' and resid 23 through 36 removed outlier: 3.693A pdb=" N GLY0K 31 " --> pdb=" O LYS0K 27 " (cutoff:3.500A) Proline residue: 0K 33 - end of helix Processing helix chain '0K' and resid 47 through 59 removed outlier: 3.777A pdb=" N ILE0K 56 " --> pdb=" O GLU0K 52 " (cutoff:3.500A) Processing helix chain '0K' and resid 68 through 96 removed outlier: 3.920A pdb=" N PHE0K 72 " --> pdb=" O THR0K 68 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS0K 73 " --> pdb=" O GLU0K 69 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE0K 74 " --> pdb=" O GLY0K 70 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU0K 77 " --> pdb=" O LYS0K 73 " (cutoff:3.500A) Proline residue: 0K 85 - end of helix removed outlier: 3.787A pdb=" N LYS0K 89 " --> pdb=" O PRO0K 85 " (cutoff:3.500A) Processing helix chain '0K' and resid 263 through 273 Processing helix chain '0K' and resid 276 through 284 Processing helix chain '0L' and resid 8 through 16 removed outlier: 4.194A pdb=" N TRP0L 15 " --> pdb=" O TYR0L 11 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER0L 16 " --> pdb=" O ILE0L 12 " (cutoff:3.500A) Processing helix chain '0L' and resid 23 through 36 removed outlier: 3.693A pdb=" N GLY0L 31 " --> pdb=" O LYS0L 27 " (cutoff:3.500A) Proline residue: 0L 33 - end of helix Processing helix chain '0L' and resid 47 through 59 removed outlier: 3.777A pdb=" N ILE0L 56 " --> pdb=" O GLU0L 52 " (cutoff:3.500A) Processing helix chain '0L' and resid 68 through 96 removed outlier: 3.920A pdb=" N PHE0L 72 " --> pdb=" O THR0L 68 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS0L 73 " --> pdb=" O GLU0L 69 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE0L 74 " --> pdb=" O GLY0L 70 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU0L 77 " --> pdb=" O LYS0L 73 " (cutoff:3.500A) Proline residue: 0L 85 - end of helix removed outlier: 3.787A pdb=" N LYS0L 89 " --> pdb=" O PRO0L 85 " (cutoff:3.500A) Processing helix chain '0L' and resid 263 through 273 Processing helix chain '0L' and resid 276 through 284 Processing helix chain 'A' and resid 31 through 61 removed outlier: 3.633A pdb=" N LEU A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'B' and resid 34 through 68 Processing helix chain 'C' and resid 34 through 65 removed outlier: 3.576A pdb=" N VAL C 52 " --> pdb=" O GLU C 48 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN C 54 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 72 removed outlier: 3.519A pdb=" N LEU C 72 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 61 removed outlier: 3.584A pdb=" N LEU D 35 " --> pdb=" O GLU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 68 Processing helix chain 'E' and resid 34 through 68 Processing helix chain 'F' and resid 34 through 65 removed outlier: 3.576A pdb=" N VAL F 52 " --> pdb=" O GLU F 48 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR F 53 " --> pdb=" O ILE F 49 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN F 54 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU F 55 " --> pdb=" O LYS F 51 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL F 63 " --> pdb=" O GLU F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 72 removed outlier: 3.518A pdb=" N LEU F 72 " --> pdb=" O ASN F 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 61 removed outlier: 3.528A pdb=" N LEU G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 68 Processing helix chain 'H' and resid 34 through 68 Processing helix chain 'I' and resid 34 through 65 removed outlier: 3.576A pdb=" N VAL I 52 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR I 53 " --> pdb=" O ILE I 49 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN I 54 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL I 63 " --> pdb=" O GLU I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 72 removed outlier: 3.520A pdb=" N LEU I 72 " --> pdb=" O ASN I 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 61 removed outlier: 3.556A pdb=" N LEU J 35 " --> pdb=" O GLU J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 68 Processing helix chain 'K' and resid 34 through 68 Processing helix chain 'L' and resid 34 through 65 removed outlier: 3.576A pdb=" N VAL L 52 " --> pdb=" O GLU L 48 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR L 53 " --> pdb=" O ILE L 49 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN L 54 " --> pdb=" O GLY L 50 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU L 55 " --> pdb=" O LYS L 51 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL L 63 " --> pdb=" O GLU L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 72 removed outlier: 3.519A pdb=" N LEU L 72 " --> pdb=" O ASN L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 61 removed outlier: 3.594A pdb=" N LEU M 35 " --> pdb=" O GLU M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 68 Processing helix chain 'N' and resid 34 through 68 Processing helix chain 'O' and resid 34 through 65 removed outlier: 3.575A pdb=" N VAL O 52 " --> pdb=" O GLU O 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR O 53 " --> pdb=" O ILE O 49 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN O 54 " --> pdb=" O GLY O 50 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU O 55 " --> pdb=" O LYS O 51 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL O 63 " --> pdb=" O GLU O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 72 removed outlier: 3.519A pdb=" N LEU O 72 " --> pdb=" O ASN O 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 31 through 61 removed outlier: 3.590A pdb=" N LEU P 35 " --> pdb=" O GLU P 31 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 68 Processing helix chain 'Q' and resid 34 through 68 Processing helix chain 'R' and resid 34 through 65 removed outlier: 3.576A pdb=" N VAL R 52 " --> pdb=" O GLU R 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR R 53 " --> pdb=" O ILE R 49 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU R 55 " --> pdb=" O LYS R 51 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL R 63 " --> pdb=" O GLU R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 72 removed outlier: 3.519A pdb=" N LEU R 72 " --> pdb=" O ASN R 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 