Starting phenix.real_space_refine on Mon Mar 11 06:03:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0u_12679/03_2024/7o0u_12679_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0u_12679/03_2024/7o0u_12679.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0u_12679/03_2024/7o0u_12679_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0u_12679/03_2024/7o0u_12679_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0u_12679/03_2024/7o0u_12679_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0u_12679/03_2024/7o0u_12679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0u_12679/03_2024/7o0u_12679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0u_12679/03_2024/7o0u_12679_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0u_12679/03_2024/7o0u_12679_updated.pdb" } resolution = 2.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 5 7.16 5 P 33 5.49 5 Mg 108 5.21 5 S 277 5.16 5 C 38473 2.51 5 N 7254 2.21 5 O 9608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "BK PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H2 PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bp PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 55758 Number of models: 1 Model: "" Number of chains: 236 Chain: "AA" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AB" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AC" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 384 Classifications: {'peptide': 48} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AD" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 384 Classifications: {'peptide': 48} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AE" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AF" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AG" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AH" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AI" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AJ" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AK" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AL" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AM" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AN" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AO" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AP" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AQ" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AR" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AS" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AT" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AU" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AV" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AW" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AX" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "BA" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BB" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BC" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BD" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BE" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BF" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BG" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BH" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BI" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BJ" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BK" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BL" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BM" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BN" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BO" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BP" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BQ" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BR" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BS" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BT" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BU" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BV" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BW" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BX" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "C" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2337 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 23, 'TRANS': 277} Chain: "C1" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 806 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 10, 'TRANS': 92} Chain: "H1" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 522 Classifications: {'peptide': 62} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H2" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1371 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 15, 'TRANS': 160} Chain: "L" Number of atoms: 2165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2165 Classifications: {'peptide': 273} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 257} Chain: "M" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2611 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 21, 'TRANS': 301} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "aa" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ab" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ac" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 443 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ad" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ae" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "af" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ag" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ah" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ai" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "aj" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ak" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 542 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 6, 'TRANS': 64} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "al" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "am" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "an" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 542 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 6, 'TRANS': 64} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ao" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ap" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 543 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 64} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ba" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bb" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bc" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bd" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "be" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bf" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bg" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bh" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bi" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bj" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bk" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bl" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bm" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bn" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "bo" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bp" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "MG" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'MAN': 1, 'RAM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "CG" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'MAN': 1, 'RAM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "AA" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AB" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 278 Unusual residues: {'BCL': 3, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "AC" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "AD" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AE" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 292 Unusual residues: {'BCL': 2, 'LMT': 2, 'V7N': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "AF" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AG" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AH" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 247 Unusual residues: {'BCL': 2, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "AI" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AJ" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 212 Unusual residues: {'0V9': 1, 'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "AK" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 202 Unusual residues: {'BCL': 2, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AL" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 202 Unusual residues: {'BCL': 2, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AM" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AN" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 268 Unusual residues: {'BCL': 3, 'LMT': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "AO" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "AP" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AQ" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 257 Unusual residues: {'0V9': 1, 'BCL': 2, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "AR" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AS" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 233 Unusual residues: {'BCL': 3, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AT" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AU" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AV" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 233 Unusual residues: {'BCL': 3, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AW" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 212 Unusual residues: {'BCL': 2, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AX" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BA" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 206 Unusual residues: {'BCL': 1, 'LMT': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BB" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BC" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BD" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 206 Unusual residues: {'BCL': 1, 'LMT': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BE" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BF" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 171 Unusual residues: {'BCL': 1, 'LMT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BG" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BH" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BI" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 206 Unusual residues: {'BCL': 1, 'LMT': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BJ" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BK" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BL" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 251 Unusual residues: {'BCL': 1, 'LMT': 4, 'V7N': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "BM" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BN" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BO" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BP" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BQ" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BR" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 171 Unusual residues: {'BCL': 1, 'LMT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BS" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 251 Unusual residues: {'BCL': 1, 'LMT': 4, 'V7N': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "BT" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BU" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 171 Unusual residues: {'BCL': 1, 'LMT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BV" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BW" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BX" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 136 Unusual residues: {'BCL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'HEC': 4, 'NDG': 1, 'V75': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H1" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 180 Unusual residues: {'0V9': 1, 'CD4': 1, 'PGW': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "H2" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 470 Unusual residues: {'0V9': 1, 'BCL': 2, 'BPH': 1, 'LMT': 5, 'MQ8': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "M" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 516 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'CD4': 2, 'CRT': 1, 'LMT': 1, 'MQ8': 1, 'V75': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "aa" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ab" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ac" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "ad" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 150 Unusual residues: {'BCL': 1, 'CD4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "ae" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 150 Unusual residues: {'BCL': 1, 'CD4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "af" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 169 Unusual residues: {'BCL': 1, 'V7B': 1, 'V7N': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "ag" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 208 Unusual residues: {'BCL': 1, 'CD4': 1, 'V7B': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "ah" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ai" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 121 Unusual residues: {'BCL': 1, 'UYH': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "aj" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'0V9': 1, 'BCL': 1, 'V7N': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "ak" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "al" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "am" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "an" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ao" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 