Starting phenix.real_space_refine (version: dev) on Wed Feb 22 12:16:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0v_12680/02_2023/7o0v_12680_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0v_12680/02_2023/7o0v_12680.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0v_12680/02_2023/7o0v_12680_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0v_12680/02_2023/7o0v_12680_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0v_12680/02_2023/7o0v_12680_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0v_12680/02_2023/7o0v_12680.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0v_12680/02_2023/7o0v_12680.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0v_12680/02_2023/7o0v_12680_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0v_12680/02_2023/7o0v_12680_updated.pdb" } resolution = 2.5 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "BE PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BM TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H2 PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 55475 Number of models: 1 Model: "" Number of chains: 238 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: 2325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2325 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 23, 'TRANS': 275} 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: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1354 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 15, 'TRANS': 158} 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: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2536 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 21, 'TRANS': 293} Chain breaks: 1 Chain: "aa" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 433 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "ab" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} 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: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} 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: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} 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: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} 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: "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: "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: "AA" 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: "AB" 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: "AC" 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: "AD" 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: "AE" 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: "AF" 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: "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: 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: "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: 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: "AK" 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: "AL" 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: "AM" 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: "AN" 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: "AO" 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: "AP" 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: "AQ" 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: "AR" 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: "AS" 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: "AT" 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: "AU" 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: "AV" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 198 Unusual residues: {'BCL': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AW" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "AX" 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: "BA" 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: "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: 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: "BD" 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: "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: 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: "BG" 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: "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: 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: "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: 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: "BL" 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: "BM" 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: "BN" 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: "BO" 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: "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: 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: "BR" 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: "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: 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: "BU" 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: "BV" 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: "BW" 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: "BX" 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: "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: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'0V9': 1, 'NDG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H1" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 264 Unusual residues: {'0V9': 1, 'CD4': 2, 