Starting phenix.real_space_refine (version: dev) on Sun Dec 11 23:56:14 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0u_12679/12_2022/7o0u_12679_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0u_12679/12_2022/7o0u_12679.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0u_12679/12_2022/7o0u_12679_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0u_12679/12_2022/7o0u_12679_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0u_12679/12_2022/7o0u_12679_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0u_12679/12_2022/7o0u_12679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0u_12679/12_2022/7o0u_12679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0u_12679/12_2022/7o0u_12679_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0u_12679/12_2022/7o0u_12679_updated.pdb" } resolution = 2.35 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "BK PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H2 PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bp PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 55758 Number of models: 1 Model: "" Number of chains: 236 Chain: "AA" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AB" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AC" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 384 Classifications: {'peptide': 48} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AD" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 384 Classifications: {'peptide': 48} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AE" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AF" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AG" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AH" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AI" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AJ" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AK" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AL" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AM" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AN" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AO" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AP" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AQ" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AR" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AS" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AT" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AU" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AV" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AW" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AX" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "BA" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BB" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BC" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BD" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BE" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BF" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BG" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BH" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BI" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BJ" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BK" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BL" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BM" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BN" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BO" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BP" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BQ" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BR" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BS" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BT" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BU" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BV" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BW" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BX" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "C" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2337 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 23, 'TRANS': 277} Chain: "C1" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 806 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 10, 'TRANS': 92} Chain: "H1" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 522 Classifications: {'peptide': 62} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H2" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1371 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 15, 'TRANS': 160} Chain: "L" Number of atoms: 2165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2165 Classifications: {'peptide': 273} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 257} Chain: "M" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2611 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 21, 'TRANS': 301} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "aa" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ab" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ac" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 443 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ad" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ae" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "af" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ag" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ah" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ai" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "aj" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ak" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 542 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 6, 'TRANS': 64} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "al" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "am" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "an" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 542 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 6, 'TRANS': 64} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ao" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ap" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 543 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 64} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ba" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bb" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bc" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bd" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "be" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bf" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bg" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bh" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bi" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bj" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bk" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bl" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bm" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bn" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "bo" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bp" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "MG" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'MAN': 1, 'RAM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "CG" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'MAN': 1, 'RAM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "AA" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AB" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 278 Unusual residues: {'BCL': 3, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "AC" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "AD" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AE" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 292 Unusual residues: {'BCL': 2, 'LMT': 2, 'V7N': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "AF" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AG" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AH" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 247 Unusual residues: {'BCL': 2, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "AI" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AJ" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 