119 Unusual residues: {'BCL': 1, 'MQ8': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "ap" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ba" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 146 Unusual residues: {'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "bb" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 236 Unusual residues: {'0V9': 2, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "bc" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bd" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "be" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 226 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bf" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bg" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "bh" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'V7N': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "bi" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 271 Unusual residues: {'0V9': 2, 'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "bj" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bk" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 146 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bl" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bm" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bn" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bo" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 226 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bp" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "AA" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AB" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AC" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AD" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AF" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AG" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "AH" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "AI" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AJ" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "AK" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AL" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AM" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AN" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AO" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AP" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AQ" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AR" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AS" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AT" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AU" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AV" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AW" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AX" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "BG" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "C1" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "H1" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "H2" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "L" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "M" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "aa" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "ab" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "ac" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "ad" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "ae" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "af" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "ag" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "ah" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "ai" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "aj" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "ak" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "al" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "am" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "an" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "ao" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "ap" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "ba" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "bb" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "bc" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "bd" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "be" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "bf" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "bg" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "bh" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "bi" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "bj" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "bk" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "bl" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "bm" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "bn" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "bo" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "bp" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 21.69, per 1000 atoms: 0.39 Number of scatterers: 55758 At special positions: 0 Unit cell: (197.893, 196.894, 145.921, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 5 26.01 S 277 16.00 P 33 15.00 Mg 108 11.99 O 9608 8.00 N 7254 7.00 C 38473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=115, symmetry=0 Links applied BETA1-4 " MANCG 1 " - " RAMCG 2 " ~> Even though RAM is an alpha isomer, a beta linkage is required... " MANMG 1 " - " RAMMG 2 " MAN-SER " MANMG 1 " - " SER M 331 " MAN-THR " MANCG 1 " - " THR C 108 " Number of additional bonds: simple=115, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.67 Conformation dependent library (CDL) restraints added in 5.0 seconds 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9042 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 220 helices and 4 sheets defined 66.2% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.46 Creating SS restraints... Processing helix chain 'AA' and resid 3 through 5 No H-bonds generated for 'chain 'AA' and resid 3 through 5' Processing helix chain 'AA' and resid 10 through 36 Processing helix chain 'AA' and resid 40 through 46 Processing helix chain 'AB' and resid 3 through 5 No H-bonds generated for 'chain 'AB' and resid 3 through 5' Processing helix chain 'AB' and resid 10 through 36 Processing helix chain 'AB' and resid 40 through 46 Processing helix chain 'AC' and resid 3 through 5 No H-bonds generated for 'chain 'AC' and resid 3 through 5' Processing helix chain 'AC' and resid 10 through 36 Processing helix chain 'AC' and resid 40 through 45 Processing helix chain 'AD' and resid 3 through 5 No H-bonds generated for 'chain 'AD' and resid 3 through 5' Processing helix chain 'AD' and resid 10 through 36 Processing helix chain 'AD' and resid 40 through 46 Processing helix chain 'AE' and resid 3 through 7 removed outlier: 4.414A pdb=" N GLYAE 7 " --> pdb=" O ILEAE 4 " (cutoff:3.500A) Processing helix chain 'AE' and resid 10 through 35 Processing helix chain 'AE' and resid 40 through 46 removed outlier: 3.527A pdb=" N TYRAE 46 " --> pdb=" O LEUAE 42 " (cutoff:3.500A) Processing helix chain 'AF' and resid 3 through 5 No H-bonds generated for 'chain 'AF' and resid 3 through 5' Processing helix chain 'AF' and resid 10 through 36 Processing helix chain 'AF' and resid 40 through 46 removed outlier: 3.551A pdb=" N TYRAF 46 " --> pdb=" O LEUAF 42 " (cutoff:3.500A) Processing helix chain 'AG' and resid 3 through 5 No H-bonds generated for 'chain 'AG' and resid 3 through 5' Processing helix chain 'AG' and resid 10 through 36 Processing helix chain 'AG' and resid 40 through 46 Processing helix chain 'AH' and resid 3 through 5 No H-bonds generated for 'chain 'AH' and resid 3 through 5' Processing helix chain 'AH' and resid 10 through 35 removed outlier: 3.558A pdb=" N GLYAH 34 " --> pdb=" O ILEAH 30 " (cutoff:3.500A) Processing helix chain 'AH' and resid 40 through 46 Processing helix chain 'AI' and resid 3 through 5 No H-bonds generated for 'chain 'AI' and resid 3 through 5' Processing helix chain 'AI' and resid 10 through 36 Processing helix chain 'AI' and resid 40 through 46 removed outlier: 3.593A pdb=" N TYRAI 46 " --> pdb=" O LEUAI 42 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 3 through 5 No H-bonds generated for 'chain 'AJ' and resid 3 through 5' Processing helix chain 'AJ' and resid 10 through 36 Processing helix chain 'AJ' and resid 40 through 45 Processing helix chain 'AK' and resid 3 through 5 No H-bonds generated for 'chain 'AK' and resid 3 through 5' Processing helix chain 'AK' and resid 10 through 35 Processing helix chain 'AK' and resid 40 through 46 removed outlier: 3.515A pdb=" N TYRAK 46 " --> pdb=" O LEUAK 42 " (cutoff:3.500A) Processing helix chain 'AL' and resid 3 through 5 No H-bonds generated for 'chain 'AL' and resid 3 through 5' Processing helix chain 'AL' and resid 10 through 36 Processing helix chain 'AL' and resid 40 through 46 Processing helix chain 'AM' and resid 3 through 5 No H-bonds generated for 'chain 'AM' and resid 3 through 5' Processing helix chain 'AM' and resid 10 through 35 Processing helix chain 'AM' and resid 40 through 46 Processing helix chain 'AN' and resid 3 through 5 No H-bonds generated for 'chain 'AN' and resid 3 through 5' Processing helix chain 'AN' and resid 10 through 35 removed outlier: 3.514A pdb=" N GLYAN 34 " --> pdb=" O ILEAN 30 " (cutoff:3.500A) Processing helix chain 'AN' and resid 40 through 46 removed outlier: 3.604A pdb=" N TYRAN 46 " --> pdb=" O LEUAN 42 " (cutoff:3.500A) Processing helix chain 'AO' and resid 3 through 5 No H-bonds generated for 'chain 'AO' and resid 3 through 5' Processing helix chain 'AO' and resid 10 through 36 Processing helix chain 'AO' and resid 40 through 46 removed outlier: 3.511A pdb=" N TYRAO 46 " --> pdb=" O LEUAO 42 " (cutoff:3.500A) Processing helix chain 'AP' and resid 3 through 5 No H-bonds generated for 'chain 'AP' and resid 3 through 5' Processing helix chain 'AP' and resid 10 through 36 Processing helix chain 'AP' and resid 40 through 46 Processing helix chain 'AQ' and resid 3 through 5 No H-bonds generated for 'chain 'AQ' and resid 3 through 5' Processing helix chain 'AQ' and resid 10 through 35 Processing helix chain 'AQ' and resid 40 through 46 removed outlier: 3.625A pdb=" N TYRAQ 46 " --> pdb=" O LEUAQ 42 " (cutoff:3.500A) Processing helix chain 'AR' and resid 3 through 5 No H-bonds generated for 'chain 'AR' and resid 3 through 5' Processing helix chain 'AR' and resid 10 through 36 Processing helix chain 'AR' and resid 40 through 46 Processing helix chain 'AS' and resid 3 through 5 No H-bonds generated for 'chain 'AS' and resid 3 through 5' Processing helix chain 'AS' and resid 10 through 36 Processing helix chain 'AS' and resid 40 through 46 Processing helix chain 'AT' and resid 3 through 5 No H-bonds generated for 'chain 'AT' and resid 3 through 5' Processing helix chain 'AT' and resid 10 through 35 Processing helix chain 'AT' and resid 40 through 46 removed outlier: 3.564A pdb=" N TYRAT 46 " --> pdb=" O LEUAT 42 " (cutoff:3.500A) Processing helix chain 'AU' and resid 3 through 5 No H-bonds generated for 'chain 'AU' and resid 3 through 5' Processing helix chain 'AU' and resid 10 through 36 Processing helix chain 'AU' and resid 40 through 46 removed outlier: 3.511A pdb=" N TYRAU 46 " --> pdb=" O LEUAU 42 " (cutoff:3.500A) Processing helix chain 'AV' and resid 3 through 5 No H-bonds generated for 'chain 'AV' and resid 3 through 5' Processing helix chain 'AV' and resid 10 through 36 Processing helix chain 'AV' and resid 40 through 46 Processing helix chain 'AW' and resid 3 through 5 No H-bonds generated for 'chain 'AW' and resid 3 through 5' Processing helix chain 'AW' and resid 10 through 35 Processing helix chain 'AW' and resid 40 through 46 Processing helix chain 'AX' and resid 10 through 36 Processing helix chain 'AX' and resid 40 through 46 Processing helix chain 'BA' and resid 9 through 40 Processing helix chain 'BB' and resid 9 through 40 removed outlier: 3.545A pdb=" N GLYBB 17 " --> pdb=" O ARGBB 13 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYRBB 18 " --> pdb=" O ARGBB 14 " (cutoff:3.500A) Processing helix chain 'BC' and resid 9 through 40 removed outlier: 3.570A pdb=" N GLYBC 17 " --> pdb=" O ARGBC 13 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYRBC 18 " --> pdb=" O ARGBC 14 " (cutoff:3.500A) Processing helix chain 'BD' and resid 9 through 40 removed outlier: 3.623A pdb=" N TYRBD 18 " --> pdb=" O ARGBD 14 " (cutoff:3.500A) Processing helix chain 'BE' and resid 9 through 40 removed outlier: 3.510A pdb=" N ARGBE 14 " --> pdb=" O GLUBE 10 " (cutoff:3.500A) Processing helix chain 'BF' and resid 9 through 40 Processing helix chain 'BG' and resid 9 through 40 removed outlier: 3.593A pdb=" N GLYBG 17 " --> pdb=" O ARGBG 13 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYRBG 18 " --> pdb=" O ARGBG 14 " (cutoff:3.500A) Processing helix chain 'BH' and resid 9 through 40 removed outlier: 3.580A pdb=" N ARGBH 14 " --> pdb=" O GLUBH 10 " (cutoff:3.500A) Processing helix chain 'BI' and resid 9 through 40 Processing helix chain 'BJ' and resid 9 through 40 Processing helix chain 'BK' and resid 9 through 40 removed outlier: 3.681A pdb=" N TYRBK 18 " --> pdb=" O ARGBK 14 " (cutoff:3.500A) Processing helix chain 'BL' and resid 9 through 40 removed outlier: 3.529A pdb=" N GLYBL 17 " --> pdb=" O ARGBL 13 " (cutoff:3.500A) Processing helix chain 'BM' and resid 9 through 40 Processing helix chain 'BN' and resid 9 through 40 removed outlier: 3.619A pdb=" N GLYBN 17 " --> pdb=" O ARGBN 13 " (cutoff:3.500A) Processing helix chain 'BO' and resid 9 through 40 removed outlier: 3.612A pdb=" N GLYBO 17 " --> pdb=" O ARGBO 13 " (cutoff:3.500A) Processing helix chain 'BP' and resid 9 through 40 removed outlier: 3.507A pdb=" N GLYBP 17 " --> pdb=" O ARGBP 13 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYRBP 18 " --> pdb=" O ARGBP 14 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 9 through 40 removed outlier: 3.572A pdb=" N TYRBQ 18 " --> pdb=" O ARGBQ 14 " (cutoff:3.500A) Processing helix chain 'BR' and resid 9 through 40 Processing helix chain 'BS' and resid 9 through 40 removed outlier: 3.531A pdb=" N TYRBS 18 " --> pdb=" O ARGBS 14 " (cutoff:3.500A) Processing helix chain 'BT' and resid 9 through 40 removed outlier: 3.582A pdb=" N GLYBT 17 " --> pdb=" O ARGBT 13 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYRBT 18 " --> pdb=" O ARGBT 14 " (cutoff:3.500A) Processing helix chain 'BU' and resid 9 through 40 Processing helix chain 'BV' and resid 9 through 40 removed outlier: 3.519A pdb=" N GLYBV 17 " --> pdb=" O ARGBV 13 " (cutoff:3.500A) Processing helix chain 'BW' and resid 9 through 40 removed outlier: 3.519A pdb=" N TYRBW 18 " --> pdb=" O ARGBW 14 " (cutoff:3.500A) Processing helix chain 'BX' and resid 9 through 40 removed outlier: 3.769A pdb=" N ARGBX 14 " --> pdb=" O GLUBX 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 27 No H-bonds generated for 'chain 'C' and resid 25 through 27' Processing helix chain 'C' and resid 35 through 46 Processing helix chain 'C' and resid 75 through 90 Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 116 through 134 Processing helix chain 'C' and resid 136 through 139 No H-bonds generated for 'chain 'C' and resid 136 through 139' Processing helix chain 'C' and resid 146 through 150 Processing helix chain 'C' and resid 168 through 172 Processing helix chain 'C' and resid 195 through 212 Processing helix chain 'C' and resid 216 through 218 No H-bonds generated for 'chain 'C' and resid 216 through 218' Processing helix chain 'C' and resid 233 through 251 removed outlier: 3.548A pdb=" N ASN C 249 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN C 250 " --> pdb=" O ASP C 247 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN C 251 " --> pdb=" O VAL C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 258 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 276 through 280 Processing helix chain 'C' and resid 286 through 289 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 297 through 299 No H-bonds generated for 'chain 'C' and resid 297 through 299' Processing helix chain 'C1' and resid 127 through 129 No H-bonds generated for 'chain 'C1' and resid 127 through 129' Processing helix chain 'C1' and resid 136 through 142 Processing helix chain 'C1' and resid 161 through 163 No H-bonds generated for 'chain 'C1' and resid 161 through 163' Processing helix chain 'C1' and resid 172 through 175 No H-bonds generated for 'chain 'C1' and resid 172 through 175' Processing helix chain 'C1' and resid 183 through 189 removed outlier: 3.597A pdb=" N ARGC1 189 " --> pdb=" O ALAC1 185 " (cutoff:3.500A) Processing helix chain 'C1' and resid 197 through 199 No H-bonds generated for 'chain 'C1' and resid 197 through 199' Processing helix chain 'H1' and resid 7 through 31 removed outlier: 3.517A pdb=" N LYSH1 31 " --> pdb=" O ARGH1 27 " (cutoff:3.500A) Processing helix chain 'H2' and resid 22 through 25 No H-bonds generated for 'chain 'H2' and resid 22 through 25' Processing helix chain 'H2' and resid 28 through 30 No H-bonds generated for 'chain 'H2' and resid 28 through 30' Processing helix chain 'H2' and resid 54 through 56 No H-bonds generated for 'chain 'H2' and resid 54 through 56' Processing helix chain 'H2' and resid 115 through 117 No H-bonds generated for 'chain 'H2' and resid 115 through 117' Processing helix chain 'H2' and resid 121 through 124 Processing helix chain 'H2' and resid 140 through 143 Processing helix chain 'H2' and resid 155 through 171 removed outlier: 4.279A pdb=" N HISH2 169 " --> pdb=" O TYRH2 165 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N METH2 170 " --> pdb=" O ALAH2 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 9 No H-bonds generated for 'chain 'L' and resid 7 through 9' Processing helix chain 'L' and resid 32 through 55 Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'L' and resid 84 through 110 Processing helix chain 'L' and resid 116 through 132 removed outlier: 3.509A pdb=" N GLY L 123 " --> pdb=" O TRP L 119 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 139 Processing helix chain 'L' and resid 142 through 144 No H-bonds generated for 'chain 'L' and resid 142 through 144' Processing helix chain 'L' and resid 152 through 164 removed outlier: 3.950A pdb=" N TYR L 164 " --> pdb=" O VAL L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 169 No H-bonds generated for 'chain 'L' and resid 167 through 169' Processing helix chain 'L' and resid 171 through 198 Processing helix chain 'L' and resid 209 through 220 Processing helix chain 'L' and resid 226 through 249 removed outlier: 3.837A pdb=" N HIS L 230 " --> pdb=" O ALA L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 260 through 267 removed outlier: 3.595A pdb=" N TRP L 265 " --> pdb=" O TRP L 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 8 No H-bonds generated for 'chain 'M' and resid 6 through 8' Processing helix chain 'M' and resid 54 through 79 Processing helix chain 'M' and resid 83 through 88 Processing helix chain 'M' and resid 90 through 92 No H-bonds generated for 'chain 'M' and resid 90 through 92' Processing helix chain 'M' and resid 100 through 102 No H-bonds generated for 'chain 'M' and resid 100 through 102' Processing helix chain 'M' and resid 113 through 139 Processing helix chain 'M' and resid 145 through 167 removed outlier: 3.507A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE M 160 " --> pdb=" O LEU M 156 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE M 161 " --> pdb=" O TYR M 157 " (cutoff:3.500A) Proline residue: M 164 - end of helix Processing helix chain 'M' and resid 170 through 172 No H-bonds generated for 'chain 'M' and resid 170 through 172' Processing helix chain 'M' and resid 178 through 191 removed outlier: 3.827A pdb=" N LEU M 182 " --> pdb=" O ILE M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 197 No H-bonds generated for 'chain 'M' and resid 195 through 197' Processing helix chain 'M' and resid 199 through 228 removed outlier: 4.948A pdb=" N ARG M 227 " --> pdb=" O LEU M 223 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N MET M 228 " --> pdb=" O ALA M 224 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 238 Processing helix chain 'M' and resid 242 through 255 removed outlier: 3.531A pdb=" N TRP M 251 " --> pdb=" O SER M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 285 removed outlier: 3.905A pdb=" N THR M 276 " --> pdb=" O ALA M 272 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 300 Processing helix chain 'M' and resid 314 through 319 Processing helix chain 'aa' and resid 3 through 7 Processing helix chain 'aa' and resid 10 through 34 removed outlier: 3.742A pdb=" N VALaa 15 " --> pdb=" O ARGaa 11 " (cutoff:3.500A) Processing helix chain 'aa' and resid 40 through 43 No H-bonds generated for 'chain 'aa' and resid 40 through 43' Processing helix chain 'ab' and resid 3 through 7 Processing helix chain 'ab' and resid 10 through 34 removed outlier: 3.777A pdb=" N VALab 15 " --> pdb=" O ARGab 11 " (cutoff:3.500A) Processing helix chain 'ab' and resid 40 through 43 No H-bonds generated for 'chain 'ab' and resid 40 through 43' Processing helix chain 'ac' and resid 3 through 7 Processing helix chain 'ac' and resid 10 through 34 removed outlier: 3.824A pdb=" N VALac 15 " --> pdb=" O ARGac 11 " (cutoff:3.500A) Processing helix chain 'ac' and resid 40 through 43 No H-bonds generated for 'chain 'ac' and resid 40 through 43' Processing helix chain 'ad' and resid 3 through 7 Processing helix chain 'ad' and resid 10 through 34 removed outlier: 3.789A pdb=" N VALad 15 " --> pdb=" O ARGad 11 " (cutoff:3.500A) Processing helix chain 'ad' and resid 40 through 43 No H-bonds generated for 'chain 'ad' and resid 40 through 43' Processing helix chain 'ae' and resid 3 through 7 Processing helix chain 'ae' and resid 10 through 34 removed outlier: 3.764A pdb=" N VALae 15 " --> pdb=" O ARGae 11 " (cutoff:3.500A) Processing helix chain 'ae' and resid 40 through 43 No H-bonds generated for 'chain 'ae' and resid 40 through 43' Processing helix chain 'af' and resid 3 through 7 Processing helix chain 'af' and resid 10 through 34 removed outlier: 3.514A pdb=" N VALaf 15 " --> pdb=" O ARGaf 11 " (cutoff:3.500A) Processing helix chain 'af' and resid 40 through 43 No H-bonds generated for 'chain 'af' and resid 40 through 43' Processing helix chain 'ag' and resid 3 through 7 Processing helix chain 'ag' and resid 10 through 34 removed outlier: 3.928A pdb=" N VALag 15 " --> pdb=" O ARGag 11 " (cutoff:3.500A) Processing helix chain 'ag' and resid 40 through 43 No H-bonds generated for 'chain 'ag' and resid 40 through 43' Processing helix chain 'ah' and resid 3 through 7 Processing helix chain 'ah' and resid 10 through 34 Processing helix chain 'ah' and resid 40 through 43 No H-bonds generated for 'chain 'ah' and resid 40 through 43' Processing helix chain 'ai' and resid 3 through 7 Processing helix chain 'ai' and resid 10 through 34 Processing helix chain 'ai' and resid 40 through 43 No H-bonds generated for 'chain 'ai' and resid 40 through 43' Processing helix chain 'aj' and resid 3 through 7 Processing helix chain 'aj' and resid 10 through 34 removed outlier: 3.802A pdb=" N VALaj 15 " --> pdb=" O ARGaj 11 " (cutoff:3.500A) Processing helix chain 'aj' and resid 40 through 43 No H-bonds generated for 'chain 'aj' and resid 40 through 43' Processing helix chain 'ak' and resid 3 through 7 Processing helix chain 'ak' and resid 10 through 34 removed outlier: 3.930A pdb=" N VALak 15 " --> pdb=" O ARGak 11 " (cutoff:3.500A) Processing helix chain 'ak' and resid 40 through 43 No H-bonds generated for 'chain 'ak' and resid 40 through 43' Processing helix chain 'al' and resid 3 through 7 Processing helix chain 'al' and resid 10 through 34 Processing helix chain 'al' and resid 40 through 43 No H-bonds generated for 'chain 'al' and resid 40 through 43' Processing helix chain 'am' and resid 3 through 7 Processing helix chain 'am' and resid 10 through 34 Processing helix chain 'am' and resid 40 through 43 No H-bonds generated for 'chain 'am' and resid 40 through 43' Processing helix chain 'an' and resid 3 through 7 Processing helix chain 'an' and resid 10 through 34 removed outlier: 3.603A pdb=" N VALan 15 " --> pdb=" O ARGan 11 " (cutoff:3.500A) Processing helix chain 'an' and resid 40 through 43 No H-bonds generated for 'chain 'an' and resid 40 through 43' Processing helix chain 'ao' and resid 3 through 7 Processing helix chain 'ao' and resid 10 through 34 Processing helix chain 'ao' and resid 40 through 43 No H-bonds generated for 'chain 'ao' and resid 40 through 43' Processing helix chain 'ap' and resid 3 through 7 Processing helix chain 'ap' and resid 10 through 34 Processing helix chain 'ap' and resid 40 through 43 No H-bonds generated for 'chain 'ap' and resid 40 through 43' Processing helix chain 'ba' and resid 9 through 40 removed outlier: 3.555A pdb=" N TYRba 18 " --> pdb=" O ARGba 14 " (cutoff:3.500A) Processing helix chain 'bb' and resid 9 through 40 removed outlier: 3.579A pdb=" N GLYbb 17 " --> pdb=" O ARGbb 13 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYRbb 18 " --> pdb=" O ARGbb 14 " (cutoff:3.500A) Processing helix chain 'bc' and resid 9 through 40 Processing helix chain 'bd' and resid 9 through 40 removed outlier: 3.582A pdb=" N TYRbd 18 " --> pdb=" O ARGbd 14 " (cutoff:3.500A) Processing helix chain 'be' and resid 9 through 40 Processing helix chain 'bf' and resid 9 through 40 removed outlier: 3.680A pdb=" N TYRbf 18 " --> pdb=" O ARGbf 14 " (cutoff:3.500A) Processing helix chain 'bg' and resid 9 through 40 Processing helix chain 'bh' and resid 9 through 40 removed outlier: 3.573A pdb=" N GLYbh 17 " --> pdb=" O ARGbh 13 " (cutoff:3.500A) Processing helix chain 'bi' and resid 9 through 40 Processing helix chain 'bj' and resid 9 through 40 removed outlier: 3.802A pdb=" N TYRbj 18 " --> pdb=" O ARGbj 14 " (cutoff:3.500A) Processing helix chain 'bk' and resid 9 through 40 removed outlier: 3.523A pdb=" N TYRbk 18 " --> pdb=" O ARGbk 14 " (cutoff:3.500A) Processing helix chain 'bl' and resid 9 through 40 removed outlier: 3.701A pdb=" N TYRbl 18 " --> pdb=" O ARGbl 14 " (cutoff:3.500A) Processing helix chain 'bm' and resid 9 through 40 Processing helix chain 'bn' and resid 9 through 40 removed outlier: 3.538A pdb=" N TYRbn 18 " --> pdb=" O ARGbn 14 " (cutoff:3.500A) Processing helix chain 'bo' and resid 9 through 40 Processing helix chain 'bp' and resid 9 through 40 removed outlier: 3.801A pdb=" N TYRbp 18 " --> pdb=" O ARGbp 14 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 17 through 21 Processing sheet with id= B, first strand: chain 'H2' and resid 5 through 7 Processing sheet with id= C, first strand: chain 'H2' and resid 51 through 53 removed outlier: 6.744A pdb=" N GLUH2 101 " --> pdb=" O VALH2 86 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEUH2 88 " --> pdb=" O TYRH2 99 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYRH2 99 " --> pdb=" O LEUH2 88 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H2' and resid 118 through 120 removed outlier: 7.623A pdb=" N VALH2 133 " --> pdb=" O PROH2 73 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILEH2 75 " --> pdb=" O VALH2 133 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLYH2 83 " --> pdb=" O VALH2 74 " (cutoff:3.500A) 2420 hydrogen bonds defined for protein. 7092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.46 Time building geometry restraints manager: 19.