Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 02:26:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0x_12682/04_2023/7o0x_12682_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0x_12682/04_2023/7o0x_12682.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0x_12682/04_2023/7o0x_12682_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0x_12682/04_2023/7o0x_12682_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0x_12682/04_2023/7o0x_12682_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0x_12682/04_2023/7o0x_12682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0x_12682/04_2023/7o0x_12682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0x_12682/04_2023/7o0x_12682_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0x_12682/04_2023/7o0x_12682_updated.pdb" } resolution = 2.44 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 5 7.16 5 P 33 5.49 5 Mg 108 5.21 5 S 278 5.16 5 C 38880 2.51 5 N 7407 2.21 5 O 9735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "BK PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BO PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H2 TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 56446 Number of models: 1 Model: "" Number of chains: 237 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: "C2" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 766 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} 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: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1404 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 163} 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: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2694 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 22, 'TRANS': 312} 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: "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 chiralities: 2 Chain: "CG" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'MAN': 1, 'RAM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "AA" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AB" Number of atoms: 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: "AC" 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: "AD" 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: "AE" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 177 Unusual residues: {'BCL': 2, 'V7N': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AF" 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: "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: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 282 Unusual residues: {'BCL': 2, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: 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: "AK" 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: "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: 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: "AO" 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: "AP" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AQ" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 198 Unusual residues: {'BCL': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AR" 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: "AS" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 233 Unusual residues: {'BCL': 3, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AT" Number of atoms: 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: "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: 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: "AW" 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: "AX" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BA" Number of atoms: 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: "BB" 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: "BC" 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: "BD" 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: "BE" 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: "BF" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 171 Unusual residues: {'BCL': 1, 'LMT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BG" Number of atoms: 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: "BH" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BI" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 206 Unusual residues: {'BCL': 1, 'LMT': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BJ" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BK" Number of atoms: 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: 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: "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: 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: "BQ" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BR" Number of atoms: 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: "BS" 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: "BT" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BU" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 171 Unusual residues: {'BCL': 1, 'LMT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BV" Number of atoms: 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: "BW" 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: "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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NDG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H1" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 180 Unusual residues: {'0V9': 1, 'CD4': 1, 'PGW': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "L" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 470 Unusual residues: {'0V9': 1, 'BCL': 2, 'BPH': 1, 'LMT': 5, 'MQ8': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "M" Number of atoms: 