Starting phenix.real_space_refine on Sat Apr 6 08:34:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0x_12682/04_2024/7o0x_12682_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0x_12682/04_2024/7o0x_12682.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0x_12682/04_2024/7o0x_12682_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0x_12682/04_2024/7o0x_12682_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0x_12682/04_2024/7o0x_12682_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0x_12682/04_2024/7o0x_12682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0x_12682/04_2024/7o0x_12682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0x_12682/04_2024/7o0x_12682_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o0x_12682/04_2024/7o0x_12682_updated.pdb" } resolution = 2.44 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 5 7.16 5 P 33 5.49 5 Mg 108 5.21 5 S 278 5.16 5 C 38880 2.51 5 N 7407 2.21 5 O 9735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "BK PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BO PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H2 TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 56446 Number of models: 1 Model: "" Number of chains: 237 Chain: "AA" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AB" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AC" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 384 Classifications: {'peptide': 48} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AD" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 384 Classifications: {'peptide': 48} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AE" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AF" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AG" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AH" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AI" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AJ" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AK" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AL" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AM" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AN" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AO" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AP" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AQ" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AR" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AS" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AT" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AU" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AV" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AW" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AX" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 391 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "BA" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BB" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BC" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BD" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BE" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BF" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BG" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BH" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BI" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BJ" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BK" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BL" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BM" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BN" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BO" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BP" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BQ" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BR" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BS" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BT" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BU" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "BV" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BW" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "BX" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "C" Number of atoms: 2325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2325 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 23, 'TRANS': 275} Chain: "C1" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 806 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 10, 'TRANS': 92} Chain: "C2" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 766 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "H1" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 522 Classifications: {'peptide': 62} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H2" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1404 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 163} Chain: "L" Number of atoms: 2165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2165 Classifications: {'peptide': 273} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 257} Chain: "M" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2694 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 22, 'TRANS': 312} Chain: "aa" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 433 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "ab" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ac" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 443 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ad" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ae" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "af" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ag" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ah" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ai" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "aj" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ak" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 542 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 6, 'TRANS': 64} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "al" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "am" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "an" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 542 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 6, 'TRANS': 64} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ao" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 465 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ap" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 543 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 64} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ba" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bb" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bc" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bd" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "be" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bf" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bg" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bh" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bi" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bj" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bk" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bl" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bm" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bn" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "bo" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "bp" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "MG" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'MAN': 1, 'RAM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 202 Unusual residues: {'BCL': 2, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AC" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AD" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 202 Unusual residues: {'BCL': 2, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AE" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 177 Unusual residues: {'BCL': 2, 'V7N': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AF" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AG" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AH" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 282 Unusual residues: {'BCL': 2, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "AI" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AJ" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AK" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AL" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AM" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AN" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 202 Unusual residues: {'BCL': 2, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AO" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AP" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AQ" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 198 Unusual residues: {'BCL': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AR" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AS" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 233 Unusual residues: {'BCL': 3, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AT" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 146 Unusual residues: {'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AU" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AV" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AW" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 233 Unusual residues: {'BCL': 3, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AX" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BA" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 251 Unusual residues: {'BCL': 1, 'LMT': 4, 'V7N': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "BB" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BC" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BD" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 251 Unusual residues: {'BCL': 1, 'LMT': 4, 'V7N': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "BE" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 251 Unusual residues: {'BCL': 1, 'LMT': 4, 'V7N': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "BF" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 171 Unusual residues: {'BCL': 1, 'LMT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BG" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BH" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BI" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 206 Unusual residues: {'BCL': 1, 'LMT': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BJ" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BK" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 251 Unusual residues: {'BCL': 1, 'LMT': 4, 'V7N': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "BL" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BM" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BN" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 251 Unusual residues: {'BCL': 1, 'LMT': 4, 'V7N': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "BO" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BP" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 251 Unusual residues: {'BCL': 1, 'LMT': 4, 'V7N': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "BQ" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BR" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 251 Unusual residues: {'BCL': 1, 'LMT': 4, 'V7N': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "BS" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BT" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'BCL': 1, 'LMT': 3, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "BU" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 171 Unusual residues: {'BCL': 1, 'LMT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BV" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "BW" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 251 Unusual residues: {'BCL': 1, 'LMT': 4, 'V7N': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "BX" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 204 Unusual residues: {'HEC': 4, 'NDG': 1, 'V75': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen 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: "L" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 470 Unusual residues: {'0V9': 1, 'BCL': 2, 'BPH': 1, 'LMT': 5, 'MQ8': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "M" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 432 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'CD4': 1, 'CRT': 1, 'LMT': 1, 'MQ8': 1, 'V75': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "aa" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ab" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ac" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "ad" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 150 Unusual residues: {'BCL': 1, 'CD4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "ae" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "af" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 