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.36: 13904 1.36 - 1.57: 42624 1.57 - 1.77: 201 1.77 - 1.98: 458 1.98 - 2.18: 448 Bond restraints: 57635 Sorted by residual: bond pdb=" C27 V7Nbn 101 " pdb=" C28 V7Nbn 101 " ideal model delta sigma weight residual 1.348 1.524 -0.176 2.00e-02 2.50e+03 7.78e+01 bond pdb=" C27 V7Nba 102 " pdb=" C28 V7Nba 102 " ideal model delta sigma weight residual 1.348 1.524 -0.176 2.00e-02 2.50e+03 7.73e+01 bond pdb=" C27 V7NAE 101 " pdb=" C28 V7NAE 101 " ideal model delta sigma weight residual 1.348 1.523 -0.175 2.00e-02 2.50e+03 7.63e+01 bond pdb=" C27 V7NBH1001 " pdb=" C28 V7NBH1001 " ideal model delta sigma weight residual 1.348 1.522 -0.174 2.00e-02 2.50e+03 7.60e+01 bond pdb=" C27 V7NAW 104 " pdb=" C28 V7NAW 104 " ideal model delta sigma weight residual 1.348 1.522 -0.174 2.00e-02 2.50e+03 7.59e+01 ... (remaining 57630 not shown) Histogram of bond angle deviations from ideal: 84.75 - 103.58: 1754 103.58 - 122.40: 67588 122.40 - 141.23: 9608 141.23 - 160.05: 305 160.05 - 178.88: 30 Bond angle restraints: 79285 Sorted by residual: angle pdb=" C34 V7NBK1001 " pdb=" C9 V7NBK1001 " pdb=" C8 V7NBK1001 " ideal model delta sigma weight residual 68.18 124.09 -55.91 3.00e+00 1.11e-01 3.47e+02 angle pdb=" C34 V7NBB 101 " pdb=" C9 V7NBB 101 " pdb=" C8 V7NBB 101 " ideal model delta sigma weight residual 68.18 124.03 -55.85 3.00e+00 1.11e-01 3.47e+02 angle pdb=" C34 V7NBG1001 " pdb=" C9 V7NBG1001 " pdb=" C8 V7NBG1001 " ideal model delta sigma weight residual 68.18 123.94 -55.76 3.00e+00 1.11e-01 3.45e+02 angle pdb=" C34 V7NBJ1001 " pdb=" C9 V7NBJ1001 " pdb=" C8 V7NBJ1001 " ideal model delta sigma weight residual 68.18 123.87 -55.69 3.00e+00 1.11e-01 3.45e+02 angle pdb=" C34 V7NBT1001 " pdb=" C9 V7NBT1001 " pdb=" C8 V7NBT1001 " ideal model delta sigma weight residual 68.18 123.83 -55.65 3.00e+00 1.11e-01 3.44e+02 ... (remaining 79280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 34293 35.64 - 71.28: 1334 71.28 - 106.92: 497 106.92 - 142.56: 142 142.56 - 178.20: 74 Dihedral angle restraints: 36340 sinusoidal: 22195 harmonic: 14145 Sorted by residual: dihedral pdb=" C1 BCLAK 103 " pdb=" C2 BCLAK 103 " pdb=" C3 BCLAK 103 " pdb=" C5 BCLAK 103 " ideal model delta sinusoidal sigma weight residual 180.00 4.34 175.66 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCLAV 104 " pdb=" CGA BCLAV 104 " pdb=" O2A BCLAV 104 " pdb=" CBA BCLAV 104 " ideal model delta sinusoidal sigma weight residual 180.00 147.70 32.30 1 6.00e+00 2.78e-02 4.13e+01 dihedral pdb=" C1 BCLBS1006 " pdb=" CGA BCLBS1006 " pdb=" O2A BCLBS1006 " pdb=" CBA BCLBS1006 " ideal model delta sinusoidal sigma weight residual -180.00 -147.71 -32.29 1 6.00e+00 2.78e-02 4.12e+01 ... (remaining 36337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 7182 0.092 - 0.184: 694 0.184 - 0.277: 199 0.277 - 0.369: 3 0.369 - 0.461: 8 Chirality restraints: 8086 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 -2.05 -0.46 2.00e-01 2.50e+01 5.32e+00 chirality pdb=" C4 UYHai 102 " pdb=" C3 UYHai 102 " pdb=" C5 UYHai 102 " pdb=" O4 UYHai 102 " both_signs ideal model delta sigma weight residual False -2.49 -2.94 0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" C3 UYHai 102 " pdb=" C2 UYHai 102 " pdb=" C4 UYHai 102 " pdb=" O3 UYHai 102 " both_signs ideal model delta sigma weight residual False 2.48 2.90 -0.42 2.00e-01 2.50e+01 4.46e+00 ... (remaining 8083 not shown) Planarity restraints: 8977 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C26 V7NBB 101 " 0.163 2.00e-02 2.50e+03 3.25e-01 1.06e+03 pdb=" C27 V7NBB 101 " -0.442 2.00e-02 2.50e+03 pdb=" C28 V7NBB 101 " 0.424 2.00e-02 2.50e+03 pdb=" C29 V7NBB 101 " -0.144 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C26 V7Naf 103 " 0.249 2.00e-02 2.50e+03 2.54e-01 6.43e+02 pdb=" C27 V7Naf 103 " -0.240 2.00e-02 2.50e+03 pdb=" C28 V7Naf 103 " -0.267 2.00e-02 2.50e+03 pdb=" C29 V7Naf 103 " 0.257 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C26 V7Nbi 102 " -0.218 2.00e-02 2.50e+03 2.14e-01 4.60e+02 pdb=" C27 V7Nbi 102 " 0.234 2.00e-02 2.50e+03 pdb=" C28 V7Nbi 102 " 0.194 2.00e-02 2.50e+03 pdb=" C29 V7Nbi 102 " -0.210 2.00e-02 2.50e+03 ... (remaining 8974 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 1119 2.68 - 3.23: 49399 3.23 - 3.79: 92182 3.79 - 4.34: 134483 4.34 - 4.90: 212047 Nonbonded interactions: 489230 Sorted by model distance: nonbonded pdb=" NE2 HIS C 280 " pdb="FE HEC C 404 " model vdw 2.121 3.080 nonbonded pdb=" NE2 HIS L 190 " pdb="FE FE M 401 " model vdw 2.158 2.340 nonbonded pdb=" OE2 GLU M 233 " pdb="FE FE M 401 " model vdw 2.165 2.260 nonbonded pdb=" NE2 HIS M 218 " pdb="FE FE M 401 " model vdw 2.185 2.340 nonbonded pdb=" OG1 THRBE 8 " pdb=" OE1 GLUBE 11 " model vdw 2.264 2.440 ... (remaining 489225 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'AA' and resid 1 through 48) selection = (chain 'AB' and resid 1 through 48) selection = (chain 'AC' and resid 1 through 48) selection = (chain 'AD' and resid 1 through 48) selection = (chain 'AE' and resid 1 through 48) selection = (chain 'AF' and resid 1 through 48) selection = (chain 'AG' and resid 1 through 48) selection = (chain 'AH' and resid 1 through 48) selection = (chain 'AI' and resid 1 through 48) selection = (chain 'AJ' and resid 1 through 48) selection = (chain 'AK' and resid 1 through 48) selection = (chain 'AL' and resid 1 through 48) selection = (chain 'AM' and resid 1 through 48) selection = (chain 'AN' and resid 1 through 48) selection = (chain 'AO' and resid 1 through 48) selection = (chain 'AP' and resid 1 through 48) selection = (chain 'AQ' and resid 1 through 48) selection = (chain 'AR' and resid 1 through 48) selection = (chain 'AS' and resid 1 through 48) selection = (chain 'AT' and resid 1 through 48) selection = (chain 'AU' and resid 1 through 48) selection = (chain 'AV' and resid 1 through 48) selection = (chain 'AW' and resid 1 through 48) selection = (chain 'AX' and resid 1 through 48) } ncs_group { reference = (chain 'BA' and resid 6 through 44) selection = (chain 'BB' and resid 6 through 44) selection = (chain 'BC' and resid 6 through 44) selection = (chain 'BD' and resid 6 through 44) selection = (chain 'BE' and resid 6 through 44) selection = (chain 'BF' and resid 6 through 44) selection = (chain 'BG' and resid 6 through 44) selection = (chain 'BH' and resid 6 through 44) selection = (chain 'BI' and resid 6 through 44) selection = (chain 'BJ' and resid 6 through 44) selection = (chain 'BK' and resid 6 through 44) selection = (chain 'BL' and resid 6 through 44) selection = (chain 'BM' and resid 6 through 44) selection = (chain 'BN' and resid 6 through 44) selection = (chain 'BO' and resid 6 through 44) selection = (chain 'BP' and resid 6 through 44) selection = (chain 'BQ' and resid 6 through 44) selection = (chain 'BR' and resid 6 through 44) selection = (chain 'BS' and resid 6 through 44) selection = (chain 'BT' and resid 6 through 44) selection = (chain 'BU' and resid 6 through 44) selection = (chain 'BV' and resid 6 through 44) selection = (chain 'BW' and resid 6 through 44) selection = (chain 'BX' and resid 6 through 44) selection = (chain 'ba' and resid 6 through 44) selection = (chain 'bb' and resid 6 through 44) selection = (chain 'bc' and resid 6 through 44) selection = (chain 'bd' and resid 6 through 44) selection = (chain 'be' and resid 6 through 44) selection = (chain 'bf' and resid 6 through 44) selection = (chain 'bg' and resid 6 through 44) selection = (chain 'bh' and resid 6 through 44) selection = (chain 'bi' and resid 6 through 44) selection = (chain 'bj' and resid 6 through 44) selection = (chain 'bk' and resid 6 through 44) selection = (chain 'bl' and resid 6 through 44) selection = (chain 'bm' and resid 6 through 44) selection = (chain 'bn' and resid 6 through 44) selection = (chain 'bo' and resid 6 through 44) selection = (chain 'bp' and resid 6 through 44) } ncs_group { reference = chain 'CG' selection = chain 'MG' } ncs_group { reference = (chain 'aa' and resid 1 through 56) selection = (chain 'ab' and resid 1 through 56) selection = (chain 'ac' and resid 1 through 56) selection = (chain 'ad' and resid 1 through 56) selection = (chain 'ae' and resid 1 through 56) selection = (chain 'af' and resid 1 through 56) selection = (chain 'ag' and resid 1 through 56) selection = (chain 'ah' and resid 1 through 56) selection = (chain 'ai' and resid 1 through 56) selection = (chain 'aj' and resid 1 through 56) selection = (chain 'al' and resid 1 through 56) selection = (chain 'am' and resid 1 through 56) selection = (chain 'ao' and resid 1 through 56) } ncs_group { reference = chain 'ak' selection = chain 'an' selection = (chain 'ap' and (resid 1 through 70 or (resid 71 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 o \ r name NH2)) or resid 1001)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 13.740 Check model and map are aligned: 0.600 Set scattering table: 0.370 Process input model: 105.420 Find NCS groups from input model: 2.900 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 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 0.176 57635 Z= 0.871 Angle : 4.371 55.912 79285 Z= 1.485 Chirality : 0.062 0.461 8086 Planarity : 0.013 0.325 8977 Dihedral : 22.734 178.197 27298 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.20 % Favored : 98.78 % Rotamer: Outliers : 0.41 % Allowed : 1.48 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.12), residues: 4756 helix: 0.96 (0.08), residues: 3158 sheet: -0.30 (1.06), residues: 22 loop : 1.19 (0.17), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP M 148 HIS 0.014 0.002 HISAD 2 PHE 0.030 0.003 PHEbh 44 TYR 0.051 0.005 TYR L 164 ARG 0.035 0.004 ARG M 321 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 853 time to evaluate : 3.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 6 MET cc_start: 0.8109 (mtp) cc_final: 0.7889 (mtm) REVERT: AB 13 ILE cc_start: 0.9070 (mm) cc_final: 0.8862 (mp) REVERT: AC 28 MET cc_start: 0.9230 (mmm) cc_final: 0.8782 (mmm) REVERT: AF 14 MET cc_start: 0.8639 (mmm) cc_final: 0.8269 (mmm) REVERT: AH 14 MET cc_start: 0.8918 (mmm) cc_final: 0.8548 (mmp) REVERT: AI 28 MET cc_start: 0.9151 (mmm) cc_final: 0.8623 (mmm) REVERT: AK 14 MET cc_start: 0.8687 (mmm) cc_final: 0.8478 (mmm) REVERT: AL 49 PRO cc_start: 0.7595 (Cg_endo) cc_final: 0.7345 (Cg_exo) REVERT: AM 14 MET cc_start: 0.8988 (mmm) cc_final: 0.8672 (mmm) REVERT: AP 6 MET cc_start: 0.8408 (mtp) cc_final: 0.8169 (mtp) REVERT: AP 14 MET cc_start: 0.8908 (mmm) cc_final: 0.8509 (mmm) REVERT: AT 28 MET cc_start: 0.9413 (mmm) cc_final: 0.9169 (mmm) REVERT: AU 9 ASP cc_start: 0.7499 (t0) cc_final: 0.6981 (t70) REVERT: AU 12 ILE cc_start: 0.8922 (mm) cc_final: 0.8608 (mm) REVERT: BE 9 GLU cc_start: 0.7427 (tm-30) cc_final: 0.6948 (tp30) REVERT: BK 18 TYR cc_start: 0.8957 (m-80) cc_final: 0.8712 (m-80) REVERT: BN 13 ARG cc_start: 0.7362 (ttp-110) cc_final: 0.6746 (ttm-80) REVERT: C 29 MET cc_start: 0.9306 (mtp) cc_final: 0.9034 (mtp) REVERT: C 82 MET cc_start: 0.9062 (mmt) cc_final: 0.8141 (mmt) REVERT: H2 170 MET cc_start: 0.8675 (ttm) cc_final: 0.8417 (ttm) REVERT: L 174 MET cc_start: 0.9321 (mtt) cc_final: 0.9090 (mtt) REVERT: L 212 GLU cc_start: 0.7871 (pt0) cc_final: 0.7665 (pt0) REVERT: M 96 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7335 (tm-30) REVERT: M 117 MET cc_start: 0.8983 (ttm) cc_final: 0.8605 (ttm) REVERT: aa 7 MET cc_start: 0.7189 (mtm) cc_final: 0.6924 (mtp) REVERT: aa 12 ARG cc_start: 0.7233 (mmm-85) cc_final: 0.6818 (mtp-110) REVERT: aj 14 MET cc_start: 0.7672 (mmm) cc_final: 0.7420 (mmm) REVERT: ak 42 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8317 (mm-30) REVERT: am 12 ARG cc_start: 0.7619 (ttm-80) cc_final: 0.7099 (tmm-80) REVERT: an 7 MET cc_start: 0.6996 (ttp) cc_final: 0.6792 (ttt) REVERT: ao 14 MET cc_start: 0.7261 (ttp) cc_final: 0.6869 (ttp) REVERT: ap 12 ARG cc_start: 0.6717 (mtm110) cc_final: 0.6453 (mtm110) REVERT: ap 42 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8329 (mm-30) REVERT: ba 14 ARG cc_start: 0.7138 (ttp-110) cc_final: 0.6930 (tpm170) REVERT: bg 11 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7389 (mt-10) REVERT: bn 19 MET cc_start: 0.8357 (tpt) cc_final: 0.8020 (tpt) REVERT: bp 7 MET cc_start: 0.6108 (tpt) cc_final: 0.5388 (tpt) REVERT: bp 19 MET cc_start: 0.7891 (tpt) cc_final: 0.7396 (tpt) outliers start: 16 outliers final: 7 residues processed: 865 average time/residue: 1.7135 time to fit residues: 1801.9561 Evaluate side-chains 665 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 657 time to evaluate : 4.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 291 ASP Chi-restraints excluded: chain ab residue 4 ILE Chi-restraints excluded: chain ad residue 39 SER Chi-restraints excluded: chain an residue 39 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 377 optimal weight: 8.9990 chunk 338 optimal weight: 0.5980 chunk 187 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 228 optimal weight: 8.9990 chunk 181 optimal weight: 0.0980 chunk 350 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 213 optimal weight: 8.9990 chunk 260 optimal weight: 1.9990 chunk 405 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AD 37 ASN AF 37 ASN ** AH 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AN 37 ASN ** AP 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 37 ASN C1 199 GLN H2 119 GLN L 104 GLN L 213 ASN ac 36 GLN ag 50 GLN an 36 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 57635 Z= 0.231 Angle : 1.975 32.530 79285 Z= 0.678 Chirality : 0.039 0.284 8086 Planarity : 0.005 0.057 8977 Dihedral : 22.646 179.930 19007 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.94 % Allowed : 8.91 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.43 (0.12), residues: 4756 helix: 2.75 (0.08), residues: 3166 sheet: 0.36 (1.06), residues: 24 loop : 1.45 (0.17), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 81 HIS 0.012 0.001 HIS L 153 PHE 0.028 0.002 PHEbc 15 TYR 0.022 0.002 TYR L 164 ARG 0.010 0.001 ARGAT 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 676 time to evaluate : 3.