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ac" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "ad" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 150 Unusual residues: {'BCL': 1, 'CD4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "ae" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "af" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 292 Unusual residues: {'BCL': 1, 'CD4': 2, 'V7B': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 205 Unusual residues: {'BCL': 1, 'CD4': 1, 'UYH': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "aj" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'0V9': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 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: "ao" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ap" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ba" 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: "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: 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: "bf" 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: "bg" 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: "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: 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: "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: 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: "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: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bn" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bo" Number of atoms: 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: "bp" 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: "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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AD" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "AG" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AH" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} 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: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "AK" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AL" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AM" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AN" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AO" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AP" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AQ" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "AR" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AS" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "AT" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} 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: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "AX" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "BD" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "BE" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "BF" 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: "BW" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 98 Classifications: {'water': 98} Link IDs: {None: 97} Chain: "C1" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "C2" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "H1" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "H2" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "M" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "aa" Number of atoms: 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "ad" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "ae" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "af" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "aj" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "ak" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "al" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "am" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "an" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "ao" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "ap" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "bb" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "bc" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "bd" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "be" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "bk" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "bn" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "bo" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "bp" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 22.04, per 1000 atoms: 0.39 Number of scatterers: 56446 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 278 16.00 P 33 15.00 Mg 108 11.99 O 9735 8.00 N 7407 7.00 C 38880 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=112, 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=112, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.76 Conformation dependent library (CDL) restraints added in 4.5 seconds 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9226 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 223 helices and 4 sheets defined 66.2% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 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 35 Processing helix chain 'AA' and resid 40 through 46 removed outlier: 3.507A pdb=" N TYRAA 46 " --> pdb=" O LEUAA 42 " (cutoff:3.500A) 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: 3.649A pdb=" N GLYAB 34 " --> pdb=" O ILEAB 30 " (cutoff:3.500A) Processing helix chain 'AB' and resid 40 through 46 Processing helix chain 'AC' and resid 3 through 5 No H-bonds generated for 'chain 'AC' and resid 3 through 5' Processing helix chain 'AC' and resid 10 through 35 Processing helix chain 'AC' and resid 40 through 46 removed outlier: 3.581A pdb=" N TYRAC 46 " --> pdb=" O LEUAC 42 " (cutoff:3.500A) 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 5 No H-bonds generated for 'chain 'AE' and resid 3 through 5' Processing