212 Unusual residues: {'0V9': 1, 'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "AK" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 202 Unusual residues: {'BCL': 2, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AL" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 202 Unusual residues: {'BCL': 2, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AM" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AN" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 268 Unusual residues: {'BCL': 3, 'LMT': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "AO" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "AP" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AQ" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 257 Unusual residues: {'0V9': 1, 'BCL': 2, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "AR" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AS" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 233 Unusual residues: {'BCL': 3, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AT" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AU" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AV" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 233 Unusual residues: {'BCL': 3, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AW" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 212 Unusual residues: {'BCL': 2, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AX" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BA" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 206 Unusual residues: {'BCL': 1, 'LMT': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BB" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BC" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BD" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 206 Unusual residues: {'BCL': 1, 'LMT': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BE" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BF" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 171 Unusual residues: {'BCL': 1, 'LMT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BG" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BH" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BI" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 206 Unusual residues: {'BCL': 1, 'LMT': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BJ" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BK" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BL" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 251 Unusual residues: {'BCL': 1, 'LMT': 4, 'V7N': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "BM" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BN" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BO" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BP" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BQ" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BR" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 171 Unusual residues: {'BCL': 1, 'LMT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BS" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 251 Unusual residues: {'BCL': 1, 'LMT': 4, 'V7N': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "BT" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BU" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 171 Unusual residues: {'BCL': 1, 'LMT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BV" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BW" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BX" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 136 Unusual residues: {'BCL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'HEC': 4, 'NDG': 1, 'V75': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C1" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NDG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H1" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 180 Unusual residues: {'0V9': 1, 'CD4': 1, 'PGW': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "H2" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 470 Unusual residues: {'0V9': 1, 'BCL': 2, 'BPH': 1, 'LMT': 5, 'MQ8': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "M" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 516 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'CD4': 2, 'CRT': 1, 'LMT': 1, 'MQ8': 1, 'V75': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "aa" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ab" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ac" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "ad" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 150 Unusual residues: {'BCL': 1, 'CD4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "ae" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 150 Unusual residues: {'BCL': 1, 'CD4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "af" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 169 Unusual residues: {'BCL': 1, 'V7B': 1, 'V7N': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "ag" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 208 Unusual residues: {'BCL': 1, 'CD4': 1, 'V7B': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "ah" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ai" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 121 Unusual residues: {'BCL': 1, 'UYH': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "aj" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'0V9': 1, 'BCL': 1, 'V7N': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "ak" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "al" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "am" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "an" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ao" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 119 Unusual residues: {'BCL': 1, 'MQ8': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "ap" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ba" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 146 Unusual residues: {'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "bb" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 236 Unusual residues: {'0V9': 2, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "bc" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bd" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "be" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 226 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bf" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bg" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "bh" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'V7N': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "bi" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 271 Unusual residues: {'0V9': 2, 'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "bj" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bk" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 146 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bl" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bm" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bn" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bo" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 226 