31 through 61 removed outlier: 3.592A pdb=" N LEU S 35 " --> pdb=" O GLU S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 68 Processing helix chain 'T' and resid 34 through 68 Processing helix chain 'U' and resid 34 through 65 removed outlier: 3.576A pdb=" N VAL U 52 " --> pdb=" O GLU U 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR U 53 " --> pdb=" O ILE U 49 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN U 54 " --> pdb=" O GLY U 50 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU U 55 " --> pdb=" O LYS U 51 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL U 63 " --> pdb=" O GLU U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 72 removed outlier: 3.519A pdb=" N LEU U 72 " --> pdb=" O ASN U 69 " (cutoff:3.500A) Processing helix chain 'V' and resid 31 through 61 removed outlier: 3.590A pdb=" N LEU V 35 " --> pdb=" O GLU V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 62 through 68 Processing helix chain 'W' and resid 34 through 68 Processing helix chain 'X' and resid 34 through 65 removed outlier: 3.576A pdb=" N VAL X 52 " --> pdb=" O GLU X 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR X 53 " --> pdb=" O ILE X 49 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN X 54 " --> pdb=" O GLY X 50 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU X 55 " --> pdb=" O LYS X 51 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL X 63 " --> pdb=" O GLU X 59 " (cutoff:3.500A) Processing helix chain 'X' and resid 68 through 72 removed outlier: 3.519A pdb=" N LEU X 72 " --> pdb=" O ASN X 69 " (cutoff:3.500A) Processing helix chain 'Y' and resid 31 through 61 removed outlier: 3.598A pdb=" N LEU Y 35 " --> pdb=" O GLU Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 62 through 68 Processing helix chain 'Z' and resid 34 through 68 Processing helix chain 'a' and resid 34 through 65 removed outlier: 3.576A pdb=" N VAL a 52 " --> pdb=" O GLU a 48 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR a 53 " --> pdb=" O ILE a 49 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN a 54 " --> pdb=" O GLY a 50 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU a 55 " --> pdb=" O LYS a 51 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL a 63 " --> pdb=" O GLU a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 68 through 72 removed outlier: 3.519A pdb=" N LEU a 72 " --> pdb=" O ASN a 69 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 61 removed outlier: 3.567A pdb=" N LEU b 35 " --> pdb=" O GLU b 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 62 through 68 Processing helix chain 'c' and resid 34 through 68 Processing helix chain 'd' and resid 34 through 65 removed outlier: 3.576A pdb=" N VAL d 52 " --> pdb=" O GLU d 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR d 53 " --> pdb=" O ILE d 49 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN d 54 " --> pdb=" O GLY d 50 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU d 55 " --> pdb=" O LYS d 51 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL d 63 " --> pdb=" O GLU d 59 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 72 removed outlier: 3.518A pdb=" N LEU d 72 " --> pdb=" O ASN d 69 " (cutoff:3.500A) Processing helix chain 'e' and resid 31 through 61 removed outlier: 3.656A pdb=" N LEU e 35 " --> pdb=" O GLU e 31 " (cutoff:3.500A) Processing helix chain 'e' and resid 62 through 68 Processing helix chain 'f' and resid 34 through 68 Processing helix chain 'g' and resid 34 through 65 removed outlier: 3.576A pdb=" N VAL g 52 " --> pdb=" O GLU g 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR g 53 " --> pdb=" O ILE g 49 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN g 54 " --> pdb=" O GLY g 50 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU g 55 " --> pdb=" O LYS g 51 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL g 63 " --> pdb=" O GLU g 59 " (cutoff:3.500A) Processing helix chain 'g' and resid 68 through 72 removed outlier: 3.519A pdb=" N LEU g 72 " --> pdb=" O ASN g 69 " (cutoff:3.500A) Processing helix chain 'h' and resid 31 through 61 removed outlier: 3.540A pdb=" N LEU h 35 " --> pdb=" O GLU h 31 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 68 Processing helix chain 'i' and resid 34 through 68 Processing helix chain 'j' and resid 34 through 65 removed outlier: 3.576A pdb=" N VAL j 52 " --> pdb=" O GLU j 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR j 53 " --> pdb=" O ILE j 49 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN j 54 " --> pdb=" O GLY j 50 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU j 55 " --> pdb=" O LYS j 51 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL j 63 " --> pdb=" O GLU j 59 " (cutoff:3.500A) Processing helix chain 'j' and resid 68 through 72 removed outlier: 3.519A pdb=" N LEU j 72 " --> pdb=" O ASN j 69 " (cutoff:3.500A) 2568 hydrogen bonds defined for protein. 7668 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 18.48 Time building geometry restraints manager: 24.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 22326 1.33 - 1.45: 13796 1.45 - 1.57: 36262 1.57 - 1.69: 0 1.69 - 1.81: 576 Bond restraints: 72960 Sorted by residual: bond pdb=" CB PHE0k 24 " pdb=" CG PHE0k 24 " ideal model delta sigma weight residual 1.502 1.431 0.071 2.30e-02 1.89e+03 9.51e+00 bond pdb=" CB PHE0b 24 " pdb=" CG PHE0b 24 " ideal model delta sigma weight residual 1.502 1.431 0.071 2.30e-02 1.89e+03 9.50e+00 bond pdb=" CB PHE0j 24 " pdb=" CG PHE0j 24 " ideal model delta sigma weight residual 1.502 1.431 0.071 2.30e-02 1.89e+03 9.47e+00 bond pdb=" CB PHE0f 24 " pdb=" CG PHE0f 24 " ideal model delta sigma weight residual 1.502 1.432 0.070 2.30e-02 1.89e+03 9.38e+00 bond pdb=" CB PHE0l 24 " pdb=" CG PHE0l 24 " ideal model delta sigma weight residual 1.502 1.432 0.070 2.30e-02 1.89e+03 9.35e+00 ... (remaining 72955 not shown) Histogram of bond angle deviations from ideal: 98.94 - 105.97: 1112 105.97 - 113.01: 38996 113.01 - 120.04: 27210 120.04 - 127.08: 30648 127.08 - 134.12: 674 Bond angle restraints: 98640 Sorted by residual: angle pdb=" C ASP P 30 " pdb=" N GLU P 31 " pdb=" CA GLU P 31 " ideal model delta sigma weight residual 121.54 129.66 -8.12 