helix chain 'AE' and resid 10 through 36 Processing helix chain 'AE' and resid 40 through 46 Processing helix chain 'AF' and resid 10 through 36 Processing helix chain 'AF' and resid 40 through 46 removed outlier: 3.513A pdb=" N TYRAF 46 " --> pdb=" O LEUAF 42 " (cutoff:3.500A) Processing helix chain 'AG' and resid 3 through 5 No H-bonds generated for 'chain 'AG' and resid 3 through 5' Processing helix chain 'AG' and resid 10 through 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 36 removed outlier: 3.529A pdb=" N GLYAH 34 " --> pdb=" O ILEAH 30 " (cutoff:3.500A) Processing helix chain 'AH' and resid 40 through 46 removed outlier: 3.538A 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 removed outlier: 3.557A pdb=" N GLYAI 34 " --> pdb=" O ILEAI 30 " (cutoff:3.500A) Processing helix chain 'AI' and resid 40 through 46 removed outlier: 3.529A pdb=" N TYRAI 46 " --> pdb=" O LEUAI 42 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 3 through 5 No H-bonds generated for 'chain 'AJ' and resid 3 through 5' Processing helix chain 'AJ' and resid 10 through 36 Processing helix chain 'AJ' and resid 40 through 46 removed outlier: 3.548A pdb=" N TYRAJ 46 " --> pdb=" O LEUAJ 42 " (cutoff:3.500A) 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: 3.593A pdb=" N GLYAK 34 " --> pdb=" O ILEAK 30 " (cutoff:3.500A) Processing helix chain 'AK' and resid 40 through 46 removed outlier: 3.505A pdb=" N TYRAK 46 " --> pdb=" O LEUAK 42 " (cutoff:3.500A) Processing helix chain 'AL' and resid 3 through 5 No H-bonds generated for 'chain 'AL' and resid 3 through 5' Processing helix chain 'AL' and resid 10 through 36 Processing helix chain 'AL' and resid 40 through 46 Processing helix chain 'AM' and resid 3 through 5 No H-bonds generated for 'chain 'AM' and resid 3 through 5' Processing helix chain 'AM' and resid 10 through 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 36 removed outlier: 3.569A 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 removed outlier: 3.575A pdb=" N GLYAO 34 " --> pdb=" O ILEAO 30 " (cutoff:3.500A) Processing helix chain 'AO' and resid 40 through 46 removed outlier: 3.524A pdb=" N TYRAO 46 " --> pdb=" O LEUAO 42 " (cutoff:3.500A) Processing helix chain 'AP' and resid 3 through 5 No H-bonds generated for 'chain 'AP' and resid 3 through 5' Processing helix chain 'AP' and resid 10 through 35 Processing helix chain 'AP' and resid 40 through 46 removed outlier: 3.556A pdb=" N TYRAP 46 " --> pdb=" O LEUAP 42 " (cutoff:3.500A) 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 removed outlier: 3.563A pdb=" N GLYAR 34 " --> pdb=" O ILEAR 30 " (cutoff:3.500A) Processing helix chain 'AR' and resid 40 through 46 Processing helix chain 'AS' and resid 3 through 5 No H-bonds generated for 'chain 'AS' and resid 3 through 5' Processing helix chain 'AS' and resid 10 through 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 removed outlier: 3.573A pdb=" N GLYAT 34 " --> pdb=" O ILEAT 30 " (cutoff:3.500A) Processing helix chain 'AT' and resid 40 through 46 Processing helix chain 'AU' and resid 3 through 5 No H-bonds generated for 'chain 'AU' and resid 3 through 5' Processing helix chain 'AU' and resid 10 through 36 Processing helix chain 'AU' and resid 40 through 46 Processing helix chain 'AV' and resid 3 through 5 No H-bonds generated for 'chain 'AV' and resid 3 through 5' Processing helix chain 'AV' and resid 10 through 36 Processing helix chain 'AV' and resid 40 through 46 Processing helix chain 'AW' and resid 3 through 5 No H-bonds generated for 'chain 'AW' and resid 3 through 5' Processing helix chain 'AW' and resid 10 through 35 removed outlier: 3.586A pdb=" N GLYAW 34 " --> pdb=" O ILEAW 30 " (cutoff:3.500A) Processing helix chain 'AW' and resid 40 through 46 removed outlier: 3.535A pdb=" N TYRAW 46 " --> pdb=" O LEUAW 42 " (cutoff:3.500A) Processing helix chain 'AX' and resid 10 through 36 Processing helix chain 'AX' and resid 40 through 46 removed outlier: 3.529A 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 removed outlier: 3.804A 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 Processing helix chain 'BF' and resid 9 through 40 removed outlier: 3.759A pdb=" N GLYBF 17 " --> pdb=" O ARGBF 13 " (cutoff:3.500A) Processing helix chain 'BG' and resid 9 through 40 Processing helix chain 'BH' and resid 9 through 40 removed outlier: 3.618A pdb=" N GLYBH 17 " --> pdb=" O ARGBH 13 " (cutoff:3.500A) Processing helix chain 'BI' and resid 9 through 40 Processing helix chain 'BJ' and resid 9 through 40 removed outlier: 3.657A pdb=" N TYRBJ 18 " --> pdb=" O ARGBJ 14 " (cutoff:3.500A) Processing helix chain 'BK' and resid 9 through 40 removed outlier: 3.772A pdb=" N GLYBK 17 " --> pdb=" O ARGBK 13 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYRBK 18 " --> pdb=" O ARGBK 14 " (cutoff:3.500A) Processing helix chain 'BL' and resid 9 through 40 removed outlier: 3.669A pdb=" N TYRBL 18 " --> pdb=" O ARGBL 14 " (cutoff:3.500A) Processing helix chain 'BM' and resid 9 through 40 removed outlier: 3.504A pdb=" N GLYBM 17 " --> pdb=" O ARGBM 13 " (cutoff:3.500A) Processing helix chain 'BN' and resid 9 through 40 removed outlier: 3.502A pdb=" N GLYBN 17 " --> pdb=" O ARGBN 13 " (cutoff:3.500A) Processing helix chain 'BO' and resid 9 through 40 removed outlier: 3.546A pdb=" N GLYBO 17 " --> pdb=" O ARGBO 13 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYRBO 18 " --> pdb=" O ARGBO 14 " (cutoff:3.500A) Processing helix chain 'BP' and resid 9 through 40 Processing helix chain 'BQ' and resid 9 through 40 removed outlier: 3.552A pdb=" N TYRBQ 18 " --> pdb=" O ARGBQ 14 " (cutoff:3.500A) Processing helix chain 'BR' and resid 9 through 40 removed outlier: 3.535A pdb=" N TYRBR 18 " --> pdb=" O ARGBR 14 " (cutoff:3.500A) Processing helix chain 'BS' and resid 9 through 40 removed outlier: 3.749A pdb=" N