292 Unusual residues: {'BCL': 1, 'CD4': 2, 'V7B': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "ag" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 124 Unusual residues: {'BCL': 1, 'V7B': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "ah" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ai" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 205 Unusual residues: {'BCL': 1, 'CD4': 1, 'UYH': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "aj" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'0V9': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "ak" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "al" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "am" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "an" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 119 Unusual residues: {'BCL': 1, 'MQ8': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "ao" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ap" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ba" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 201 Unusual residues: {'0V9': 2, 'BCL': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "bb" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bc" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bd" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 146 Unusual residues: {'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "be" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 201 Unusual residues: {'0V9': 2, 'BCL': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "bf" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 226 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bg" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bh" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 226 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bi" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'0V9': 1, 'BCL': 1, 'V7N': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bj" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bk" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 236 Unusual residues: {'0V9': 2, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "bl" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 226 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 2, 'V7N': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bm" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bn" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bo" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 191 Unusual residues: {'0V9': 1, 'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "bp" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 146 Unusual residues: {'BCL': 1, 'LMT': 1, 'V7N': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AA" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AB" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AC" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AD" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "AG" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AH" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AI" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AJ" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "AK" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AL" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AM" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "AN" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AO" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AP" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AQ" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "AR" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "AS" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "AT" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "AV" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "AW" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "AX" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "BD" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "BE" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "BF" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "BO" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "BW" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 98 Classifications: {'water': 98} Link IDs: {None: 97} Chain: "C1" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "C2" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "H1" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "H2" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "M" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "aa" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "ab" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "ac" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "ad" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "ae" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "af" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "ag" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "ah" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "ai" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "aj" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "ak" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "al" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "am" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "an" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "ao" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "ap" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "bb" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "bc" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "bd" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "be" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "bf" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "bg" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "bh" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "bi" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "bk" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "bl" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "bm" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "bn" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "bo" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "bp" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 21.68, per 1000 atoms: 0.38 Number of scatterers: 56446 At special positions: 0 Unit cell: (199.892, 194.895, 145.921, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 5 26.01 S 278 16.00 P 33 15.00 Mg 108 11.99 O 9735 8.00 N 7407 7.00 C 38880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=112, symmetry=0 Links applied BETA1-4 " MANCG 1 " - " RAMCG 2 " ~> Even though RAM is an alpha isomer, a beta linkage is required... " MANMG 1 " - " RAMMG 2 " MAN-SER " MANMG 1 " - " SER M 331 " MAN-THR " MANCG 1 " - " THR C 108 " Number of additional bonds: simple=112, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.34 Conformation dependent library (CDL) restraints added in 5.5 seconds 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9226 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 223 helices and 4 sheets defined 66.2% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.03 Creating SS restraints... Processing helix chain 'AA' and resid 3 through 5 No H-bonds generated for 'chain 'AA' and resid 3 through 5' Processing helix chain 'AA' and resid 10 through 35 Processing helix chain 'AA' and resid 40 through 46 removed outlier: 3.507A pdb=" N TYRAA 46 " --> pdb=" O LEUAA 42 " (cutoff:3.500A) Processing helix chain 'AB' and resid 3 through 5 No H-bonds generated for 'chain 'AB' and resid 3 through 5' Processing helix chain 'AB' and resid 10 through 35 removed outlier: 3.649A pdb=" N GLYAB 34 " --> pdb=" O ILEAB 30 " (cutoff:3.500A) Processing helix chain 'AB' and resid 40 through 46 Processing helix chain 'AC' and resid 3 through 5 No H-bonds generated for 'chain 'AC' and resid 3 through 5' Processing helix chain 'AC' and resid 10 through 35 Processing helix chain 'AC' and resid 40 through 46 removed outlier: 3.581A pdb=" N TYRAC 46 " --> pdb=" O LEUAC 42 " (cutoff:3.500A) Processing helix chain 'AD' and resid 3 through 5 No H-bonds generated for 'chain 'AD' and resid 3 through 5' Processing helix chain 'AD' and resid 10 through 36 Processing helix chain 'AD' and resid 40 through 46 Processing helix chain 'AE' and resid 3 through 5 No H-bonds generated for 'chain 'AE' and resid 3 through 5' Processing helix chain 'AE' and resid 10 through 36 Processing helix chain 'AE' and resid 40 through 46 Processing helix chain 'AF' and resid 10 through 36 Processing helix chain 'AF' and resid 40 through 46 removed outlier: 3.513A pdb=" N TYRAF 46 " --> pdb=" O LEUAF 42 " (cutoff:3.500A) Processing helix chain 'AG' and resid 3 through 5 No H-bonds generated for 'chain 'AG' and resid 3 through 5' Processing helix chain 'AG' and resid 10 through 35 Processing helix chain 'AG' and resid 40 through 46 Processing helix chain 'AH' and resid 3 through 5 No H-bonds generated for 'chain 'AH' and resid 3 through 5' Processing helix chain 'AH' and resid 10 through 36 removed outlier: 3.529A pdb=" N GLYAH 34 " --> pdb=" O ILEAH 30 " (cutoff:3.500A) Processing helix chain 'AH' and resid 40 through 46 removed outlier: 3.538A pdb=" N TYRAH 46 " --> pdb=" O LEUAH 42 " (cutoff:3.500A) Processing helix chain 'AI' and resid 3 through 5 No H-bonds generated for 'chain 'AI' and resid 3 through 5' Processing helix chain 'AI' and resid 10 through 36 removed outlier: 3.557A pdb=" N GLYAI 34 " --> pdb=" O ILEAI 30 " (cutoff:3.500A) Processing helix chain 'AI' and resid 40 through 46 removed outlier: 3.529A pdb=" N TYRAI 46 " --> pdb=" O LEUAI 42 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 3 through 5 No H-bonds generated for 'chain 'AJ' and resid 3 through 5' Processing helix chain 'AJ' and resid 10 through 36 Processing helix chain 'AJ' and resid 40 through 46 removed outlier: 3.548A pdb=" N TYRAJ 46 " --> pdb=" O LEUAJ 42 " (cutoff:3.500A) Processing helix chain 'AK' and resid 3 through 5 No H-bonds generated for 'chain 'AK' and resid 3 through 5' Processing helix chain 'AK' and resid 10 through 35 removed outlier: 3.593A pdb=" N GLYAK 34 " --> pdb=" O ILEAK 30 " (cutoff:3.500A) Processing helix chain 'AK' and resid 40 through 46 removed outlier: 3.505A pdb=" N TYRAK 46 " --> pdb=" O LEUAK 42 " (cutoff:3.500A) Processing helix chain 'AL' and resid 3 through 5 No H-bonds generated for 'chain 'AL' and resid 3 through 5' Processing helix chain 'AL' and resid 10 through 36 Processing helix chain 'AL' and resid 40 through 46 Processing helix chain 'AM' and resid 3 through 5 No H-bonds generated for 'chain 'AM' and resid 3 through 5' Processing helix chain 'AM' and resid 10 through 36 Processing helix chain 'AM' and resid 40 through 46 Processing helix chain 'AN' and resid 3 through 5 No H-bonds generated for 'chain 'AN' and resid 3 through 5' Processing helix chain 'AN' and resid 10 through 36 removed outlier: 3.569A pdb=" N GLYAN 34 " --> pdb=" O ILEAN 30 " (cutoff:3.500A) Processing helix chain 'AN' and resid 40 through 46 Processing helix chain 'AO' and resid 3 through 5 No H-bonds generated for 'chain 'AO' and resid 3 through 5' Processing helix chain 'AO' and resid 10 through 35 removed outlier: 3.575A pdb=" N GLYAO 34 " --> pdb=" O ILEAO 30 " (cutoff:3.500A) Processing helix chain 'AO' and resid 40 through 46 removed outlier: 3.524A pdb=" N TYRAO 46 " --> pdb=" O LEUAO 42 " (cutoff:3.500A) Processing helix chain 'AP' and resid 3 through 5 No H-bonds generated for 'chain 'AP' and resid 3 through 5' Processing helix chain 'AP' and resid 10 through 35 Processing helix chain 'AP' and resid 40 through 46 removed outlier: 3.556A pdb=" N TYRAP 46 " --> pdb=" O LEUAP 42 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 3 through 5 No H-bonds generated for 'chain 'AQ' and resid 3 through 5' Processing helix chain 'AQ' and resid 10 through 36 Processing helix chain 'AQ' and resid 40 through 46 Processing helix chain 'AR' and resid 3 through 5 No H-bonds generated for 'chain 'AR' and resid 3 through 5' Processing helix chain 'AR' and resid 10 through 36 removed outlier: 3.563A pdb=" N GLYAR 34 " --> pdb=" O ILEAR 30 " (cutoff:3.500A) Processing helix chain 'AR' and resid 40 through 46 Processing helix chain 'AS' and resid 3 through 5 No H-bonds generated for 'chain 'AS' and resid 3 through 5' Processing helix chain 'AS' and resid 10 through 35 Processing helix chain 'AS' and resid 40 through 46 Processing helix chain 'AT' and resid 3 through 5 No H-bonds generated for 'chain 'AT' and resid 3 through 5' Processing helix chain 'AT' and resid 10 through 35 removed outlier: 3.573A pdb=" N GLYAT 34 " --> pdb=" O ILEAT 30 " (cutoff:3.500A) Processing helix chain 'AT' and resid 40 through 46 Processing helix chain 'AU' and resid 3 through 5 No H-bonds generated for 'chain 'AU' and resid 3 through 5' Processing helix chain 'AU' and resid 10 through 36 Processing helix chain 'AU' and resid 40 through 46 Processing helix chain 'AV' and resid 3 through 5 No H-bonds generated for 'chain 'AV' and resid 3 through 5' Processing helix chain 'AV' and resid 