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bp" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "AA" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AB" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AC" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AD" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AF" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AG" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "AH" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "AI" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AJ" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "AK" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AL" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AM" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AN" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AO" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AP" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AQ" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AR" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AS" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AT" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AU" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AV" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AW" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AX" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "BG" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "C1" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "H1" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "H2" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "L" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "M" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "aa" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "ab" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "ac" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "ad" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "ae" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "af" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "ag" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "ah" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "ai" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "aj" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "ak" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "al" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "am" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "an" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "ao" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "ap" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "ba" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "bb" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "bc" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "bd" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "be" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "bf" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "bg" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "bh" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "bi" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "bj" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "bk" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "bl" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "bm" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "bn" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "bo" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "bp" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 24.74, per 1000 atoms: 0.44 Number of scatterers: 55758 At special positions: 0 Unit cell: (197.893, 196.894, 145.921, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 5 26.01 S 277 16.00 P 33 15.00 Mg 108 11.99 O 9608 8.00 N 7254 7.00 C 38473 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=115, symmetry=0 Links applied BETA1-4 " MANCG 1 " - " RAMCG 2 " ~> Even though RAM is an alpha isomer, a beta linkage is required... " MANMG 1 " - " RAMMG 2 " MAN-SER " MANMG 1 " - " SER M 331 " MAN-THR " MANCG 1 " - " THR C 108 " Number of additional bonds: simple=115, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.67 Conformation dependent library (CDL) restraints added in 4.3 seconds 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9042 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 220 helices and 4 sheets defined 66.2% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'AA' and resid 3 through 5 No H-bonds generated for 'chain 'AA' and resid 3 through 5' Processing helix chain 'AA' and resid 10 through 36 Processing helix chain 'AA' and resid 40 through 46 Processing helix chain 'AB' and resid 3 through 5 No H-bonds generated for 'chain 'AB' and resid 3 through 5' Processing helix chain 'AB' and resid 10 through 36 Processing helix chain 'AB' and resid 40 through 46 Processing helix chain 'AC' and resid 3 through 5 No H-bonds generated for 'chain 'AC' and resid 3 through 5' Processing helix chain 'AC' and resid 10 through 36 Processing helix chain 'AC' and resid 40 through 45 Processing helix chain 'AD' and resid 3 through 5 No H-bonds generated for 'chain 'AD' and resid 3 through 5' Processing helix chain 'AD' and resid 10 through 36 Processing helix chain 'AD' and resid 40 through 46 Processing helix chain 'AE' and resid 3 through 7 removed outlier: 4.414A pdb=" N GLYAE 7 " --> pdb=" O ILEAE 4 " (cutoff:3.500A) Processing helix chain 'AE' and resid 10 through 35 Processing helix chain 'AE' and resid 40 through 46 removed outlier: 3.527A pdb=" N TYRAE 46 " --> pdb=" O LEUAE 42 " (cutoff:3.500A) Processing helix chain 'AF' and resid 3 through 5 No H-bonds generated for 'chain 'AF' and resid 3 through 5' Processing helix chain 'AF' and resid 10 through 36 Processing helix chain 'AF' and resid 40 through 46 removed outlier: 3.551A pdb=" N TYRAF 46 " --> pdb=" O LEUAF 42 " (cutoff:3.500A) Processing helix chain 'AG' and resid 3 through 5 No H-bonds generated for 'chain 'AG' and resid 3 through 5' Processing helix chain 'AG' and resid 10 through 36 Processing helix chain 'AG' and resid 40 through 46 Processing helix chain 'AH' and resid 3 through 5 No H-bonds generated for 'chain 'AH' and resid 3 through 5' Processing helix chain 'AH' and resid 10 through 35 removed outlier: 3.558A pdb=" N GLYAH 34 " --> pdb=" O ILEAH 30 " (cutoff:3.500A) Processing helix chain 'AH' and resid 40 through 46 Processing helix chain 'AI' and resid 3 through 5 No H-bonds generated for 'chain 'AI' and resid 3 through 5' Processing helix chain 'AI' and resid 10 through 36 Processing helix chain 'AI' and resid 40 through 46 removed outlier: 3.593A pdb=" N TYRAI 46 " --> pdb=" O LEUAI 42 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 3 through 5 No H-bonds generated for 'chain 'AJ' and resid 3 through 5' Processing helix chain 'AJ' and resid 10 through 36 Processing helix chain 'AJ' and resid 40 through 45 Processing helix chain 'AK' and resid 3 through 5 No H-bonds generated for 'chain 'AK' and resid 3 through 5' Processing helix chain 'AK' and resid 10 through 35 Processing helix chain 'AK' and resid 40 through 46 removed outlier: 3.515A pdb=" N TYRAK 46 " --> pdb=" O LEUAK 42 " (cutoff:3.500A) Processing helix chain 'AL' and resid 3 through 5 No H-bonds generated for 'chain 'AL' and resid 3 through 5' Processing helix chain 'AL' and resid 10 through 36 Processing helix chain 'AL' and resid 40 through 46 Processing helix chain 'AM' and resid 3 through 5 No H-bonds generated for 'chain 'AM' and resid 3 through 5' Processing helix chain 'AM' and resid 10 through 35 Processing helix chain 'AM' and resid 40 through 46 Processing helix chain 'AN' and resid 3 through 5 No H-bonds generated for 'chain 'AN' and resid 3 through 5' Processing helix chain 'AN' and resid 10 through 35 removed outlier: 3.514A pdb=" N GLYAN 34 " --> pdb=" O ILEAN 30 " (cutoff:3.500A) Processing helix chain 'AN' and resid 40 through 46 removed outlier: 3.604A pdb=" N TYRAN 46 " --> pdb=" O LEUAN 42 " (cutoff:3.500A) Processing helix chain 'AO' and resid 3 through 5 No H-bonds generated for 'chain 'AO' and resid 3 through 5' Processing helix chain 'AO' and resid 10 through 36 Processing helix chain 'AO' and resid 40 through 46 removed outlier: 3.511A pdb=" N TYRAO 46 " --> pdb=" O LEUAO 42 " (cutoff:3.500A) Processing helix chain 'AP' and resid 3 through 5 No H-bonds generated for 'chain 'AP' and resid 3 through 5' Processing helix chain 'AP' and resid 10 through 36 Processing helix chain 'AP' and resid 40 through 46 Processing helix chain 'AQ' and resid 3 through 5 No H-bonds generated for 'chain 'AQ' and resid 3 through 5' Processing helix chain 'AQ' and resid 10 through 35 Processing helix chain 'AQ' and resid 40 through 46 removed outlier: 3.625A pdb=" N TYRAQ 46 " --> pdb=" O LEUAQ 42 " (cutoff:3.500A) Processing helix chain 'AR' and resid 3 through 5 No H-bonds generated for 'chain 'AR' and resid 3 through 5' Processing helix chain 'AR' and resid 10 through 36 Processing helix chain 'AR' and resid 40 through 46 Processing helix chain 'AS' and resid 3 through 5 No H-bonds generated for 'chain 'AS' and resid 3 through 5' Processing helix