'PGW': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "L" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 518 Unusual residues: {'BCL': 2, 'BPH': 1, 'LMT': 6, 'MQ8': 1, 'V7B': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "M" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 432 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'CD4': 1, 'CRT': 1, 'LMT': 1, 'MQ8': 1, 'V75': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} 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: 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: "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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 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: 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: "ag" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 124 Unusual residues: {'BCL': 1, 'V7B': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 195 Unusual residues: {'0V9': 1, 'BCL': 1, 'CD4': 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: 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: "bb" 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: "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: 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: "be" 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: "bf" 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: "bg" 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: "bh" 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: "bi" 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: "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: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 201 Unusual residues: {'0V9': 2, 'BCL': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "bl" 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: "bm" 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: "bn" 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: "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: 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: "AA" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AD" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AE" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AF" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AG" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "AH" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AI" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AJ" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AM" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "AN" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AO" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AP" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} 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: "AS" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} 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: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "BB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "BI" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "BJ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "BO" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "BP" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 86 Classifications: {'water': 86} Link IDs: {None: 85} Chain: "C1" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "H1" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "H2" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "M" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "aa" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "ad" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "ae" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "af" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "ag" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "ah" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} 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: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "ak" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "al" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "am" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "an" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} 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: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "ba" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "bb" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "bc" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "bd" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "be" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "bf" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "bg" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "bh" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "bi" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "bj" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "bk" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "bl" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "bm" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "bn" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "bo" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 21.99, per 1000 atoms: 0.40 Number of scatterers: 55475 At special positions: 0 Unit cell: (199.892, 194.895, 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 275 16.00 P 33 15.00 Mg 108 11.99 O 9538 8.00 N 7224 7.00 C 38292 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=114, 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=114, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.45 