1.91e+00 2.74e-01 1.81e+01 angle pdb=" C ASP e 30 " pdb=" N GLU e 31 " pdb=" CA GLU e 31 " ideal model delta sigma weight residual 121.54 129.32 -7.78 1.91e+00 2.74e-01 1.66e+01 angle pdb=" C PHE b 29 " pdb=" N ASP b 30 " pdb=" CA ASP b 30 " ideal model delta sigma weight residual 121.90 116.78 5.12 1.26e+00 6.30e-01 1.65e+01 angle pdb=" C SER0C 3 " pdb=" N TYR0C 4 " pdb=" CA TYR0C 4 " ideal model delta sigma weight residual 121.54 129.28 -7.74 1.91e+00 2.74e-01 1.64e+01 angle pdb=" C SER0A 3 " pdb=" N TYR0A 4 " pdb=" CA TYR0A 4 " ideal model delta sigma weight residual 121.54 129.28 -7.74 1.91e+00 2.74e-01 1.64e+01 ... (remaining 98635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.74: 37972 10.74 - 21.49: 4872 21.49 - 32.23: 699 32.23 - 42.98: 329 42.98 - 53.72: 120 Dihedral angle restraints: 43992 sinusoidal: 17748 harmonic: 26244 Sorted by residual: dihedral pdb=" CA LEU0F 176 " pdb=" C LEU0F 176 " pdb=" N GLN0F 177 " pdb=" CA GLN0F 177 " ideal model delta harmonic sigma weight residual 180.00 -130.62 -49.38 0 5.00e+00 4.00e-02 9.75e+01 dihedral pdb=" CA LEU0E 176 " pdb=" C LEU0E 176 " pdb=" N GLN0E 177 " pdb=" CA GLN0E 177 " ideal model delta harmonic sigma weight residual -180.00 -130.63 -49.37 0 5.00e+00 4.00e-02 9.75e+01 dihedral pdb=" CA LEU0J 176 " pdb=" C LEU0J 176 " pdb=" N GLN0J 177 " pdb=" CA GLN0J 177 " ideal model delta harmonic sigma weight residual -180.00 -130.64 -49.36 0 5.00e+00 4.00e-02 9.75e+01 ... (remaining 43989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 6863 0.048 - 0.095: 2940 0.095 - 0.143: 778 0.143 - 0.190: 194 0.190 - 0.238: 49 Chirality restraints: 10824 Sorted by residual: chirality pdb=" CB THR0I 136 " pdb=" CA THR0I 136 " pdb=" OG1 THR0I 136 " pdb=" CG2 THR0I 136 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB THR0G 136 " pdb=" CA THR0G 136 " pdb=" OG1 THR0G 136 " pdb=" CG2 THR0G 136 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB THR0A 136 " pdb=" CA THR0A 136 " pdb=" OG1 THR0A 136 " pdb=" CG2 THR0A 136 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 10821 not shown) Planarity restraints: 12816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU K 20 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.33e+00 pdb=" C LEU K 20 " -0.053 2.00e-02 2.50e+03 pdb=" O LEU K 20 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR K 21 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU N 20 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.20e+00 pdb=" C LEU N 20 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU N 20 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR N 21 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU H 20 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C LEU H 20 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU H 20 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR H 21 " 0.018 2.00e-02 2.50e+03 ... (remaining 12813 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 3705 2.69 - 3.25: 72595 3.25 - 3.80: 120164 3.80 - 4.35: 154964 4.35 - 4.90: 247872 Nonbonded interactions: 599300 Sorted by model distance: nonbonded pdb=" OH TYR K 21 " pdb=" O GLU L 31 " model vdw 2.143 2.440 nonbonded pdb=" O ASP0B 127 " pdb=" OG1 THR0C 234 " model vdw 2.144 2.440 nonbonded pdb=" OH TYR f 21 " pdb=" O GLU g 31 " model vdw 2.154 2.440 nonbonded pdb=" OG SER0C 155 " pdb=" OG SER0D 207 " model vdw 2.155 2.440 nonbonded pdb=" OG1 THR0E 147 " pdb=" O ASN0F 215 " model vdw 2.158 2.440 ... (remaining 599295 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 '0A' selection = chain '0B' selection = chain '0C' selection = chain '0D' selection = chain '0E' selection = chain '0F' selection = chain '0G' selection = chain '0H' selection = chain '0I' selection = chain '0J' selection = chain '0K' selection = chain '0L' } ncs_group { reference = chain '0a' selection = chain '0b' selection = chain '0c' selection = chain '0d' selection = chain '0e' selection = chain '0f' selection = chain '0g' selection = chain '0h' selection = chain '0i' selection = chain '0j' selection = chain '0k' selection = chain '0l' } ncs_group { reference = (chain 'A' and resid 21 through 70) selection = (chain 'B' and resid 21 through 70) selection = (chain 'D' and resid 21 through 70) selection = (chain 'E' and resid 21 through 70) selection = (chain 'G' and resid 21 through 70) selection = (chain 'H' and resid 21 through 70) selection = (chain 'J' and resid 21 through 70) selection = (chain 'K' and resid 21 through 70) selection = (chain 'M' and resid 21 through 70) selection = (chain 'N' and resid 21 through 70) selection = (chain 'P' and resid 21 through 70) selection = (chain 'Q' and resid 21 through 70) selection = (chain 'S' and resid 21 through 70) selection = (chain 'T' and resid 21 through 70) selection = (chain 'V' and resid 21 through 70) selection = (chain 'W' and resid 21 through 70) selection = (chain 'Y' and resid 21 through 70) selection = (chain 'Z' and resid 21 through 70) selection = (chain 'b' and resid 21 through 70) selection = (chain 'c' and resid 21 through 70) selection = (chain 'e' and resid 21 through 70) selection = (chain 'f' and resid 21 through 70) selection = (chain 'h' and resid 21 through 70) selection = (chain 'i' and resid 21 through 70) } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' selection = chain 'a' selection = chain 'd' selection = chain 'g' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 300 5.16 5 C 45264 2.51 5 N 11904 2.21 5 O 14160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 35.240 Check model and map are aligned: 0.850 Convert atoms to be neutral: 0.460 Process input model: 135.000 Find NCS groups from input model: 4.420 Set up NCS constraints: 0.710 Set refine NCS operators: 0.000 Set scattering table: 0.050 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:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 184.