chain 'AS' and resid 10 through 36 Processing helix chain 'AS' and resid 40 through 46 Processing helix chain 'AT' and resid 3 through 5 No H-bonds generated for 'chain 'AT' and resid 3 through 5' Processing helix chain 'AT' and resid 10 through 35 Processing helix chain 'AT' and resid 40 through 46 removed outlier: 3.564A pdb=" N TYRAT 46 " --> pdb=" O LEUAT 42 " (cutoff:3.500A) Processing helix chain 'AU' and resid 3 through 5 No H-bonds generated for 'chain 'AU' and resid 3 through 5' Processing helix chain 'AU' and resid 10 through 36 Processing helix chain 'AU' and resid 40 through 46 removed outlier: 3.511A pdb=" N TYRAU 46 " --> pdb=" O LEUAU 42 " (cutoff:3.500A) Processing helix chain 'AV' and resid 3 through 5 No H-bonds generated for 'chain 'AV' and resid 3 through 5' Processing helix chain 'AV' and resid 10 through 36 Processing helix chain 'AV' and resid 40 through 46 Processing helix chain 'AW' and resid 3 through 5 No H-bonds generated for 'chain 'AW' and resid 3 through 5' Processing helix chain 'AW' and resid 10 through 35 Processing helix chain 'AW' and resid 40 through 46 Processing helix chain 'AX' and resid 10 through 36 Processing helix chain 'AX' and resid 40 through 46 Processing helix chain 'BA' and resid 9 through 40 Processing helix chain 'BB' and resid 9 through 40 removed outlier: 3.545A pdb=" N GLYBB 17 " --> pdb=" O ARGBB 13 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYRBB 18 " --> pdb=" O ARGBB 14 " (cutoff:3.500A) Processing helix chain 'BC' and resid 9 through 40 removed outlier: 3.570A pdb=" N GLYBC 17 " --> pdb=" O ARGBC 13 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYRBC 18 " --> pdb=" O ARGBC 14 " (cutoff:3.500A) Processing helix chain 'BD' and resid 9 through 40 removed outlier: 3.623A pdb=" N TYRBD 18 " --> pdb=" O ARGBD 14 " (cutoff:3.500A) Processing helix chain 'BE' and resid 9 through 40 removed outlier: 3.510A pdb=" N ARGBE 14 " --> pdb=" O GLUBE 10 " (cutoff:3.500A) Processing helix chain 'BF' and resid 9 through 40 Processing helix chain 'BG' and resid 9 through 40 removed outlier: 3.593A pdb=" N GLYBG 17 " --> pdb=" O ARGBG 13 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYRBG 18 " --> pdb=" O ARGBG 14 " (cutoff:3.500A) Processing helix chain 'BH' and resid 9 through 40 removed outlier: 3.580A pdb=" N ARGBH 14 " --> pdb=" O GLUBH 10 " (cutoff:3.500A) Processing helix chain 'BI' and resid 9 through 40 Processing helix chain 'BJ' and resid 9 through 40 Processing helix chain 'BK' and resid 9 through 40 removed outlier: 3.681A pdb=" N TYRBK 18 " --> pdb=" O ARGBK 14 " (cutoff:3.500A) Processing helix chain 'BL' and resid 9 through 40 removed outlier: 3.529A pdb=" N GLYBL 17 " --> pdb=" O ARGBL 13 " (cutoff:3.500A) Processing helix chain 'BM' and resid 9 through 40 Processing helix chain 'BN' and resid 9 through 40 removed outlier: 3.619A pdb=" N GLYBN 17 " --> pdb=" O ARGBN 13 " (cutoff:3.500A) Processing helix chain 'BO' and resid 9 through 40 removed outlier: 3.612A pdb=" N GLYBO 17 " --> pdb=" O ARGBO 13 " (cutoff:3.500A) Processing helix chain 'BP' and resid 9 through 40 removed outlier: 3.507A pdb=" N GLYBP 17 " --> pdb=" O ARGBP 13 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYRBP 18 " --> pdb=" O ARGBP 14 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 9 through 40 removed outlier: 3.572A pdb=" N TYRBQ 18 " --> pdb=" O ARGBQ 14 " (cutoff:3.500A) Processing helix chain 'BR' and resid 9 through 40 Processing helix chain 'BS' and resid 9 through 40 removed outlier: 3.531A pdb=" N TYRBS 18 " --> pdb=" O ARGBS 14 " (cutoff:3.500A) Processing helix chain 'BT' and resid 9 through 40 removed outlier: 3.582A pdb=" N GLYBT 17 " --> pdb=" O ARGBT 13 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYRBT 18 " --> pdb=" O ARGBT 14 " (cutoff:3.500A) Processing helix chain 'BU' and resid 9 through 40 Processing helix chain 'BV' and resid 9 through 40 removed outlier: 3.519A pdb=" N GLYBV 17 " --> pdb=" O ARGBV 13 " (cutoff:3.500A) Processing helix chain 'BW' and resid 9 through 40 removed outlier: 3.519A pdb=" N TYRBW 18 " --> pdb=" O ARGBW 14 " (cutoff:3.500A) Processing helix chain 'BX' and resid 9 through 40 removed outlier: 3.769A pdb=" N ARGBX 14 " --> pdb=" O GLUBX 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 27 No H-bonds generated for 'chain 'C' and resid 25 through 27' Processing helix chain 'C' and resid 35 through 46 Processing helix chain 'C' and resid 75 through 90 Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 116 through 134 Processing helix chain 'C' and resid 136 through 139 No H-bonds generated for 'chain 'C' and resid 136 through 139' Processing helix chain 'C' and resid 146 through 150 Processing helix chain 'C' and resid 168 through 172 Processing helix chain 'C' and resid 195 through 212 Processing helix chain 'C' and resid 216 through 218 No H-bonds generated for 'chain 'C' and resid 216 through 218' Processing helix chain 'C' and resid 233 through 251 removed outlier: 3.548A pdb=" N ASN C 249 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN C 250 " --> pdb=" O ASP C 247 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN C 251 " --> pdb=" O VAL C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 258 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 276 through 280 Processing helix chain 'C' and resid 286 through 289 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 297 through 299 No H-bonds generated for 'chain 'C' and resid 297 through 299' Processing helix chain 'C1' and resid 127 through 129 No H-bonds generated for 'chain 'C1' and resid 127 through 129' Processing helix chain 'C1' and resid 136 through 142 Processing helix chain 'C1' and resid 161 through 163 No H-bonds generated for 'chain 'C1' and resid 161 through 163' Processing helix chain 'C1' and resid 172 through 175 No H-bonds generated for 'chain 'C1' and resid 172 through 175' Processing helix chain 'C1' and resid 183 through 189 removed outlier: 3.597A pdb=" N ARGC1 189 " --> pdb=" O ALAC1 185 " (cutoff:3.500A) Processing helix chain 'C1' and resid 197 through 199 No H-bonds generated for 'chain 'C1' and resid 197 through 199' Processing helix chain 'H1' and resid 7 through 31 removed outlier: 3.517A pdb=" N LYSH1 31 " --> pdb=" O ARGH1 27 " (cutoff:3.500A) Processing helix chain 'H2' and resid 22 through 25 No H-bonds generated for 'chain 'H2' and resid 22 through 25' Processing helix chain 'H2' and resid 28 through 30 No H-bonds generated for 'chain 'H2' and resid 28 through 30' Processing helix chain 'H2' and resid 54 through 56 No H-bonds generated for 'chain 'H2' and resid 54 through 56' Processing helix chain 'H2' and resid 115 through 117 No H-bonds generated for 'chain 'H2' and resid 115 through 117' Processing helix chain 'H2' and resid 121 through 124 Processing helix chain 'H2' and resid 140 through 143 Processing helix chain 'H2' and resid 155 through 171 removed outlier: 4.279A pdb=" N HISH2 169 " --> pdb=" O TYRH2 165 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N METH2 170 " --> pdb=" O ALAH2 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 9 No H-bonds generated for 'chain 'L' and resid 7 through 9' Processing helix chain 'L' and resid 32 through 55 Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'L' and resid 84 through 110 Processing helix chain 'L' and resid 116 through 132 removed outlier: 3.509A pdb=" N GLY L 123 " --> pdb=" O TRP L 119 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 139 Processing helix chain 'L' and resid 142 through 144 No H-bonds generated for 'chain 'L' and resid 142 through 144' Processing helix chain 'L' and resid 152 through 164 removed outlier: 3.950A pdb=" N TYR L 164 " --> pdb=" O VAL L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 169 No H-bonds generated for 'chain 'L' and resid 167 through 169' Processing helix chain 'L' and resid 171 through 198 Processing helix chain 'L' and resid 209 through 220 Processing helix chain 'L' and resid 226 through 249 removed outlier: 3.837A pdb=" N HIS L 230 " --> pdb=" O ALA L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 260 through 267 removed outlier: 3.595A pdb=" N TRP L 265 " --> pdb=" O TRP L 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 