Conformation dependent library (CDL) restraints added in 4.1 seconds 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8994 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 221 helices and 5 sheets defined 66.3% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 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 35 removed outlier: 3.515A pdb=" N GLYAB 34 " --> pdb=" O ILEAB 30 " (cutoff:3.500A) Processing helix chain 'AB' and resid 40 through 46 removed outlier: 3.510A pdb=" N TYRAB 46 " --> pdb=" O LEUAB 42 " (cutoff:3.500A) Processing helix chain 'AC' and resid 10 through 36 Processing helix chain 'AC' and resid 40 through 46 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: 4.349A pdb=" N GLYAE 7 " --> pdb=" O ILEAE 4 " (cutoff:3.500A) Processing helix chain 'AE' and resid 10 through 35 removed outlier: 3.507A pdb=" N GLYAE 34 " --> pdb=" O ILEAE 30 " (cutoff:3.500A) Processing helix chain 'AE' and resid 40 through 46 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 35 Processing helix chain 'AF' and resid 40 through 46 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 35 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 Processing helix chain 'AH' and resid 40 through 46 removed outlier: 3.504A pdb=" N TYRAH 46 " --> pdb=" O LEUAH 42 " (cutoff:3.500A) 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 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 removed outlier: 3.607A pdb=" N GLYAJ 34 " --> pdb=" O ILEAJ 30 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 40 through 46 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 removed outlier: 3.620A pdb=" N GLYAK 34 " --> pdb=" O ILEAK 30 " (cutoff:3.500A) Processing helix chain 'AK' and resid 40 through 46 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 35 removed outlier: 3.547A pdb=" N GLYAL 34 " --> pdb=" O ILEAL 30 " (cutoff:3.500A) 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 36 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: 3.540A pdb=" N GLYAN 34 " --> pdb=" O ILEAN 30 " (cutoff:3.500A) Processing helix chain 'AN' and resid 40 through 46 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 35 Processing helix chain 'AO' and resid 40 through 46 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 35 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 36 Processing helix chain 'AQ' and resid 40 through 46 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 removed outlier: 3.532A pdb=" N TYRAR 46 " --> pdb=" O LEUAR 42 " (cutoff:3.500A) 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 35 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: 3.523A 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 35 Processing helix chain 'AU' and resid 40 through 46 removed outlier: 3.515A 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 35 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 3 through 5 No H-bonds generated for 'chain 'AX' and resid 3 through 5' Processing helix chain 'AX' and resid 10 through 36 removed outlier: 3.518A pdb=" N GLYAX 34 " --> pdb=" O ILEAX 30 " (cutoff:3.500A) Processing helix chain 'AX' and resid 40 through 46 removed outlier: 3.502A pdb=" N TYRAX 46 " --> pdb=" O LEUAX 42 " (cutoff:3.500A) Processing helix chain 'BA' and resid 9 through 40 Processing helix chain 'BB' and resid 9 through 40 Processing helix chain 'BC' and resid 9 through 40 Processing helix chain 'BD' and resid 9 through 40 Processing helix chain 'BE' and resid 9 through 40 Processing helix chain 'BF' and resid 9 through 40 Processing helix chain 'BG' and resid 9 through 40 removed outlier: 3.588A pdb=" N TYRBG 18 " --> pdb=" O ARGBG 14 " (cutoff:3.500A) Processing helix chain 'BH' and resid 9 through 40 Processing helix chain 'BI' and resid 9 through 40 Processing helix chain 'BJ' and resid 9 through 40 removed outlier: 3.623A pdb=" N GLYBJ 17 " --> pdb=" O ARGBJ 13 " (cutoff:3.500A) Processing helix chain 'BK' and resid 9 through 40 removed outlier: 3.536A pdb=" N GLYBK 17 " --> pdb=" O ARGBK 13 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYRBK 18 " --> pdb=" O ARGBK 14 " (cutoff:3.500A) Processing helix chain 'BL' and resid 9 through 40 removed outlier: 3.590A 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: 3.593A pdb=" N GLYBN 17 " --> pdb=" O ARGBN 13 " (cutoff:3.500A) Processing helix chain 'BO' and resid 9 through 40 removed outlier: 3.556A pdb=" N TYRBO 18 " --> pdb=" O ARGBO 14 " (cutoff:3.500A) Processing helix chain 'BP' and resid 9 through 40 removed outlier: 3.669A pdb=" N GLYBP 17 " --> pdb=" O ARGBP 13 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYRBP 18 " --> pdb=" O ARGBP 14 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 9 through 40 removed outlier: 3.536A pdb=" N TYRBQ 18 " --> pdb=" O ARGBQ 14 " (cutoff:3.500A) Processing helix chain 'BR' and resid 9 through 40 removed outlier: 3.579A pdb=" N TYRBR 18 " --> pdb=" O ARGBR 14 " (cutoff:3.500A) Processing helix chain 'BS' and resid 9 through 40 Processing helix chain 'BT' and resid 9 through 40 removed outlier: 3.592A 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 Processing helix chain 'BW' and resid 9 through 40 Processing helix chain 'BX' and resid 9 through 40 removed outlier: 3.764A pdb=" N TYRBX 18 " --> pdb=" O ARGBX 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 46 Processing helix chain 'C' and resid 75 through 89 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: 3.637A pdb=" N ASN C 249 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN C 250 " --> pdb=" O ASP C 