10 through 36 Processing helix chain 'AV' and resid 40 through 46 Processing helix chain 'AW' and resid 3 through 5 No H-bonds generated for 'chain 'AW' and resid 3 through 5' Processing helix chain 'AW' and resid 10 through 35 removed outlier: 3.586A pdb=" N GLYAW 34 " --> pdb=" O ILEAW 30 " (cutoff:3.500A) Processing helix chain 'AW' and resid 40 through 46 removed outlier: 3.535A pdb=" N TYRAW 46 " --> pdb=" O LEUAW 42 " (cutoff:3.500A) Processing helix chain 'AX' and resid 10 through 36 Processing helix chain 'AX' and resid 40 through 46 removed outlier: 3.529A pdb=" N TYRAX 46 " --> pdb=" O LEUAX 42 " (cutoff:3.500A) Processing helix chain 'BA' and resid 9 through 40 Processing helix chain 'BB' and resid 9 through 40 Processing helix chain 'BC' and resid 9 through 40 removed outlier: 3.804A pdb=" N TYRBC 18 " --> pdb=" O ARGBC 14 " (cutoff:3.500A) Processing helix chain 'BD' and resid 9 through 40 Processing helix chain 'BE' and resid 9 through 40 Processing helix chain 'BF' and resid 9 through 40 removed outlier: 3.759A pdb=" N GLYBF 17 " --> pdb=" O ARGBF 13 " (cutoff:3.500A) Processing helix chain 'BG' and resid 9 through 40 Processing helix chain 'BH' and resid 9 through 40 removed outlier: 3.618A pdb=" N GLYBH 17 " --> pdb=" O ARGBH 13 " (cutoff:3.500A) Processing helix chain 'BI' and resid 9 through 40 Processing helix chain 'BJ' and resid 9 through 40 removed outlier: 3.657A pdb=" N TYRBJ 18 " --> pdb=" O ARGBJ 14 " (cutoff:3.500A) Processing helix chain 'BK' and resid 9 through 40 removed outlier: 3.772A pdb=" N GLYBK 17 " --> pdb=" O ARGBK 13 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYRBK 18 " --> pdb=" O ARGBK 14 " (cutoff:3.500A) Processing helix chain 'BL' and resid 9 through 40 removed outlier: 3.669A pdb=" N TYRBL 18 " --> pdb=" O ARGBL 14 " (cutoff:3.500A) Processing helix chain 'BM' and resid 9 through 40 removed outlier: 3.504A pdb=" N GLYBM 17 " --> pdb=" O ARGBM 13 " (cutoff:3.500A) Processing helix chain 'BN' and resid 9 through 40 removed outlier: 3.502A pdb=" N GLYBN 17 " --> pdb=" O ARGBN 13 " (cutoff:3.500A) Processing helix chain 'BO' and resid 9 through 40 removed outlier: 3.546A pdb=" N GLYBO 17 " --> pdb=" O ARGBO 13 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYRBO 18 " --> pdb=" O ARGBO 14 " (cutoff:3.500A) Processing helix chain 'BP' and resid 9 through 40 Processing helix chain 'BQ' and resid 9 through 40 removed outlier: 3.552A pdb=" N TYRBQ 18 " --> pdb=" O ARGBQ 14 " (cutoff:3.500A) Processing helix chain 'BR' and resid 9 through 40 removed outlier: 3.535A pdb=" N TYRBR 18 " --> pdb=" O ARGBR 14 " (cutoff:3.500A) Processing helix chain 'BS' and resid 9 through 40 removed outlier: 3.749A pdb=" N TYRBS 18 " --> pdb=" O ARGBS 14 " (cutoff:3.500A) Processing helix chain 'BT' and resid 9 through 40 removed outlier: 3.654A pdb=" N GLYBT 17 " --> pdb=" O ARGBT 13 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYRBT 18 " --> pdb=" O ARGBT 14 " (cutoff:3.500A) Processing helix chain 'BU' and resid 9 through 40 Processing helix chain 'BV' and resid 9 through 40 removed outlier: 3.559A pdb=" N GLYBV 17 " --> pdb=" O ARGBV 13 " (cutoff:3.500A) Processing helix chain 'BW' and resid 9 through 40 removed outlier: 3.596A pdb=" N TYRBW 18 " --> pdb=" O ARGBW 14 " (cutoff:3.500A) Processing helix chain 'BX' and resid 9 through 40 removed outlier: 3.577A pdb=" N TYRBX 18 " --> pdb=" O ARGBX 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 46 Processing helix chain 'C' and resid 75 through 89 Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 116 through 134 Processing helix chain 'C' and resid 136 through 139 No H-bonds generated for 'chain 'C' and resid 136 through 139' Processing helix chain 'C' and resid 146 through 150 Processing helix chain 'C' and resid 168 through 172 Processing helix chain 'C' and resid 195 through 212 Processing helix chain 'C' and resid 216 through 218 No H-bonds generated for 'chain 'C' and resid 216 through 218' Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 233 through 251 removed outlier: 3.564A pdb=" N ASN C 249 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN C 250 " --> pdb=" O ASP C 247 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN C 251 " --> pdb=" O VAL C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 258 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 276 through 280 Processing helix chain 'C' and resid 286 through 289 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 297 through 299 No H-bonds generated for 'chain 'C' and resid 297 through 299' Processing helix chain 'C1' and resid 127 through 129 No H-bonds generated for 'chain 'C1' and resid 127 through 129' Processing helix chain 'C1' and resid 136 through 142 Processing helix chain 'C1' and resid 161 through 163 No H-bonds generated for 'chain 'C1' and resid 161 through 163' Processing helix chain 'C1' and resid 172 through 175 No H-bonds generated for 'chain 'C1' and resid 172 through 175' Processing helix chain 'C1' and resid 183 through 189 Processing helix chain 'C1' and resid 197 through 199 No H-bonds generated for 'chain 'C1' and resid 197 through 199' Processing helix chain 'C2' and resid 4 through 9 Processing helix chain 'C2' and resid 22 through 52 removed outlier: 3.525A pdb=" N ALAC2 33 " --> pdb=" O VALC2 29 " (cutoff:3.500A) Processing helix chain 'C2' and resid 55 through 87 removed outlier: 3.526A pdb=" N TRPC2 75 " --> pdb=" O GLUC2 71 " (cutoff:3.500A) Processing helix chain 'H1' and resid 7 through 31 removed outlier: 3.535A pdb=" N LYSH1 31 " --> pdb=" O ARGH1 27 " (cutoff:3.500A) Processing helix chain 'H2' and resid 22 through 25 No H-bonds generated for 'chain 'H2' and resid 22 through 25' Processing helix chain 'H2' and resid 28 through 30 No H-bonds generated for 'chain 'H2' and resid 28 through 30' Processing helix chain 'H2' and resid 54 through 56 No H-bonds generated for 'chain 'H2' and resid 54 through 56' Processing helix chain 'H2' and resid 115 through 117 No H-bonds generated for 'chain 'H2' and resid 115 through 117' Processing helix chain 'H2' and resid 140 through 143 Processing helix chain 'H2' and resid 155 through 171 removed outlier: 3.642A pdb=" N GLYH2 168 " --> pdb=" O TYRH2 164 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N HISH2 169 " --> pdb=" O TYRH2 165 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N METH2 170 " --> pdb=" O ALAH2 166 " (cutoff:3.500A) Processing helix chain 'H2' and resid 174 through 177 removed outlier: 3.766A pdb=" N SERH2 177 " --> pdb=" O ALAH2 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'H2' and resid 174 through 177' Processing helix chain 'L' and resid 7 through 9 No H-bonds generated for 'chain 'L' and resid 7 through 9' Processing helix chain 'L' and resid 32 through 55 Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'L' and resid 84 through 110 Processing helix chain 'L' and resid 116 through 132 removed outlier: 4.050A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 139 Processing helix chain 'L' and resid 142 through 144 No H-bonds generated for 'chain 'L' and resid 142 through 144' Processing helix chain 'L' and resid 152 through 164 removed outlier: 3.903A pdb=" N TYR L 164 " --> pdb=" O VAL L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 169 No H-bonds generated for 'chain 'L' and resid 167 through 169' Processing helix chain 'L' and resid 171 through 198 Processing helix chain 'L' and resid 209 through 220 Processing helix chain 'L' and resid 226 through 250 removed outlier: 3.681A pdb=" N HIS L 230 " --> pdb=" O ALA L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 260 through 267 removed outlier: 3.655A pdb=" N TRP L 265 " --> pdb=" O TRP L 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 43 removed outlier: 3.765A pdb=" N PHE M 43 " --> pdb=" O LEU M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 79 Processing helix chain 'M' and resid 83 through 88 Processing helix chain 'M' and resid 90 through 92 No H-bonds generated for 'chain 'M' and resid 90 through 92' Processing helix chain 'M' and resid 100 through 102 No H-bonds generated for 'chain 'M' and resid 100 through 102' Processing helix chain 'M' and resid 109 through 111 No H-bonds generated for 'chain 'M' and resid 109 through 111' Processing helix chain 'M' and resid 113 through 139 Processing helix chain 'M' and resid 145 through 167 removed outlier: 3.568A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE M 160 " --> pdb=" O LEU M 156 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE M 161 " --> pdb=" O TYR M 157 " (cutoff:3.500A) Proline residue: M 164 - end of helix Processing helix chain 'M' and resid 170 through 172 No H-bonds generated for 'chain 'M' and resid 170 through 172' Processing helix chain 'M' and resid 178 through 191 removed outlier: 3.746A pdb=" N LEU M 182 " --> pdb=" O ILE M 178 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER M 189 " --> pdb=" O THR M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 197 No H-bonds generated for 'chain 'M' and resid 195 through 197' Processing helix chain 'M' and resid 199 through 228 removed outlier: 4.683A pdb=" N ARG M 227 " --> pdb=" O LEU M 223 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N MET M 228 " --> pdb=" O ALA M 224 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 238 Processing helix chain 'M' and resid 242 through 255 removed outlier: 3.520A pdb=" N TRP M 251 " --> pdb=" O SER M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 285 removed outlier: 3.906A pdb=" N THR M 276 " --> pdb=" O ALA M 272 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 299 Processing helix chain 'M' and resid 314 through 320 Processing helix chain 'aa' and resid 3 through 7 Processing helix chain 'aa' and resid 10 through 34 Processing helix chain 'aa' and resid 40 through 43 No H-bonds generated for 'chain 'aa' and resid 40 through 43' Processing helix chain 'ab' and resid 3 through 7 Processing helix chain 'ab' and resid 10 through 33 removed outlier: 3.700A pdb=" N VALab 15 " --> pdb=" O ARGab 11 " (cutoff:3.500A) Processing helix chain 'ab' and resid 40 through 43 No H-bonds generated for 'chain 'ab' and resid 40 through 43' Processing helix chain 'ac' and resid 3 through 7 Processing helix chain 'ac' and resid 10 through 12 No H-bonds generated for 'chain 'ac' and resid 10 through 12' Processing helix chain 'ac' and resid 14 through 34 removed outlier: 3.505A pdb=" N SERac 34 " --> pdb=" O PHEac 30 " (cutoff:3.500A) Processing helix chain 'ac' and resid 40 through 43 No H-bonds generated for 'chain 'ac' and resid 40 through 43' Processing helix chain 'ad' and resid 3 through 7 Processing helix chain 'ad' and resid 10 through 34 removed outlier: 3.723A pdb=" N VALad 15 " --> pdb=" O ARGad 11 " (cutoff:3.500A) Processing helix chain 'ad' and resid 40 through 43 No H-bonds generated for 'chain 'ad' and resid 40 through 43' Processing helix chain 'ae' and resid 3 through 7 Processing helix chain 'ae' and resid 10 through 34 Processing helix chain 'ae' and resid 40 through 43 No H-bonds generated for 'chain 'ae' and resid 40 through 43' Processing helix chain 'af' and resid 3 through 7 Processing helix chain 'af' and resid 10 through 34 Processing helix chain 'af' and resid 40 through 43 No H-bonds generated for 'chain 'af' and resid 40 through 43' Processing helix chain 'ag' and resid 3 through 7 Processing helix chain 'ag' and resid 10 through 34 Processing helix chain 'ag' and resid 40 through 43 No H-bonds generated for 'chain 'ag' and resid 40 through 43' Processing helix chain 'ah' and resid 3 through 7 Processing helix chain 'ah' and resid 10 through 34 removed outlier: 3.888A pdb=" N VALah 15 " --> pdb=" O ARGah 11 " (cutoff:3.500A) Processing helix chain 'ah' and resid 40 through 43 No H-bonds generated for 'chain 'ah' and resid 40 through 43' Processing helix chain 'ai' and resid 3 through 7 Processing helix chain 'ai' and resid 10 through 34 removed outlier: 3.529A pdb=" N VALai 15 " --> pdb=" O ARGai 11 " (cutoff:3.500A) Processing helix chain 'ai' and resid 40 through 43 No H-bonds generated for 'chain 'ai' and resid 40 through 43' Processing helix chain 'aj' and resid 3 through 7 Processing helix chain 'aj' and resid 10 through 33 removed outlier: 3.665A pdb=" N VALaj 15 " --> pdb=" O ARGaj 11 " (cutoff:3.500A) Processing helix chain 'aj' and resid 40 through 43 No H-bonds generated for 'chain 'aj' and resid 40 through 43' Processing helix chain 'ak' and resid 3 through 7 Processing helix chain 'ak' and resid 10 through 34 removed outlier: 3.867A pdb=" N VALak 15 " --> pdb=" O ARGak 11 " (cutoff:3.500A) Processing helix chain 'ak' and resid 40 through 43 No H-bonds generated for 'chain 'ak' and resid 40 through 43' Processing helix chain 'al' and resid 3 through 7 Processing helix chain 'al' and resid 10 through 34 removed outlier: 3.941A pdb=" N VALal 15 " --> pdb=" O ARGal 11 " (cutoff:3.500A) Processing helix chain 'al' and resid 40 through 43 No H-bonds generated for 'chain 'al' and resid 40 through 43' Processing helix chain 'am' and resid 3 through 7 Processing helix chain 'am' and resid 10 through 34 removed outlier: 3.918A