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 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 : 0.010 0.085 72960 Z= 0.646 Angle : 1.065 9.445 98640 Z= 0.595 Chirality : 0.057 0.238 10824 Planarity : 0.006 0.051 12816 Dihedral : 10.175 53.720 27000 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.83 % Favored : 90.13 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -4.87 (0.07), residues: 8736 helix: -2.86 (0.06), residues: 3576 sheet: -4.25 (0.08), residues: 1788 loop : -2.71 (0.10), residues: 3372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4061 residues out of total 8136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 4049 time to evaluate : 6.550 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 outliers start: 12 outliers final: 6 residues processed: 4061 average time/residue: 0.6948 time to fit residues: 4663.9009 Evaluate side-chains 3342 residues out of total 8136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 3336 time to evaluate : 6.546 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.5075 time to fit residues: 14.8493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 739 optimal weight: 0.6980 chunk 663 optimal weight: 0.6980 chunk 368 optimal weight: 2.9990 chunk 226 optimal weight: 0.9980 chunk 447 optimal weight: 0.8980 chunk 354 optimal weight: 0.9980 chunk 686 optimal weight: 0.7980 chunk 265 optimal weight: 1.9990 chunk 417 optimal weight: 0.4980 chunk 511 optimal weight: 0.8980 chunk 795 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 151 ASN ** 0a 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 211 ASN 0a 275 ASN ** 0b 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 32 GLN 0b 151 ASN ** 0b 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 13 ASN 0c 32 GLN 0c 58 HIS 0c 151 ASN 0c 176 ASN 0c 215 ASN 0c 219 ASN 0d 32 GLN 0d 151 ASN ** 0d 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 32 GLN 0e 58 HIS 0e 215 ASN 0e 269 ASN 0f 32 GLN 0f 151 ASN ** 0f 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 269 ASN 0f 275 ASN 0g 151 ASN 0h 13 ASN 0h 151 ASN ** 0h 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 151 ASN 0j 32 GLN ** 0j 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 215 ASN 0j 275 ASN 0k 13 ASN 0k 32 GLN 0k 58 HIS 0l 32 GLN 0l 58 HIS 0l 211 ASN ** 0A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0A 162 ASN 0A 192 GLN 0B 75 HIS ** 0B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0B 162 ASN 0B 192 GLN 0B 279 GLN ** 0C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0C 75 HIS ** 0C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0C 162 ASN 0C 192 GLN 0C 196 HIS ** 0D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0D 162 ASN 0D 192 GLN ** 0D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0E 162 ASN 0E 192 GLN 0E 196 HIS 0E 279 GLN ** 0F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0F 75 HIS ** 0F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0F 162 ASN 0F 192 GLN ** 0G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0G 162 ASN ** 0G 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0G 237 ASN 0H 17 GLN ** 0H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0H 162 ASN 0H 192 GLN 0H 237 ASN 0I 17 GLN ** 0I 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0I 162 ASN 0I 192 GLN 0I 279 GLN 0J 17 GLN 0J 126 GLN 0J 162 ASN 0J 192 GLN ** 0K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0K 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0K 162 ASN 0K 192 GLN 0K 279 GLN ** 0K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0L 17 GLN ** 0L 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0L 162 ASN ** 0L 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0L 196 HIS 0L 237 ASN A 54 ASN B 40 ASN C 61 ASN D 40 ASN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** G 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 ASN J 44 HIS J 54 ASN K 40 ASN M 44 HIS ** M 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 ASN N 40 ASN ** O 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 ASN ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 54 ASN Y 54 ASN Z 40 ASN b 54 ASN c 40 ASN d 61 ASN f 40 ASN h 40 ASN ** h 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 72960 Z= 0.255 Angle : 0.739 9.336 98640 Z= 0.399 Chirality : 0.044 0.321 10824 Planarity : 0.005 0.109 12816 Dihedral : 6.193 33.214 9588 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer Outliers : 4.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -3.30 (0.08), residues: 8736 helix: -1.01 (0.08), residues: 3888 sheet: -3.95 (0.09), residues: 1800 loop : -2.33 (0.11), residues: 3048 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3953 residues out of total 8136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 378 poor density : 3575 time to evaluate : 6.489 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: 378 outliers final: 220 residues processed: 3726 average time/residue: 0.6939 time to fit residues: 4291.6229 Evaluate side-chains 3490 residues out of total 8136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 3270 time to evaluate : 6.976 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 220 outliers final: 4 residues processed: 220 average time/residue: 0.5781 time to fit residues: 242.5537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 442 optimal weight: 0.8980 chunk 246 optimal weight: 4.9990 chunk 662 optimal weight: 0.6980 chunk 541 optimal weight: 0.7980 chunk 219 optimal weight: 0.9990 chunk 796 optimal weight: 1.9990 chunk 860 optimal weight: 3.9990 chunk 709 optimal weight: 1.9990 chunk 790 optimal weight: 6.9990 chunk 271 optimal weight: 1.9990 chunk 639 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 32 GLN 0c 13 ASN 0c 32 GLN 0d 26 HIS 0d 32 GLN ** 0d 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 269 ASN 0e 58 HIS 0f 26 HIS ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 13 ASN ** 0h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 58 HIS 0i 32 GLN 0i 58 HIS ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 32 GLN ** 0j 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 13 ASN 0k 32 GLN 0k 176 ASN 0l 26 HIS ** 0l 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0B 192 GLN ** 0B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0E 245 ASN ** 0F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0G 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0G 279 GLN ** 0H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0H 237 ASN ** 0I 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0I 192 GLN 0J 192 GLN 0J 279 GLN ** 0K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0K 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0L 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0L 261 GLN ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 54 ASN K 40 ASN ** M 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 ASN ** O 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 54 ASN ** d 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 61 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 72960 Z= 0.292 Angle : 0.728 11.324 98640 Z= 0.388 Chirality : 0.044 0.364 10824 Planarity : 0.005 0.126 12816 Dihedral : 5.923 31.405 9588 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 23.