8 No H-bonds generated for 'chain 'M' and resid 6 through 8' Processing helix chain 'M' and resid 54 through 79 Processing helix chain 'M' and resid 83 through 88 Processing helix chain 'M' and resid 90 through 92 No H-bonds generated for 'chain 'M' and resid 90 through 92' Processing helix chain 'M' and resid 100 through 102 No H-bonds generated for 'chain 'M' and resid 100 through 102' Processing helix chain 'M' and resid 113 through 139 Processing helix chain 'M' and resid 145 through 167 removed outlier: 3.507A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE M 160 " --> pdb=" O LEU M 156 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE M 161 " --> pdb=" O TYR M 157 " (cutoff:3.500A) Proline residue: M 164 - end of helix Processing helix chain 'M' and resid 170 through 172 No H-bonds generated for 'chain 'M' and resid 170 through 172' Processing helix chain 'M' and resid 178 through 191 removed outlier: 3.827A pdb=" N LEU M 182 " --> pdb=" O ILE M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 197 No H-bonds generated for 'chain 'M' and resid 195 through 197' Processing helix chain 'M' and resid 199 through 228 removed outlier: 4.948A pdb=" N ARG M 227 " --> pdb=" O LEU M 223 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N MET M 228 " --> pdb=" O ALA M 224 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 238 Processing helix chain 'M' and resid 242 through 255 removed outlier: 3.531A pdb=" N TRP M 251 " --> pdb=" O SER M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 285 removed outlier: 3.905A pdb=" N THR M 276 " --> pdb=" O ALA M 272 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 300 Processing helix chain 'M' and resid 314 through 319 Processing helix chain 'aa' and resid 3 through 7 Processing helix chain 'aa' and resid 10 through 34 removed outlier: 3.742A pdb=" N VALaa 15 " --> pdb=" O ARGaa 11 " (cutoff:3.500A) Processing helix chain 'aa' and resid 40 through 43 No H-bonds generated for 'chain 'aa' and resid 40 through 43' Processing helix chain 'ab' and resid 3 through 7 Processing helix chain 'ab' and resid 10 through 34 removed outlier: 3.777A pdb=" N VALab 15 " --> pdb=" O ARGab 11 " (cutoff:3.500A) Processing helix chain 'ab' and resid 40 through 43 No H-bonds generated for 'chain 'ab' and resid 40 through 43' Processing helix chain 'ac' and resid 3 through 7 Processing helix chain 'ac' and resid 10 through 34 removed outlier: 3.824A pdb=" N VALac 15 " --> pdb=" O ARGac 11 " (cutoff:3.500A) Processing helix chain 'ac' and resid 40 through 43 No H-bonds generated for 'chain 'ac' and resid 40 through 43' Processing helix chain 'ad' and resid 3 through 7 Processing helix chain 'ad' and resid 10 through 34 removed outlier: 3.789A pdb=" N VALad 15 " --> pdb=" O ARGad 11 " (cutoff:3.500A) Processing helix chain 'ad' and resid 40 through 43 No H-bonds generated for 'chain 'ad' and resid 40 through 43' Processing helix chain 'ae' and resid 3 through 7 Processing helix chain 'ae' and resid 10 through 34 removed outlier: 3.764A pdb=" N VALae 15 " --> pdb=" O ARGae 11 " (cutoff:3.500A) Processing helix chain 'ae' and resid 40 through 43 No H-bonds generated for 'chain 'ae' and resid 40 through 43' Processing helix chain 'af' and resid 3 through 7 Processing helix chain 'af' and resid 10 through 34 removed outlier: 3.514A pdb=" N VALaf 15 " --> pdb=" O ARGaf 11 " (cutoff:3.500A) Processing helix chain 'af' and resid 40 through 43 No H-bonds generated for 'chain 'af' and resid 40 through 43' Processing helix chain 'ag' and resid 3 through 7 Processing helix chain 'ag' and resid 10 through 34 removed outlier: 3.928A pdb=" N VALag 15 " --> pdb=" O ARGag 11 " (cutoff:3.500A) Processing helix chain 'ag' and resid 40 through 43 No H-bonds generated for 'chain 'ag' and resid 40 through 43' Processing helix chain 'ah' and resid 3 through 7 Processing helix chain 'ah' and resid 10 through 34 Processing helix chain 'ah' and resid 40 through 43 No H-bonds generated for 'chain 'ah' and resid 40 through 43' Processing helix chain 'ai' and resid 3 through 7 Processing helix chain 'ai' and resid 10 through 34 Processing helix chain 'ai' and resid 40 through 43 No H-bonds generated for 'chain 'ai' and resid 40 through 43' Processing helix chain 'aj' and resid 3 through 7 Processing helix chain 'aj' and resid 10 through 34 removed outlier: 3.802A pdb=" N VALaj 15 " --> pdb=" O ARGaj 11 " (cutoff:3.500A) Processing helix chain 'aj' and resid 40 through 43 No H-bonds generated for 'chain 'aj' and resid 40 through 43' Processing helix chain 'ak' and resid 3 through 7 Processing helix chain 'ak' and resid 10 through 34 removed outlier: 3.930A pdb=" N VALak 15 " --> pdb=" O ARGak 11 " (cutoff:3.500A) Processing helix chain 'ak' and resid 40 through 43 No H-bonds generated for 'chain 'ak' and resid 40 through 43' Processing helix chain 'al' and resid 3 through 7 Processing helix chain 'al' and resid 10 through 34 Processing helix chain 'al' and resid 40 through 43 No H-bonds generated for 'chain 'al' and resid 40 through 43' Processing helix chain 'am' and resid 3 through 7 Processing helix chain 'am' and resid 10 through 34 Processing helix chain 'am' and resid 40 through 43 No H-bonds generated for 'chain 'am' and resid 40 through 43' Processing helix chain 'an' and resid 3 through 7 Processing helix chain 'an' and resid 10 through 34 removed outlier: 3.603A pdb=" N VALan 15 " --> pdb=" O ARGan 11 " (cutoff:3.500A) Processing helix chain 'an' and resid 40 through 43 No H-bonds generated for 'chain 'an' and resid 40 through 43' Processing helix chain 'ao' and resid 3 through 7 Processing helix chain 'ao' and resid 10 through 34 Processing helix chain 'ao' and resid 40 through 43 No H-bonds generated for 'chain 'ao' and resid 40 through 43' Processing helix chain 'ap' and resid 3 through 7 Processing helix chain 'ap' and resid 10 through 34 Processing helix chain 'ap' and resid 40 through 43 No H-bonds generated for 'chain 'ap' and resid 40 through 43' Processing helix chain 'ba' and resid 9 through 40 removed outlier: 3.555A pdb=" N TYRba 18 " --> pdb=" O ARGba 14 " (cutoff:3.500A) Processing helix chain 'bb' and resid 9 through 40 removed outlier: 3.579A pdb=" N GLYbb 17 " --> pdb=" O ARGbb 13 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYRbb 18 " --> pdb=" O ARGbb 14 " (cutoff:3.500A) Processing helix chain 'bc' and resid 9 through 40 Processing helix chain 'bd' and resid 9 through 40 removed outlier: 3.582A pdb=" N TYRbd 18 " --> pdb=" O ARGbd 14 " (cutoff:3.500A) Processing helix chain 'be' and resid 9 through 40 Processing helix chain 'bf' and resid 9 through 40 removed outlier: 3.680A pdb=" N TYRbf 18 " --> pdb=" O ARGbf 14 " (cutoff:3.500A) Processing helix chain 'bg' and resid 9 through 40 Processing helix chain 'bh' and resid 9 through 40 removed outlier: 3.573A pdb=" N GLYbh 17 " --> pdb=" O ARGbh 13 " (cutoff:3.500A) Processing helix chain 'bi' and resid 9 through 40 Processing helix chain 'bj' and resid 9 through 40 removed outlier: 3.802A pdb=" N TYRbj 18 " --> pdb=" O ARGbj 14 " (cutoff:3.500A) Processing helix chain 'bk' and resid 9 through 40 removed outlier: 3.523A pdb=" N TYRbk 18 " --> pdb=" O ARGbk 14 " (cutoff:3.500A) Processing helix chain 'bl' and resid 9 through 40 removed outlier: 3.701A pdb=" N TYRbl 18 " --> pdb=" O ARGbl 14 " (cutoff:3.500A) Processing helix chain 'bm' and resid 9 through 40 Processing helix chain 'bn' and resid 9 through 40 removed outlier: 3.538A pdb=" N TYRbn 18 " --> pdb=" O ARGbn 14 " (cutoff:3.500A) Processing helix chain 'bo' and resid 9 through 40 Processing helix chain 'bp' and resid 9 through 40 removed outlier: 3.801A pdb=" N TYRbp 18 " --> pdb=" O ARGbp 14 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 17 through 21 Processing sheet with id= B, first strand: chain 'H2' and resid 5 through 7 Processing sheet with id= C, first strand: chain 'H2' and resid 51 through 53 removed outlier: 6.744A pdb=" N GLUH2 101 " --> pdb=" O VALH2 86 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEUH2 88 " --> pdb=" O TYRH2 99 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYRH2 99 " --> pdb=" O LEUH2 88 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H2' and resid 118 through 120 removed outlier: 7.623A pdb=" N VALH2 133 " --> pdb=" O PROH2 73 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILEH2 75 " --> pdb=" O VALH2 133 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLYH2 83 " --> pdb=" O VALH2 74 " (cutoff:3.500A) 2420 hydrogen bonds defined for protein. 