247 " (cutoff:3.500A) removed outlier: 4.000A 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 141 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: 3.538A 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 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 140 through 143 Processing helix chain 'H2' and resid 155 through 166 Processing helix chain 'H2' and resid 168 through 171 No H-bonds generated for 'chain 'H2' and resid 168 through 171' 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 111 Processing helix chain 'L' and resid 116 through 132 removed outlier: 3.546A pdb=" N GLY L 123 " --> pdb=" O TRP L 119 " (cutoff:3.500A) removed outlier: 4.020A 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: 3.936A 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: 3.844A pdb=" N HIS L 230 " --> pdb=" O ALA L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 260 through 267 removed outlier: 3.642A pdb=" N TRP L 265 " --> pdb=" O TRP L 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 79 removed outlier: 3.563A pdb=" N VAL M 79 " --> pdb=" O MET M 75 " (cutoff:3.500A) 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 109 through 111 No H-bonds generated for 'chain 'M' and resid 109 through 111' Processing helix chain 'M' and resid 113 through 139 Processing helix chain 'M' and resid 145 through 167 removed outlier: 3.699A pdb=" N PHE M 160 " --> pdb=" O LEU M 156 " (cutoff:3.500A) removed outlier: 3.979A 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: 3.774A 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 224 Processing helix chain 'M' and resid 226 through 228 No H-bonds generated for 'chain 'M' and resid 226 through 228' Processing helix chain 'M' and resid 233 through 238 Processing helix chain 'M' and resid 242 through 255 removed outlier: 3.527A pdb=" N TRP M 251 " --> pdb=" O SER M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 285 removed outlier: 3.906A 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 removed outlier: 3.624A pdb=" N ASP M 318 " --> pdb=" O PRO M 314 " (cutoff:3.500A) Processing helix chain 'aa' and resid 4 through 7 No H-bonds generated for 'chain 'aa' and resid 4 through 7' Processing helix chain 'aa' and resid 10 through 34 removed outlier: 4.289A 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: 4.126A 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: 3.911A 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: 3.739A 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 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 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 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 removed outlier: 3.891A pdb=" N VALah 15 " --> pdb=" O ARGah 11 " (cutoff:3.500A) 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 'ai' and resid 48 through 50 No H-bonds generated for 'chain 'ai' and resid 48 through 50' Processing helix chain 'aj' and resid 3 through 7 Processing helix chain 'aj' and resid 10 through 33 removed outlier: 3.707A 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: 4.077A 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 removed outlier: 3.901A pdb=" N VALal 15 " --> pdb=" O ARGal 11 " (cutoff:3.500A) 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 removed outlier: 3.780A pdb=" N VALam 15 " --> pdb=" O ARGam 11 " (cutoff:3.500A) Processing helix chain 'am' and resid 40 through 43 No H-bonds generated for 'chain 'am' and resid 40 through 43' Processing helix chain 'am' and resid 48 through 50 No H-bonds generated for 'chain 'am' and resid 48 through 50' Processing helix chain 'an' and resid 3 through 7 Processing helix chain 'an' and resid 10 through 34 removed outlier: 3.859A pdb=" N METan 14 " --> pdb=" O PROan 10 " (cutoff:3.500A) removed outlier: 3.913A 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 removed outlier: 3.743A pdb=" N VALao 15 " --> pdb=" O ARGao 11 " (cutoff:3.500A) 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 removed outlier: 3.920A pdb=" N VALap 15 " --> pdb=" O ARGap 11 " (cutoff:3.500A) 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 Processing helix chain 'bb' and resid 9 through 40 Processing helix chain 'bc' and resid 9 through 40 removed outlier: 3.758A pdb=" N TYRbc 18 " --> pdb=" O ARGbc 14 " (cutoff:3.500A) Processing helix chain 'bd' and resid 9 through 40 Processing helix chain 'be' and resid 9 through 40 removed outlier: 3.771A pdb=" N TYRbe 18 " --> pdb=" O ARGbe 14 " (cutoff:3.500A) Processing helix chain 'bf' and resid 9 through 40 Processing helix chain 'bg' and resid 9 through 40 removed outlier: 3.515A pdb=" N TYRbg 18 " --> pdb=" O ARGbg 14 " (cutoff:3.500A) Processing helix chain 'bh' and resid 9 through 40 Processing helix chain 'bi' and resid 9 through 40 removed outlier: 3.660A pdb=" N TYRbi 18 " --> pdb=" O ARGbi 14 " (cutoff:3.500A) Processing helix chain 'bj' and resid 9 through 40 removed outlier: 3.604A pdb=" N TYRbj 18 " --> pdb=" O ARGbj 14 " (cutoff:3.500A) Processing helix chain 'bk' and resid 9 through 40 removed outlier: 3.602A pdb=" N TYRbk 18 " --> pdb=" O ARGbk 14 " (cutoff:3.500A) Processing helix chain 'bl' and resid 9 through 40 Processing helix chain 'bm' and resid 9 through 40 removed outlier: 3.666A pdb=" N TYRbm 18 " --> pdb=" O ARGbm 14 " (cutoff:3.500A) Processing helix chain 'bn' and resid 9 through 40 Processing helix chain 'bo' and resid 9 through 40 Processing helix chain 'bp' and resid 9 through 40 removed outlier: 3.786A pdb=" N ARGbp 14 " --> pdb=" O GLUbp 10 " (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: 6.684A pdb=" N GLUH2 101 " --> pdb=" O VALH2 86 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEUH2 88 " --> pdb=" O TYRH2 99 " (cutoff:3.500A) removed outlier: 6.839A 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: 7.705A pdb=" N VALH2 133 " --> pdb=" O PROH2 73 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILEH2 75 " --> pdb=" O VALH2 133 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLYH2 83 " --> pdb=" O VALH2 74 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'M' and resid 41 through 43 removed outlier: 3.733A pdb=" N ALA M 46 " --> pdb=" O PHE M 43 " (cutoff:3.500A) 2415 hydrogen bonds defined for protein. 