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AB 13 ILE cc_start: 0.9021 (mm) cc_final: 0.8819 (mp) REVERT: AC 28 MET cc_start: 0.9196 (mmm) cc_final: 0.8805 (mmm) REVERT: AF 14 MET cc_start: 0.8649 (mmm) cc_final: 0.8252 (mmm) REVERT: AH 12 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8660 (mp) REVERT: AH 14 MET cc_start: 0.9008 (mmm) cc_final: 0.8636 (mmp) REVERT: AI 28 MET cc_start: 0.9119 (mmm) cc_final: 0.8617 (mmm) REVERT: AL 49 PRO cc_start: 0.7503 (Cg_endo) cc_final: 0.7271 (Cg_exo) REVERT: AP 6 MET cc_start: 0.8532 (mtp) cc_final: 0.8279 (mtm) REVERT: AU 9 ASP cc_start: 0.7545 (t0) cc_final: 0.6954 (t70) REVERT: AU 12 ILE cc_start: 0.8951 (mm) cc_final: 0.8568 (mm) REVERT: BA 9 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6857 (tt0) REVERT: BE 9 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6312 (tp30) REVERT: BK 13 ARG cc_start: 0.8284 (ttm-80) cc_final: 0.8082 (ttm170) REVERT: BL 9 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7060 (tm-30) REVERT: BR 9 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7352 (tm-30) REVERT: BU 19 MET cc_start: 0.8248 (tpp) cc_final: 0.8038 (tpp) REVERT: C 29 MET cc_start: 0.9313 (mtp) cc_final: 0.9017 (mtp) REVERT: H2 149 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.6927 (mtp180) REVERT: H2 170 MET cc_start: 0.8692 (ttm) cc_final: 0.8448 (ttm) REVERT: L 174 MET cc_start: 0.9210 (mtt) cc_final: 0.9005 (mtt) REVERT: M 96 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8120 (mm-30) REVERT: M 117 MET cc_start: 0.8889 (ttm) cc_final: 0.8532 (ttm) REVERT: aa 7 MET cc_start: 0.7395 (mtm) cc_final: 0.7032 (mtp) REVERT: aa 39 SER cc_start: 0.9205 (OUTLIER) cc_final: 0.8976 (t) REVERT: af 3 ARG cc_start: 0.7538 (mtp180) cc_final: 0.7176 (mmm-85) REVERT: am 12 ARG cc_start: 0.7255 (ttm-80) cc_final: 0.6995 (mtm110) REVERT: an 7 MET cc_start: 0.6957 (ttp) cc_final: 0.6708 (ttt) REVERT: an 12 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.6694 (tmt170) REVERT: ap 42 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8362 (mm-30) REVERT: ba 14 ARG cc_start: 0.7353 (ttp-110) cc_final: 0.7099 (tpm170) REVERT: bf 9 GLU cc_start: 0.7343 (tt0) cc_final: 0.7059 (tt0) REVERT: bj 19 MET cc_start: 0.8472 (tpp) cc_final: 0.8230 (tpp) REVERT: bm 11 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6914 (mt-10) REVERT: bn 19 MET cc_start: 0.8330 (tpt) cc_final: 0.8028 (tpt) REVERT: bp 7 MET cc_start: 0.6101 (tpt) cc_final: 0.5480 (tpt) REVERT: bp 19 MET cc_start: 0.7864 (tpt) cc_final: 0.7357 (tpt) outliers start: 76 outliers final: 32 residues processed: 710 average time/residue: 1.7074 time to fit residues: 1474.7707 Evaluate side-chains 667 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 629 time to evaluate : 3.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 48 THR Chi-restraints excluded: chain AC residue 48 THR Chi-restraints excluded: chain AG residue 15 SER Chi-restraints excluded: chain AH residue 12 ILE Chi-restraints excluded: chain AP residue 48 THR Chi-restraints excluded: chain AR residue 19 SER Chi-restraints excluded: chain AV residue 48 THR Chi-restraints excluded: chain AW residue 15 SER Chi-restraints excluded: chain AW residue 48 THR Chi-restraints excluded: chain AX residue 48 THR Chi-restraints excluded: chain BA residue 9 GLU Chi-restraints excluded: chain BB residue 31 SER Chi-restraints excluded: chain BH residue 24 LEU Chi-restraints excluded: chain BH residue 31 SER Chi-restraints excluded: chain BM residue 24 LEU Chi-restraints excluded: chain BW residue 39 SER Chi-restraints excluded: chain C1 residue 174 SER Chi-restraints excluded: chain C1 residue 181 ARG Chi-restraints excluded: chain H2 residue 128 ASN Chi-restraints excluded: chain H2 residue 149 ARG Chi-restraints excluded: chain L residue 20 ASP Chi-restraints excluded: chain L residue 220 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 291 ASP Chi-restraints excluded: chain aa residue 6 LEU Chi-restraints excluded: chain aa residue 39 SER Chi-restraints excluded: chain ab residue 7 MET Chi-restraints excluded: chain ab residue 26 LEU Chi-restraints excluded: chain an residue 12 ARG Chi-restraints excluded: chain an residue 14 MET Chi-restraints excluded: chain an residue 39 SER Chi-restraints excluded: chain ap residue 13 VAL Chi-restraints excluded: chain ba residue 8 THR Chi-restraints excluded: chain bh residue 24 LEU Chi-restraints excluded: chain bl residue 13 ARG Chi-restraints excluded: chain bp residue 8 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 225 optimal weight: 0.0670 chunk 125 optimal weight: 9.9990 chunk 337 optimal weight: 2.9990 chunk 276 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 406 optimal weight: 1.9990 chunk 439 optimal weight: 4.9990 chunk 362 optimal weight: 0.5980 chunk 403 optimal weight: 8.9990 chunk 138 optimal weight: 0.9990 chunk 326 optimal weight: 5.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AH 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 37 ASN ** AS 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AW 35 GLN C1 199 GLN H2 119 GLN M 6 ASN ac 36 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 57635 Z= 0.169 Angle : 1.798 30.683 79285 Z= 0.612 Chirality : 0.036 0.281 8086 Planarity : 0.004 0.050 8977 Dihedral : 21.126 179.899 19003 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.12 % Allowed : 10.26 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.05 (0.12), residues: 4756 helix: 3.35 (0.08), residues: 3144 sheet: 0.41 (1.15), residues: 24 loop : 1.41 (0.17), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPH2 126 HIS 0.009 0.001 HIS L 153 PHE 0.027 0.002 PHEbc 15 TYR 0.016 0.001 TYR L 164 ARG 0.027 0.001 ARGAL 3 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 677 time to evaluate : 4.053 Fit side-chains revert: symmetry clash REVERT: AC 28 MET cc_start: 0.9221 (mmm) cc_final: 0.8690 (mmm) REVERT: AF 14 MET cc_start: 0.8577 (mmm) cc_final: 0.8165 (mmm) REVERT: AH 14 MET cc_start: 0.9016 (mmm) cc_final: 0.8641 (mmp) REVERT: AI 28 MET cc_start: 0.9081 (mmm) cc_final: 0.8594 (mmm) REVERT: AL 49 PRO cc_start: 0.7228 (Cg_endo) cc_final: 0.7001 (Cg_exo) REVERT: AM 14 MET cc_start: 0.9053 (mmm) cc_final: 0.8832 (mmm) REVERT: AP 6 MET cc_start: 0.8537 (mtp) cc_final: 0.8204 (mtm) REVERT: AU 9 ASP cc_start: 0.7484 (t0) cc_final: 0.6924 (t70) REVERT: AU 12 ILE cc_start: 0.8920 (mm) cc_final: 0.8570 (mm) REVERT: AW 28 MET cc_start: 0.9217 (mmm) cc_final: 0.8991 (mmm) REVERT: BB 13 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7797 (ttm110) REVERT: BD 13 ARG cc_start: 0.7470 (ttp-110) cc_final: 0.7246 (ttm-80) REVERT: BI 10 GLU cc_start: 0.6319 (tp30) cc_final: 0.6077 (tp30) REVERT: BK 13 ARG cc_start: 0.8252 (ttm-80) cc_final: 0.8037 (ttm170) REVERT: BN 9 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7163 (tm-30) REVERT: BN 13 ARG cc_start: 0.7470 (ttm-80) cc_final: 0.7175 (ttp-110) REVERT: BV 11 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6970 (mt-10) REVERT: BX 9 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6065 (tp30) REVERT: C 82 MET cc_start: 0.9051 (mmt) cc_final: 0.7881 (mmt) REVERT: H2 149 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6848 (mtp180) REVERT: M 96 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8134 (mm-30) REVERT: M 117 MET cc_start: 0.8807 (ttm) cc_final: 0.8506 (ttm) REVERT: aa 11 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.7143 (mtm-85) REVERT: ai 12 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.6169 (mtm180) REVERT: aj 49 ASP cc_start: 0.7438 (p0) cc_final: 0.7206 (p0) REVERT: an 7 MET cc_start: 0.6951 (ttp) cc_final: 0.6700 (mtp) REVERT: ap 13 VAL cc_start: 0.8105 (t) cc_final: 0.7840 (p) REVERT: ap 42 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8417 (mm-30) REVERT: ap 63 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7040 (pt0) REVERT: ba 14 ARG cc_start: 0.7411 (ttp-110) cc_final: 0.7129 (tpt170) REVERT: bb 19 MET cc_start: 0.8149 (tpp) cc_final: 0.7921 (tpp) REVERT: bd 19 MET cc_start: 0.8439 (mmm) cc_final: 0.8152 (mmm) REVERT: bh 7 MET cc_start: 0.7232 (mmt) cc_final: 0.6727 (tpp) REVERT: bj 14 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8558 (ttp-170) REVERT: bj 19 MET cc_start: 0.8253 (tpp) cc_final: 0.8017 (tpp) REVERT: bl 13 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6387 (ttt90) REVERT: bm 11 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6930 (mt-10) REVERT: bm 13 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.7316 (mtt-85) REVERT: bn 13 ARG cc_start: 0.7434 (ttp-110) cc_final: 0.7157 (ptm-80) REVERT: bn 19 MET cc_start: 0.8280 (tpt) cc_final: 0.8022 (tpt) REVERT: bp 7 MET cc_start: 0.5891 (tpt) cc_final: 0.5296 (tpt) REVERT: bp 19 MET cc_start: 0.7750 (tpt) cc_final: 0.7329 (tpt) outliers start: 83 outliers final: 24 residues processed: 716 average time/residue: 1.6875 time to fit residues: 1474.3525 Evaluate side-chains 656 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 622 time to evaluate : 3.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 48 THR Chi-restraints excluded: chain AC residue 48 THR Chi-restraints excluded: chain AF residue 15 SER Chi-restraints excluded: chain AP residue 48 THR Chi-restraints excluded: chain AR residue 19 SER Chi-restraints excluded: chain AS residue 30 ILE Chi-restraints excluded: chain AW residue 15 SER Chi-restraints excluded: chain AX residue 19 SER Chi-restraints excluded: chain AX residue 48 THR Chi-restraints excluded: chain BB residue 13 ARG Chi-restraints excluded: chain BB residue 31 SER Chi-restraints excluded: chain BC residue 39 SER Chi-restraints excluded: chain BM residue 24 LEU Chi-restraints excluded: chain BS residue 8 THR Chi-restraints excluded: chain BX residue 9 GLU Chi-restraints excluded: chain C1 residue 174 SER Chi-restraints excluded: chain H2 residue 59 THR Chi-restraints excluded: chain H2 residue 149 ARG Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 291 ASP Chi-restraints excluded: chain aa residue 6 LEU Chi-restraints excluded: chain aa residue 11 ARG Chi-restraints excluded: chain ab residue 26 LEU Chi-restraints excluded: chain af residue 18 VAL Chi-restraints excluded: chain ai residue 12 ARG Chi-restraints excluded: chain ak residue 39 SER Chi-restraints excluded: chain am residue 39 SER Chi-restraints excluded: chain ap residue 63 GLU Chi-restraints excluded: chain bj residue 14 ARG Chi-restraints excluded: chain bl residue 13 ARG Chi-restraints excluded: chain bm residue 13 ARG Chi-restraints excluded: chain bp residue 8 THR Chi-restraints excluded: chain bp residue 21 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 401 optimal weight: 9.9990 chunk 305 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 273 optimal weight: 0.6980 chunk 408 optimal weight: 0.9980 chunk 432 optimal weight: 0.9990 chunk 213 optimal weight: 9.9990 chunk 386 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AH 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 11 HIS AS 11 HIS C1 199 GLN H2 122 ASN H2 169 HIS ac 36 GLN af 2 HIS ak 50 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 57635 Z= 0.224 Angle : 1.774 27.830 79285 Z= 0.606 Chirality : 0.037 0.269 8086 Planarity : 0.004 0.050 8977 Dihedral : 20.690 179.890 19000 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.63 % Allowed : 10.72 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.96 (0.12), residues: 4756 helix: 3.23 (0.08), residues: 3200 sheet: 0.21 (1.14), residues: 24 loop : 1.42 (0.18), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPbd 43 HIS 0.012 0.001 HIS L 153 PHE 0.028 0.002 PHEbc 15 TYR 0.022 0.001 TYR L 164 ARG 0.008 0.000 ARGAL 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 627 time to evaluate : 4.123 Fit side-chains revert: symmetry clash REVERT: AC 28 MET cc_start: 0.9225 (mmm) cc_final: 0.8728 (mmm) REVERT: AF 14 MET cc_start: 0.8622 (mmm) cc_final: 0.8268 (mmm) REVERT: AH 14 MET cc_start: 0.9000 (mmm) cc_final: 0.8613 (mmp) REVERT: AH 28 MET cc_start: 0.9367 (mmm) cc_final: 0.9164 (mmm) REVERT: AI 28 MET cc_start: 0.9134 (mmm) cc_final: 0.8667 (mmm) REVERT: AL 6 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.7103 (mtt) REVERT: AP 6 MET cc_start: 0.8540 (mtp) cc_final: 0.8184 (mtm) REVERT: AU 6 MET cc_start: 0.8366 (mtp) cc_final: 0.8070 (mtp) REVERT: AW 28 MET cc_start: 0.9263 (mmm) cc_final: 0.9051 (mmm) REVERT: BA 9 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6901 (tt0) REVERT: BL 13 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7439 (ttp-110) REVERT: BN 9 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7250 (tm-30) REVERT: BU 19 MET cc_start: 0.7998 (tpp) cc_final: 0.7733 (tpp) REVERT: BV 19 MET cc_start: 0.7960 (tpp) cc_final: 0.7717 (tpp) REVERT: BX 9 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6700 (tp30) REVERT: C 82 MET cc_start: 0.9023 (mmt) cc_final: 0.7878 (mmt) REVERT: H2 122 ASN cc_start: 0.7400 (m110) cc_final: 0.7126 (m-40) REVERT: H2 149 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.6911 (mtp180) REVERT: M 96 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8058 (mm-30) REVERT: M 117 MET cc_start: 0.8836 (ttm) cc_final: 0.8543 (ttm) REVERT: M 138 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7372 (mmp-170) REVERT: aa 11 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.7189 (mtm-85) REVERT: ai 12 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.6396 (mtm180) REVERT: an 7 MET cc_start: 0.6912 (ttp) cc_final: 0.6711 (mtp) REVERT: an 12 ARG cc_start: 0.6741 (tmt170) cc_final: 0.6459 (ttp80) REVERT: ap 13 VAL cc_start: 0.8116 (OUTLIER) cc_final: 0.7851 (p) REVERT: ap 42 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8384 (mm-30) REVERT: ap 63 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7034 (pt0) REVERT: ba 14 ARG cc_start: 0.7432 (ttp-110) cc_final: 0.7126 (mmt180) REVERT: bd 7 MET cc_start: 0.8062 (ptp) cc_final: 0.7715 (ptm) REVERT: bh 7 MET cc_start: 0.7327 (mmt) cc_final: 0.6887 (tpp) REVERT: bj 14 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8564 (ttp-170) REVERT: bj 19 MET cc_start: 0.8328 (tpp) cc_final: 0.8087 (tpp) REVERT: bl 13 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6384 (ttt90) REVERT: bl 19 MET cc_start: 0.7983 (tpp) cc_final: 0.7752 (mmm) REVERT: bm 7 MET cc_start: 0.6405 (ttm) cc_final: 0.6100 (ttt) REVERT: bm 11 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6667 (mt-10) REVERT: bn 13 ARG cc_start: 0.7496 (ttp-110) cc_final: 0.7238 (ptm-80) REVERT: bp 7 MET cc_start: 0.5963 (tpt) cc_final: 0.5389 (tpt) REVERT: bp 19 MET cc_start: 0.7817 (tpt) cc_final: 0.7408 (tpt) outliers start: 103 outliers final: 45 residues processed: 675 average time/residue: 1.6915 time to fit residues: 1397.6296 Evaluate side-chains 668 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 610 time to evaluate : 3.