TYRBS 18 " --> pdb=" O ARGBS 14 " (cutoff:3.500A) Processing helix chain 'BT' and resid 9 through 40 removed outlier: 3.654A pdb=" N GLYBT 17 " --> pdb=" O ARGBT 13 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYRBT 18 " --> pdb=" O ARGBT 14 " (cutoff:3.500A) Processing helix chain 'BU' and resid 9 through 40 Processing helix chain 'BV' and resid 9 through 40 removed outlier: 3.559A pdb=" N GLYBV 17 " --> pdb=" O ARGBV 13 " (cutoff:3.500A) Processing helix chain 'BW' and resid 9 through 40 removed outlier: 3.596A pdb=" N TYRBW 18 " --> pdb=" O ARGBW 14 " (cutoff:3.500A) Processing helix chain 'BX' and resid 9 through 40 removed outlier: 3.577A 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 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 233 through 251 removed outlier: 3.564A pdb=" N ASN C 249 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN C 250 " --> pdb=" O ASP C 247 " (cutoff:3.500A) removed outlier: 4.050A 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 276 through 280 Processing helix chain 'C' and resid 286 through 289 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 297 through 299 No H-bonds generated for 'chain 'C' and resid 297 through 299' Processing helix chain 'C1' and resid 127 through 129 No H-bonds generated for 'chain 'C1' and resid 127 through 129' Processing helix chain 'C1' and resid 136 through 142 Processing helix chain 'C1' and resid 161 through 163 No H-bonds generated for 'chain 'C1' and resid 161 through 163' Processing helix chain 'C1' and resid 172 through 175 No H-bonds generated for 'chain 'C1' and resid 172 through 175' Processing helix chain 'C1' and resid 183 through 189 Processing helix chain 'C1' and resid 197 through 199 No H-bonds generated for 'chain 'C1' and resid 197 through 199' Processing helix chain 'C2' and resid 4 through 9 Processing helix chain 'C2' and resid 22 through 52 removed outlier: 3.525A pdb=" N ALAC2 33 " --> pdb=" O VALC2 29 " (cutoff:3.500A) Processing helix chain 'C2' and resid 55 through 87 removed outlier: 3.526A pdb=" N TRPC2 75 " --> pdb=" O GLUC2 71 " (cutoff:3.500A) Processing helix chain 'H1' and resid 7 through 31 removed outlier: 3.535A pdb=" N LYSH1 31 " --> pdb=" O ARGH1 27 " (cutoff:3.500A) Processing helix chain 'H2' and resid 22 through 25 No H-bonds generated for 'chain 'H2' and resid 22 through 25' Processing helix chain 'H2' and resid 28 through 30 No H-bonds generated for 'chain 'H2' and resid 28 through 30' Processing helix chain 'H2' and resid 54 through 56 No H-bonds generated for 'chain 'H2' and resid 54 through 56' Processing helix chain 'H2' and resid 115 through 117 No H-bonds generated for 'chain 'H2' and resid 115 through 117' Processing helix chain 'H2' and resid 140 through 143 Processing helix chain 'H2' and resid 155 through 171 removed outlier: 3.642A pdb=" N GLYH2 168 " --> pdb=" O TYRH2 164 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N HISH2 169 " --> pdb=" O TYRH2 165 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N METH2 170 " --> pdb=" O ALAH2 166 " (cutoff:3.500A) Processing helix chain 'H2' and resid 174 through 177 removed outlier: 3.766A pdb=" N SERH2 177 " --> pdb=" O ALAH2 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'H2' and resid 174 through 177' Processing helix chain 'L' and resid 7 through 9 No H-bonds generated for 'chain 'L' and resid 7 through 9' Processing helix chain 'L' and resid 32 through 55 Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'L' and resid 84 through 110 Processing helix chain 'L' and resid 116 through 132 removed outlier: 4.050A 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: 3.903A 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 250 removed outlier: 3.681A pdb=" N HIS L 230 " --> pdb=" O ALA L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 260 through 267 removed outlier: 3.655A pdb=" N TRP L 265 " --> pdb=" O TRP L 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 43 removed outlier: 3.765A pdb=" N PHE M 43 " --> pdb=" O LEU M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 79 Processing helix chain 'M' and resid 83 through 88 Processing helix chain 'M' and resid 90 through 92 No H-bonds generated for 'chain 'M' and resid 90 through 92' Processing helix chain 'M' and resid 100 through 102 No H-bonds generated for 'chain 'M' and resid 100 through 102' Processing helix chain 'M' and resid 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: 3.568A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE M 160 " --> pdb=" O LEU M 156 " (cutoff:3.500A) removed outlier: 3.969A 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: 3.746A pdb=" N LEU M 182 " --> pdb=" O ILE M 178 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER M 189 " --> pdb=" O THR M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 197 No H-bonds generated for 'chain 'M' and resid 195 through 197' Processing helix chain 'M' and resid 199 through 228 removed outlier: 4.683A pdb=" N ARG M 227 " --> pdb=" O LEU M 223 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N MET M 228 " --> pdb=" O ALA M 224 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 238 Processing helix chain 'M' and resid 242 through 255 removed outlier: 3.520A 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 299 Processing helix chain 'M' and resid 314 through 320 Processing helix chain 'aa' and resid 3 through 7 Processing helix chain 'aa' and resid 10 through 34 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 33 removed outlier: 3.700A 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 12 No H-bonds generated for 'chain 'ac' and resid 10 through 12' Processing helix chain 'ac' and resid 14 through 34 removed outlier: 3.505A pdb=" N SERac 34 " --> pdb=" O PHEac 30 " (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: 3.723A 