7092 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: 14.32 Time building geometry restraints manager: 20.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.36: 13904 1.36 - 1.57: 42624 1.57 - 1.77: 201 1.77 - 1.98: 458 1.98 - 2.18: 448 Bond restraints: 57635 Sorted by residual: bond pdb=" C27 V7Nbn 101 " pdb=" C28 V7Nbn 101 " ideal model delta sigma weight residual 1.350 1.524 -0.174 2.00e-02 2.50e+03 7.61e+01 bond pdb=" C27 V7Nba 102 " pdb=" C28 V7Nba 102 " ideal model delta sigma weight residual 1.350 1.524 -0.174 2.00e-02 2.50e+03 7.56e+01 bond pdb=" C27 V7NAE 101 " pdb=" C28 V7NAE 101 " ideal model delta sigma weight residual 1.350 1.523 -0.173 2.00e-02 2.50e+03 7.45e+01 bond pdb=" C27 V7NBH1001 " pdb=" C28 V7NBH1001 " ideal model delta sigma weight residual 1.350 1.522 -0.172 2.00e-02 2.50e+03 7.42e+01 bond pdb=" C27 V7NAW 104 " pdb=" C28 V7NAW 104 " ideal model delta sigma weight residual 1.350 1.522 -0.172 2.00e-02 2.50e+03 7.42e+01 ... (remaining 57630 not shown) Histogram of bond angle deviations from ideal: 84.75 - 103.58: 1754 103.58 - 122.40: 67588 122.40 - 141.23: 9608 141.23 - 160.05: 305 160.05 - 178.88: 30 Bond angle restraints: 79285 Sorted by residual: angle pdb=" C34 V7NBK1001 " pdb=" C9 V7NBK1001 " pdb=" C8 V7NBK1001 " ideal model delta sigma weight residual 68.18 124.09 -55.91 3.00e+00 1.11e-01 3.47e+02 angle pdb=" C34 V7NBB 101 " pdb=" C9 V7NBB 101 " pdb=" C8 V7NBB 101 " ideal model delta sigma weight residual 68.18 124.03 -55.85 3.00e+00 1.11e-01 3.47e+02 angle pdb=" C34 V7NBG1001 " pdb=" C9 V7NBG1001 " pdb=" C8 V7NBG1001 " ideal model delta sigma weight residual 68.18 123.94 -55.76 3.00e+00 1.11e-01 3.45e+02 angle pdb=" C34 V7NBJ1001 " pdb=" C9 V7NBJ1001 " pdb=" C8 V7NBJ1001 " ideal model delta sigma weight residual 68.18 123.87 -55.69 3.00e+00 1.11e-01 3.45e+02 angle pdb=" C34 V7NBT1001 " pdb=" C9 V7NBT1001 " pdb=" C8 V7NBT1001 " ideal model delta sigma weight residual 68.18 123.83 -55.65 3.00e+00 1.11e-01 3.44e+02 ... (remaining 79280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 27505 35.73 - 71.46: 881 71.46 - 107.19: 301 107.19 - 142.92: 93 142.92 - 178.65: 56 Dihedral angle restraints: 28836 sinusoidal: 14691 harmonic: 14145 Sorted by residual: dihedral pdb=" C1 BCLAK 103 " pdb=" C2 BCLAK 103 " pdb=" C3 BCLAK 103 " pdb=" C5 BCLAK 103 " ideal model delta sinusoidal sigma weight residual 180.00 4.34 175.66 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCLAV 104 " pdb=" CGA BCLAV 104 " pdb=" O2A BCLAV 104 " pdb=" CBA BCLAV 104 " ideal model delta sinusoidal sigma weight residual 180.00 147.70 32.30 1 6.00e+00 2.78e-02 4.13e+01 dihedral pdb=" C1 BCLBS1006 " pdb=" CGA BCLBS1006 " pdb=" O2A BCLBS1006 " pdb=" CBA BCLBS1006 " ideal model delta sinusoidal sigma weight residual -180.00 -147.71 -32.29 1 6.00e+00 2.78e-02 4.12e+01 ... (remaining 28833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 7555 0.090 - 0.181: 520 0.181 - 0.271: 15 0.271 - 0.361: 2 0.361 - 0.452: 6 Chirality restraints: 8098 Sorted by residual: chirality pdb=" C4 UYHai 102 " pdb=" C3 UYHai 102 " pdb=" C5 UYHai 102 " pdb=" O4 UYHai 102 " both_signs ideal model delta sigma weight residual False -2.49 -2.94 0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" C3 UYHai 102 " pdb=" C2 UYHai 102 " pdb=" C4 UYHai 102 " pdb=" O3 UYHai 102 " both_signs ideal model delta sigma weight residual False 2.48 2.90 -0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" C5 UYHai 102 " pdb=" C4 UYHai 102 " pdb=" C6 UYHai 102 " pdb=" O6 UYHai 102 " both_signs ideal model delta sigma weight residual False -2.52 -2.93 0.41 2.00e-01 2.50e+01 4.24e+00 ... (remaining 8095 not shown) Planarity restraints: 8977 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C26 V7NBB 101 " 0.163 2.00e-02 2.50e+03 3.25e-01 1.06e+03 pdb=" C27 V7NBB 101 " -0.442 2.00e-02 2.50e+03 pdb=" C28 V7NBB 101 " 0.424 2.00e-02 2.50e+03 pdb=" C29 V7NBB 101 " -0.144 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C26 V7Naf 103 " 0.249 2.00e-02 2.50e+03 2.54e-01 6.43e+02 pdb=" C27 V7Naf 103 " -0.240 2.00e-02 2.50e+03 pdb=" C28 V7Naf 103 " -0.267 2.00e-02 2.50e+03 pdb=" C29 V7Naf 103 " 0.257 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C26 V7Nbi 102 " -0.218 2.00e-02 2.50e+03 2.14e-01 4.60e+02 pdb=" C27 V7Nbi 102 " 0.234 2.00e-02 2.50e+03 pdb=" C28 V7Nbi 102 " 0.194 2.00e-02 2.50e+03 pdb=" C29 V7Nbi 102 " -0.210 2.00e-02 2.50e+03 ... (remaining 8974 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 1119 2.68 - 3.23: 49399 3.23 - 3.79: 92182 3.79 - 4.34: 134483 4.34 - 4.90: 212047 Nonbonded interactions: 489230 Sorted by model distance: nonbonded pdb=" NE2 HIS C 280 " pdb="FE HEC C 404 " model vdw 2.121 3.080 nonbonded pdb=" NE2 HIS L 190 " pdb="FE FE M 401 " model vdw 2.158 2.340 nonbonded pdb=" OE2 GLU M 233 " pdb="FE FE M 401 " model vdw 2.165 2.260 nonbonded pdb=" NE2 HIS M 218 " pdb="FE FE M 401 " model vdw 2.185 2.340 nonbonded pdb=" OG1 THRBE 8 " pdb=" OE1 GLUBE 11 " model vdw 2.264 2.440 ... (remaining 489225 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 'AA' and resid 1 through 48) selection = (chain 'AB' and resid 1 through 48) selection = (chain 'AC' and resid 1 through 48) selection = (chain 'AD' and resid 1 through 48) selection = (chain 'AE' and resid 1 through 48) selection = (chain 'AF' and resid 1 through 48) selection = (chain 'AG' and resid 1 through 48) selection = (chain 'AH' and resid 1 through 48) selection = (chain 'AI' and resid 1 through 48) selection = (chain 'AJ' and resid 1 through 48) selection = (chain 'AK' and resid 1 through 48) selection = (chain 'AL' and resid 1 through 48) selection = (chain 'AM' and resid 1 through 48) selection = (chain 'AN' and resid 1 through 48) selection = (chain 'AO' and resid 1 through 48) selection = (chain 'AP' and resid 1 through 48) selection = (chain 'AQ' and resid 1 through 48) selection = (chain 'AR' and resid 1 through 48) selection = (chain 'AS' and resid 1 through 48) selection = (chain 'AT' and resid 1 through 48) selection = (chain 'AU' and resid 1 through 48) selection = (chain 'AV' and resid 1 through 48) selection = (chain 'AW' and resid 1 through 48) selection = (chain 'AX' and resid 1 through 48) } ncs_group { reference = (chain 'BA' and resid 6 through 44) selection = (chain 'BB' and resid 6 through 44) selection = (chain 'BC' and resid 6 through 44) selection = (chain 'BD' and resid 6 through 44) selection = (chain 'BE' and resid 6 through 44) selection = (chain 'BF' and resid 6 through 44) selection = (chain 'BG' and resid 6 through 44) selection = (chain 'BH' and resid 6 through 44) selection = (chain 'BI' and resid 6 through 44) selection = (chain 'BJ' and resid 6 through 44) selection = (chain 'BK' and resid 6 through 44) selection = (chain 'BL' and resid 6 through 44) selection = (chain 'BM' and resid 6 through 44) selection = (chain 'BN' and resid 6 through 44) selection = (chain 'BO' and resid 6 through 44) selection = (chain 'BP' and resid 6 through 44) selection = (chain 'BQ' and resid 6 through 44) selection = (chain 'BR' and resid 6 through 44) selection = (chain 'BS' and resid 6 through 44) selection = (chain 'BT' and resid 6 through 44) selection = (chain 'BU' and resid 6 through 44) selection = (chain 'BV' and resid 6 through 44) selection = (chain 'BW' and resid 6 through 44) selection = (chain 'BX' and resid 6 through 44) selection = (chain 'ba' and resid 6 through 44) selection = (chain 'bb' and resid 6 through 44) selection = (chain 'bc' and resid 6 through 44) selection = (chain 'bd' and resid 6 through 44) selection = (chain 'be' and resid 6 through 44) selection = (chain 'bf' and resid 6 through 44) selection = (chain 'bg' and resid 6 through 44) selection = (chain 'bh' and resid 6 through 44) selection = (chain 'bi' and resid 6 through 44) selection = (chain 'bj' and resid 6 through 44) selection = (chain 'bk' and resid 6 through 44) selection = (chain 'bl' and resid 6 through 44) selection = (chain 'bm' and resid 6 through 44) selection = (chain 'bn' and resid 6 through 44) selection = (chain 'bo' and resid 6 through 44) selection = (chain 'bp' and resid 6 through 44) } ncs_group { reference = chain 'CG' selection = chain 'MG' } ncs_group { reference = (chain 'aa' and resid 1 through 56) selection = (chain 'ab' and resid 1 through 56) selection = (chain 'ac' and resid 1 through 56) selection = (chain 'ad' and resid 1 through 56) selection = (chain 'ae' and resid 1 through 56) selection = (chain 'af' and resid 1 through 56) selection = (chain 'ag' and resid 1 through 56) selection = (chain 'ah' and resid 1 through 56) selection = (chain 'ai' and resid 1 through 56) selection = (chain 'aj' and resid 1 through 56) selection = (chain 'al' and resid 1 through 56) selection = (chain 'am' and resid 1 through 56) selection = (chain 'ao' and resid 1 through 56) } ncs_group { reference = chain 'ak' selection = chain 'an' selection = (chain 'ap' and (resid 1 through 70 or (resid 71 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 o \ r name NH2)) or resid 1001)) } 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: 7 Type Number sf(0) Gaussians Fe 5 7.16 5 P 33 5.49 5 Mg 108 5.21 5 S 277 5.16 5 C 38473 2.51 5 N 7254 2.21 5 O 9608 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 0.030 Extract box with map and model: 15.710 Check model and map are aligned: 0.640 Convert atoms to be neutral: 0.380 Process input model: 106.500 Find NCS groups from input model: 3.160 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 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 : 0.017 0.174 57635 Z= 0.783 Angle : 4.330 55.912 79285 Z= 1.476 Chirality : 0.048 0.452 8098 Planarity : 0.013 0.325 8977 Dihedral : 22.248 178.651 19794 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.20 % Favored : 98.78 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: 1.39 (0.12), residues: 4756 helix: 0.96 (0.08), residues: 3158 sheet: -0.30 (1.06), residues: 22 loop : 1.19 (0.17), residues: 1576 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 853 time to evaluate : 4.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 865 average time/residue: 1.5916 time to fit residues: 1684.5794 Evaluate side-chains 663 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 656 time to evaluate : 4.110 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 1 average time/residue: 0.4040 time to fit residues: 5.3644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 377 optimal weight: 3.9990 chunk 338 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 228 optimal weight: 8.9990 chunk 181 optimal weight: 4.9990 chunk 350 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 chunk 260 optimal weight: 2.9990 chunk 405 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AD 37 ASN AF 37 ASN ** AH 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AN 37 ASN ** AP 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 37 ASN C1 199 GLN H2 119 GLN L 104 GLN L 213 ASN ac 36 GLN ag 50 GLN an 36 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 57635 Z= 0.239 Angle : 2.013 25.421 79285 Z= 0.692 Chirality : 0.039 0.262 8098 Planarity : 0.005 0.057 8977 Dihedral : 24.565 179.697 11490 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer Outliers : 2.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.47 (0.12), residues: 4756 helix: 2.79 (0.08), residues: 3166 sheet: 0.36 (1.06), residues: 24 loop : 1.45 (0.17), residues: 1566 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 677 time to evaluate : 4.065 Fit side-chains revert: symmetry clash outliers start: 84 outliers final: 35 residues processed: 712 average time/residue: 1.5826 time to fit residues: 1382.3892 Evaluate side-chains 661 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 626 time to evaluate : 4.131 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 25 residues processed: 11 average time/residue: 0.6725 time to fit residues: 15.9938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 225 optimal weight: 0.0770 chunk 125 optimal weight: 9.9990 chunk 337 optimal weight: 2.9990 chunk 276 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 406 optimal weight: 1.9990 chunk 439 optimal weight: 4.9990 chunk 362 optimal weight: 0.6980 chunk 403 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 326 optimal weight: 5.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 2 HIS ** AH 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 37 ASN C1 199 GLN H2 119 GLN M 6 ASN ac 36 GLN aj 50 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 57635 Z= 0.177 Angle : 1.878 25.465 79285 Z= 0.641 Chirality : 0.035 0.274 8098 Planarity : 0.004 0.053 8977 Dihedral : 23.583 179.961 11490 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.93 (0.12), residues: 4756 helix: 3.25 (0.08), residues: 3145 sheet: 0.36 (1.09), residues: 24 loop : 1.40 (0.17), residues: 1587 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 665 time to evaluate : 4.210 Fit side-chains revert: symmetry clash outliers start: 88 outliers final: 35 residues processed: 711 average time/residue: 1.5506 time to fit residues: 1362.1907 Evaluate side-chains 663 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 628 time to evaluate : 4.106 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 26 residues processed: 9 average time/residue: 0.3980 time to fit residues: 11.4013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 401 optimal weight: 9.9990 chunk 305 optimal weight: 10.0000 chunk 211 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 194 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 408 optimal weight: 6.9990 chunk 432 optimal weight: 5.9990 chunk 213 optimal weight: 0.8980 chunk 386 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AH 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 35 GLN AP 11 HIS AS 11 HIS C1 199 GLN H2 119 GLN H2 169 HIS ac 36 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 57635 Z= 0.309 Angle : 1.886 26.815 79285 Z= 0.649 Chirality : 0.040 0.260 8098 Planarity : 0.004 0.051 8977 Dihedral : 23.356 179.923 11490 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.67 (0.12), residues: 4756 helix: 3.00 (0.08), residues: 3193 sheet: 0.19 (1.12), residues: 24 loop : 1.35 (0.18), residues: 1539 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 634 time to evaluate : 4.209 Fit side-chains revert: symmetry clash outliers start: 116 outliers final: 52 residues processed: 690 average time/residue: 1.6150 time to fit residues: 1370.8225 Evaluate side-chains 672 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 620 time to evaluate : 4.087 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 35 residues processed: 18 average time/residue: 0.5445 time to fit residues: 20.8924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 359 optimal weight: 9.9990 chunk 245 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 321 optimal weight: 0.1980 chunk 178 optimal weight: 9.9990 chunk 368 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 220 optimal weight: 7.9990 chunk 387 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AH 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 35 GLN AQ 35 GLN AV 35 GLN AW 35 GLN C1 199 GLN H2 169 HIS ac 36 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 57635 Z= 0.195 Angle : 1.800 25.471 79285 Z= 0.615 Chirality : 0.036 0.266 8098 Planarity : 0.004 0.048 8977 Dihedral : 22.757 179.944 11490 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: 4.02 (0.12), residues: 4756 helix: 3.38 (0.08), residues: 3140 sheet: 0.02 (1.13), residues: 24 loop : 1.30 (0.17), residues: 1592 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 639 time to evaluate : 4.745 Fit side-chains revert: symmetry clash outliers start: 101 outliers final: 53 residues processed: 690 average time/residue: 1.5995 time to fit residues: 1367.0091 Evaluate side-chains 666 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 613 time to evaluate : 4.116 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 39 residues processed: 14 average time/residue: 0.5980 time to fit residues: 18.1577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 145 optimal weight: 6.9990 chunk 389 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 253 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 432 optimal weight: 4.9990 chunk 359 optimal weight: 10.0000 chunk 200 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 227 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AE 35 GLN ** AH 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 35 GLN AS 35 GLN C1 199 GLN H2 103 GLN H2 122 ASN H2 169 HIS ac 36 GLN ak 50 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 57635 Z= 0.378 Angle : 1.853 26.156 79285 Z= 0.640 Chirality : 0.041 0.262 8098 Planarity : 0.005 0.057 8977 Dihedral : 22.986 179.928 11490 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer Outliers : 2.