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 48 THR Chi-restraints excluded: chain AC residue 48 THR Chi-restraints excluded: chain AF residue 15 SER Chi-restraints excluded: chain AG residue 15 SER Chi-restraints excluded: chain AI residue 8 THR Chi-restraints excluded: chain AL residue 6 MET Chi-restraints excluded: chain AM residue 15 SER Chi-restraints excluded: chain AP residue 48 THR Chi-restraints excluded: chain AR residue 15 SER Chi-restraints excluded: chain AS residue 30 ILE Chi-restraints excluded: chain AW residue 48 THR Chi-restraints excluded: chain AX residue 48 THR Chi-restraints excluded: chain BA residue 9 GLU Chi-restraints excluded: chain BA residue 24 LEU Chi-restraints excluded: chain BB residue 31 SER Chi-restraints excluded: chain BB residue 39 SER Chi-restraints excluded: chain BC residue 39 SER Chi-restraints excluded: chain BF residue 24 LEU Chi-restraints excluded: chain BH residue 24 LEU Chi-restraints excluded: chain BK residue 31 SER Chi-restraints excluded: chain BL residue 13 ARG Chi-restraints excluded: chain BM residue 24 LEU Chi-restraints excluded: chain BQ residue 39 SER Chi-restraints excluded: chain BU residue 31 SER Chi-restraints excluded: chain BV residue 24 LEU Chi-restraints excluded: chain BX residue 9 GLU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C1 residue 174 SER Chi-restraints excluded: chain H2 residue 59 THR Chi-restraints excluded: chain H2 residue 128 ASN Chi-restraints excluded: chain H2 residue 149 ARG Chi-restraints excluded: chain L residue 20 ASP Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 138 ARG Chi-restraints excluded: chain M residue 291 ASP Chi-restraints excluded: chain aa residue 6 LEU Chi-restraints excluded: chain aa residue 7 MET Chi-restraints excluded: chain aa residue 11 ARG Chi-restraints excluded: chain aa residue 39 SER Chi-restraints excluded: chain ab residue 26 LEU Chi-restraints excluded: chain ad residue 39 SER Chi-restraints excluded: chain af residue 18 VAL Chi-restraints excluded: chain ai residue 12 ARG Chi-restraints excluded: chain ai residue 18 VAL Chi-restraints excluded: chain ak residue 39 SER Chi-restraints excluded: chain am residue 39 SER Chi-restraints excluded: chain ap residue 13 VAL Chi-restraints excluded: chain ap residue 63 GLU Chi-restraints excluded: chain ba residue 39 SER Chi-restraints excluded: chain bg residue 8 THR Chi-restraints excluded: chain bi residue 7 MET Chi-restraints excluded: chain bj residue 14 ARG Chi-restraints excluded: chain bl residue 13 ARG Chi-restraints excluded: chain bp residue 8 THR Chi-restraints excluded: chain bp residue 21 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 359 optimal weight: 10.0000 chunk 245 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 321 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 chunk 368 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 220 optimal weight: 7.9990 chunk 387 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AE 35 GLN ** AH 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 35 GLN C 157 ASN C1 199 GLN H2 103 GLN H2 169 HIS ac 36 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 57635 Z= 0.382 Angle : 1.842 24.517 79285 Z= 0.635 Chirality : 0.042 0.255 8086 Planarity : 0.005 0.058 8977 Dihedral : 21.174 179.907 19000 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.91 % Allowed : 11.31 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.47 (0.12), residues: 4756 helix: 2.86 (0.08), residues: 3204 sheet: 0.06 (1.14), residues: 24 loop : 1.22 (0.18), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPH2 126 HIS 0.015 0.002 HIS L 153 PHE 0.031 0.002 PHEbc 15 TYR 0.029 0.002 TYR L 164 ARG 0.008 0.001 ARGAG 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 624 time to evaluate : 3.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AA 9 ASP cc_start: 0.7694 (t0) cc_final: 0.7490 (t0) REVERT: AC 28 MET cc_start: 0.9209 (mmm) cc_final: 0.8721 (mmm) REVERT: AD 42 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8986 (tp) REVERT: AF 14 MET cc_start: 0.8664 (mmm) cc_final: 0.8239 (mmm) REVERT: AH 14 MET cc_start: 0.8978 (mmm) cc_final: 0.8597 (mmp) REVERT: AI 28 MET cc_start: 0.9187 (mmm) cc_final: 0.8708 (mmm) REVERT: AL 6 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.7082 (mtt) REVERT: AP 6 MET cc_start: 0.8536 (mtp) cc_final: 0.8281 (mtm) REVERT: AU 6 MET cc_start: 0.8374 (mtp) cc_final: 0.8132 (mtp) REVERT: BG 9 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7388 (tp30) REVERT: BH 7 MET cc_start: 0.8753 (mtm) cc_final: 0.8428 (mtm) REVERT: BL 13 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7422 (ttp-110) REVERT: BN 13 ARG cc_start: 0.7410 (ttm-80) cc_final: 0.7193 (ttm-80) REVERT: BT 9 GLU cc_start: 0.7707 (tp30) cc_final: 0.7421 (tp30) REVERT: BV 19 MET cc_start: 0.8090 (tpp) cc_final: 0.7751 (tpp) REVERT: BX 9 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6636 (tp30) REVERT: C 82 MET cc_start: 0.9082 (mmt) cc_final: 0.7949 (mmt) REVERT: H2 122 ASN cc_start: 0.7562 (m110) cc_final: 0.7305 (m-40) REVERT: H2 149 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7132 (mtp180) REVERT: M 96 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7992 (mm-30) REVERT: M 138 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7537 (mmp-170) REVERT: ai 12 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6467 (mtm180) REVERT: an 12 ARG cc_start: 0.6725 (tmt170) cc_final: 0.6438 (ttp80) REVERT: ap 13 VAL cc_start: 0.8099 (OUTLIER) cc_final: 0.7826 (p) REVERT: ap 42 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8336 (mm-30) REVERT: ap 63 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7192 (pt0) REVERT: ba 14 ARG cc_start: 0.7441 (ttp-110) cc_final: 0.7124 (mmt180) REVERT: bd 7 MET cc_start: 0.7968 (ptp) cc_final: 0.7566 (ptm) REVERT: bh 7 MET cc_start: 0.7325 (mmt) cc_final: 0.6858 (tpp) REVERT: bj 14 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8572 (ttp-170) REVERT: bj 19 MET cc_start: 0.8399 (tpp) cc_final: 0.7988 (tpp) REVERT: bm 7 MET cc_start: 0.6490 (ttm) cc_final: 0.6039 (ttt) REVERT: bn 13 ARG cc_start: 0.7554 (ttp-110) cc_final: 0.7144 (ptm-80) REVERT: bp 7 MET cc_start: 0.6015 (tpt) cc_final: 0.5279 (tpt) REVERT: bp 19 MET cc_start: 0.7890 (tpt) cc_final: 0.7394 (tpt) outliers start: 114 outliers final: 60 residues processed: 683 average time/residue: 1.7190 time to fit residues: 1431.1802 Evaluate side-chains 685 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 613 time to evaluate : 3.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 48 THR Chi-restraints excluded: chain AC residue 48 THR Chi-restraints excluded: chain AD residue 42 LEU Chi-restraints excluded: chain AF residue 15 SER Chi-restraints excluded: chain AG residue 15 SER Chi-restraints excluded: chain AL residue 6 MET Chi-restraints excluded: chain AM residue 15 SER Chi-restraints excluded: chain AP residue 12 ILE Chi-restraints excluded: chain AP residue 48 THR Chi-restraints excluded: chain AR residue 15 SER Chi-restraints excluded: chain AS residue 30 ILE Chi-restraints excluded: chain AW residue 15 SER Chi-restraints excluded: chain AW residue 48 THR Chi-restraints excluded: chain AX residue 19 SER Chi-restraints excluded: chain AX residue 48 THR Chi-restraints excluded: chain BA residue 24 LEU Chi-restraints excluded: chain BB residue 31 SER Chi-restraints excluded: chain BB residue 39 SER Chi-restraints excluded: chain BC residue 39 SER Chi-restraints excluded: chain BF residue 24 LEU Chi-restraints excluded: chain BG residue 9 GLU Chi-restraints excluded: chain BH residue 24 LEU Chi-restraints excluded: chain BH residue 31 SER Chi-restraints excluded: chain BI residue 9 GLU Chi-restraints excluded: chain BK residue 31 SER Chi-restraints excluded: chain BL residue 13 ARG Chi-restraints excluded: chain BM residue 24 LEU Chi-restraints excluded: chain BP residue 8 THR Chi-restraints excluded: chain BS residue 8 THR Chi-restraints excluded: chain BT residue 39 SER Chi-restraints excluded: chain BU residue 31 SER Chi-restraints excluded: chain BU residue 39 SER Chi-restraints excluded: chain BX residue 9 GLU Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C1 residue 174 SER Chi-restraints excluded: chain H2 residue 59 THR Chi-restraints excluded: chain H2 residue 128 ASN Chi-restraints excluded: chain H2 residue 149 ARG Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 138 ARG Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 291 ASP Chi-restraints excluded: chain aa residue 6 LEU Chi-restraints excluded: chain aa residue 39 SER Chi-restraints excluded: chain ab residue 7 MET Chi-restraints excluded: chain ab residue 26 LEU Chi-restraints excluded: chain ad residue 12 ARG Chi-restraints excluded: chain ad residue 39 SER Chi-restraints excluded: chain af residue 18 VAL Chi-restraints excluded: chain ai residue 12 ARG Chi-restraints excluded: chain aj residue 26 LEU Chi-restraints excluded: chain ak residue 39 SER Chi-restraints excluded: chain am residue 39 SER Chi-restraints excluded: chain an residue 6 LEU Chi-restraints excluded: chain ap residue 13 VAL Chi-restraints excluded: chain ap residue 18 VAL Chi-restraints excluded: chain ap residue 63 GLU Chi-restraints excluded: chain ba residue 39 SER Chi-restraints excluded: chain be residue 8 THR Chi-restraints excluded: chain bf residue 9 GLU Chi-restraints excluded: chain bg residue 8 THR Chi-restraints excluded: chain bh residue 24 LEU Chi-restraints excluded: chain bi residue 7 MET Chi-restraints excluded: chain bj residue 14 ARG Chi-restraints excluded: chain bl residue 13 ARG Chi-restraints excluded: chain bp residue 8 THR Chi-restraints excluded: chain bp residue 21 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 145 optimal weight: 1.9990 chunk 389 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 253 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 432 optimal weight: 8.9990 chunk 359 optimal weight: 8.9990 chunk 200 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 227 optimal weight: 0.0060 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AH 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 35 GLN AV 35 GLN C1 199 GLN H2 169 HIS ac 36 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 57635 Z= 0.197 Angle : 1.744 25.398 79285 Z= 0.594 Chirality : 0.036 0.272 8086 Planarity : 0.004 0.052 8977 Dihedral : 20.460 179.919 19000 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.50 % Allowed : 12.33 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.86 (0.12), residues: 4756 helix: 3.22 (0.08), residues: 3180 sheet: 0.16 (1.15), residues: 24 loop : 1.23 (0.18), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRPH2 126 HIS 0.013 0.001 HIS M 181 PHE 0.031 0.002 PHEbc 15 TYR 0.020 0.001 TYR L 164 ARG 0.011 0.000 ARGab 3 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 622 time to evaluate : 4.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AA 9 ASP cc_start: 0.7579 (t0) cc_final: 0.7370 (t0) REVERT: AC 28 MET cc_start: 0.9198 (mmm) cc_final: 0.8728 (mmm) REVERT: AF 14 MET cc_start: 0.8658 (mmm) cc_final: 0.8286 (mmm) REVERT: AH 14 MET cc_start: 0.9010 (mmm) cc_final: 0.8615 (mmp) REVERT: AI 28 MET cc_start: 0.9133 (mmm) cc_final: 0.8680 (mmm) REVERT: AP 6 MET cc_start: 0.8541 (mtp) cc_final: 0.8234 (mtm) REVERT: AU 3 ARG cc_start: 0.8605 (mtt90) cc_final: 0.8261 (mtt90) REVERT: AU 6 MET cc_start: 0.8348 (mtp) cc_final: 0.8064 (mtp) REVERT: AU 9 ASP cc_start: 0.7483 (t0) cc_final: 0.6938 (t70) REVERT: AW 28 MET cc_start: 0.9166 (mmm) cc_final: 0.8914 (mmm) REVERT: BB 9 GLU cc_start: 0.7453 (tm-30) cc_final: 0.7251 (tm-30) REVERT: BH 7 MET cc_start: 0.8728 (mtm) cc_final: 0.8367 (mtm) REVERT: BI 13 ARG cc_start: 0.7720 (ttm-80) cc_final: 0.7472 (ttm-80) REVERT: BL 13 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7422 (ttp-110) REVERT: BV 19 MET cc_start: 0.8021 (tpp) cc_final: 0.7620 (tpp) REVERT: C 82 MET cc_start: 0.9021 (mmt) cc_final: 0.8176 (mmt) REVERT: H2 122 ASN cc_start: 0.7596 (m110) cc_final: 0.7380 (m-40) REVERT: H2 128 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.7187 (m110) REVERT: H2 149 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6984 (mtp180) REVERT: M 96 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8041 (mm-30) REVERT: M 138 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7355 (mmp-170) REVERT: ai 12 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.6345 (mtm180) REVERT: an 12 ARG cc_start: 0.6821 (tmt170) cc_final: 0.6556 (ttp80) REVERT: ap 13 VAL cc_start: 0.8104 (OUTLIER) cc_final: 0.7842 (p) REVERT: ap 42 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8349 (mm-30) REVERT: ap 63 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7084 (pt0) REVERT: ba 14 ARG cc_start: 0.7425 (ttp-110) cc_final: 0.7157 (mmt180) REVERT: bd 7 MET cc_start: 0.7956 (ptp) cc_final: 0.7539 (ptm) REVERT: bh 7 MET cc_start: 0.7356 (mmt) cc_final: 0.6771 (tpp) REVERT: bj 14 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8550 (ttp-170) REVERT: bj 19 MET cc_start: 0.8363 (tpp) cc_final: 0.8099 (tpp) REVERT: bn 13 ARG cc_start: 0.7546 (ttp-110) cc_final: 0.7252 (ptm-80) REVERT: bo 14 ARG cc_start: 0.7230 (ttp-110) cc_final: 0.7001 (ttp-110) REVERT: bp 7 MET cc_start: 0.5959 (tpt) cc_final: 0.5214 (tpt) REVERT: bp 19 MET cc_start: 0.7832 (tpt) cc_final: 0.7413 (tpt) outliers start: 98 outliers final: 51 residues processed: 674 average time/residue: 1.6758 time to fit residues: 1384.5334 Evaluate side-chains 668 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 608 time to evaluate : 3.