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: 3.888A 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 removed outlier: 3.529A pdb=" N VALai 15 " --> pdb=" O ARGai 11 " (cutoff:3.500A) Processing helix chain 'ai' and resid 40 through 43 No H-bonds generated for 'chain 'ai' and resid 40 through 43' Processing helix chain 'aj' and resid 3 through 7 Processing helix chain 'aj' and resid 10 through 33 removed outlier: 3.665A pdb=" N VALaj 15 " --> pdb=" O ARGaj 11 " (cutoff:3.500A) Processing helix chain 'aj' and resid 40 through 43 No H-bonds generated for 'chain 'aj' and resid 40 through 43' Processing helix chain 'ak' and resid 3 through 7 Processing helix chain 'ak' and resid 10 through 34 removed outlier: 3.867A 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: 3.941A 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: 3.918A 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 'an' and resid 3 through 7 Processing helix chain 'an' and resid 10 through 34 removed outlier: 3.576A 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: 3.777A 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 removed outlier: 3.724A pdb=" N METap 7 " --> pdb=" O ILEap 4 " (cutoff:3.500A) Processing helix chain 'ap' and resid 10 through 34 Processing helix chain 'ap' and resid 40 through 43 No H-bonds generated for 'chain 'ap' and resid 40 through 43' Processing helix chain 'ba' and resid 9 through 40 removed outlier: 3.736A pdb=" N TYRba 18 " --> pdb=" O ARGba 14 " (cutoff:3.500A) 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 41 Processing helix chain 'be' and resid 9 through 40 removed outlier: 3.732A pdb=" N TYRbe 18 " --> pdb=" O ARGbe 14 " (cutoff:3.500A) Processing helix chain 'bf' and resid 9 through 40 removed outlier: 3.543A pdb=" N TYRbf 18 " --> pdb=" O ARGbf 14 " (cutoff:3.500A) Processing helix chain 'bg' and resid 9 through 40 removed outlier: 3.519A pdb=" N GLYbg 17 " --> pdb=" O ARGbg 13 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYRbg 18 " --> pdb=" O ARGbg 14 " (cutoff:3.500A) Processing helix chain 'bh' and resid 9 through 40 removed outlier: 3.622A pdb=" N ARGbh 14 " --> pdb=" O GLUbh 10 " (cutoff:3.500A) Processing helix chain 'bi' and resid 9 through 40 removed outlier: 3.617A pdb=" N TYRbi 18 " --> pdb=" O ARGbi 14 " (cutoff:3.500A) Processing helix chain 'bj' and resid 9 through 41 Processing helix chain 'bk' and resid 9 through 40 removed outlier: 3.764A 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: 3.657A 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 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: 6.818A pdb=" N GLUH2 101 " --> pdb=" O VALH2 86 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEUH2 88 " --> pdb=" O TYRH2 99 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYRH2 99 " --> pdb=" O LEUH2 88 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H2' and resid 130 through 132 removed outlier: 3.788A pdb=" N GLYH2 83 " --> pdb=" O VALH2 74 " (cutoff:3.500A) 2464 hydrogen bonds defined for protein. 7224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.01 Time building geometry restraints manager: 21.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.35: 13620 1.35 - 1.56: 43567 1.56 - 1.77: 178 1.77 - 1.98: 500 1.98 - 2.18: 448 Bond restraints: 58313 Sorted by residual: bond pdb=" C27 V7Nba 101 " pdb=" C28 V7Nba 101 " ideal model delta sigma weight residual 1.348 1.522 -0.174 2.00e-02 2.50e+03 7.56e+01 bond pdb=" C27 V7NBV1001 " pdb=" C28 V7NBV1001 " ideal model delta sigma weight residual 1.348 1.522 -0.174 2.00e-02 2.50e+03 7.55e+01 bond pdb=" C27 V7Nbp 102 " pdb=" C28 V7Nbp 102 " ideal model delta sigma weight residual 1.348 1.522 -0.174 2.00e-02 2.50e+03 7.55e+01 bond pdb=" C27 V7Nbl 102 " pdb=" C28 V7Nbl 102 " ideal model delta sigma weight residual 1.348 1.521 -0.173 2.00e-02 2.50e+03 7.52e+01 bond pdb=" C27 V7Nbg 101 " pdb=" C28 V7Nbg 101 " ideal model delta sigma weight residual 1.348 1.521 -0.173 2.00e-02 2.50e+03 7.52e+01 ... (remaining 58308 not shown) Histogram of bond angle deviations from ideal: 84.79 - 103.09: 1319 103.09 - 121.40: 62259 121.40 - 139.70: 16312 139.70 - 158.00: 124 158.00 - 176.31: 210 Bond angle restraints: 80224 Sorted by residual: angle pdb=" C34 V7NBM1001 " pdb=" C9 V7NBM1001 " pdb=" C8 V7NBM1001 " ideal model delta sigma weight residual 68.18 124.10 -55.92 3.00e+00 1.11e-01 3.47e+02 angle pdb=" C34 V7NBD 101 " pdb=" C9 V7NBD 101 " pdb=" C8 V7NBD 101 " ideal model delta sigma weight residual 68.18 123.92 -55.74 3.00e+00 1.11e-01 3.45e+02 angle pdb=" C34 V7Nbm 101 " pdb=" C9 V7Nbm 101 " pdb=" C8 V7Nbm 101 " ideal model delta sigma weight residual 68.18 123.15 -54.97 3.00e+00 1.11e-01 3.36e+02 angle pdb=" C19 V7NBP1001 " pdb=" C18 V7NBP1001 " pdb=" C36 V7NBP1001 " ideal model delta sigma weight residual 68.14 122.90 -54.76 3.00e+00 1.11e-01 3.33e+02 angle pdb=" C19 V7NBD 101 " pdb=" C18 V7NBD 101 " pdb=" C36 V7NBD 101 " ideal model delta sigma weight residual 68.14 122.74 -54.60 3.00e+00 1.11e-01 3.31e+02 ... (remaining 80219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 28282 35.40 - 70.80: 1160 70.80 - 106.20: 446 106.20 - 141.60: 122 141.60 - 177.00: 88 Dihedral angle restraints: 30098 sinusoidal: 15667 harmonic: 14431 Sorted by residual: dihedral pdb=" CBD BCLAQ 103 " pdb=" CGD BCLAQ 103 " pdb=" O2D BCLAQ 103 " pdb=" CED BCLAQ 103 " ideal model delta sinusoidal sigma weight residual -180.00 -13.49 -166.51 1 5.00e+00 4.00e-02 7.57e+02 dihedral pdb=" C1 BCLAK 103 " pdb=" C2 BCLAK 103 " pdb=" C3 BCLAK 103 " pdb=" C5 BCLAK 103 " ideal model delta sinusoidal sigma weight residual 180.00 3.00 177.00 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCLAQ 103 " pdb=" CGA BCLAQ 103 " pdb=" O2A BCLAQ 103 " pdb=" CBA BCLAQ 103 " ideal model delta sinusoidal sigma weight residual -180.00 -149.94 -30.06 1 6.00e+00 2.78e-02 3.59e+01 ... (remaining 30095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 7306 0.098 - 0.196: 765 0.196 - 0.294: 86 0.294 - 0.392: 4 0.392 - 0.490: 5 Chirality restraints: 8166 Sorted by residual: chirality pdb=" C5' LMTBK1004 " pdb=" C4' LMTBK1004 " pdb=" C6' LMTBK1004 " pdb=" O5' LMTBK1004 " both_signs ideal model delta sigma weight residual False -2.51 -2.02 -0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" C4 UYHai 101 " pdb=" C3 UYHai 101 " pdb=" C5 UYHai 101 " pdb=" O4 UYHai 101 " both_signs ideal model delta sigma weight residual False -2.49 -2.93 0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" C5 UYHai 101 " pdb=" C4 UYHai 101 " pdb=" C6 UYHai 101 " pdb=" O6 UYHai 101 " both_signs ideal model delta sigma weight residual False -2.52 -2.95 0.43 2.00e-01 2.50e+01 4.64e+00 ... (remaining 8163 not shown) Planarity restraints: 9122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C26 V7Nbg 101 " -0.185 2.00e-02 2.50e+03 1.94e-01 3.75e+02 pdb=" C27 V7Nbg 101 " 0.159 2.00e-02 2.50e+03 pdb=" C28 V7Nbg 101 " 0.226 2.00e-02 2.50e+03 pdb=" C29 V7Nbg 101 " -0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C26 V7NBV1001 " 0.186 2.00e-02 2.50e+03 1.88e-01 3.55e+02 pdb=" C27 V7NBV1001 " -0.178 2.00e-02 2.50e+03 pdb=" C28 V7NBV1001 " -0.198 2.00e-02 2.50e+03 pdb=" C29 V7NBV1001 " 0.191 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C26 V7NBQ1001 " -0.127 2.00e-02 2.50e+03 1.25e-01 1.57e+02 pdb=" C27 V7NBQ1001 " 0.142 2.00e-02 2.50e+03 pdb=" C28 V7NBQ1001 " 0.107 2.00e-02 2.50e+03 pdb=" C29 V7NBQ1001 " -0.122 2.00e-02 2.50e+03 ... (remaining 9119 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 960 2.66 - 3.22: 48675 3.22 - 3.78: 93166 3.78 - 4.34: 136759 4.34 - 4.90: 215962 Nonbonded interactions: 495522 Sorted by model distance: nonbonded pdb=" OE2 GLU M 233 " pdb="FE FE M 401 " model vdw 2.099 2.260 nonbonded pdb=" NE2 HIS M 218 " pdb="FE FE M 401 " model vdw 2.111 2.340 nonbonded pdb=" NE2 HIS C 138 " pdb="FE HEC C1002 " model vdw 2.131 3.080 nonbonded pdb=" O HOHAQ 202 " pdb=" O HOHAQ 204 " model vdw 2.210 2.440 nonbonded pdb=" O HOHAA1101 " pdb=" O HOHAA1103 " model vdw 2.259 2.440 ... (remaining 495517 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' and resid 1 through 71) selection = (chain 'an' and resid 1 through 71) 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)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 15.880 Check model and map are aligned: 0.660 Set scattering table: 0.390 Process input model: 104.980 Find NCS groups from input model: 2.720 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 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 : 0.018 0.174 58313 Z= 0.839 Angle : 4.336 55.917 80224 Z= 1.476 Chirality : 0.062 0.490 8166 Planarity : 0.012 0.194 9122 Dihedral : 24.660 177.004 20872 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.42 % Favored : 98.56 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.11), residues: 4858 helix: 0.84 (0.08), residues: 3312 sheet: -0.09 (1.05), residues: 21 loop : 1.36 (0.18), residues: 1525 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 788 time to evaluate : 4.292 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 797 average time/residue: 1.7430 time to fit residues: 1693.1982 Evaluate side-chains 593 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 588 time to evaluate : 4.160 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 1 average time/residue: 1.2561 time to fit residues: 6.3717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 381 optimal weight: 4.9990 chunk 342 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 231 optimal weight: 7.9990 chunk 183 optimal weight: 0.0020 chunk 354 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 215 optimal weight: 0.0370 chunk 263 optimal weight: 2.9990 chunk 410 optimal weight: 5.9990 overall best weight: 0.5870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AD 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 37 ASN AL 37 ASN AM 11 HIS AP 37 ASN AQ 37 ASN C1 157 GLN C1 158 GLN C2 24 HIS H2 12 ASN H2 119 GLN L 104 GLN L 116 HIS L 213 ASN M 316 GLN aa 2 HIS ad 50 GLN ah 50 GLN ai 36 GLN ap 2 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 58313 Z= 0.186 Angle : 1.961 27.635 80224 Z= 0.671 Chirality : 0.037 0.266 8166 Planarity : 0.004 0.056 9122 Dihedral : 25.856 179.822 12380 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.64 (0.12), residues: 4858 helix: 2.99 (0.08), residues: 3204 sheet: 0.00 (0.95), residues: 27 loop : 1.39 (0.17), residues: 1627 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 638 time to evaluate : 4.166 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 30 residues processed: 668 average time/residue: 1.6906 time to fit residues: 1389.9557 Evaluate side-chains 600 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 570 time to evaluate : 4.197 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 16 residues processed: 15 average time/residue: 0.8887 time to fit residues: 23.8147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 228 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 341 optimal weight: 0.0070 chunk 279 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 411 optimal weight: 5.9990 chunk 444 optimal weight: 3.9990 chunk 366 optimal weight: 3.9990 chunk 407 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 329 optimal weight: 3.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AD 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 37 ASN AW 35 GLN C1 157 GLN ad 50 GLN ** ag 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ah 50 GLN ak 50 GLN an 50 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 58313 Z= 0.328 Angle : 1.886 28.498 80224 Z= 0.650 Chirality : 0.042 0.256 8166 Planarity : 0.005 0.064 9122 Dihedral : 25.074 179.695 12380 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer Outliers : 2.