pdb=" N VALam 15 " --> pdb=" O ARGam 11 " (cutoff:3.500A) Processing helix chain 'am' and resid 40 through 43 No H-bonds generated for 'chain 'am' and resid 40 through 43' Processing helix chain 'an' and resid 3 through 7 Processing helix chain 'an' and resid 10 through 34 removed outlier: 3.576A pdb=" N VALan 15 " --> pdb=" O ARGan 11 " (cutoff:3.500A) Processing helix chain 'an' and resid 40 through 43 No H-bonds generated for 'chain 'an' and resid 40 through 43' Processing helix chain 'ao' and resid 3 through 7 Processing helix chain 'ao' and resid 10 through 34 removed outlier: 3.777A pdb=" N VALao 15 " --> pdb=" O ARGao 11 " (cutoff:3.500A) Processing helix chain 'ao' and resid 40 through 43 No H-bonds generated for 'chain 'ao' and resid 40 through 43' Processing helix chain 'ap' and resid 3 through 7 removed outlier: 3.724A pdb=" N METap 7 " --> pdb=" O ILEap 4 " (cutoff:3.500A) Processing helix chain 'ap' and resid 10 through 34 Processing helix chain 'ap' and resid 40 through 43 No H-bonds generated for 'chain 'ap' and resid 40 through 43' Processing helix chain 'ba' and resid 9 through 40 removed outlier: 3.736A pdb=" N TYRba 18 " --> pdb=" O ARGba 14 " (cutoff:3.500A) Processing helix chain 'bb' and resid 9 through 40 Processing helix chain 'bc' and resid 9 through 40 Processing helix chain 'bd' and resid 9 through 41 Processing helix chain 'be' and resid 9 through 40 removed outlier: 3.732A pdb=" N TYRbe 18 " --> pdb=" O ARGbe 14 " (cutoff:3.500A) Processing helix chain 'bf' and resid 9 through 40 removed outlier: 3.543A pdb=" N TYRbf 18 " --> pdb=" O ARGbf 14 " (cutoff:3.500A) Processing helix chain 'bg' and resid 9 through 40 removed outlier: 3.519A pdb=" N GLYbg 17 " --> pdb=" O ARGbg 13 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYRbg 18 " --> pdb=" O ARGbg 14 " (cutoff:3.500A) Processing helix chain 'bh' and resid 9 through 40 removed outlier: 3.622A pdb=" N ARGbh 14 " --> pdb=" O GLUbh 10 " (cutoff:3.500A) Processing helix chain 'bi' and resid 9 through 40 removed outlier: 3.617A pdb=" N TYRbi 18 " --> pdb=" O ARGbi 14 " (cutoff:3.500A) Processing helix chain 'bj' and resid 9 through 41 Processing helix chain 'bk' and resid 9 through 40 removed outlier: 3.764A pdb=" N TYRbk 18 " --> pdb=" O ARGbk 14 " (cutoff:3.500A) Processing helix chain 'bl' and resid 9 through 40 Processing helix chain 'bm' and resid 9 through 40 removed outlier: 3.657A pdb=" N TYRbm 18 " --> pdb=" O ARGbm 14 " (cutoff:3.500A) Processing helix chain 'bn' and resid 9 through 40 Processing helix chain 'bo' and resid 9 through 40 Processing helix chain 'bp' and resid 9 through 40 Processing sheet with id= A, first strand: chain 'C' and resid 17 through 21 Processing sheet with id= B, first strand: chain 'H2' and resid 5 through 7 Processing sheet with id= C, first strand: chain 'H2' and resid 51 through 53 removed outlier: 6.818A pdb=" N GLUH2 101 " --> pdb=" O VALH2 86 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEUH2 88 " --> pdb=" O TYRH2 99 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYRH2 99 " --> pdb=" O LEUH2 88 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H2' and resid 130 through 132 removed outlier: 3.788A pdb=" N GLYH2 83 " --> pdb=" O VALH2 74 " (cutoff:3.500A) 2464 hydrogen bonds defined for protein. 7224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.87 Time building geometry restraints manager: 20.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.35: 13620 1.35 - 1.56: 43567 1.56 - 1.77: 178 1.77 - 1.98: 500 1.98 - 2.18: 448 Bond restraints: 58313 Sorted by residual: bond pdb=" C12 V7NBM1001 " pdb=" C13 V7NBM1001 " ideal model delta sigma weight residual 1.583 1.403 0.180 2.00e-02 2.50e+03 8.14e+01 bond pdb=" C12 V7NBA 101 " pdb=" C13 V7NBA 101 " ideal model delta sigma weight residual 1.583 1.403 0.180 2.00e-02 2.50e+03 8.07e+01 bond pdb=" C12 V7NBJ1001 " pdb=" C13 V7NBJ1001 " ideal model delta sigma weight residual 1.583 1.404 0.179 2.00e-02 2.50e+03 8.02e+01 bond pdb=" C12 V7Nbe 101 " pdb=" C13 V7Nbe 101 " ideal model delta sigma weight residual 1.583 1.404 0.179 2.00e-02 2.50e+03 8.01e+01 bond pdb=" C27 V7Nba 101 " pdb=" C28 V7Nba 101 " ideal model delta sigma weight residual 1.343 1.522 -0.179 2.00e-02 2.50e+03 8.00e+01 ... (remaining 58308 not shown) Histogram of bond angle deviations from ideal: 84.79 - 103.09: 1319 103.09 - 121.40: 62259 121.40 - 139.70: 16312 139.70 - 158.00: 124 158.00 - 176.31: 210 Bond angle restraints: 80224 Sorted by residual: angle pdb=" C34 V7NBM1001 " pdb=" C9 V7NBM1001 " pdb=" C8 V7NBM1001 " ideal model delta sigma weight residual 68.18 124.10 -55.92 3.00e+00 1.11e-01 3.47e+02 angle pdb=" C34 V7NBD 101 " pdb=" C9 V7NBD 101 " pdb=" C8 V7NBD 101 " ideal model delta sigma weight residual 68.18 123.92 -55.74 3.00e+00 1.11e-01 3.45e+02 angle pdb=" C34 V7Nbm 101 " pdb=" C9 V7Nbm 101 " pdb=" C8 V7Nbm 101 " ideal model delta sigma weight residual 68.18 123.15 -54.97 3.00e+00 1.11e-01 3.36e+02 angle pdb=" C19 V7NBP1001 " pdb=" C18 V7NBP1001 " pdb=" C36 V7NBP1001 " ideal model delta sigma weight residual 68.20 122.90 -54.70 3.00e+00 1.11e-01 3.32e+02 angle pdb=" C19 V7NBD 101 " pdb=" C18 V7NBD 101 " pdb=" C36 V7NBD 101 " ideal model delta sigma weight residual 68.20 122.74 -54.54 3.00e+00 1.11e-01 3.31e+02 ... (remaining 80219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 34054 35.40 - 70.80: 1270 70.80 - 106.20: 269 106.20 - 141.60: 80 141.60 - 177.00: 75 Dihedral angle restraints: 35748 sinusoidal: 21317 harmonic: 14431 Sorted by residual: dihedral pdb=" CBD BCLAQ 103 " pdb=" CGD BCLAQ 103 " pdb=" O2D BCLAQ 103 " pdb=" CED BCLAQ 103 " ideal model delta sinusoidal sigma weight residual -180.00 -13.49 -166.51 1 5.00e+00 4.00e-02 7.57e+02 dihedral pdb=" C1 BCLAK 103 " pdb=" C2 BCLAK 103 " pdb=" C3 BCLAK 103 " pdb=" C5 BCLAK 103 " ideal model delta sinusoidal sigma weight residual 180.00 3.00 177.00 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCLAQ 103 " pdb=" CGA BCLAQ 103 " pdb=" O2A BCLAQ 103 " pdb=" CBA BCLAQ 103 " ideal model delta sinusoidal sigma weight residual -180.00 -149.94 -30.06 1 6.00e+00 2.78e-02 3.59e+01 ... (remaining 35745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 7313 0.098 - 0.196: 766 0.196 - 0.294: 89 0.294 - 0.392: 5 0.392 - 0.490: 5 Chirality restraints: 8178 Sorted by residual: chirality pdb=" C5' LMTBK1004 " pdb=" C4' LMTBK1004 " pdb=" C6' LMTBK1004 " pdb=" O5' LMTBK1004 " both_signs ideal model delta sigma weight residual False -2.51 -2.02 -0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" C4 UYHai 101 " pdb=" C3 UYHai 101 " pdb=" C5 UYHai 101 " pdb=" O4 UYHai 101 " both_signs ideal model delta sigma weight residual False -2.49 -2.93 0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" C5 UYHai 101 " pdb=" C4 UYHai 101 " pdb=" C6 UYHai 101 " pdb=" O6 UYHai 101 " both_signs ideal model delta sigma weight residual False -2.52 -2.95 0.43 2.00e-01 2.50e+01 4.64e+00 ... (remaining 8175 not shown) Planarity restraints: 9122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C26 V7Nbg 101 " -0.185 2.00e-02 2.50e+03 1.94e-01 3.75e+02 pdb=" C27 V7Nbg 101 " 0.159 2.00e-02 2.50e+03 pdb=" C28 V7Nbg 101 " 0.226 2.00e-02 2.50e+03 pdb=" C29 V7Nbg 101 " -0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C26 V7NBV1001 " 0.186 2.00e-02 2.50e+03 1.88e-01 3.55e+02 pdb=" C27 V7NBV1001 " -0.178 2.00e-02 2.50e+03 pdb=" C28 V7NBV1001 " -0.198 2.00e-02 2.50e+03 pdb=" C29 V7NBV1001 " 0.191 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C26 V7NBQ1001 " -0.127 2.00e-02 2.50e+03 1.25e-01 1.57e+02 pdb=" C27 V7NBQ1001 " 0.142 2.00e-02 2.50e+03 pdb=" C28 V7NBQ1001 " 0.107 2.00e-02 2.50e+03 pdb=" C29 V7NBQ1001 " -0.122 2.00e-02 2.50e+03 ... (remaining 9119 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 960 2.66 - 3.22: 48675 3.22 - 3.78: 93166 3.78 - 4.34: 136759 4.34 - 4.90: 215962 Nonbonded interactions: 495522 Sorted by model distance: nonbonded pdb=" OE2 GLU M 233 " pdb="FE FE M 401 " model vdw 2.099 2.260 nonbonded pdb=" NE2 HIS M 218 " pdb="FE FE M 401 " model vdw 2.111 2.340 nonbonded pdb=" NE2 HIS C 138 " pdb="FE HEC C1002 " model vdw 2.131 3.080 nonbonded pdb=" O HOHAQ 202 " pdb=" O HOHAQ 204 " model vdw 2.210 2.440 nonbonded pdb=" O HOHAA1101 " pdb=" O HOHAA1103 " model vdw 2.259 2.440 ... (remaining 495517 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'AA' and resid 1 through 48) selection = (chain 'AB' and resid 1 through 48) selection = (chain 'AC' and resid 1 through 48) selection = (chain 'AD' and resid 1 through 48) selection = (chain 'AE' and resid 1 through 48) selection = (chain 'AF' and resid 1 through 48) selection = (chain 'AG' and resid 1 through 48) selection = (chain 'AH' and resid 1 through 48) selection = (chain 'AI' and resid 1 through 48) selection = (chain 'AJ' and resid 1 through 48) selection = (chain 'AK' and resid 1 through 48) selection = (chain 'AL' and resid 1 through 48) selection = (chain 'AM' and resid 1 through 48) selection = (chain 'AN' and resid 1 through 48) selection = (chain 'AO' and resid 1 through 48) selection = (chain 'AP' and resid 1 through 48) selection = (chain 'AQ' and resid 1 through 48) selection = (chain 'AR' and resid 1 through 48) selection = (chain 'AS' and resid 1 through 48) selection = (chain 'AT' and resid 1 through 48) selection = (chain 'AU' and resid 1 through 48) selection = (chain 'AV' and resid 1 through 48) selection = (chain 'AW' and resid 1 through 48) selection = (chain 'AX' and resid 1 through 48) } ncs_group { reference = (chain 'BA' and resid 6 through 44) selection = (chain 'BB' and resid 6 through 44) selection = (chain 'BC' and resid 6 through 44) selection = (chain 'BD' and resid 6 through 44) selection = (chain 'BE' and resid 6 through 44) selection = (chain 'BF' and resid 6 through 44) selection = (chain 'BG' and resid 6 through 44) selection = (chain 'BH' and resid 6 through 44) selection = (chain 'BI' and resid 6 through 44) selection = (chain 'BJ' and resid 6 through 44) selection = (chain 'BK' and resid 6 through 44) selection = (chain 'BL' and resid 6 through 44) selection = (chain 'BM' and resid 6 through 44) selection = (chain 'BN' and resid 6 through 44) selection = (chain 'BO' and resid 6 through 44) selection = (chain 'BP' and resid 6 through 44) selection = (chain 'BQ' and resid 6 through 44) selection = (chain 'BR' and resid 6 through 44) selection = (chain 'BS' and resid 6 through 44) selection = (chain 'BT' and resid 6 through 44) selection = (chain 'BU' and resid 6 through 44) selection = (chain 'BV' and resid 6 through 44) selection = (chain 'BW' and resid 6 through 44) selection = (chain 'BX' and resid 6 through 44) selection = (chain 'ba' and resid 6 through 44) selection = (chain 'bb' and resid 6 through 44) selection = (chain 'bc' and resid 6 through 44) selection = (chain 'bd' and resid 6 through 44) selection = (chain 'be' and resid 6 through 44) selection = (chain 'bf' and resid 6 through 44) selection = (chain 'bg' and resid 6 through 44) selection = (chain 'bh' and resid 6 through 44) selection = (chain 'bi' and resid 6 through 44) selection = (chain 'bj' and resid 6 through 44) selection = (chain 'bk' and resid 6 through 44) selection = (chain 'bl' and resid 6 through 44) selection = (chain 'bm' and resid 6 through 44) selection = (chain 'bn' and resid 6 through 44) selection = (chain 'bo' and resid 6 through 44) selection = (chain 'bp' and resid 6 through 44) } ncs_group { reference = chain 'CG' selection = chain 'MG' } ncs_group { reference = (chain 'aa' and resid 2 through 56) selection = (chain 'ab' and resid 2 through 56) selection = (chain 'ac' and resid 2 through 56) selection = (chain 'ad' and resid 2 through 56) selection = (chain 'ae' and resid 2 through 56) selection = (chain 'af' and resid 2 through 56) selection = (chain 'ag' and resid 2 through 56) selection = (chain 'ah' and resid 2 through 56) selection = (chain 'ai' and resid 2 through 56) selection = (chain 'aj' and resid 2 through 56) selection = (chain 'al' and resid 2 through 56) selection = (chain 'am' and resid 2 through 56) selection = (chain 'ao' and resid 2 through 56) } ncs_group { reference = (chain 'ak' and resid 1 through 71) selection = (chain 'an' and resid 1 through 71) selection = (chain 'ap' and (resid 1 through 70 or (resid 71 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 o \ r name NH2)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 14.760 Check model and map are aligned: 0.870 Set scattering table: 0.530 Process input model: 106.730 Find NCS groups from input model: 3.030 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.180 58313 Z= 0.855 Angle : 4.443 55.917 80224 Z= 1.510 Chirality : 0.062 0.490 8178 Planarity : 0.012 0.194 9122 Dihedral : 20.406 177.004 26522 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.42 % Favored : 98.56 % Rotamer: Outliers : 0.23 % Allowed : 1.25 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.11), residues: 4858 helix: 0.84 (0.08), residues: 3312 sheet: -0.09 (1.05), residues: 21 loop : 1.36 (0.18), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRPbe 40 HIS 0.011 0.002 HIS M 300 PHE 0.027 0.003 PHEbk 44 TYR 0.042 0.006 TYRap 38 ARG 