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 48 THR Chi-restraints excluded: chain AC residue 48 THR Chi-restraints excluded: chain AE residue 15 SER Chi-restraints excluded: chain AF residue 15 SER Chi-restraints excluded: chain AM residue 15 SER Chi-restraints excluded: chain AP residue 48 THR Chi-restraints excluded: chain AR residue 15 SER Chi-restraints excluded: chain AR residue 19 SER Chi-restraints excluded: chain AS residue 12 ILE Chi-restraints excluded: chain AS residue 30 ILE Chi-restraints excluded: chain AX residue 19 SER Chi-restraints excluded: chain AX residue 48 THR Chi-restraints excluded: chain BA residue 24 LEU Chi-restraints excluded: chain BB residue 31 SER Chi-restraints excluded: chain BB residue 39 SER Chi-restraints excluded: chain BC residue 39 SER Chi-restraints excluded: chain BH residue 24 LEU Chi-restraints excluded: chain BH residue 31 SER Chi-restraints excluded: chain BK residue 31 SER Chi-restraints excluded: chain BL residue 13 ARG Chi-restraints excluded: chain BL residue 24 LEU Chi-restraints excluded: chain BM residue 24 LEU Chi-restraints excluded: chain BP residue 8 THR Chi-restraints excluded: chain BT residue 39 SER Chi-restraints excluded: chain BU residue 31 SER Chi-restraints excluded: chain BU residue 39 SER Chi-restraints excluded: chain BV residue 24 LEU Chi-restraints excluded: chain BW residue 39 SER Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C1 residue 174 SER Chi-restraints excluded: chain C1 residue 181 ARG Chi-restraints excluded: chain H2 residue 59 THR Chi-restraints excluded: chain H2 residue 128 ASN Chi-restraints excluded: chain H2 residue 149 ARG Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 138 ARG Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 291 ASP Chi-restraints excluded: chain aa residue 6 LEU Chi-restraints excluded: chain aa residue 39 SER Chi-restraints excluded: chain ab residue 26 LEU Chi-restraints excluded: chain ad residue 12 ARG Chi-restraints excluded: chain af residue 18 VAL Chi-restraints excluded: chain ai residue 12 ARG Chi-restraints excluded: chain ak residue 39 SER Chi-restraints excluded: chain am residue 39 SER Chi-restraints excluded: chain an residue 6 LEU Chi-restraints excluded: chain ap residue 13 VAL Chi-restraints excluded: chain ap residue 63 GLU Chi-restraints excluded: chain ba residue 39 SER Chi-restraints excluded: chain bc residue 8 THR Chi-restraints excluded: chain bg residue 8 THR Chi-restraints excluded: chain bh residue 24 LEU Chi-restraints excluded: chain bj residue 14 ARG Chi-restraints excluded: chain bl residue 13 ARG Chi-restraints excluded: chain bp residue 8 THR Chi-restraints excluded: chain bp residue 21 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 416 optimal weight: 0.0170 chunk 48 optimal weight: 10.0000 chunk 246 optimal weight: 0.7980 chunk 315 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 364 optimal weight: 9.9990 chunk 241 optimal weight: 4.9990 chunk 430 optimal weight: 1.9990 chunk 269 optimal weight: 0.0770 chunk 262 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AH 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 35 GLN AV 35 GLN C1 163 ASN C1 199 GLN H2 169 HIS ac 36 GLN ** ak 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 57635 Z= 0.170 Angle : 1.709 23.613 79285 Z= 0.581 Chirality : 0.035 0.269 8086 Planarity : 0.004 0.051 8977 Dihedral : 19.780 179.844 19000 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.94 % Allowed : 12.87 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.17 (0.12), residues: 4756 helix: 3.52 (0.08), residues: 3139 sheet: 0.27 (1.17), residues: 24 loop : 1.29 (0.17), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRPH2 126 HIS 0.011 0.001 HIS M 181 PHE 0.030 0.001 PHEBL 15 TYR 0.017 0.001 TYR L 164 ARG 0.010 0.000 ARGBN 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 630 time to evaluate : 3.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AC 28 MET cc_start: 0.9196 (mmm) cc_final: 0.8736 (mmm) REVERT: AF 14 MET cc_start: 0.8635 (mmm) cc_final: 0.8296 (mmm) REVERT: AH 14 MET cc_start: 0.8995 (mmm) cc_final: 0.8638 (mmp) REVERT: AI 28 MET cc_start: 0.9108 (mmm) cc_final: 0.8648 (mmm) REVERT: AP 6 MET cc_start: 0.8557 (mtp) cc_final: 0.8260 (mtm) REVERT: AU 6 MET cc_start: 0.8327 (mtp) cc_final: 0.8033 (mtp) REVERT: AU 9 ASP cc_start: 0.7483 (t0) cc_final: 0.6955 (t70) REVERT: AW 28 MET cc_start: 0.9143 (mmm) cc_final: 0.8852 (mmm) REVERT: BE 9 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.5993 (tp30) REVERT: BH 7 MET cc_start: 0.8706 (mtm) cc_final: 0.8462 (mtm) REVERT: BI 13 ARG cc_start: 0.7707 (ttm-80) cc_final: 0.7499 (ttm-80) REVERT: BT 9 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7349 (tp30) REVERT: BV 19 MET cc_start: 0.7952 (tpp) cc_final: 0.7590 (tpp) REVERT: C 82 MET cc_start: 0.8933 (mmt) cc_final: 0.8000 (mmt) REVERT: H2 128 ASN cc_start: 0.7576 (OUTLIER) cc_final: 0.7183 (m110) REVERT: H2 149 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6901 (mtp180) REVERT: M 96 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8074 (mm-30) REVERT: M 138 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7328 (mmp-170) REVERT: ah 56 SER cc_start: 0.7830 (p) cc_final: 0.7373 (t) REVERT: ai 12 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.6363 (mtm180) REVERT: an 12 ARG cc_start: 0.6805 (tmt170) cc_final: 0.6558 (tmt170) REVERT: ap 13 VAL cc_start: 0.8096 (OUTLIER) cc_final: 0.7840 (p) REVERT: ap 42 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8373 (mm-30) REVERT: ap 63 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7057 (pt0) REVERT: ba 14 ARG cc_start: 0.7386 (ttp-110) cc_final: 0.7167 (mmt180) REVERT: bd 7 MET cc_start: 0.7993 (ptp) cc_final: 0.7552 (ptm) REVERT: bh 7 MET cc_start: 0.7270 (mmt) cc_final: 0.6841 (tpp) REVERT: bj 14 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8533 (ttp-170) REVERT: bn 13 ARG cc_start: 0.7527 (ttp-110) cc_final: 0.7287 (ptm-80) REVERT: bp 7 MET cc_start: 0.5921 (tpt) cc_final: 0.5336 (tpt) REVERT: bp 19 MET cc_start: 0.7810 (tpt) cc_final: 0.7303 (tpt) outliers start: 76 outliers final: 42 residues processed: 670 average time/residue: 1.6737 time to fit residues: 1369.8107 Evaluate side-chains 658 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 606 time to evaluate : 3.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 48 THR Chi-restraints excluded: chain AG residue 15 SER Chi-restraints excluded: chain AM residue 15 SER Chi-restraints excluded: chain AP residue 48 THR Chi-restraints excluded: chain AS residue 30 ILE Chi-restraints excluded: chain AX residue 19 SER Chi-restraints excluded: chain AX residue 48 THR Chi-restraints excluded: chain BA residue 24 LEU Chi-restraints excluded: chain BB residue 31 SER Chi-restraints excluded: chain BC residue 39 SER Chi-restraints excluded: chain BE residue 9 GLU Chi-restraints excluded: chain BH residue 24 LEU Chi-restraints excluded: chain BH residue 31 SER Chi-restraints excluded: chain BI residue 9 GLU Chi-restraints excluded: chain BK residue 31 SER Chi-restraints excluded: chain BM residue 24 LEU Chi-restraints excluded: chain BP residue 8 THR Chi-restraints excluded: chain BT residue 9 GLU Chi-restraints excluded: chain BT residue 39 SER Chi-restraints excluded: chain BU residue 39 SER Chi-restraints excluded: chain BV residue 24 LEU Chi-restraints excluded: chain BW residue 39 SER Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C1 residue 174 SER Chi-restraints excluded: chain C1 residue 181 ARG Chi-restraints excluded: chain H2 residue 59 THR Chi-restraints excluded: chain H2 residue 128 ASN Chi-restraints excluded: chain H2 residue 149 ARG Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 138 ARG Chi-restraints excluded: chain M residue 291 ASP Chi-restraints excluded: chain aa residue 6 LEU Chi-restraints excluded: chain aa residue 39 SER Chi-restraints excluded: chain ab residue 26 LEU Chi-restraints excluded: chain ad residue 12 ARG Chi-restraints excluded: chain ad residue 39 SER Chi-restraints excluded: chain af residue 18 VAL Chi-restraints excluded: chain ai residue 12 ARG Chi-restraints excluded: chain aj residue 26 LEU Chi-restraints excluded: chain am residue 39 SER Chi-restraints excluded: chain an residue 6 LEU Chi-restraints excluded: chain ap residue 2 HIS Chi-restraints excluded: chain ap residue 13 VAL Chi-restraints excluded: chain ap residue 63 GLU Chi-restraints excluded: chain bg residue 8 THR Chi-restraints excluded: chain bh residue 24 LEU Chi-restraints excluded: chain bi residue 7 MET Chi-restraints excluded: chain bj residue 14 ARG Chi-restraints excluded: chain bp residue 8 THR Chi-restraints excluded: chain bp residue 21 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 266 optimal weight: 0.1980 chunk 172 optimal weight: 1.9990 chunk 257 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 83 optimal weight: 0.8980 chunk 273 optimal weight: 0.5980 chunk 293 optimal weight: 0.9980 chunk 213 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 338 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AH 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 35 GLN C1 198 ASN C1 199 GLN H2 169 HIS ac 36 GLN ** ak 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 57635 Z= 0.168 Angle : 1.694 23.497 79285 Z= 0.576 Chirality : 0.034 0.266 8086 Planarity : 0.003 0.050 8977 Dihedral : 19.297 179.852 19000 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.84 % Allowed : 13.38 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.22 (0.12), residues: 4756 helix: 3.42 (0.08), residues: 3202 sheet: -0.02 (0.99), residues: 30 loop : 1.57 (0.18), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRPH2 126 HIS 0.011 0.001 HIS M 181 PHE 0.027 0.001 PHEbc 15 TYR 0.017 0.001 TYR L 164 ARG 0.011 0.000 ARGab 3 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 626 time to evaluate : 3.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AC 28 MET cc_start: 0.9207 (mmm) cc_final: 0.8757 (mmm) REVERT: AF 14 MET cc_start: 0.8624 (mmm) cc_final: 0.8306 (mmm) REVERT: AH 14 MET cc_start: 0.9017 (mmm) cc_final: 0.8651 (mmp) REVERT: AI 28 MET cc_start: 0.9105 (mmm) cc_final: 0.8638 (mmm) REVERT: AP 6 MET cc_start: 0.8564 (mtp) cc_final: 0.8262 (mtm) REVERT: AU 6 MET cc_start: 0.8355 (mtp) cc_final: 0.8063 (mtp) REVERT: AU 9 ASP cc_start: 0.7548 (t0) cc_final: 0.7012 (t70) REVERT: AV 3 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8112 (tpp-160) REVERT: AW 28 MET cc_start: 0.9148 (mmm) cc_final: 0.8829 (mmm) REVERT: BB 9 GLU cc_start: 0.7405 (tm-30) cc_final: 0.7149 (tp30) REVERT: BH 7 MET cc_start: 0.8660 (mtm) cc_final: 0.8443 (mtm) REVERT: BS 10 GLU cc_start: 0.6979 (tp30) cc_final: 0.6770 (tp30) REVERT: BV 19 MET cc_start: 0.7931 (tpp) cc_final: 0.7555 (tpp) REVERT: BX 9 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.5899 (tp30) REVERT: C 82 MET cc_start: 0.8886 (mmt) cc_final: 0.7984 (mmt) REVERT: H2 149 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6843 (mtp180) REVERT: M 96 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8054 (mm-30) REVERT: M 138 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7295 (mmp-170) REVERT: ah 56 SER cc_start: 0.7841 (p) cc_final: 0.7361 (t) REVERT: ai 12 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.6442 (mtm180) REVERT: an 12 ARG cc_start: 0.6795 (tmt170) cc_final: 0.6549 (tmt170) REVERT: ao 50 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7993 (mp-120) REVERT: ap 13 VAL cc_start: 0.8173 (OUTLIER) cc_final: 0.7920 (p) REVERT: ap 42 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8381 (mm-30) REVERT: bb 21 THR cc_start: 0.8805 (m) cc_final: 0.8546 (m) REVERT: bd 7 MET cc_start: 0.7993 (ptp) cc_final: 0.7552 (ptm) REVERT: bh 7 MET cc_start: 0.7157 (mmt) cc_final: 0.6769 (tpp) REVERT: bp 7 MET cc_start: 0.5963 (tpt) cc_final: 0.5385 (tpt) REVERT: bp 19 MET cc_start: 0.7815 (tpt) cc_final: 0.7303 (tpt) outliers start: 72 outliers final: 40 residues processed: 661 average time/residue: 1.6789 time to fit residues: 1358.1078 Evaluate side-chains 661 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 613 time to evaluate : 3.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 48 THR Chi-restraints excluded: chain AG residue 15 SER Chi-restraints excluded: chain AM residue 15 SER Chi-restraints excluded: chain AS residue 30 ILE Chi-restraints excluded: chain AV residue 3 ARG Chi-restraints excluded: chain AX residue 19 SER Chi-restraints excluded: chain BA residue 24 LEU Chi-restraints excluded: chain BB residue 31 SER Chi-restraints excluded: chain BB residue 39 SER Chi-restraints excluded: chain BC residue 39 SER Chi-restraints excluded: chain BH residue 24 LEU Chi-restraints excluded: chain BH residue 31 SER Chi-restraints excluded: chain BT residue 39 SER Chi-restraints excluded: chain BU residue 39 SER Chi-restraints excluded: chain BV residue 24 LEU Chi-restraints excluded: chain BW residue 39 SER Chi-restraints excluded: chain BX residue 9 GLU Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C1 residue 174 SER Chi-restraints excluded: chain C1 residue 181 ARG Chi-restraints excluded: chain H2 residue 59 THR Chi-restraints excluded: chain H2 residue 128 ASN Chi-restraints excluded: chain H2 residue 149 ARG Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 138 ARG Chi-restraints excluded: chain M residue 291 ASP Chi-restraints excluded: chain aa residue 6 LEU Chi-restraints excluded: chain aa residue 39 SER Chi-restraints excluded: chain ab residue 26 LEU Chi-restraints excluded: chain ad residue 12 ARG Chi-restraints excluded: chain ad residue 39 SER Chi-restraints excluded: chain af residue 18 VAL Chi-restraints excluded: chain ai residue 12 ARG Chi-restraints excluded: chain aj residue 26 LEU Chi-restraints excluded: chain aj residue 39 SER Chi-restraints excluded: chain ak residue 39 SER Chi-restraints excluded: chain am residue 39 SER Chi-restraints excluded: chain ao residue 50 GLN Chi-restraints excluded: chain ap residue 2 HIS Chi-restraints excluded: chain ap residue 13 VAL Chi-restraints excluded: chain bc residue 8 THR Chi-restraints excluded: chain be residue 8 THR Chi-restraints excluded: chain bg residue 8 THR Chi-restraints excluded: chain bh residue 24 LEU Chi-restraints excluded: chain bi residue 7 MET Chi-restraints excluded: chain bp residue 8 THR Chi-restraints excluded: chain bp residue 21 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 391 optimal weight: 10.0000 chunk 412 optimal weight: 0.6980 chunk 376 optimal weight: 0.8980 chunk 401 optimal weight: 10.0000 chunk 241 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 315 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 362 optimal weight: 0.7980 chunk 379 optimal weight: 2.9990 chunk 400 optimal weight: 7.