7083 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.51 Time building geometry restraints manager: 18.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.35: 13243 1.35 - 1.56: 42985 1.56 - 1.77: 176 1.77 - 1.97: 496 1.97 - 2.18: 448 Bond restraints: 57348 Sorted by residual: bond pdb=" C27 V7Nbn 102 " pdb=" C28 V7Nbn 102 " ideal model delta sigma weight residual 1.348 1.523 -0.175 2.00e-02 2.50e+03 7.64e+01 bond pdb=" C27 V7NBI1001 " pdb=" C28 V7NBI1001 " ideal model delta sigma weight residual 1.348 1.522 -0.174 2.00e-02 2.50e+03 7.61e+01 bond pdb=" C27 V7NBC 101 " pdb=" C28 V7NBC 101 " ideal model delta sigma weight residual 1.348 1.522 -0.174 2.00e-02 2.50e+03 7.58e+01 bond pdb=" C27 V7NBK1001 " pdb=" C28 V7NBK1001 " ideal model delta sigma weight residual 1.348 1.522 -0.174 2.00e-02 2.50e+03 7.54e+01 bond pdb=" C27 V7NBP1001 " pdb=" C28 V7NBP1001 " ideal model delta sigma weight residual 1.348 1.522 -0.174 2.00e-02 2.50e+03 7.54e+01 ... (remaining 57343 not shown) Histogram of bond angle deviations from ideal: 84.72 - 103.46: 1699 103.46 - 122.20: 66068 122.20 - 140.94: 10799 140.94 - 159.68: 266 159.68 - 178.42: 70 Bond angle restraints: 78902 Sorted by residual: angle pdb=" C34 V7NBD 101 " pdb=" C9 V7NBD 101 " pdb=" C8 V7NBD 101 " ideal model delta sigma weight residual 68.18 123.70 -55.52 3.00e+00 1.11e-01 3.42e+02 angle pdb=" C34 V7NBK1001 " pdb=" C9 V7NBK1001 " pdb=" C8 V7NBK1001 " ideal model delta sigma weight residual 68.18 123.65 -55.47 3.00e+00 1.11e-01 3.42e+02 angle pdb=" C34 V7Nbk 101 " pdb=" C9 V7Nbk 101 " pdb=" C8 V7Nbk 101 " ideal model delta sigma weight residual 68.18 123.60 -55.42 3.00e+00 1.11e-01 3.41e+02 angle pdb=" C34 V7NBM1001 " pdb=" C9 V7NBM1001 " pdb=" C8 V7NBM1001 " ideal model delta sigma weight residual 68.18 123.46 -55.28 3.00e+00 1.11e-01 3.39e+02 angle pdb=" C34 V7Nbm 101 " pdb=" C9 V7Nbm 101 " pdb=" C8 V7Nbm 101 " ideal model delta sigma weight residual 68.18 123.01 -54.83 3.00e+00 1.11e-01 3.34e+02 ... (remaining 78897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 27796 35.67 - 71.33: 1136 71.33 - 107.00: 424 107.00 - 142.66: 113 142.66 - 178.33: 93 Dihedral angle restraints: 29562 sinusoidal: 15491 harmonic: 14071 Sorted by residual: dihedral pdb=" CBD BCLAR 102 " pdb=" CGD BCLAR 102 " pdb=" O2D BCLAR 102 " pdb=" CED BCLAR 102 " ideal model delta sinusoidal sigma weight residual 180.00 33.80 146.20 1 5.00e+00 4.00e-02 7.03e+02 dihedral pdb=" C1 BCLBO1004 " pdb=" CGA BCLBO1004 " pdb=" O2A BCLBO1004 " pdb=" CBA BCLBO1004 " ideal model delta sinusoidal sigma weight residual -180.00 -1.67 -178.33 1 6.00e+00 2.78e-02 5.33e+02 dihedral pdb=" C1 BCLBX1002 " pdb=" CGA BCLBX1002 " pdb=" O2A BCLBX1002 " pdb=" CBA BCLBX1002 " ideal model delta sinusoidal sigma weight residual -180.00 -20.94 -159.06 1 6.00e+00 2.78e-02 5.16e+02 ... (remaining 29559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 7424 0.086 - 0.171: 580 0.171 - 0.257: 18 0.257 - 0.343: 2 0.343 - 0.428: 6 Chirality restraints: 8030 Sorted by residual: 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 2.91 -0.43 2.00e-01 2.50e+01 4.58e+00 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 -2.92 0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" C2 UYHai 102 " pdb=" C1 UYHai 102 " pdb=" C3 UYHai 102 " pdb=" O2 UYHai 102 " both_signs ideal model delta sigma weight residual False -2.50 -2.92 0.42 2.00e-01 2.50e+01 4.33e+00 ... (remaining 8027 not shown) Planarity restraints: 8942 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C26 V7Nba 101 " 0.329 2.00e-02 2.50e+03 3.19e-01 1.02e+03 pdb=" C27 V7Nba 101 " -0.356 2.00e-02 2.50e+03 pdb=" C28 V7Nba 101 " -0.279 2.00e-02 2.50e+03 pdb=" C29 V7Nba 101 " 0.307 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C26 V7Nbb 101 " 0.154 2.00e-02 2.50e+03 3.02e-01 9.09e+02 pdb=" C27 V7Nbb 101 " -0.402 2.00e-02 2.50e+03 pdb=" C28 V7Nbb 101 " 0.395 2.00e-02 2.50e+03 pdb=" C29 V7Nbb 101 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C26 V7Nbe 101 " 0.176 2.00e-02 2.50e+03 1.86e-01 3.48e+02 pdb=" C27 V7Nbe 101 " -0.145 2.00e-02 2.50e+03 pdb=" C28 V7Nbe 101 " -0.224 2.00e-02 2.50e+03 pdb=" C29 V7Nbe 101 " 0.193 2.00e-02 2.50e+03 ... (remaining 8939 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 1068 2.67 - 3.23: 48616 3.23 - 3.79: 91791 3.79 - 4.34: 133943 4.34 - 4.90: 211354 Nonbonded interactions: 486772 Sorted by model distance: nonbonded pdb=" NE2 HIS C 138 " pdb="FE HEC C 404 " model vdw 2.117 3.080 nonbonded pdb=" NE2 HIS M 218 " pdb="FE FE M 401 " model vdw 2.125 2.340 nonbonded pdb=" OE2 GLU M 233 " pdb="FE FE M 401 " model vdw 2.129 2.260 nonbonded pdb=" O HOHAP 203 " pdb=" O HOHAP 204 " model vdw 2.236 2.440 nonbonded pdb=" NE2 HIS L 190 " pdb="FE FE M 401 " model vdw 2.256 2.340 ... (remaining 486767 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 2 through 56) selection = (chain 'ab' and resid 2 through 56) selection = (chain 'ac' and resid 2 through 56) selection = (chain 'ad' and resid 2 through 56) selection = (chain 'ae' and resid 2 through 56) selection = (chain 'af' and resid 2 through 56) selection = (chain 'ag' and resid 2 through 56) selection = (chain 'ah' and resid 2 through 56) selection = (chain 'ai' and resid 2 through 56) selection = (chain 'aj' and resid 2 through 56) selection = (chain 'al' and resid 2 through 56) selection = (chain 'am' and resid 2 through 56) selection = (chain 'ao' and resid 2 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 275 5.16 5 C 38292 2.51 5 N 7224 2.21 5 O 9538 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: 3.760 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: 15.580 Check model and map are aligned: 0.590 Process input model: 94.820 Find NCS groups from input model: 2.730 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.360 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:9.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 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 0.175 57348 Z= 0.747 Angle : 4.336 55.517 78902 Z= 1.477 Chirality : 0.047 0.428 8030 Planarity : 0.013 0.319 8942 Dihedral : 24.730 178.327 20568 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.24 % 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: 1.63 (0.12), residues: 4733 helix: 1.23 (0.08), residues: 3092 sheet: 0.46 (1.11), residues: 22 loop : 1.10 (0.17), residues: 1619 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 792 time to evaluate : 3.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 802 average time/residue: 1.6995 time to fit residues: 1658.0243 Evaluate side-chains 613 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 606 time to evaluate : 3.925 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 3 average time/residue: 1.2635 time to fit residues: 9.5624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 371 optimal weight: 4.9990 chunk 333 optimal weight: 0.0270 chunk 185 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 chunk 178 optimal weight: 0.0170 chunk 344 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 209 optimal weight: 0.8980 chunk 256 optimal weight: 4.9990 chunk 399 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 37 ASN AF 37 ASN ** AK 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 37 ASN C1 164 GLN H2 49 HIS H2 103 GLN L 104 GLN L 144 HIS L 166 HIS L 264 ASN L 268 ASN M 141 GLN M 316 GLN ab 36 GLN ai 36 GLN am 50 GLN an 50 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 57348 Z= 0.193 Angle : 1.962 29.982 78902 Z= 0.671 Chirality : 0.036 0.235 8030 Planarity : 0.004 0.054 8942 Dihedral : 26.232 179.999 12290 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 0.68 % Favored : 99.30 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.24 % 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: 3.66 (0.12), residues: 4733 helix: 3.02 (0.08), residues: 3132 sheet: 0.34 (1.06), residues: 28 loop : 1.35 (0.18), residues: 1573 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 631 time to evaluate : 3.900 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 31 residues processed: 669 average time/residue: 1.6425 time to fit residues: 1351.3126 Evaluate side-chains 605 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 574 time to evaluate : 3.842 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 20 residues processed: 12 average time/residue: 0.6117 time to fit residues: 16.3804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 222 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 332 optimal weight: 4.9990 chunk 272 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 400 optimal weight: 0.9980 chunk 432 optimal weight: 4.9990 chunk 356 optimal weight: 0.6980 chunk 396 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 chunk 321 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 35 GLN AB 37 ASN AC 37 ASN ** AK 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** am 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 57348 Z= 0.240 Angle : 1.843 27.707 78902 Z= 0.631 Chirality : 0.037 0.231 8030 Planarity : 0.004 0.058 8942 Dihedral : 25.380 179.895 12290 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer Outliers : 2.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.24 % 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: 3.79 (0.12), residues: 4733 helix: 3.20 (0.08), residues: 3160 sheet: 0.36 (1.06), residues: 28 loop : 1.16 (0.18), residues: 1545 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 595 time to evaluate : 3.868 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 45 residues processed: 642 average time/residue: 1.6215 time to fit residues: 1284.7523 Evaluate side-chains 609 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 564 time to evaluate : 3.882 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 27 residues processed: 18 average time/residue: 0.7415 time to fit residues: 24.7792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 395 optimal weight: 10.0000 chunk 300 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 44 optimal weight: 20.0000 chunk 191 optimal weight: 3.9990 chunk 268 optimal weight: 20.0000 chunk 401 optimal weight: 6.9990 chunk 425 optimal weight: 9.9990 chunk 209 optimal weight: 0.8980 chunk 380 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AD 35 GLN ** AK 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 35 GLN C1 109 GLN C1 164 GLN H2 12 ASN L 264 ASN am 50 GLN ** an 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.092 57348 Z= 0.562 Angle : 1.960 25.904 78902 Z= 0.683 Chirality : 0.049 0.274 8030 Planarity : 0.006 0.067 8942 Dihedral : 26.129 179.935 12290 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.12), residues: 4733 helix: 2.61 (0.08), residues: 3155 sheet: -1.18 (1.27), residues: 18 loop : 0.80 (0.17), residues: 1560 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 590 time to evaluate : 3.