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer Outliers : 3.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.09), residues: 8736 helix: -0.53 (0.08), residues: 3984 sheet: -3.79 (0.09), residues: 1788 loop : -2.17 (0.12), residues: 2964 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3718 residues out of total 8136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 3436 time to evaluate : 6.391 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 outliers start: 282 outliers final: 151 residues processed: 3529 average time/residue: 0.7152 time to fit residues: 4215.1245 Evaluate side-chains 3426 residues out of total 8136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 3275 time to evaluate : 6.535 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 151 outliers final: 1 residues processed: 151 average time/residue: 0.5512 time to fit residues: 164.5558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 787 optimal weight: 0.8980 chunk 599 optimal weight: 0.3980 chunk 413 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 380 optimal weight: 1.9990 chunk 535 optimal weight: 0.9990 chunk 799 optimal weight: 7.9990 chunk 846 optimal weight: 0.7980 chunk 417 optimal weight: 0.9990 chunk 758 optimal weight: 0.0370 chunk 228 optimal weight: 3.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 26 HIS ** 0b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 13 ASN 0c 32 GLN ** 0c 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 58 HIS 0d 176 ASN ** 0e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 58 HIS ** 0f 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 32 GLN ** 0g 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 219 ASN 0h 26 HIS ** 0h 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 152 GLN ** 0i 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 173 GLN 0j 176 ASN ** 0j 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 58 HIS 0k 59 GLN 0k 249 GLN ** 0l 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0B 126 GLN ** 0C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0C 261 GLN ** 0D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0D 103 ASN 0D 126 GLN ** 0E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0G 126 GLN 0G 237 ASN ** 0G 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0G 279 GLN ** 0H 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0H 126 GLN 0H 279 GLN ** 0I 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0K 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0K 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0L 126 GLN A 54 ASN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN E 40 ASN ** G 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 54 ASN H 40 ASN ** J 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN ** M 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 ASN ** O 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 61 ASN Z 40 ASN ** a 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 54 ASN ** c 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 61 ASN h 40 ASN ** h 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 72960 Z= 0.230 Angle : 0.705 12.132 98640 Z= 0.371 Chirality : 0.044 0.409 10824 Planarity : 0.005 0.097 12816 Dihedral : 5.643 27.699 9588 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer Outliers : 3.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.09), residues: 8736 helix: -0.25 (0.08), residues: 3936 sheet: -3.57 (0.09), residues: 1848 loop : -1.75 (0.12), residues: 2952 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3654 residues out of total 8136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 3384 time to evaluate : 6.605 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 outliers start: 270 outliers final: 145 residues processed: 3460 average time/residue: 0.6938 time to fit residues: 3998.2189 Evaluate side-chains 3382 residues out of total 8136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 3237 time to evaluate : 6.556 Switching outliers to nearest non-outliers outliers start: 145 outliers final: 0 residues processed: 145 average time/residue: 0.5683 time to fit residues: 158.2951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 705 optimal weight: 4.9990 chunk 480 optimal weight: 0.0170 chunk 12 optimal weight: 3.9990 chunk 630 optimal weight: 0.6980 chunk 349 optimal weight: 3.9990 chunk 722 optimal weight: 0.9990 chunk 585 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 432 optimal weight: 1.9990 chunk 760 optimal weight: 0.8980 chunk 213 optimal weight: 0.9990 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0a 26 HIS 0a 32 GLN ** 0a 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 13 ASN 0c 26 HIS ** 0c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 58 HIS 0e 151 ASN 0e 211 ASN ** 0e 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 269 ASN ** 0f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 151 ASN 0f 211 ASN 0f 249 GLN ** 0f 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 176 ASN 0h 58 HIS ** 0j 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 249 GLN ** 0k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 58 HIS 0k 151 ASN ** 0k 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 211 ASN ** 0k 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 26 HIS ** 0l 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0D 75 HIS 0D 103 ASN ** 0E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0F 