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AD 35 GLN ** AH 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 35 GLN C 94 ASN H2 122 ASN ac 36 GLN ai 36 GLN ** ak 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 57635 Z= 0.185 Angle : 1.699 23.590 79285 Z= 0.578 Chirality : 0.035 0.263 8086 Planarity : 0.004 0.050 8977 Dihedral : 19.180 179.887 19000 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.79 % Allowed : 13.71 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.17 (0.12), residues: 4756 helix: 3.37 (0.08), residues: 3201 sheet: -0.02 (0.99), residues: 30 loop : 1.56 (0.18), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRPH2 126 HIS 0.012 0.001 HIS M 181 PHE 0.036 0.001 PHEBL 15 TYR 0.019 0.001 TYR L 164 ARG 0.011 0.000 ARGad 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 618 time to evaluate : 3.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AC 28 MET cc_start: 0.9212 (mmm) cc_final: 0.8762 (mmm) REVERT: AF 14 MET cc_start: 0.8642 (mmm) cc_final: 0.8314 (mmm) REVERT: AH 12 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8579 (mp) REVERT: AH 14 MET cc_start: 0.9015 (mmm) cc_final: 0.8672 (mmp) REVERT: AI 28 MET cc_start: 0.9113 (mmm) cc_final: 0.8642 (mmm) REVERT: AL 6 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6860 (mtt) REVERT: AP 6 MET cc_start: 0.8564 (mtp) cc_final: 0.8246 (mtm) REVERT: AU 6 MET cc_start: 0.8319 (mtp) cc_final: 0.8033 (mtp) REVERT: AW 28 MET cc_start: 0.9159 (mmm) cc_final: 0.8856 (mmm) REVERT: BA 7 MET cc_start: 0.8050 (ttp) cc_final: 0.7401 (ttm) REVERT: BB 19 MET cc_start: 0.8328 (mmm) cc_final: 0.8118 (mmp) REVERT: BD 11 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7668 (mt-10) REVERT: BH 7 MET cc_start: 0.8666 (mtm) cc_final: 0.8444 (mtm) REVERT: BP 44 PHE cc_start: 0.8651 (m-80) cc_final: 0.8441 (m-80) REVERT: BU 13 ARG cc_start: 0.7508 (ttm-80) cc_final: 0.7202 (mtp85) REVERT: BV 19 MET cc_start: 0.7945 (tpp) cc_final: 0.7552 (tpp) REVERT: BX 9 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.5842 (tp30) REVERT: C 82 MET cc_start: 0.8911 (mmt) cc_final: 0.7994 (mmt) REVERT: H2 149 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6876 (mtp180) REVERT: M 96 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8078 (mm-30) REVERT: M 138 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7320 (mmp-170) REVERT: ag 3 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7326 (mtm180) REVERT: ah 56 SER cc_start: 0.7848 (p) cc_final: 0.7368 (t) REVERT: ai 12 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.6457 (mtm180) REVERT: an 12 ARG cc_start: 0.6819 (tmt170) cc_final: 0.6576 (tmt170) REVERT: ap 13 VAL cc_start: 0.8143 (t) cc_final: 0.7899 (p) REVERT: ap 42 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8378 (mm-30) REVERT: bb 21 THR cc_start: 0.8824 (m) cc_final: 0.8568 (m) REVERT: bd 7 MET cc_start: 0.7984 (ptp) cc_final: 0.7537 (ptm) REVERT: bh 7 MET cc_start: 0.7138 (mmt) cc_final: 0.6781 (tpp) REVERT: bp 7 MET cc_start: 0.5978 (tpt) cc_final: 0.5406 (tpt) REVERT: bp 19 MET cc_start: 0.7819 (tpt) cc_final: 0.7278 (mmm) outliers start: 70 outliers final: 46 residues processed: 660 average time/residue: 1.6765 time to fit residues: 1353.6393 Evaluate side-chains 663 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 609 time to evaluate : 3.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 48 THR Chi-restraints excluded: chain AF residue 15 SER Chi-restraints excluded: chain AG residue 15 SER Chi-restraints excluded: chain AH residue 12 ILE Chi-restraints excluded: chain AL residue 6 MET Chi-restraints excluded: chain AM residue 15 SER Chi-restraints excluded: chain AP residue 48 THR Chi-restraints excluded: chain AR residue 19 SER Chi-restraints excluded: chain AS residue 30 ILE Chi-restraints excluded: chain AX residue 19 SER Chi-restraints excluded: chain AX residue 48 THR Chi-restraints excluded: chain BA residue 24 LEU Chi-restraints excluded: chain BB residue 7 MET Chi-restraints excluded: chain BB residue 31 SER Chi-restraints excluded: chain BB residue 39 SER Chi-restraints excluded: chain BC residue 39 SER Chi-restraints excluded: chain BH residue 24 LEU Chi-restraints excluded: chain BH residue 31 SER Chi-restraints excluded: chain BJ residue 24 LEU Chi-restraints excluded: chain BP residue 8 THR Chi-restraints excluded: chain BT residue 39 SER Chi-restraints excluded: chain BU residue 39 SER Chi-restraints excluded: chain BV residue 24 LEU Chi-restraints excluded: chain BW residue 39 SER Chi-restraints excluded: chain BX residue 9 GLU Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C1 residue 174 SER Chi-restraints excluded: chain C1 residue 181 ARG Chi-restraints excluded: chain H2 residue 59 THR Chi-restraints excluded: chain H2 residue 128 ASN Chi-restraints excluded: chain H2 residue 149 ARG Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 138 ARG Chi-restraints excluded: chain M residue 291 ASP Chi-restraints excluded: chain aa residue 6 LEU Chi-restraints excluded: chain aa residue 39 SER Chi-restraints excluded: chain ab residue 26 LEU Chi-restraints excluded: chain ad residue 12 ARG Chi-restraints excluded: chain ad residue 39 SER Chi-restraints excluded: chain af residue 18 VAL Chi-restraints excluded: chain ag residue 3 ARG Chi-restraints excluded: chain ai residue 12 ARG Chi-restraints excluded: chain aj residue 26 LEU Chi-restraints excluded: chain aj residue 39 SER Chi-restraints excluded: chain am residue 39 SER Chi-restraints excluded: chain ap residue 2 HIS Chi-restraints excluded: chain bc residue 8 THR Chi-restraints excluded: chain be residue 8 THR Chi-restraints excluded: chain bg residue 8 THR Chi-restraints excluded: chain bh residue 24 LEU Chi-restraints excluded: chain bi residue 7 MET Chi-restraints excluded: chain bp residue 8 THR Chi-restraints excluded: chain bp residue 21 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 263 optimal weight: 4.9990 chunk 424 optimal weight: 0.6980 chunk 259 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 295 optimal weight: 0.0980 chunk 445 optimal weight: 5.9990 chunk 409 optimal weight: 5.9990 chunk 354 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 273 optimal weight: 0.6980 chunk 217 optimal weight: 8.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AH 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ac 36 GLN ** ak 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 57635 Z= 0.220 Angle : 1.716 23.730 79285 Z= 0.587 Chirality : 0.036 0.258 8086 Planarity : 0.004 0.051 8977 Dihedral : 19.231 179.964 19000 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.61 % Allowed : 14.04 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.05 (0.12), residues: 4756 helix: 3.26 (0.08), residues: 3203 sheet: 0.31 (1.17), residues: 24 loop : 1.56 (0.18), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRPH2 126 HIS 0.013 0.001 HIS L 153 PHE 0.030 0.002 PHEbc 15 TYR 0.022 0.001 TYR L 164 ARG 0.010 0.001 ARGad 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9512 Ramachandran restraints generated. 4756 Oldfield, 0 Emsley, 4756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 614 time to evaluate : 3.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AC 28 MET cc_start: 0.9219 (mmm) cc_final: 0.8756 (mmm) REVERT: AF 6 MET cc_start: 0.7515 (mtp) cc_final: 0.7298 (mtm) REVERT: AF 14 MET cc_start: 0.8647 (mmm) cc_final: 0.8280 (mmm) REVERT: AH 12 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8624 (mp) REVERT: AH 14 MET cc_start: 0.9014 (mmm) cc_final: 0.8675 (mmp) REVERT: AI 28 MET cc_start: 0.9146 (mmm) cc_final: 0.8672 (mmm) REVERT: AL 6 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.7014 (mtt) REVERT: AP 6 MET cc_start: 0.8580 (mtp) cc_final: 0.8295 (mtm) REVERT: AU 6 MET cc_start: 0.8357 (mtp) cc_final: 0.8085 (mtp) REVERT: AU 9 ASP cc_start: 0.7529 (t0) cc_final: 0.6985 (t70) REVERT: AW 28 MET cc_start: 0.9182 (mmm) cc_final: 0.8866 (mmm) REVERT: BD 11 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7807 (mt-10) REVERT: BH 7 MET cc_start: 0.8711 (mtm) cc_final: 0.8435 (mtm) REVERT: BT 9 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7242 (tp30) REVERT: BV 19 MET cc_start: 0.7962 (tpp) cc_final: 0.7593 (tpp) REVERT: BX 9 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6313 (tp30) REVERT: C 82 MET cc_start: 0.8981 (mmt) cc_final: 0.8023 (mmt) REVERT: H2 149 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.6942 (mtp180) REVERT: M 14 ARG cc_start: 0.6994 (mmm160) cc_final: 0.6753 (mmm160) REVERT: M 96 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8050 (mm-30) REVERT: M 138 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7342 (mmp-170) REVERT: ag 3 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7305 (mtm180) REVERT: ai 12 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.6444 (mtm180) REVERT: an 12 ARG cc_start: 0.6798 (tmt170) cc_final: 0.6539 (tmt170) REVERT: ap 13 VAL cc_start: 0.8125 (t) cc_final: 0.7867 (p) REVERT: ap 42 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8371 (mm-30) REVERT: bb 7 MET cc_start: 0.7079 (ttm) cc_final: 0.6798 (ttt) REVERT: bb 21 THR cc_start: 0.8823 (m) cc_final: 0.8560 (m) REVERT: bd 7 MET cc_start: 0.7947 (ptp) cc_final: 0.7489 (ptm) REVERT: bh 7 MET cc_start: 0.7242 (mmt) cc_final: 0.6827 (tpp) REVERT: bp 7 MET cc_start: 0.5998 (tpt) cc_final: 0.5438 (tpt) REVERT: bp 19 MET cc_start: 0.7837 (tpt) cc_final: 0.7301 (mmm) outliers start: 63 outliers final: 47 residues processed: 655 average time/residue: 1.6569 time to fit residues: 1332.9532 Evaluate side-chains 668 residues out of total 3917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 612 time to evaluate : 3.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 48 THR Chi-restraints excluded: chain AC residue 48 THR Chi-restraints excluded: chain AF residue 15 SER Chi-restraints excluded: chain AG residue 15 SER Chi-restraints excluded: chain AH residue 12 ILE Chi-restraints excluded: chain AL residue 6 MET Chi-restraints excluded: chain AM residue 15 SER Chi-restraints excluded: chain AP residue 48 THR Chi-restraints excluded: chain AS residue 30 ILE Chi-restraints excluded: chain AX residue 19 SER Chi-restraints excluded: chain AX residue 48 THR Chi-restraints excluded: chain BA residue 24 LEU Chi-restraints excluded: chain BB residue 31 SER Chi-restraints excluded: chain BB residue 39 SER Chi-restraints excluded: chain BC residue 39 SER Chi-restraints excluded: chain BH residue 24 LEU Chi-restraints excluded: chain BH residue 31 SER Chi-restraints excluded: chain BK residue 31 SER Chi-restraints excluded: chain BP residue 8 THR Chi-restraints excluded: chain BT residue 9 GLU Chi-restraints excluded: chain BT residue 39 SER Chi-restraints excluded: chain BU residue 39 SER Chi-restraints excluded: chain BV residue 24 LEU Chi-restraints excluded: chain BW residue 39 SER Chi-restraints excluded: chain BX residue 9 GLU Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C1 residue 174 SER Chi-restraints excluded: chain C1 residue 181 ARG Chi-restraints excluded: chain H2 residue 59 THR Chi-restraints excluded: chain H2 residue 128 ASN Chi-restraints excluded: chain H2 residue 149 ARG Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 138 ARG Chi-restraints excluded: chain M residue 291 ASP Chi-restraints excluded: chain aa residue 6 LEU Chi-restraints excluded: chain aa residue 39 SER Chi-restraints excluded: chain ab residue 26 LEU Chi-restraints excluded: chain ad residue 12 ARG Chi-restraints excluded: chain ad residue 39 SER Chi-restraints excluded: chain af residue 18 VAL Chi-restraints excluded: chain ag residue 3 ARG Chi-restraints excluded: chain ai residue 12 ARG Chi-restraints excluded: chain aj residue 26 LEU Chi-restraints excluded: chain aj residue 39 SER Chi-restraints excluded: chain ak residue 39 SER Chi-restraints excluded: chain am residue 39 SER Chi-restraints excluded: chain ap residue 2 HIS Chi-restraints excluded: chain bc residue 8 THR Chi-restraints excluded: chain be residue 8 THR Chi-restraints excluded: chain bg residue 8 THR Chi-restraints excluded: chain bh residue 24 LEU Chi-restraints excluded: chain bi residue 7 MET Chi-restraints excluded: chain bp residue 8 THR Chi-restraints excluded: chain bp residue 21 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 281 optimal weight: 0.7980 chunk 377 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 326 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 355 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 364 optimal weight: 0.0010 chunk 44 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AH 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 35 GLN C1 199 GLN H2 122 ASN ac 36 GLN ** ak 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.104451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.076878 restraints weight = 88976.872| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.21 r_work: 0.2813 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 57635 Z= 0.181 Angle : 1.692 23.565 79285 Z= 0.577 Chirality : 0.035 0.263 8086 Planarity : 0.004 0.051 8977 Dihedral : 19.002 179.987 19000 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.61 % Allowed : 14.17 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.13 (0.12), residues: 4756 helix: 3.33 (0.08), residues: 3203 sheet: 0.01 (0.98), residues: 30 loop : 1.57 (0.18), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRPH2 126 HIS 0.011 0.001 HIS M 181 PHE 0.041 0.001 PHEBL 15 TYR 0.019 0.001 TYR L 164 ARG 0.010 0.000 ARGad 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20416.78 seconds wall clock time: 354 minutes 51.44 seconds (21291.44 seconds total)