0.033 0.004 ARGH1 59 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 788 time to evaluate : 3.882 Fit side-chains revert: symmetry clash REVERT: AD 6 MET cc_start: 0.8028 (mtm) cc_final: 0.7666 (mtm) REVERT: AG 9 ASP cc_start: 0.7583 (t0) cc_final: 0.7361 (t0) REVERT: AH 14 MET cc_start: 0.8979 (mmm) cc_final: 0.8562 (mmm) REVERT: AJ 9 ASP cc_start: 0.8001 (t0) cc_final: 0.7715 (t0) REVERT: AK 14 MET cc_start: 0.8838 (mmm) cc_final: 0.8333 (mmm) REVERT: AL 9 ASP cc_start: 0.7688 (t0) cc_final: 0.7154 (t70) REVERT: AQ 4 ILE cc_start: 0.8394 (tp) cc_final: 0.8189 (tt) REVERT: AR 4 ILE cc_start: 0.8631 (tp) cc_final: 0.8422 (tp) REVERT: AS 14 MET cc_start: 0.8811 (mmm) cc_final: 0.8610 (mmp) REVERT: AT 14 MET cc_start: 0.8667 (mmm) cc_final: 0.8318 (mmm) REVERT: AU 9 ASP cc_start: 0.7750 (t0) cc_final: 0.7449 (t0) REVERT: AU 12 ILE cc_start: 0.8744 (mm) cc_final: 0.8506 (mt) REVERT: AV 6 MET cc_start: 0.8510 (mtp) cc_final: 0.8198 (mtp) REVERT: AW 14 MET cc_start: 0.8624 (mmm) cc_final: 0.8415 (mmm) REVERT: BB 14 ARG cc_start: 0.8401 (mtm-85) cc_final: 0.8197 (mtm-85) REVERT: BC 13 ARG cc_start: 0.6945 (ttm110) cc_final: 0.6592 (ttm-80) REVERT: BD 7 MET cc_start: 0.7332 (tpp) cc_final: 0.6874 (tpp) REVERT: BD 11 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7401 (mt-10) REVERT: BG 9 GLU cc_start: 0.7346 (tm-30) cc_final: 0.7123 (tm-30) REVERT: BI 13 ARG cc_start: 0.7337 (tpp80) cc_final: 0.7134 (ttm-80) REVERT: BN 7 MET cc_start: 0.8041 (ttp) cc_final: 0.7728 (ttp) REVERT: BP 18 TYR cc_start: 0.8789 (m-80) cc_final: 0.8564 (m-80) REVERT: BR 11 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6791 (mt-10) REVERT: BU 9 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7092 (tm-30) REVERT: BV 13 ARG cc_start: 0.7917 (ttp-110) cc_final: 0.7671 (ttp-110) REVERT: BW 14 ARG cc_start: 0.8596 (ttp-170) cc_final: 0.8270 (ttp80) REVERT: C 29 MET cc_start: 0.9228 (mtp) cc_final: 0.8929 (mtp) REVERT: C 85 MET cc_start: 0.8792 (mtp) cc_final: 0.8405 (mtm) REVERT: L 212 GLU cc_start: 0.7887 (pt0) cc_final: 0.7609 (tt0) REVERT: aa 8 TYR cc_start: 0.5988 (m-80) cc_final: 0.5772 (m-80) REVERT: aa 42 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8194 (mm-30) REVERT: af 14 MET cc_start: 0.7994 (mmm) cc_final: 0.7741 (mmp) REVERT: af 50 GLN cc_start: 0.8195 (mp10) cc_final: 0.7791 (mt0) REVERT: ag 2 HIS cc_start: 0.7522 (p-80) cc_final: 0.7129 (p90) REVERT: ah 12 ARG cc_start: 0.7107 (mtm110) cc_final: 0.6682 (mmm-85) REVERT: ai 49 ASP cc_start: 0.7574 (p0) cc_final: 0.7248 (p0) REVERT: aj 14 MET cc_start: 0.8063 (mmm) cc_final: 0.7754 (mmm) REVERT: ak 11 ARG cc_start: 0.7676 (mtp-110) cc_final: 0.7273 (mtm180) REVERT: ak 12 ARG cc_start: 0.7238 (mtm180) cc_final: 0.6834 (mtm-85) REVERT: al 11 ARG cc_start: 0.7575 (ttm110) cc_final: 0.7199 (mtp-110) REVERT: am 12 ARG cc_start: 0.7605 (mmt180) cc_final: 0.7057 (ttp80) REVERT: an 12 ARG cc_start: 0.7483 (mmt-90) cc_final: 0.6754 (ttt180) REVERT: be 13 ARG cc_start: 0.7405 (tpp80) cc_final: 0.7183 (tpt90) REVERT: bl 8 THR cc_start: 0.8203 (p) cc_final: 0.7399 (t) REVERT: bl 19 MET cc_start: 0.8117 (tpt) cc_final: 0.7698 (tpt) REVERT: bn 11 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7512 (mt-10) REVERT: bo 24 LEU cc_start: 0.8900 (tt) cc_final: 0.8612 (mt) outliers start: 9 outliers final: 5 residues processed: 797 average time/residue: 1.6946 time to fit residues: 1643.0634 Evaluate side-chains 604 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 599 time to evaluate : 3.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BB residue 19 MET Chi-restraints excluded: chain H2 residue 159 ASP Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain ad residue 39 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 381 optimal weight: 4.9990 chunk 342 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 231 optimal weight: 7.9990 chunk 183 optimal weight: 0.0020 chunk 354 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 215 optimal weight: 0.0370 chunk 263 optimal weight: 2.9990 chunk 410 optimal weight: 5.9990 overall best weight: 0.8072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AD 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 37 ASN AL 37 ASN AP 37 ASN AQ 37 ASN C1 157 GLN C1 158 GLN C2 24 HIS H2 12 ASN H2 119 GLN L 104 GLN L 116 HIS L 213 ASN M 316 GLN aa 2 HIS ad 50 GLN ah 50 GLN ai 36 GLN ap 2 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 58313 Z= 0.192 Angle : 2.009 29.095 80224 Z= 0.688 Chirality : 0.038 0.269 8178 Planarity : 0.004 0.057 9122 Dihedral : 20.476 179.860 18038 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.98 % Allowed : 7.88 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.12), residues: 4858 helix: 2.94 (0.08), residues: 3204 sheet: -0.06 (0.94), residues: 27 loop : 1.37 (0.17), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRPbe 40 HIS 0.009 0.001 HIS L 153 PHE 0.038 0.002 PHEBO 15 TYR 0.016 0.001 TYR C 135 ARG 0.007 0.001 ARGBO 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 638 time to evaluate : 3.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AC 3 ARG cc_start: 0.8222 (ptp90) cc_final: 0.7978 (ptm160) REVERT: AC 17 LEU cc_start: 0.8887 (tp) cc_final: 0.8676 (tm) REVERT: AD 6 MET cc_start: 0.8082 (mtm) cc_final: 0.7727 (mtm) REVERT: AG 6 MET cc_start: 0.7883 (mtm) cc_final: 0.7652 (mtm) REVERT: AH 4 ILE cc_start: 0.8133 (tp) cc_final: 0.7881 (pt) REVERT: AJ 9 ASP cc_start: 0.7947 (t0) cc_final: 0.7658 (t0) REVERT: AK 14 MET cc_start: 0.8775 (mmm) cc_final: 0.8352 (mmm) REVERT: AL 9 ASP cc_start: 0.7672 (t0) cc_final: 0.7355 (t70) REVERT: AQ 4 ILE cc_start: 0.8278 (tp) cc_final: 0.8058 (tt) REVERT: AR 4 ILE cc_start: 0.8641 (tp) cc_final: 0.8437 (tp) REVERT: AT 14 MET cc_start: 0.8691 (mmm) cc_final: 0.8319 (mmm) REVERT: AU 9 ASP cc_start: 0.7893 (t0) cc_final: 0.7660 (t0) REVERT: AU 12 ILE cc_start: 0.8720 (mm) cc_final: 0.8442 (mt) REVERT: AU 42 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8580 (tp) REVERT: AW 3 ARG cc_start: 0.8346 (mtp-110) cc_final: 0.7967 (mtp-110) REVERT: AW 14 MET cc_start: 0.8635 (mmm) cc_final: 0.8406 (mmm) REVERT: AX 6 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.8049 (ptm) REVERT: BB 31 SER cc_start: 0.9077 (m) cc_final: 0.8858 (p) REVERT: BD 7 MET cc_start: 0.7486 (tpp) cc_final: 0.6872 (tpp) REVERT: BF 24 LEU cc_start: 0.8704 (tt) cc_final: 0.8406 (mt) REVERT: BJ 9 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7121 (tm-30) REVERT: BQ 8 THR cc_start: 0.7779 (p) cc_final: 0.7386 (p) REVERT: BR 24 LEU cc_start: 0.8975 (mm) cc_final: 0.8586 (mt) REVERT: BW 7 MET cc_start: 0.7976 (mtm) cc_final: 0.7698 (mtm) REVERT: BW 14 ARG cc_start: 0.8630 (ttp-170) cc_final: 0.8383 (ttp80) REVERT: C 113 LYS cc_start: 0.8138 (mttp) cc_final: 0.7922 (mptm) REVERT: M 45 ASP cc_start: 0.6575 (m-30) cc_final: 0.6336 (m-30) REVERT: M 315 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7146 (pm20) REVERT: aa 8 TYR cc_start: 0.5860 (m-80) cc_final: 0.5534 (m-80) REVERT: aa 11 ARG cc_start: 0.6106 (ttp80) cc_final: 0.5820 (ttp80) REVERT: aa 36 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7896 (mm-40) REVERT: aa 42 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8235 (mm-30) REVERT: ac 7 MET cc_start: 0.8294 (mtm) cc_final: 0.7952 (ttm) REVERT: af 50 GLN cc_start: 0.8165 (mp10) cc_final: 0.7835 (mp10) REVERT: ah 11 ARG cc_start: 0.7333 (ttm110) cc_final: 0.6544 (ttt-90) REVERT: ah 12 ARG cc_start: 0.7095 (mtm110) cc_final: 0.6626 (mmm160) REVERT: aj 14 MET cc_start: 0.8110 (mmm) cc_final: 0.7844 (mmm) REVERT: ak 11 ARG cc_start: 0.7585 (mtp-110) cc_final: 0.7215 (mtm180) REVERT: ak 12 ARG cc_start: 0.7048 (mtm180) cc_final: 0.6689 (mtm-85) REVERT: am 12 ARG cc_start: 0.7446 (mmt180) cc_final: 0.6998 (mtp85) REVERT: ap 6 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8690 (mm) REVERT: be 13 ARG cc_start: 0.7284 (tpp80) cc_final: 0.6861 (mtp85) REVERT: bm 13 ARG cc_start: 0.7447 (ttp80) cc_final: 0.7141 (ttt-90) REVERT: bo 24 LEU cc_start: 0.8890 (tt) cc_final: 0.8617 (mt) outliers start: 79 outliers final: 30 residues processed: 667 average time/residue: 1.6374 time to fit residues: 1339.0710 Evaluate side-chains 613 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 579 time to evaluate : 3.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 48 THR Chi-restraints excluded: chain AE residue 48 THR Chi-restraints excluded: chain AG residue 48 THR Chi-restraints excluded: chain AH residue 6 MET Chi-restraints excluded: chain AJ residue 19 SER Chi-restraints excluded: chain AU residue 15 SER Chi-restraints excluded: chain AU residue 42 LEU Chi-restraints excluded: chain AV residue 48 THR Chi-restraints excluded: chain AW residue 48 THR Chi-restraints excluded: chain AX residue 6 MET Chi-restraints excluded: chain BB residue 19 MET Chi-restraints excluded: chain BD residue 31 SER Chi-restraints excluded: chain BE residue 39 SER Chi-restraints excluded: chain BG residue 10 GLU Chi-restraints excluded: chain BH residue 24 LEU Chi-restraints excluded: chain BI residue 21 THR Chi-restraints excluded: chain BI residue 24 LEU Chi-restraints excluded: chain BM residue 19 MET Chi-restraints excluded: chain BN residue 19 MET Chi-restraints excluded: chain BT residue 31 SER Chi-restraints excluded: chain BU residue 39 SER Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C2 residue 49 VAL Chi-restraints excluded: chain H2 residue 159 ASP Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 315 GLU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain aa residue 14 MET Chi-restraints excluded: chain ab residue 49 ASP Chi-restraints excluded: chain ac residue 49 ASP Chi-restraints excluded: chain ao residue 49 ASP Chi-restraints excluded: chain ap residue 6 LEU Chi-restraints excluded: chain ap residue 7 MET Chi-restraints excluded: chain bm residue 8 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 228 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 341 optimal weight: 9.9990 chunk 279 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 411 optimal weight: 5.9990 chunk 444 optimal weight: 3.9990 chunk 366 optimal weight: 4.9990 chunk 407 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 329 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 35 GLN ** AD 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 35 GLN AS 37 ASN AW 35 GLN C1 157 GLN H2 119 GLN M 145 HIS aa 2 HIS ad 50 GLN ah 50 GLN ak 50 GLN an 50 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 58313 Z= 0.499 Angle : 2.067 28.776 80224 Z= 0.714 Chirality : 0.050 0.347 8178 Planarity : 0.006 0.074 9122 Dihedral : 20.371 179.606 18036 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.95 % Allowed : 8.63 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.12), residues: 4858 helix: 2.56 (0.08), residues: 3235 sheet: -0.41 (0.91), residues: 27 loop : 0.98 (0.17), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRPbe 40 HIS 0.011 0.002 HIS L 153 PHE 0.034 0.003 PHEBO 15 TYR 0.031 0.003 TYR L 164 ARG 0.010 0.001 ARGBO 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 590 time to evaluate : 3.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AC 3 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7970 (ptm160) REVERT: AD 6 MET cc_start: 0.8031 (mtm) cc_final: 0.7654 (mtm) REVERT: AF 3 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.7083 (ttm170) REVERT: AG 45 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8786 (ttmt) REVERT: AH 14 MET cc_start: 0.8872 (mmm) cc_final: 0.8619 (mmm) REVERT: AJ 9 ASP cc_start: 0.7985 (t0) cc_final: 0.7529 (t0) REVERT: AK 14 MET cc_start: 0.8828 (mmm) cc_final: 0.8107 (mmm) REVERT: AL 9 ASP cc_start: 0.7748 (t0) cc_final: 0.7371 (t70) REVERT: AQ 43 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8404 (tttt) REVERT: AT 14 MET cc_start: 0.8665 (mmm) cc_final: 0.8227 (mmm) REVERT: AT 42 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8613 (tp) REVERT: AU 9 ASP cc_start: 0.8009 (t0) cc_final: 0.7775 (t0) REVERT: AU 12 ILE cc_start: 0.8807 (mm) cc_final: 0.8571 (mt) REVERT: AU 42 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8632 (tp) REVERT: AW 3 ARG cc_start: 0.8194 (mtp-110) cc_final: 0.7810 (mtp-110) REVERT: BD 7 MET cc_start: 0.7500 (tpp) cc_final: 0.6974 (tpp) REVERT: BD 9 GLU cc_start: 0.7382 (tm-30) cc_final: 0.7133 (tm-30) REVERT: BD 11 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7294 (mt-10) REVERT: BG 19 MET cc_start: 0.8144 (tpp) cc_final: 0.7871 (mmm) REVERT: BM 9 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6782 (tm-30) REVERT: BN 19 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7067 (mmp) REVERT: BP 11 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7860 (mt-10) REVERT: BQ 8 THR cc_start: 0.7800 (p) cc_final: 0.7398 (p) REVERT: BR 13 ARG cc_start: 0.7077 (ttm110) cc_final: 0.6875 (ttm110) REVERT: BV 9 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.6962 (tm-30) REVERT: BV 13 ARG cc_start: 0.8136 (ttp-110) cc_final: 0.7205 (ttp-110) REVERT: BW 14 ARG cc_start: 0.8584 (ttp-170) cc_final: 0.8348 (ttp80) REVERT: C 82 MET cc_start: 0.9144 (mmt) cc_final: 0.7456 (mmt) REVERT: C2 71 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7170 (tp30) REVERT: H1 3 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: L 7 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8616 (ttmt) REVERT: M 14 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.8030 (mmp-170) REVERT: M 315 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7167 (pm20) REVERT: aa 11 ARG cc_start: 0.6158 (ttp80) cc_final: 0.5531 (tmm-80) REVERT: ac 7 MET cc_start: 0.8371 (mtm) cc_final: 0.8037 (ttm) REVERT: ad 3 ARG cc_start: 0.8150 (mtm-85) cc_final: 0.7934 (mtt90) REVERT: ad 12 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8482 (ptt180) REVERT: af 50 GLN cc_start: 0.8268 (mp10) cc_final: 0.7885 (mt0) REVERT: ah 12 ARG cc_start: 0.7073 (mtm110) cc_final: 0.6601 (mmm160) REVERT: ah 36 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7962 (mp10) REVERT: ai 3 ARG cc_start: 0.7707 (ttp-170) cc_final: 0.7394 (ttp-170) REVERT: ai 7 MET cc_start: 0.7903 (mtp) cc_final: 0.7544 (mtp) REVERT: ai 49 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7312 (p0) REVERT: aj 9 ASP cc_start: 0.8173 (t0) cc_final: 0.7858 (t0) REVERT: aj 11 ARG cc_start: 0.7562 (mtt-85) cc_final: 0.7166 (mtm-85) REVERT: ak 11 ARG cc_start: 0.7598 (mtp-110) cc_final: 0.7229 (mtm110) REVERT: ak 12 ARG cc_start: 0.7047 (mtm180) cc_final: 0.6641 (mtm-85) REVERT: am 12 ARG cc_start: 0.7425 (mmt180) cc_final: 0.7165 (mmm160) REVERT: an 12 ARG cc_start: 0.7374 (mmt-90) cc_final: 0.6548 (ttt180) REVERT: ap 3 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6861 (mtm180) REVERT: ap 7 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.6853 (ttp) REVERT: bd 9 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7402 (tp30) REVERT: be 13 ARG cc_start: 0.7554 (tpp80) cc_final: 0.6997 (mtp85) REVERT: bf 11 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7667 (pt0) REVERT: bo 10 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7114 (tm-30) REVERT: bo 24 LEU cc_start: 0.8901 (tt) cc_final: 0.8668 (mt) outliers start: 118 outliers final: 61 residues processed: 643 average time/residue: 1.6485 time to fit residues: 1300.6173 Evaluate side-chains 656 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 575 time to evaluate : 3.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 48 THR Chi-restraints excluded: chain AB residue 17 LEU Chi-restraints excluded: chain AC residue 3 ARG Chi-restraints excluded: chain AC residue 48 THR Chi-restraints excluded: chain AD residue 15 SER Chi-restraints excluded: chain AE residue 15 SER Chi-restraints excluded: chain AE residue 48 THR Chi-restraints excluded: chain AF residue 3 ARG Chi-restraints excluded: chain AF residue 15 SER Chi-restraints excluded: chain AG residue 45 LYS Chi-restraints excluded: chain AK residue 15 SER Chi-restraints excluded: chain AK residue 48 THR Chi-restraints excluded: chain AN residue 48 THR Chi-restraints excluded: chain AP residue 19 SER Chi-restraints excluded: chain AQ residue 8 THR Chi-restraints excluded: chain AQ residue 43 LYS Chi-restraints excluded: chain AR residue 48 THR Chi-restraints excluded: chain AT residue 42 LEU Chi-restraints excluded: chain AU residue 15 SER Chi-restraints excluded: chain AU residue 42 LEU Chi-restraints excluded: chain AV residue 48 THR Chi-restraints excluded: chain AW residue 48 THR Chi-restraints excluded: chain AX residue 6 MET Chi-restraints excluded: chain BB residue 19 MET Chi-restraints excluded: chain BC residue 28 VAL Chi-restraints excluded: chain BD residue 31 SER Chi-restraints excluded: chain BE residue 24 LEU Chi-restraints excluded: chain BE residue 31 SER Chi-restraints excluded: chain BE residue 39 SER Chi-restraints excluded: chain BG residue 10 GLU Chi-restraints excluded: chain BH residue 24 LEU Chi-restraints excluded: chain BI residue 21 THR Chi-restraints excluded: chain BI residue 24 LEU Chi-restraints excluded: chain BI residue 39 SER Chi-restraints excluded: chain BK residue 7 MET Chi-restraints excluded: chain BM residue 9 GLU Chi-restraints excluded: chain BN residue 19 MET Chi-restraints excluded: chain BO residue 13 ARG Chi-restraints excluded: chain BR residue 19 MET Chi-restraints excluded: chain BT residue 31 SER Chi-restraints excluded: chain BU residue 39 SER Chi-restraints excluded: chain BV residue 9 GLU Chi-restraints excluded: chain BX residue 24 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C1 residue 107 THR Chi-restraints excluded: chain C1 residue 135 ASN Chi-restraints excluded: chain C2 residue 49 VAL Chi-restraints excluded: chain C2 residue 71 GLU Chi-restraints excluded: chain H1 residue 3 GLU Chi-restraints excluded: chain H2 residue 3 VAL Chi-restraints excluded: chain H2 residue 159 ASP Chi-restraints excluded: chain L residue 7 LYS Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 14 ARG Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 315 GLU Chi-restraints excluded: chain aa residue 13 VAL Chi-restraints excluded: chain aa residue 14 MET Chi-restraints excluded: chain aa residue 15 VAL Chi-restraints excluded: chain ab residue 49 ASP Chi-restraints excluded: chain ac residue 15 VAL Chi-restraints excluded: chain ac residue 49 ASP Chi-restraints excluded: chain ad residue 12 ARG Chi-restraints excluded: chain ag residue 36 GLN Chi-restraints excluded: chain ah residue 36 GLN Chi-restraints excluded: chain ai residue 49 ASP Chi-restraints excluded: chain ak residue 39 SER Chi-restraints excluded: chain ao residue 49 ASP Chi-restraints excluded: chain ap residue 3 ARG Chi-restraints excluded: chain ap residue 6 LEU Chi-restraints excluded: chain ap residue 7 MET Chi-restraints excluded: chain ap residue 64 MET Chi-restraints excluded: chain bb residue 8 THR Chi-restraints excluded: chain bc residue 8 THR Chi-restraints excluded: chain bd residue 9 GLU Chi-restraints excluded: chain bh residue 7 MET Chi-restraints excluded: chain bi residue 24 LEU Chi-restraints excluded: chain bk residue 13 ARG Chi-restraints excluded: chain bl residue 8 THR Chi-restraints excluded: chain bm residue 8 THR Chi-restraints excluded: chain bp residue 7 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 406 optimal weight: 7.9990 chunk 309 optimal weight: 0.9990 chunk 213 optimal weight: 0.3980 chunk 45 optimal weight: 9.9990 chunk 196 optimal weight: 0.5980 chunk 276 optimal weight: 0.6980 chunk 412 optimal weight: 1.9990 chunk 436 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 391 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 2 HIS AD 37 ASN AH 35 GLN AM 11 HIS AR 35 GLN C 137 GLN C1 157 GLN H2 119 GLN M 311 GLN aa 2 HIS ad 50 GLN af 50 GLN ah 50 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 58313 Z= 0.173 Angle : 1.845 25.442 80224 Z= 0.626 Chirality : 0.037 0.260 8178 Planarity : 0.004 0.062 9122 Dihedral : 18.494 179.757 18036 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.95 % Allowed : 10.35 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.12), residues: 4858 helix: 3.23 (0.08), residues: 3236 sheet: -0.43 (0.91), residues: 28 loop : 1.08 (0.17), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 270 HIS 0.009 0.001 HIS L 153 PHE 0.034 0.002 PHEBO 15 TYR 0.015 0.001 TYR C 135 ARG 0.007 0.000 ARGbi 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 607 time to evaluate : 4.400 Fit side-chains revert: symmetry clash REVERT: AA 28 MET cc_start: 0.9220 (mmm) cc_final: 0.8875 (mmm) REVERT: AD 6 MET cc_start: 0.8087 (mtm) cc_final: 0.7645 (mtm) REVERT: AD 37 ASN cc_start: 0.8941 (OUTLIER) cc_final: 0.8718 (t0) REVERT: AG 45 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8697 (ttmt) REVERT: AH 4 ILE cc_start: 0.8063 (tp) cc_final: 0.7835 (pt) REVERT: AH 14 MET cc_start: 0.8893 (mmm) cc_final: 0.8671 (mmm) REVERT: AJ 9 ASP cc_start: 0.7888 (t0) cc_final: 0.7648 (t0) REVERT: AK 14 MET cc_start: 0.8838 (mmm) cc_final: 0.8378 (mmm) REVERT: AL 9 ASP cc_start: 0.7696 (t0) cc_final: 0.7235 (t70) REVERT: AT 8 THR cc_start: 0.8885 (p) cc_final: 0.8680 (p) REVERT: AT 14 MET cc_start: 0.8687 (mmm) cc_final: 0.8463 (mmm) REVERT: AU 9 ASP cc_start: 0.8065 (t0) cc_final: 0.7828 (t0) REVERT: AU 12 ILE cc_start: 0.8727 (mm) cc_final: 0.8511 (mt) REVERT: AV 6 MET cc_start: 0.8696 (mtp) cc_final: 0.8486 (mtp) REVERT: AW 3 ARG cc_start: 0.8110 (mtp-110) cc_final: 0.7840 (mtp-110) REVERT: AW 6 MET cc_start: 0.7399 (mtp) cc_final: 0.7090 (mtt) REVERT: AX 6 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7956 (ptm) REVERT: BD 7 MET cc_start: 0.7584 (tpp) cc_final: 0.7151 (tpp) REVERT: BD 11 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7168 (mt-10) REVERT: BF 7 MET cc_start: 0.4768 (ttm) cc_final: 0.4507 (ttp) REVERT: BG 19 MET cc_start: 0.8013 (tpp) cc_final: 0.7813 (mmm) REVERT: BN 19 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7400 (tpp) REVERT: BO 15 PHE cc_start: 0.8142 (t80) cc_final: 0.7866 (t80) REVERT: BP 11 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7807 (mt-10) REVERT: BQ 8 THR cc_start: 0.7641 (p) cc_final: 0.7290 (p) REVERT: BR 24 LEU cc_start: 0.9004 (mm) cc_final: 0.8594 (mt) REVERT: BW 14 ARG cc_start: 0.8461 (ttp-170) cc_final: 0.8178 (ttp80) REVERT: C 82 MET cc_start: 0.9129 (mmt) cc_final: 0.7535 (mmt) REVERT: C 205 MET cc_start: 0.9232 (mmt) cc_final: 0.9028 (mmt) REVERT: M 42 LYS cc_start: 0.6628 (OUTLIER) cc_final: 0.6345 (mttt) REVERT: M 315 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7301 (pm20) REVERT: M 321 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.8005 (ptm160) REVERT: aa 11 ARG cc_start: 0.6144 (ttp80) cc_final: 0.5526 (tmm-80) REVERT: aa 14 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6721 (ttp) REVERT: aa 36 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7973 (mm-40) REVERT: ac 7 MET cc_start: 0.8281 (mtm) cc_final: 0.8045 (ttm) REVERT: af 50 GLN cc_start: 0.8041 (mp-120) cc_final: 0.7783 (mt0) REVERT: ah 12 ARG cc_start: 0.7086 (mtm110) cc_final: 0.6721 (mmm160) REVERT: ah 36 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7948 (mp10) REVERT: ai 3 ARG cc_start: 0.7670 (ttp-170) cc_final: 0.7374 (ttp-170) REVERT: aj 9 ASP cc_start: 0.8105 (t0) cc_final: 0.7789 (t0) REVERT: aj 11 ARG cc_start: 0.7433 (mtt-85) cc_final: 0.6977 (mtm-85) REVERT: aj 14 MET cc_start: 0.8147 (mmm) cc_final: 0.7755 (mmm) REVERT: ak 11 ARG cc_start: 0.7430 (mtp-110) cc_final: 0.7197 (mtm-85) REVERT: ak 12 ARG cc_start: 0.6915 (mtm180) cc_final: 0.6675 (mtp180) REVERT: ap 7 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.6654 (ttp) REVERT: be 13 ARG cc_start: 0.7326 (tpp80) cc_final: 0.6880 (mtp85) REVERT: bh 13 ARG cc_start: 0.7788 (tpp-160) cc_final: 0.7500 (mtt90) REVERT: bm 13 ARG cc_start: 0.7481 (ttp80) cc_final: 0.7218 (ptm-80) outliers start: 78 outliers final: 23 residues processed: 638 average time/residue: 1.6150 time to fit residues: 1265.8426 Evaluate side-chains 602 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 569 time to evaluate : 3.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 17 LEU Chi-restraints excluded: chain AD residue 37 ASN Chi-restraints excluded: chain AE residue 48 THR Chi-restraints excluded: chain AG residue 45 LYS Chi-restraints excluded: chain AH residue 6 MET Chi-restraints excluded: chain AJ residue 19 SER Chi-restraints excluded: chain AK residue 15 SER Chi-restraints excluded: chain AO residue 15 SER Chi-restraints excluded: chain AU residue 15 SER Chi-restraints excluded: chain AX residue 6 MET Chi-restraints excluded: chain BB residue 19 MET Chi-restraints excluded: chain BB residue 31 SER Chi-restraints excluded: chain BD residue 24 LEU Chi-restraints excluded: chain BI residue 39 SER Chi-restraints excluded: chain BN residue 19 MET Chi-restraints excluded: chain BT residue 31 SER Chi-restraints excluded: chain C1 residue 154 SER Chi-restraints excluded: chain C2 residue 49 VAL Chi-restraints excluded: chain H2 residue 159 ASP Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 315 GLU Chi-restraints excluded: chain M residue 321 ARG Chi-restraints excluded: chain aa residue 14 MET Chi-restraints excluded: chain ab residue 3 ARG Chi-restraints excluded: chain ah residue 36 GLN Chi-restraints excluded: chain an residue 64 MET Chi-restraints excluded: chain ao residue 49 ASP Chi-restraints excluded: chain ap residue 7 MET Chi-restraints excluded: chain bi residue 24 LEU Chi-restraints excluded: chain bl residue 8 THR Chi-restraints excluded: chain bm residue 8 THR Chi-restraints excluded: chain bp residue 7 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 363 optimal weight: 0.0020 chunk 248 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 325 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 372 optimal weight: 3.9990 chunk 302 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 223 optimal weight: 7.9990 chunk 392 optimal weight: 2.9990 chunk 110 optimal weight: 0.0870 overall best weight: 1.6172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 2 HIS AD 37 ASN C1 157 GLN H2 119 GLN aa 2 HIS ad 50 GLN ah 50 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 58313 Z= 0.216 Angle : 1.815 25.526 80224 Z= 0.618 Chirality : 0.037 0.236 8178 Planarity : 0.004 0.054 9122 Dihedral : 17.993 179.736 18036 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.05 % Allowed : 11.13 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.88 (0.12), residues: 4858 helix: 3.34 (0.08), residues: 3211 sheet: -0.57 (0.89), residues: 28 loop : 1.09 (0.17), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 270 HIS 0.011 0.001 HIS L 153 PHE 0.028 0.002 PHEBO 15 TYR 0.018 0.001 TYR L 164 ARG 0.009 0.000 ARGbi 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 582 time to evaluate : 3.