75 HIS ** 0F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0F 237 ASN ** 0F 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0G 58 ASN ** 0G 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0G 279 GLN 0H 58 ASN ** 0H 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0I 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0I 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0J 103 ASN ** 0K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0K 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0K 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0L 126 GLN ** 0L 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 54 ASN L 47 ASN M 54 ASN ** P 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 ASN ** S 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 54 ASN ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 54 ASN ** X 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 54 ASN e 61 ASN f 40 ASN i 40 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.089 72960 Z= 0.252 Angle : 0.722 16.094 98640 Z= 0.377 Chirality : 0.044 0.245 10824 Planarity : 0.005 0.151 12816 Dihedral : 5.560 27.799 9588 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 23.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.09), residues: 8736 helix: -0.04 (0.08), residues: 3912 sheet: -3.48 (0.10), residues: 1824 loop : -1.71 (0.12), residues: 3000 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3508 residues out of total 8136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 3301 time to evaluate : 6.572 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 outliers start: 207 outliers final: 107 residues processed: 3357 average time/residue: 0.6883 time to fit residues: 3845.1698 Evaluate side-chains 3293 residues out of total 8136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 3186 time to evaluate : 6.561 Switching outliers to nearest non-outliers outliers start: 107 outliers final: 0 residues processed: 107 average time/residue: 0.5468 time to fit residues: 116.4196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 284 optimal weight: 0.7980 chunk 762 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 497 optimal weight: 0.0980 chunk 209 optimal weight: 0.9990 chunk 847 optimal weight: 5.9990 chunk 703 optimal weight: 0.7980 chunk 392 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 280 optimal weight: 2.9990 chunk 444 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0a 32 GLN ** 0a 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 59 GLN 0c 13 ASN ** 0c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 26 HIS 0e 58 HIS ** 0e 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 151 ASN ** 0f 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 173 GLN 0k 249 GLN ** 0l 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0F 75 HIS ** 0F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0F 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0G 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0G 279 GLN 0H 7 GLN 0H 261 GLN 0I 237 ASN ** 0I 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0J 126 GLN 0J 237 ASN ** 0K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0K 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0K 286 GLN ** 0L 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN ** G 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 ASN ** M 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 ASN N 40 ASN ** P 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 ASN ** S 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 40 ASN V 54 ASN Y 54 ASN b 54 ASN d 47 ASN e 54 ASN e 61 ASN i 40 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 72960 Z= 0.231 Angle : 0.730 13.168 98640 Z= 0.379 Chirality : 0.044 0.334 10824 Planarity : 0.004 0.073 12816 Dihedral : 5.441 25.938 9588 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 23.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.09), residues: 8736 helix: 0.04 (0.08), residues: 3924 sheet: -3.42 (0.10), residues: 1608 loop : -1.72 (0.12), residues: 3204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3477 residues out of total 8136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 3285 time to evaluate : 6.662 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 outliers start: 192 outliers final: 108 residues processed: 3329 average time/residue: 0.6928 time to fit residues: 3834.7821 Evaluate side-chains 3273 residues out of total 8136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 3165 time to evaluate : 6.499 Switching outliers to nearest non-outliers outliers start: 108 outliers final: 0 residues processed: 108 average time/residue: 0.5657 time to fit residues: 120.5089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 817 optimal weight: 0.0570 chunk 95 optimal weight: 5.9990 chunk 482 optimal weight: 0.9990 chunk 618 optimal weight: 3.9990 chunk 479 optimal weight: 0.8980 chunk 713 optimal weight: 1.9990 chunk 473 optimal weight: 3.9990 chunk 844 optimal weight: 0.4980 chunk 528 optimal weight: 3.9990 chunk 514 optimal weight: 2.9990 chunk 389 optimal weight: 0.8980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0c 13 ASN ** 0c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 153 ASN ** 0d 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 37 GLN ** 0d 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 58 HIS ** 0e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 211 ASN 0e 215 ASN ** 0e 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 151 ASN ** 0f 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 211 ASN ** 0f 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 211 ASN 0i 215 ASN ** 0j 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 176 ASN 0k 211 ASN ** 0l 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0B 54 HIS ** 0B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0E 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0F 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0F 75 HIS ** 0F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0F 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0G 261 GLN 0H 261 GLN ** 0I 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0J 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0K 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0L 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN ** G 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 ASN ** M 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 ASN ** P 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 54 ASN Y 61 ASN b 54 ASN b 61 ASN e 54 ASN e 61 ASN ** g 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 40 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.6158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 72960 Z= 0.249 Angle : 0.762 14.943 98640 Z= 0.394 Chirality : 0.045 0.287 10824 Planarity : 0.004 0.095 12816 Dihedral : 5.441 25.766 9588 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 24.