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.52 (0.12), residues: 4858 helix: 2.96 (0.08), residues: 3225 sheet: -0.19 (0.94), residues: 27 loop : 1.17 (0.17), residues: 1606 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 586 time to evaluate : 5.322 Fit side-chains revert: symmetry clash outliers start: 106 outliers final: 50 residues processed: 637 average time/residue: 1.7215 time to fit residues: 1352.2318 Evaluate side-chains 615 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 565 time to evaluate : 4.263 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 30 residues processed: 20 average time/residue: 0.7269 time to fit residues: 27.1378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 406 optimal weight: 10.0000 chunk 309 optimal weight: 0.9980 chunk 213 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 chunk 276 optimal weight: 0.8980 chunk 412 optimal weight: 0.9980 chunk 436 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 391 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AD 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 35 GLN AQ 35 GLN C1 157 GLN ** ag 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** ah 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ah 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 58313 Z= 0.204 Angle : 1.787 26.576 80224 Z= 0.609 Chirality : 0.037 0.246 8166 Planarity : 0.004 0.053 9122 Dihedral : 24.004 179.821 12380 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.81 (0.12), residues: 4858 helix: 3.22 (0.08), residues: 3230 sheet: -0.46 (0.92), residues: 28 loop : 1.17 (0.17), residues: 1600 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 587 time to evaluate : 4.280 Fit side-chains revert: symmetry clash outliers start: 90 outliers final: 42 residues processed: 635 average time/residue: 1.6977 time to fit residues: 1336.1466 Evaluate side-chains 607 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 565 time to evaluate : 4.188 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 28 residues processed: 15 average time/residue: 0.7826 time to fit residues: 22.3227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 363 optimal weight: 10.0000 chunk 248 optimal weight: 0.3980 chunk 6 optimal weight: 10.0000 chunk 325 optimal weight: 0.9980 chunk 180 optimal weight: 0.4980 chunk 372 optimal weight: 4.9990 chunk 302 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 223 optimal weight: 7.9990 chunk 392 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 35 GLN AB 2 HIS AD 37 ASN AR 35 GLN C 137 GLN C1 157 GLN M 311 GLN aa 36 GLN ah 50 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 58313 Z= 0.164 Angle : 1.729 26.192 80224 Z= 0.587 Chirality : 0.035 0.219 8166 Planarity : 0.003 0.047 9122 Dihedral : 23.024 179.782 12380 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.05 (0.12), residues: 4858 helix: 3.43 (0.08), residues: 3230 sheet: -0.37 (0.92), residues: 28 loop : 1.19 (0.17), residues: 1600 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 593 time to evaluate : 4.264 Fit side-chains revert: symmetry clash outliers start: 86 outliers final: 43 residues processed: 640 average time/residue: 1.6720 time to fit residues: 1325.7819 Evaluate side-chains 606 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 563 time to evaluate : 4.233 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 30 residues processed: 13 average time/residue: 0.9722 time to fit residues: 22.9821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 146 optimal weight: 6.9990 chunk 393 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 256 optimal weight: 0.0870 chunk 107 optimal weight: 10.0000 chunk 437 optimal weight: 7.9990 chunk 363 optimal weight: 0.0870 chunk 202 optimal weight: 0.3980 chunk 36 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 229 optimal weight: 0.8980 overall best weight: 1.0938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 157 GLN ah 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 58313 Z= 0.168 Angle : 1.717 23.623 80224 Z= 0.583 Chirality : 0.035 0.220 8166 Planarity : 0.003 0.047 9122 Dihedral : 22.438 179.778 12380 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.07 (0.12), residues: 4858 helix: 3.45 (0.08), residues: 3225 sheet: -0.16 (0.92), residues: 27 loop : 1.20 (0.17), residues: 1606 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 575 time to evaluate : 4.385 Fit side-chains revert: symmetry clash outliers start: 79 outliers final: 43 residues processed: 615 average time/residue: 1.6541 time to fit residues: 1261.7593 Evaluate side-chains 599 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 556 time to evaluate : 4.152 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 31 residues processed: 12 average time/residue: 0.6417 time to fit residues: 17.0447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 421 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 249 optimal weight: 3.9990 chunk 319 optimal weight: 5.9990 chunk 247 optimal weight: 0.9990 chunk 368 optimal weight: 6.9990 chunk 244 optimal weight: 0.4980 chunk 435 optimal weight: 3.9990 chunk 272 optimal weight: 5.9990 chunk 265 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AX 35 GLN C1 157 GLN H2 119 GLN M 311 GLN aa 36 GLN ad 50 GLN ** ah 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ah 50 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 58313 Z= 0.189 Angle : 1.719 23.541 80224 Z= 0.584 Chirality : 0.036 0.223 8166 Planarity : 0.004 0.052 9122 Dihedral : 22.314 179.788 12380 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.00 (0.12), residues: 4858 helix: 3.41 (0.08), residues: 3224 sheet: -0.31 (0.91), residues: 27 loop : 1.17 (0.17), residues: 1607 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 570 time to evaluate : 5.