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AA 6 MET cc_start: 0.8408 (mtm) cc_final: 0.8173 (mtp) REVERT: AA 28 MET cc_start: 0.9276 (mmm) cc_final: 0.8881 (mmm) REVERT: AD 6 MET cc_start: 0.8085 (mtm) cc_final: 0.7714 (mtm) REVERT: AH 14 MET cc_start: 0.8917 (mmm) cc_final: 0.8683 (mmm) REVERT: AJ 9 ASP cc_start: 0.7919 (t0) cc_final: 0.7675 (t0) REVERT: AK 6 MET cc_start: 0.8104 (mtm) cc_final: 0.7890 (mtm) REVERT: AK 14 MET cc_start: 0.8848 (mmm) cc_final: 0.8373 (mmm) REVERT: AL 9 ASP cc_start: 0.7553 (t0) cc_final: 0.7104 (t70) REVERT: AN 15 SER cc_start: 0.8780 (t) cc_final: 0.8560 (t) REVERT: AQ 43 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8187 (tttt) REVERT: AT 8 THR cc_start: 0.8865 (p) cc_final: 0.8638 (p) REVERT: AT 42 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8489 (tp) REVERT: AU 9 ASP cc_start: 0.8078 (t0) cc_final: 0.7820 (t0) REVERT: AU 12 ILE cc_start: 0.8760 (mm) cc_final: 0.8554 (mt) REVERT: AU 42 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8554 (tp) REVERT: AV 6 MET cc_start: 0.8729 (mtp) cc_final: 0.8479 (mtp) REVERT: AW 3 ARG cc_start: 0.8113 (mtp-110) cc_final: 0.7838 (mtp-110) REVERT: AW 6 MET cc_start: 0.7378 (mtp) cc_final: 0.7077 (mtt) REVERT: AX 6 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8078 (ptm) REVERT: BD 7 MET cc_start: 0.7595 (tpp) cc_final: 0.7193 (tpp) REVERT: BD 11 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7138 (mt-10) REVERT: BF 7 MET cc_start: 0.4808 (ttm) cc_final: 0.4557 (ttp) REVERT: BF 9 GLU cc_start: 0.6744 (tp30) cc_final: 0.6520 (mm-30) REVERT: BF 11 GLU cc_start: 0.6455 (mt-10) cc_final: 0.5920 (pt0) REVERT: BF 18 TYR cc_start: 0.7041 (OUTLIER) cc_final: 0.6742 (m-10) REVERT: BG 19 MET cc_start: 0.7957 (tpp) cc_final: 0.7730 (mmm) REVERT: BM 9 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6538 (tm-30) REVERT: BN 19 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7339 (tpp) REVERT: BO 15 PHE cc_start: 0.8197 (t80) cc_final: 0.7922 (t80) REVERT: BP 11 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7785 (mt-10) REVERT: BQ 8 THR cc_start: 0.7672 (p) cc_final: 0.7370 (p) REVERT: BR 24 LEU cc_start: 0.8998 (mm) cc_final: 0.8593 (mt) REVERT: C2 43 GLU cc_start: 0.7950 (pt0) cc_final: 0.7631 (mt-10) REVERT: C2 74 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7769 (m-30) REVERT: M 315 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7330 (pm20) REVERT: aa 11 ARG cc_start: 0.6151 (ttp80) cc_final: 0.5527 (tmm-80) REVERT: ac 7 MET cc_start: 0.8261 (mtm) cc_final: 0.8030 (ttm) REVERT: af 50 GLN cc_start: 0.8103 (mp-120) cc_final: 0.7714 (mt0) REVERT: ah 12 ARG cc_start: 0.7131 (mtm110) cc_final: 0.6703 (mmm160) REVERT: ah 36 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.8013 (mp10) REVERT: ai 3 ARG cc_start: 0.7707 (ttp-170) cc_final: 0.7245 (ttp-170) REVERT: aj 9 ASP cc_start: 0.8150 (t0) cc_final: 0.7810 (t0) REVERT: aj 11 ARG cc_start: 0.7401 (mtt-85) cc_final: 0.6956 (mtm-85) REVERT: aj 12 ARG cc_start: 0.8059 (mtt-85) cc_final: 0.6735 (ptt90) REVERT: ak 11 ARG cc_start: 0.7429 (mtp-110) cc_final: 0.7084 (mtm180) REVERT: ak 12 ARG cc_start: 0.6873 (mtm180) cc_final: 0.6612 (mtp180) REVERT: am 12 ARG cc_start: 0.7090 (mmm160) cc_final: 0.6506 (mtp85) REVERT: ap 3 ARG cc_start: 0.7315 (ttm110) cc_final: 0.7100 (tpp80) REVERT: ap 7 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.6642 (ttp) REVERT: bb 19 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.6983 (tpt) REVERT: be 13 ARG cc_start: 0.7341 (tpp80) cc_final: 0.6922 (mtp85) REVERT: bh 13 ARG cc_start: 0.7765 (tpp-160) cc_final: 0.7525 (mtt90) REVERT: bm 13 ARG cc_start: 0.7517 (ttp80) cc_final: 0.7261 (ptm-80) REVERT: bp 11 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7029 (mt-10) outliers start: 82 outliers final: 32 residues processed: 620 average time/residue: 1.6441 time to fit residues: 1251.2281 Evaluate side-chains 613 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 569 time to evaluate : 3.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 17 LEU Chi-restraints excluded: chain AE residue 48 THR Chi-restraints excluded: chain AK residue 15 SER Chi-restraints excluded: chain AO residue 15 SER Chi-restraints excluded: chain AQ residue 43 LYS Chi-restraints excluded: chain AT residue 42 LEU Chi-restraints excluded: chain AU residue 15 SER Chi-restraints excluded: chain AU residue 42 LEU Chi-restraints excluded: chain AV residue 48 THR Chi-restraints excluded: chain AX residue 6 MET Chi-restraints excluded: chain BB residue 19 MET Chi-restraints excluded: chain BD residue 24 LEU Chi-restraints excluded: chain BE residue 24 LEU Chi-restraints excluded: chain BF residue 18 TYR Chi-restraints excluded: chain BI residue 21 THR Chi-restraints excluded: chain BI residue 39 SER Chi-restraints excluded: chain BM residue 9 GLU Chi-restraints excluded: chain BN residue 19 MET Chi-restraints excluded: chain BS residue 39 SER Chi-restraints excluded: chain BT residue 24 LEU Chi-restraints excluded: chain BT residue 31 SER Chi-restraints excluded: chain BU residue 39 SER Chi-restraints excluded: chain BX residue 24 LEU Chi-restraints excluded: chain C1 residue 107 THR Chi-restraints excluded: chain C1 residue 135 ASN Chi-restraints excluded: chain C1 residue 154 SER Chi-restraints excluded: chain C2 residue 49 VAL Chi-restraints excluded: chain C2 residue 74 ASP Chi-restraints excluded: chain H2 residue 34 GLU Chi-restraints excluded: chain H2 residue 159 ASP Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 315 GLU Chi-restraints excluded: chain ab residue 6 LEU Chi-restraints excluded: chain ac residue 49 ASP Chi-restraints excluded: chain ad residue 39 SER Chi-restraints excluded: chain ah residue 36 GLN Chi-restraints excluded: chain ak residue 39 SER Chi-restraints excluded: chain an residue 64 MET Chi-restraints excluded: chain ao residue 49 ASP Chi-restraints excluded: chain ap residue 7 MET Chi-restraints excluded: chain bb residue 19 MET Chi-restraints excluded: chain bi residue 24 LEU Chi-restraints excluded: chain bl residue 8 THR Chi-restraints excluded: chain bm residue 8 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 146 optimal weight: 3.9990 chunk 393 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 256 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 437 optimal weight: 10.0000 chunk 363 optimal weight: 0.0050 chunk 202 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 229 optimal weight: 5.9990 overall best weight: 2.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 157 GLN H2 10 ASN M 311 GLN ad 50 GLN ah 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 58313 Z= 0.270 Angle : 1.818 24.890 80224 Z= 0.620 Chirality : 0.039 0.243 8178 Planarity : 0.004 0.051 9122 Dihedral : 17.925 179.656 18036 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.28 % Allowed : 11.40 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.12), residues: 4858 helix: 3.20 (0.08), residues: 3204 sheet: -0.70 (0.87), residues: 27 loop : 1.04 (0.17), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPbh 43 HIS 0.012 0.001 HIS L 153 PHE 0.028 0.002 PHEBO 15 TYR 0.021 0.002 TYR L 164 ARG 0.011 0.001 ARGbi 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 583 time to evaluate : 3.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AA 6 MET cc_start: 0.8386 (mtm) cc_final: 0.8177 (mtp) REVERT: AA 28 MET cc_start: 0.9300 (mmm) cc_final: 0.8881 (mmm) REVERT: AB 42 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8331 (tp) REVERT: AD 6 MET cc_start: 0.8040 (mtm) cc_final: 0.7630 (mtm) REVERT: AG 45 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8729 (ttmt) REVERT: AH 14 MET cc_start: 0.8904 (mmm) cc_final: 0.8637 (mmm) REVERT: AJ 9 ASP cc_start: 0.7913 (t0) cc_final: 0.7670 (t0) REVERT: AK 14 MET cc_start: 0.8862 (mmm) cc_final: 0.8256 (mmm) REVERT: AL 9 ASP cc_start: 0.7535 (t0) cc_final: 0.7070 (t70) REVERT: AN 15 SER cc_start: 0.8754 (t) cc_final: 0.8528 (t) REVERT: AQ 14 MET cc_start: 0.8652 (mmm) cc_final: 0.8401 (mmm) REVERT: AQ 43 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8248 (tttt) REVERT: AT 42 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8471 (tp) REVERT: AU 9 ASP cc_start: 0.8086 (t0) cc_final: 0.7820 (t0) REVERT: AU 42 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8543 (tp) REVERT: AV 6 MET cc_start: 0.8740 (mtp) cc_final: 0.8493 (mtp) REVERT: AW 3 ARG cc_start: 0.8102 (mtp-110) cc_final: 0.7654 (mtp85) REVERT: AX 45 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8402 (ttpt) REVERT: BD 7 MET cc_start: 0.7570 (tpp) cc_final: 0.7157 (tpp) REVERT: BD 11 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7136 (mt-10) REVERT: BF 9 GLU cc_start: 0.6917 (tp30) cc_final: 0.6700 (mm-30) REVERT: BF 18 TYR cc_start: 0.6952 (OUTLIER) cc_final: 0.6673 (m-10) REVERT: BG 19 MET cc_start: 0.7969 (tpp) cc_final: 0.7739 (mmm) REVERT: BG 24 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8321 (mm) REVERT: BJ 9 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7271 (tp30) REVERT: BM 9 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6562 (tm-30) REVERT: BO 15 PHE cc_start: 0.8209 (t80) cc_final: 0.7928 (t80) REVERT: BP 11 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7796 (mt-10) REVERT: BQ 8 THR cc_start: 0.7733 (p) cc_final: 0.7399 (p) REVERT: BV 10 GLU cc_start: 0.6939 (tp30) cc_final: 0.6275 (tp30) REVERT: BV 13 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7171 (ttp80) REVERT: C 72 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7640 (p0) REVERT: C2 43 GLU cc_start: 0.8050 (pt0) cc_final: 0.7696 (mt-10) REVERT: M 315 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7311 (pm20) REVERT: aa 11 ARG cc_start: 0.6114 (ttp80) cc_final: 0.5497 (tmm-80) REVERT: aa 14 MET cc_start: 0.6585 (OUTLIER) cc_final: 0.6349 (ttp) REVERT: ac 7 MET cc_start: 0.8257 (mtm) cc_final: 0.8008 (ttm) REVERT: ac 11 ARG cc_start: 0.7629 (ptp-170) cc_final: 0.7120 (ptt90) REVERT: ad 12 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8350 (ptt180) REVERT: af 50 GLN cc_start: 0.8052 (mp-120) cc_final: 0.7729 (mt0) REVERT: ah 12 ARG cc_start: 0.7135 (mtm110) cc_final: 0.6677 (mmm160) REVERT: ah 36 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.8004 (mp10) REVERT: ai 3 ARG cc_start: 0.7660 (ttp-170) cc_final: 0.7371 (ttp-170) REVERT: aj 9 ASP cc_start: 0.8158 (t0) cc_final: 0.7883 (t0) REVERT: aj 11 ARG cc_start: 0.7429 (mtt-85) cc_final: 0.7166 (mtm-85) REVERT: aj 12 ARG cc_start: 0.8068 (mtt-85) cc_final: 0.6724 (ptt90) REVERT: ak 11 ARG cc_start: 0.7440 (mtp-110) cc_final: 0.7112 (mtm180) REVERT: am 12 ARG cc_start: 0.7123 (mmm160) cc_final: 0.6487 (mtp85) REVERT: an 64 MET cc_start: 0.3592 (OUTLIER) cc_final: 0.2872 (mtm) REVERT: ap 7 MET cc_start: 0.6923 (OUTLIER) cc_final: 0.6692 (ttp) REVERT: bd 9 GLU cc_start: 0.7588 (tt0) cc_final: 0.7381 (tp30) REVERT: be 13 ARG cc_start: 0.7437 (tpp80) cc_final: 0.6993 (mtp85) REVERT: bh 13 ARG cc_start: 0.7763 (ttp-170) cc_final: 0.7454 (mtt90) REVERT: bl 7 MET cc_start: 0.7592 (mtt) cc_final: 0.7352 (ptp) REVERT: bm 13 ARG cc_start: 0.7528 (ttp80) cc_final: 0.7271 (ptm-80) outliers start: 91 outliers final: 44 residues processed: 623 average time/residue: 1.6462 time to fit residues: 1261.3624 Evaluate side-chains 635 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 573 time to evaluate : 3.