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer Outliers : 2.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.09), residues: 8736 helix: 0.10 (0.08), residues: 3972 sheet: -3.32 (0.11), residues: 1632 loop : -1.69 (0.12), residues: 3132 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3382 residues out of total 8136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 3217 time to evaluate : 6.755 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 outliers start: 165 outliers final: 100 residues processed: 3248 average time/residue: 0.6965 time to fit residues: 3759.8310 Evaluate side-chains 3233 residues out of total 8136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 3133 time to evaluate : 6.536 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 0 residues processed: 100 average time/residue: 0.5697 time to fit residues: 111.4806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 522 optimal weight: 0.9990 chunk 337 optimal weight: 0.0070 chunk 504 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 536 optimal weight: 0.4980 chunk 575 optimal weight: 1.9990 chunk 417 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 663 optimal weight: 0.0030 overall best weight: 0.4608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0a 59 GLN 0b 77 ASN 0c 13 ASN ** 0c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 58 HIS ** 0e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 77 ASN 0e 211 ASN ** 0e 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 32 GLN 0f 151 ASN ** 0f 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 173 GLN ** 0f 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 32 GLN ** 0g 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 37 GLN ** 0k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0B 54 HIS ** 0B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0D 126 GLN ** 0E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0E 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0F 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0F 126 GLN 0F 286 GLN 0G 261 GLN 0H 126 GLN 0H 279 GLN 0I 261 GLN ** 0J 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0J 245 ASN ** 0K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0K 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0L 237 ASN ** 0L 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN E 61 ASN ** G 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN ** M 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 ASN N 40 ASN ** P 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 54 ASN ** S 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 54 ASN X 40 ASN Z 40 ASN ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 44 HIS b 61 ASN e 61 ASN ** g 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 40 ASN ** j 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.6423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.094 72960 Z= 0.233 Angle : 0.777 16.857 98640 Z= 0.399 Chirality : 0.045 0.297 10824 Planarity : 0.004 0.085 12816 Dihedral : 5.361 24.405 9588 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 24.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.09), residues: 8736 helix: 0.27 (0.08), residues: 3828 sheet: -3.26 (0.11), residues: 1656 loop : -1.63 (0.12), residues: 3252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3342 residues out of total 8136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 3203 time to evaluate : 6.558 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 outliers start: 139 outliers final: 82 residues processed: 3233 average time/residue: 0.7016 time to fit residues: 3778.6739 Evaluate side-chains 3224 residues out of total 8136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 3142 time to evaluate : 6.416 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 0 residues processed: 82 average time/residue: 0.5564 time to fit residues: 91.8280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 768 optimal weight: 0.1980 chunk 808 optimal weight: 0.8980 chunk 737 optimal weight: 0.8980 chunk 786 optimal weight: 6.9990 chunk 473 optimal weight: 2.9990 chunk 342 optimal weight: 5.9990 chunk 617 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 chunk 710 optimal weight: 0.9990 chunk 744 optimal weight: 0.5980 chunk 784 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0b 77 ASN 0c 13 ASN ** 0c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 58 HIS ** 0e 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 211 ASN ** 0e 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0B 7 GLN ** 0B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0C 237 ASN ** 0D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0E 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0F 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0H 261 GLN 0I 261 GLN 0J 261 GLN ** 0K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0K 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0K 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0L 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN L 47 ASN ** M 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 ASN N 40 ASN ** P 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 ASN ** S 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 40 ASN ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 54 ASN Y 61 ASN Z 40 ASN b 61 ASN d 47 ASN e 61 ASN ** h 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.6646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 72960 Z= 0.266 Angle : 0.818 16.911 98640 Z= 0.421 Chirality : 0.046 0.286 10824 Planarity : 0.005 0.081 12816 Dihedral : 5.441 25.417 9588 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 25.