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 47 residues processed: 613 average time/residue: 1.6707 time to fit residues: 1277.1670 Evaluate side-chains 604 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 557 time to evaluate : 4.286 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 33 residues processed: 14 average time/residue: 0.8556 time to fit residues: 22.1926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 269 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 chunk 260 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 276 optimal weight: 0.6980 chunk 296 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 342 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 157 GLN M 311 GLN aa 36 GLN ad 50 GLN ** ag 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ah 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 58313 Z= 0.196 Angle : 1.717 23.601 80224 Z= 0.585 Chirality : 0.036 0.226 8166 Planarity : 0.004 0.062 9122 Dihedral : 22.191 179.770 12380 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.98 (0.12), residues: 4858 helix: 3.40 (0.08), residues: 3220 sheet: -0.34 (0.90), residues: 27 loop : 1.13 (0.17), residues: 1611 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 564 time to evaluate : 4.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 40 residues processed: 603 average time/residue: 1.6709 time to fit residues: 1254.9632 Evaluate side-chains 594 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 554 time to evaluate : 4.290 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 32 residues processed: 8 average time/residue: 0.5980 time to fit residues: 13.0447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 396 optimal weight: 0.9980 chunk 417 optimal weight: 2.9990 chunk 380 optimal weight: 3.9990 chunk 405 optimal weight: 6.9990 chunk 244 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 318 optimal weight: 0.0670 chunk 124 optimal weight: 10.0000 chunk 366 optimal weight: 0.9990 chunk 383 optimal weight: 7.9990 chunk 404 optimal weight: 8.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 157 GLN aa 36 GLN ad 50 GLN ** ag 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ah 50 GLN ai 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 58313 Z= 0.161 Angle : 1.693 23.468 80224 Z= 0.575 Chirality : 0.035 0.221 8166 Planarity : 0.003 0.055 9122 Dihedral : 21.815 179.826 12380 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.09 (0.12), residues: 4858 helix: 3.51 (0.08), residues: 3218 sheet: -0.43 (0.92), residues: 28 loop : 1.13 (0.17), residues: 1612 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 568 time to evaluate : 4.264 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 34 residues processed: 607 average time/residue: 1.6633 time to fit residues: 1259.4860 Evaluate side-chains 589 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 555 time to evaluate : 4.161 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 32 residues processed: 2 average time/residue: 0.8486 time to fit residues: 7.2111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 266 optimal weight: 2.9990 chunk 429 optimal weight: 3.9990 chunk 262 optimal weight: 7.9990 chunk 203 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 chunk 450 optimal weight: 8.9990 chunk 414 optimal weight: 3.9990 chunk 358 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 276 optimal weight: 0.5980 chunk 219 optimal weight: 0.6980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 157 GLN M 311 GLN aa 36 GLN ad 50 GLN ** ag 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ah 50 GLN aj 50 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 58313 Z= 0.207 Angle : 1.711 23.662 80224 Z= 0.583 Chirality : 0.036 0.232 8166 Planarity : 0.004 0.065 9122 Dihedral : 21.913 179.807 12380 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.95 (0.12), residues: 4858 helix: 3.38 (0.08), residues: 3229 sheet: -0.36 (0.91), residues: 27 loop : 1.10 (0.17), residues: 1602 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 565 time to evaluate : 4.248 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 35 residues processed: 599 average time/residue: 1.6842 time to fit residues: 1260.5673 Evaluate side-chains 589 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 554 time to evaluate : 4.211 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 30 residues processed: 5 average time/residue: 0.7285 time to fit residues: 10.4100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 284 optimal weight: 3.9990 chunk 381 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 330 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 359 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 368 optimal weight: 0.2980 chunk 45 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 157 GLN M 311 GLN ad 50 GLN ** ag 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ah 50 GLN ai 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.102405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.076117 restraints weight = 92231.554| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.24 r_work: 0.2836 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 58313 Z= 0.219 Angle : 1.716 23.661 80224 Z= 0.585 Chirality : 0.037 0.232 8166 Planarity : 0.004 0.064 9122 Dihedral : 21.991 179.768 12380 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.90 (0.12), residues: 4858 helix: 3.34 (0.08), residues: 3227 sheet: -0.38 (0.92), residues: 27 loop : 1.09 (0.17), residues: 1604 =============================================================================== Job complete usr+sys time: 19153.91 seconds wall clock time: 333 minutes 33.80 seconds (20013.80 seconds total)