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 59 residues processed: 650 average time/residue: 1.6182 time to fit residues: 1296.4612 Evaluate side-chains 627 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 568 time to evaluate : 3.843 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 38 residues processed: 22 average time/residue: 0.7078 time to fit residues: 28.0524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 354 optimal weight: 0.9990 chunk 241 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 316 optimal weight: 0.9990 chunk 175 optimal weight: 0.2980 chunk 362 optimal weight: 0.5980 chunk 293 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 217 optimal weight: 0.9990 chunk 381 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AE 35 GLN AK 35 GLN ** AK 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 11 HIS ** AN 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 35 GLN L 264 ASN am 50 GLN ** an 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 57348 Z= 0.168 Angle : 1.763 24.610 78902 Z= 0.600 Chirality : 0.035 0.213 8030 Planarity : 0.004 0.063 8942 Dihedral : 24.672 179.986 12290 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer Outliers : 2.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.24 % 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: 3.76 (0.12), residues: 4733 helix: 3.27 (0.08), residues: 3155 sheet: -1.02 (1.22), residues: 18 loop : 0.93 (0.17), residues: 1560 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 593 time to evaluate : 3.913 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 39 residues processed: 641 average time/residue: 1.6132 time to fit residues: 1280.5379 Evaluate side-chains 602 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 563 time to evaluate : 3.852 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 35 residues processed: 5 average time/residue: 0.7511 time to fit residues: 10.0819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 143 optimal weight: 0.9980 chunk 383 optimal weight: 0.2980 chunk 84 optimal weight: 10.0000 chunk 249 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 425 optimal weight: 8.9990 chunk 353 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 223 optimal weight: 0.0970 overall best weight: 2.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AK 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 164 GLN H2 12 ASN L 264 ASN M 47 GLN ** an 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 57348 Z= 0.258 Angle : 1.782 24.485 78902 Z= 0.610 Chirality : 0.037 0.219 8030 Planarity : 0.004 0.064 8942 Dihedral : 24.299 179.876 12290 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.24 % 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: 3.71 (0.12), residues: 4733 helix: 3.07 (0.08), residues: 3218 sheet: -1.30 (1.05), residues: 24 loop : 1.23 (0.18), residues: 1491 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 576 time to evaluate : 3.879 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 49 residues processed: 629 average time/residue: 1.6128 time to fit residues: 1255.2302 Evaluate side-chains 608 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 559 time to evaluate : 3.821 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 38 residues processed: 11 average time/residue: 0.6189 time to fit residues: 15.2861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 410 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 chunk 310 optimal weight: 8.9990 chunk 240 optimal weight: 3.9990 chunk 358 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 424 optimal weight: 10.0000 chunk 265 optimal weight: 0.9990 chunk 258 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AK 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2 12 ASN ** H2 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 264 ASN am 50 GLN ** an 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ao 2 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 57348 Z= 0.257 Angle : 1.771 24.122 78902 Z= 0.606 Chirality : 0.037 0.216 8030 Planarity : 0.004 0.068 8942 Dihedral : 23.974 179.894 12290 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.24 % 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: 3.66 (0.12), residues: 4733 helix: 3.19 (0.08), residues: 3161 sheet: -1.28 (1.04), residues: 24 loop : 0.88 (0.18), residues: 1548 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 573 time to evaluate : 4.913 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 49 residues processed: 626 average time/residue: 1.6274 time to fit residues: 1261.5065 Evaluate side-chains 604 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 555 time to evaluate : 3.854 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 41 residues processed: 8 average time/residue: 0.5967 time to fit residues: 12.1992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 262 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 253 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 269 optimal weight: 1.9990 chunk 288 optimal weight: 7.9990 