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.12), residues: 4756 helix: 3.00 (0.08), residues: 3165 sheet: 0.05 (1.15), residues: 24 loop : 1.26 (0.17), residues: 1567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 627 time to evaluate : 4.157 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 62 residues processed: 684 average time/residue: 1.5689 time to fit residues: 1328.5024 Evaluate side-chains 682 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 620 time to evaluate : 4.134 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 43 residues processed: 19 average time/residue: 0.6359 time to fit residues: 23.6652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 416 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 246 optimal weight: 0.8980 chunk 315 optimal weight: 0.9980 chunk 244 optimal weight: 0.6980 chunk 364 optimal weight: 8.9990 chunk 241 optimal weight: 4.9990 chunk 430 optimal weight: 0.7980 chunk 269 optimal weight: 0.0040 chunk 262 optimal weight: 0.7980 chunk 198 optimal weight: 0.8980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AD 35 GLN ** AH 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 35 GLN C1 199 GLN H2 119 GLN H2 169 HIS ac 36 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 57635 Z= 0.162 Angle : 1.759 25.706 79285 Z= 0.600 Chirality : 0.035 0.268 8098 Planarity : 0.004 0.050 8977 Dihedral : 22.324 179.877 11490 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: 4.06 (0.12), residues: 4756 helix: 3.43 (0.08), residues: 3138 sheet: 0.10 (1.16), residues: 24 loop : 1.27 (0.17), residues: 1594 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 635 time to evaluate : 4.119 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 44 residues processed: 679 average time/residue: 1.5436 time to fit residues: 1303.8512 Evaluate side-chains 654 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 610 time to evaluate : 4.111 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 36 residues processed: 8 average time/residue: 0.6269 time to fit residues: 12.5268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 266 optimal weight: 0.1980 chunk 172 optimal weight: 0.8980 chunk 257 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 273 optimal weight: 2.9990 chunk 293 optimal weight: 0.7980 chunk 213 optimal weight: 0.0270 chunk 40 optimal weight: 10.0000 chunk 338 optimal weight: 0.7980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AH 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 35 GLN AP 35 GLN AT 35 GLN C1 163 ASN C1 198 ASN C1 199 GLN H2 169 HIS ac 36 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 57635 Z= 0.152 Angle : 1.728 25.847 79285 Z= 0.589 Chirality : 0.034 0.266 8098 Planarity : 0.004 0.049 8977 Dihedral : 21.717 179.880 11490 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: 4.18 (0.12), residues: 4756 helix: 3.55 (0.08), residues: 3138 sheet: -0.13 (0.99), residues: 30 loop : 1.26 (0.18), residues: 1588 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 642 time to evaluate : 4.208 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 36 residues processed: 683 average time/residue: 1.5669 time to fit residues: 1330.8639 Evaluate side-chains 639 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 603 time to evaluate : 4.087 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 33 residues processed: 4 average time/residue: 0.7821 time to fit residues: 9.2319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 391 optimal weight: 9.9990 chunk 412 optimal weight: 0.9980 chunk 376 optimal weight: 2.9990 chunk 401 optimal weight: 0.8980 chunk 241 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 315 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 362 optimal weight: 0.8980 chunk 379 optimal weight: 4.9990 chunk 400 optimal weight: 7.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AH 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2 122 ASN ac 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 57635 Z= 0.196 Angle : 1.727 25.853 79285 Z= 0.591 Chirality : 0.035 0.265 8098 Planarity : 0.004 0.053 8977 Dihedral : 21.642 179.916 11490 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: 4.06 (0.12), residues: 4756 helix: 3.44 (0.08), residues: 3144 sheet: -0.14 (0.99), residues: 30 loop : 1.24 (0.18), residues: 1582 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 615 time to evaluate : 4.174 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 42 residues processed: 652 average time/residue: 1.5977 time to fit residues: 1291.7869 Evaluate side-chains 644 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 602 time to evaluate : 4.192 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 35 residues processed: 9 average time/residue: 0.9966 time to fit residues: 17.1616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 263 optimal weight: 0.9990 chunk 424 optimal weight: 4.9990 chunk 259 optimal weight: 0.8980 chunk 201 optimal weight: 0.6980 chunk 295 optimal weight: 0.5980 chunk 445 optimal weight: 0.9990 chunk 409 optimal weight: 2.9990 chunk 354 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 273 optimal weight: 0.9980 chunk 217 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AH 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ac 36 GLN ai 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 57635 Z= 0.165 Angle : 1.705 25.706 79285 Z= 0.582 Chirality : 0.034 0.266 8098 Planarity : 0.004 0.049 8977 Dihedral : 21.358 179.950 11490 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: 4.10 (0.12), residues: 4756 helix: 3.47 (0.08), residues: 3145 sheet: -0.18 (0.98), residues: 30 loop : 1.24 (0.18), residues: 1581 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 625 time to evaluate : 4.248 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 35 residues processed: 660 average time/residue: 1.6024 time to fit residues: 1316.8076 Evaluate side-chains 637 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 602 time to evaluate : 4.119 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 35 residues processed: 1 average time/residue: 0.4494 time to fit residues: 5.4981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 281 optimal weight: 0.5980 chunk 377 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 326 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 355 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 chunk 364 optimal weight: 0.5980 chunk 44 optimal weight: 10.0000 chunk 65 optimal weight: 0.3980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AH 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 37 ASN C 94 ASN ac 36 GLN ** af 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.104630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.075605 restraints weight = 89408.286| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.41 r_work: 0.2789 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 57635 Z= 0.179 Angle : 1.704 25.803 79285 Z= 0.583 Chirality : 0.035 0.265 8098 Planarity : 0.004 0.049 8977 Dihedral : 21.217 179.844 11490 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % 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: 4.04 (0.12), residues: 4756 helix: 3.42 (0.08), residues: 3145 sheet: -0.13 (0.99), residues: 30 loop : 1.24 (0.18), residues: 1581 =============================================================================== Job complete usr+sys time: 19732.18 seconds wall clock time: 342 minutes 3.03 seconds (20523.03 seconds total)