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.09), residues: 8736 helix: 0.14 (0.08), residues: 3876 sheet: -3.17 (0.11), residues: 1632 loop : -1.67 (0.12), residues: 3228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3261 residues out of total 8136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 3169 time to evaluate : 6.921 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 outliers start: 92 outliers final: 56 residues processed: 3186 average time/residue: 0.6942 time to fit residues: 3677.8702 Evaluate side-chains 3180 residues out of total 8136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 3124 time to evaluate : 6.441 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.5708 time to fit residues: 66.4484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 516 optimal weight: 1.9990 chunk 831 optimal weight: 0.9980 chunk 507 optimal weight: 0.0070 chunk 394 optimal weight: 0.7980 chunk 578 optimal weight: 0.6980 chunk 872 optimal weight: 0.7980 chunk 803 optimal weight: 0.5980 chunk 694 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 536 optimal weight: 0.8980 chunk 426 optimal weight: 0.9980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0a 37 GLN 0a 59 GLN ** 0a 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 77 ASN 0c 13 ASN ** 0c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 152 GLN 0e 211 ASN 0f 173 GLN ** 0f 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 37 GLN ** 0h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 168 GLN 0k 176 ASN ** 0l 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0B 54 HIS ** 0B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0C 261 GLN ** 0D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0F 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0G 261 GLN ** 0H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0H 261 GLN ** 0I 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0I 261 GLN ** 0K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0K 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0L 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 ASN ** P 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 ASN ** S 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 54 ASN ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 44 HIS ** h 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.6867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 72960 Z= 0.258 Angle : 0.854 18.883 98640 Z= 0.436 Chirality : 0.047 0.305 10824 Planarity : 0.005 0.145 12816 Dihedral : 5.443 25.178 9588 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 25.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.09), residues: 8736 helix: 0.17 (0.08), residues: 3840 sheet: -3.11 (0.11), residues: 1632 loop : -1.69 (0.11), residues: 3264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17472 Ramachandran restraints generated. 8736 Oldfield, 0 Emsley, 8736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3226 residues out of total 8136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 3153 time to evaluate : 7.062 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 outliers start: 73 outliers final: 50 residues processed: 3160 average time/residue: 0.6987 time to fit residues: 3675.1272 Evaluate side-chains 3139 residues out of total 8136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 3089 time to evaluate : 6.472 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.5931 time to fit residues: 61.4150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 876 random chunks: chunk 552 optimal weight: 2.9990 chunk 740 optimal weight: 0.9980 chunk 212 optimal weight: 3.9990 chunk 640 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 193 optimal weight: 0.0870 chunk 696 optimal weight: 0.7980 chunk 291 optimal weight: 10.0000 chunk 714 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0a 37 GLN ** 0b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 77 ASN 0c 13 ASN ** 0d 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 211 ASN ** 0f 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 32 GLN ** 0h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 211 ASN 0k 215 ASN 0l 37 GLN ** 0A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0C 261 GLN ** 0D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0D 261 GLN ** 0E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0E 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0F 83 ASN 0G 261 GLN 0H 261 GLN 0I 261 GLN 0J 261 GLN ** 0K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0K 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0L 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0L 261 GLN ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 ASN N 40 ASN ** P 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 ASN ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 47 ASN ** h 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.163248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.122864 restraints weight = 160269.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.124772 restraints weight = 89614.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.126398 restraints weight = 57167.257| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.6982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.095 72960 Z= 0.311 Angle : 0.889 18.132 98640 Z= 0.456 Chirality : 0.048 0.335 10824 Planarity : 0.005 0.168 12816 Dihedral : 5.585 26.802 9588 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 28.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.09), residues: 8736 helix: 0.11 (0.08), residues: 3852 sheet: -3.17 (0.11), residues: 1632 loop : -1.72 (0.11), residues: 3252 =============================================================================== Job complete usr+sys time: 45541.43 seconds wall clock time: 782 minutes 47.76 seconds (46967.76 seconds total)