chunk 209 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 333 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AK 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 35 GLN C1 164 GLN H2 12 ASN ** H2 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 264 ASN ao 2 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 57348 Z= 0.205 Angle : 1.745 23.840 78902 Z= 0.595 Chirality : 0.036 0.214 8030 Planarity : 0.004 0.064 8942 Dihedral : 23.494 179.905 12290 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.24 % 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: 3.79 (0.12), residues: 4733 helix: 3.31 (0.08), residues: 3161 sheet: -1.25 (1.04), residues: 24 loop : 0.90 (0.18), residues: 1548 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 566 time to evaluate : 3.946 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 49 residues processed: 613 average time/residue: 1.6248 time to fit residues: 1233.5080 Evaluate side-chains 604 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 555 time to evaluate : 3.856 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 41 residues processed: 8 average time/residue: 0.7973 time to fit residues: 13.8687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 385 optimal weight: 3.9990 chunk 406 optimal weight: 9.9990 chunk 370 optimal weight: 0.9980 chunk 395 optimal weight: 0.9980 chunk 237 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 310 optimal weight: 9.9990 chunk 121 optimal weight: 0.9990 chunk 357 optimal weight: 0.3980 chunk 373 optimal weight: 6.9990 chunk 393 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AK 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2 122 ASN L 264 ASN am 50 GLN ao 2 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 57348 Z= 0.172 Angle : 1.719 23.512 78902 Z= 0.585 Chirality : 0.034 0.215 8030 Planarity : 0.004 0.068 8942 Dihedral : 22.997 179.854 12290 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.24 % 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: 3.98 (0.12), residues: 4733 helix: 3.29 (0.08), residues: 3214 sheet: -1.14 (1.04), residues: 24 loop : 1.28 (0.18), residues: 1495 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 561 time to evaluate : 3.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 48 residues processed: 607 average time/residue: 1.6566 time to fit residues: 1248.7377 Evaluate side-chains 597 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 549 time to evaluate : 3.855 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 41 residues processed: 7 average time/residue: 1.0440 time to fit residues: 14.4887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 259 optimal weight: 0.7980 chunk 417 optimal weight: 7.9990 chunk 255 optimal weight: 0.9990 chunk 198 optimal weight: 0.9990 chunk 290 optimal weight: 3.9990 chunk 438 optimal weight: 9.9990 chunk 403 optimal weight: 10.0000 chunk 349 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 269 optimal weight: 8.9990 chunk 214 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AK 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 164 GLN H2 12 ASN L 264 ASN M 47 GLN am 50 GLN ao 2 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 57348 Z= 0.253 Angle : 1.748 23.903 78902 Z= 0.598 Chirality : 0.037 0.326 8030 Planarity : 0.004 0.064 8942 Dihedral : 23.117 179.930 12290 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.24 % 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: 3.78 (0.12), residues: 4733 helix: 3.29 (0.08), residues: 3157 sheet: -1.19 (1.06), residues: 24 loop : 0.94 (0.18), residues: 1552 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9466 Ramachandran restraints generated. 4733 Oldfield, 0 Emsley, 4733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 559 time to evaluate : 3.911 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 45 residues processed: 603 average time/residue: 1.6460 time to fit residues: 1235.1981 Evaluate side-chains 602 residues out of total 3906 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 557 time to evaluate : 3.863 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 41 residues processed: 5 average time/residue: 1.0316 time to fit residues: 11.6318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 277 optimal weight: 5.9990 chunk 371 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 321 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 349 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 359 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AK 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 264 ASN am 50 GLN ** an 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ao 2 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.098285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.069897 restraints weight = 94855.633| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.50 r_work: 0.2668 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.090 57348 Z= 0.503 Angle : 1.862 24.932 78902 Z= 0.646 Chirality : 0.046 0.342 8030 Planarity : 0.005 0.089 8942 Dihedral : 24.172 179.243 12290 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.24 % 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: 3.14 (0.12), residues: 4733 helix: 2.77 (0.08), residues: 3155 sheet: -1.34 (1.14), residues: 20 loop : 0.75 (0.17), residues: 1558 =============================================================================== Job complete usr+sys time: 18801.96 seconds wall clock time: 326 minutes 37.54 seconds (19597.54 seconds total)