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 17 LEU Chi-restraints excluded: chain AB residue 42 LEU Chi-restraints excluded: chain AC residue 48 THR Chi-restraints excluded: chain AD residue 15 SER Chi-restraints excluded: chain AE residue 48 THR Chi-restraints excluded: chain AG residue 45 LYS Chi-restraints excluded: chain AK residue 15 SER Chi-restraints excluded: chain AN residue 48 THR Chi-restraints excluded: chain AO residue 15 SER Chi-restraints excluded: chain AQ residue 43 LYS Chi-restraints excluded: chain AR residue 48 THR Chi-restraints excluded: chain AT residue 42 LEU Chi-restraints excluded: chain AU residue 15 SER Chi-restraints excluded: chain AU residue 42 LEU Chi-restraints excluded: chain AV residue 48 THR Chi-restraints excluded: chain AX residue 6 MET Chi-restraints excluded: chain AX residue 45 LYS Chi-restraints excluded: chain BB residue 19 MET Chi-restraints excluded: chain BD residue 8 THR Chi-restraints excluded: chain BD residue 24 LEU Chi-restraints excluded: chain BE residue 24 LEU Chi-restraints excluded: chain BF residue 18 TYR Chi-restraints excluded: chain BG residue 24 LEU Chi-restraints excluded: chain BI residue 21 THR Chi-restraints excluded: chain BI residue 39 SER Chi-restraints excluded: chain BJ residue 9 GLU Chi-restraints excluded: chain BK residue 7 MET Chi-restraints excluded: chain BM residue 9 GLU Chi-restraints excluded: chain BS residue 39 SER Chi-restraints excluded: chain BT residue 24 LEU Chi-restraints excluded: chain BT residue 31 SER Chi-restraints excluded: chain BU residue 39 SER Chi-restraints excluded: chain BV residue 13 ARG Chi-restraints excluded: chain BX residue 24 LEU Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C1 residue 107 THR Chi-restraints excluded: chain C1 residue 135 ASN Chi-restraints excluded: chain C1 residue 154 SER Chi-restraints excluded: chain C2 residue 49 VAL Chi-restraints excluded: chain H2 residue 34 GLU Chi-restraints excluded: chain H2 residue 159 ASP Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain M residue 315 GLU Chi-restraints excluded: chain aa residue 14 MET Chi-restraints excluded: chain ab residue 6 LEU Chi-restraints excluded: chain ab residue 49 ASP Chi-restraints excluded: chain ac residue 49 ASP Chi-restraints excluded: chain ad residue 12 ARG Chi-restraints excluded: chain ad residue 39 SER Chi-restraints excluded: chain af residue 56 SER Chi-restraints excluded: chain ah residue 36 GLN Chi-restraints excluded: chain ak residue 39 SER Chi-restraints excluded: chain an residue 64 MET Chi-restraints excluded: chain ao residue 49 ASP Chi-restraints excluded: chain ap residue 7 MET Chi-restraints excluded: chain bc residue 8 THR Chi-restraints excluded: chain bc residue 13 ARG Chi-restraints excluded: chain bi residue 24 LEU Chi-restraints excluded: chain bl residue 8 THR Chi-restraints excluded: chain bm residue 8 THR Chi-restraints excluded: chain bn residue 10 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 421 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 249 optimal weight: 8.9990 chunk 319 optimal weight: 0.7980 chunk 247 optimal weight: 1.9990 chunk 368 optimal weight: 1.9990 chunk 244 optimal weight: 0.5980 chunk 435 optimal weight: 0.9980 chunk 272 optimal weight: 6.9990 chunk 265 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 157 GLN H2 10 ASN M 311 GLN ad 50 GLN ah 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 58313 Z= 0.167 Angle : 1.745 24.708 80224 Z= 0.592 Chirality : 0.035 0.214 8178 Planarity : 0.003 0.055 9122 Dihedral : 17.226 179.762 18036 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.73 % Allowed : 12.70 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.01 (0.12), residues: 4858 helix: 3.48 (0.08), residues: 3210 sheet: -0.75 (0.88), residues: 28 loop : 1.05 (0.17), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 270 HIS 0.009 0.001 HIS L 153 PHE 0.028 0.001 PHEBO 15 TYR 0.014 0.001 TYR C 135 ARG 0.013 0.000 ARGbi 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 591 time to evaluate : 3.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 28 MET cc_start: 0.9273 (mmm) cc_final: 0.8895 (mmm) REVERT: AB 42 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8308 (tp) REVERT: AD 6 MET cc_start: 0.8040 (mtm) cc_final: 0.7618 (mtm) REVERT: AF 19 SER cc_start: 0.8839 (m) cc_final: 0.8630 (p) REVERT: AJ 9 ASP cc_start: 0.7912 (t0) cc_final: 0.7689 (t0) REVERT: AJ 12 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8986 (mp) REVERT: AK 14 MET cc_start: 0.8829 (mmm) cc_final: 0.8369 (mmm) REVERT: AL 9 ASP cc_start: 0.7403 (t0) cc_final: 0.6934 (t70) REVERT: AN 15 SER cc_start: 0.8753 (t) cc_final: 0.8527 (t) REVERT: AQ 43 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8149 (tttt) REVERT: AT 8 THR cc_start: 0.8853 (p) cc_final: 0.8628 (p) REVERT: AU 9 ASP cc_start: 0.8167 (t0) cc_final: 0.7896 (t0) REVERT: AU 42 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8510 (tp) REVERT: AW 3 ARG cc_start: 0.8078 (mtp-110) cc_final: 0.7728 (mtp85) REVERT: AW 9 ASP cc_start: 0.8099 (t0) cc_final: 0.7832 (t0) REVERT: AX 6 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7985 (ptm) REVERT: BD 7 MET cc_start: 0.7577 (tpp) cc_final: 0.6915 (tpp) REVERT: BD 11 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7141 (mt-10) REVERT: BF 18 TYR cc_start: 0.6808 (OUTLIER) cc_final: 0.6517 (m-10) REVERT: BK 10 GLU cc_start: 0.7359 (tp30) cc_final: 0.7044 (tp30) REVERT: BN 19 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7329 (tpp) REVERT: BO 15 PHE cc_start: 0.8150 (t80) cc_final: 0.7835 (t80) REVERT: BP 11 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7771 (mt-10) REVERT: BQ 8 THR cc_start: 0.7754 (p) cc_final: 0.7523 (p) REVERT: BR 24 LEU cc_start: 0.9016 (mm) cc_final: 0.8630 (mt) REVERT: BU 18 TYR cc_start: 0.8125 (m-80) cc_final: 0.7828 (m-80) REVERT: C 113 LYS cc_start: 0.8155 (mttp) cc_final: 0.7929 (mptm) REVERT: C2 43 GLU cc_start: 0.7976 (pt0) cc_final: 0.7691 (mt-10) REVERT: H2 108 GLU cc_start: 0.6112 (mm-30) cc_final: 0.5667 (tp30) REVERT: M 315 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7272 (pm20) REVERT: aa 11 ARG cc_start: 0.6074 (ttp80) cc_final: 0.5517 (tmm-80) REVERT: ac 11 ARG cc_start: 0.7611 (ptp-170) cc_final: 0.7112 (ptt90) REVERT: ad 12 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8083 (ptt180) REVERT: ah 12 ARG cc_start: 0.7063 (mtm110) cc_final: 0.6681 (mmm160) REVERT: ah 36 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.8013 (mp10) REVERT: ai 3 ARG cc_start: 0.7621 (ttp-170) cc_final: 0.7217 (tpp-160) REVERT: aj 9 ASP cc_start: 0.8078 (t0) cc_final: 0.7799 (t0) REVERT: aj 11 ARG cc_start: 0.7403 (mtt-85) cc_final: 0.7032 (mtm-85) REVERT: aj 12 ARG cc_start: 0.7984 (mtt-85) cc_final: 0.6731 (ptt90) REVERT: ak 11 ARG cc_start: 0.7372 (mtp-110) cc_final: 0.7027 (mtm180) REVERT: am 12 ARG cc_start: 0.7050 (mmm160) cc_final: 0.6620 (mmm160) REVERT: an 64 MET cc_start: 0.3505 (OUTLIER) cc_final: 0.2798 (mtm) REVERT: bd 9 GLU cc_start: 0.7571 (tt0) cc_final: 0.7309 (tp30) REVERT: be 13 ARG cc_start: 0.7332 (tpp80) cc_final: 0.6911 (mtp85) REVERT: bh 13 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7441 (mtt90) REVERT: bp 11 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7026 (mt-10) outliers start: 69 outliers final: 27 residues processed: 618 average time/residue: 1.6371 time to fit residues: 1247.4580 Evaluate side-chains 606 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 567 time to evaluate : 3.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 17 LEU Chi-restraints excluded: chain AB residue 42 LEU Chi-restraints excluded: chain AE residue 48 THR Chi-restraints excluded: chain AJ residue 12 ILE Chi-restraints excluded: chain AK residue 15 SER Chi-restraints excluded: chain AO residue 15 SER Chi-restraints excluded: chain AQ residue 43 LYS Chi-restraints excluded: chain AU residue 15 SER Chi-restraints excluded: chain AU residue 42 LEU Chi-restraints excluded: chain AX residue 6 MET Chi-restraints excluded: chain BB residue 19 MET Chi-restraints excluded: chain BC residue 31 SER Chi-restraints excluded: chain BD residue 24 LEU Chi-restraints excluded: chain BD residue 39 SER Chi-restraints excluded: chain BF residue 18 TYR Chi-restraints excluded: chain BI residue 21 THR Chi-restraints excluded: chain BN residue 19 MET Chi-restraints excluded: chain BT residue 31 SER Chi-restraints excluded: chain C1 residue 135 ASN Chi-restraints excluded: chain C2 residue 49 VAL Chi-restraints excluded: chain H2 residue 159 ASP Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain M residue 315 GLU Chi-restraints excluded: chain ab residue 3 ARG Chi-restraints excluded: chain ab residue 6 LEU Chi-restraints excluded: chain ab residue 49 ASP Chi-restraints excluded: chain ac residue 49 ASP Chi-restraints excluded: chain ad residue 12 ARG Chi-restraints excluded: chain af residue 56 SER Chi-restraints excluded: chain ah residue 36 GLN Chi-restraints excluded: chain an residue 64 MET Chi-restraints excluded: chain ao residue 49 ASP Chi-restraints excluded: chain bc residue 13 ARG Chi-restraints excluded: chain bh residue 13 ARG Chi-restraints excluded: chain bi residue 24 LEU Chi-restraints excluded: chain bl residue 8 THR Chi-restraints excluded: chain bm residue 8 THR Chi-restraints excluded: chain bn residue 10 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 269 optimal weight: 4.9990 chunk 173 optimal weight: 0.6980 chunk 260 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 276 optimal weight: 0.5980 chunk 296 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 342 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 157 GLN H2 10 ASN aa 36 GLN ad 50 GLN ah 50 GLN aj 50 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 58313 Z= 0.212 Angle : 1.757 24.692 80224 Z= 0.598 Chirality : 0.037 0.221 8178 Planarity : 0.004 0.071 9122 Dihedral : 17.144 179.743 18036 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.85 % Allowed : 12.83 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.92 (0.12), residues: 4858 helix: 3.39 (0.08), residues: 3208 sheet: -0.68 (0.88), residues: 28 loop : 1.05 (0.17), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 270 HIS 0.012 0.001 HIS M 181 PHE 0.026 0.002 PHEBO 15 TYR 0.018 0.001 TYR L 164 ARG 0.016 0.000 ARGbi 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 574 time to evaluate : 3.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AA 28 MET cc_start: 0.9287 (mmm) cc_final: 0.8885 (mmm) REVERT: AB 42 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8352 (tp) REVERT: AD 6 MET cc_start: 0.8034 (mtm) cc_final: 0.7656 (mtm) REVERT: AF 3 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6969 (ttm170) REVERT: AF 19 SER cc_start: 0.8827 (m) cc_final: 0.8614 (p) REVERT: AJ 9 ASP cc_start: 0.7919 (t0) cc_final: 0.7688 (t0) REVERT: AK 6 MET cc_start: 0.8090 (mtm) cc_final: 0.7858 (mtm) REVERT: AK 14 MET cc_start: 0.8833 (mmm) cc_final: 0.8351 (mmm) REVERT: AL 9 ASP cc_start: 0.7383 (t0) cc_final: 0.6941 (t70) REVERT: AN 15 SER cc_start: 0.8809 (t) cc_final: 0.8595 (t) REVERT: AQ 43 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8188 (tttt) REVERT: AT 8 THR cc_start: 0.8847 (p) cc_final: 0.8628 (p) REVERT: AT 42 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8446 (tp) REVERT: AU 9 ASP cc_start: 0.8164 (t0) cc_final: 0.7861 (t0) REVERT: AU 42 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8523 (tp) REVERT: AW 3 ARG cc_start: 0.8079 (mtp-110) cc_final: 0.7752 (mtp85) REVERT: AW 28 MET cc_start: 0.9318 (mmm) cc_final: 0.9056 (mmm) REVERT: BD 7 MET cc_start: 0.7558 (tpp) cc_final: 0.6980 (tpp) REVERT: BF 18 TYR cc_start: 0.6810 (OUTLIER) cc_final: 0.6512 (m-10) REVERT: BN 19 MET cc_start: 0.7650 (mmm) cc_final: 0.7329 (tpp) REVERT: BO 15 PHE cc_start: 0.8188 (t80) cc_final: 0.7914 (t80) REVERT: BP 11 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7790 (mt-10) REVERT: BQ 8 THR cc_start: 0.7752 (p) cc_final: 0.7511 (p) REVERT: C 82 MET cc_start: 0.9099 (mmt) cc_final: 0.7793 (mmt) REVERT: C 113 LYS cc_start: 0.8155 (mttp) cc_final: 0.7923 (mptm) REVERT: C 205 MET cc_start: 0.9339 (mmt) cc_final: 0.8950 (mmt) REVERT: C2 43 GLU cc_start: 0.8000 (pt0) cc_final: 0.7773 (mt-10) REVERT: C2 74 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7773 (m-30) REVERT: H2 108 GLU cc_start: 0.6095 (mm-30) cc_final: 0.5656 (tp30) REVERT: M 315 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7276 (pm20) REVERT: aa 14 MET cc_start: 0.6525 (ttp) cc_final: 0.6215 (ttt) REVERT: ac 11 ARG cc_start: 0.7619 (ptp-170) cc_final: 0.7155 (ptt90) REVERT: ad 12 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8248 (ptt180) REVERT: ah 12 ARG cc_start: 0.7089 (mtm110) cc_final: 0.6745 (mmm-85) REVERT: ah 36 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7979 (mp10) REVERT: ai 3 ARG cc_start: 0.7657 (ttp-170) cc_final: 0.7272 (tpp-160) REVERT: aj 9 ASP cc_start: 0.8097 (t0) cc_final: 0.7813 (t0) REVERT: aj 11 ARG cc_start: 0.7396 (mtt-85) cc_final: 0.7012 (mtm-85) REVERT: aj 12 ARG cc_start: 0.8031 (mtt-85) cc_final: 0.6747 (ptt90) REVERT: ak 11 ARG cc_start: 0.7415 (mtp-110) cc_final: 0.7079 (mtm180) REVERT: am 12 ARG cc_start: 0.7048 (mmm160) cc_final: 0.6625 (mmm160) REVERT: an 64 MET cc_start: 0.3365 (OUTLIER) cc_final: 0.2672 (mtm) REVERT: be 13 ARG cc_start: 0.7335 (tpp80) cc_final: 0.6913 (mtp85) REVERT: bh 13 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7530 (mtt90) REVERT: bj 7 MET cc_start: 0.7940 (tpt) cc_final: 0.7737 (ttm) REVERT: bp 11 GLU cc_start: 0.7378 (mt-10) cc_final: 0.6998 (mt-10) outliers start: 74 outliers final: 35 residues processed: 604 average time/residue: 1.6433 time to fit residues: 1222.2784 Evaluate side-chains 616 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 569 time to evaluate : 3.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 17 LEU Chi-restraints excluded: chain AB residue 42 LEU Chi-restraints excluded: chain AC residue 48 THR Chi-restraints excluded: chain AE residue 48 THR Chi-restraints excluded: chain AF residue 3 ARG Chi-restraints excluded: chain AK residue 15 SER Chi-restraints excluded: chain AO residue 15 SER Chi-restraints excluded: chain AQ residue 43 LYS Chi-restraints excluded: chain AT residue 42 LEU Chi-restraints excluded: chain AU residue 15 SER Chi-restraints excluded: chain AU residue 42 LEU Chi-restraints excluded: chain AX residue 6 MET Chi-restraints excluded: chain BB residue 19 MET Chi-restraints excluded: chain BD residue 8 THR Chi-restraints excluded: chain BD residue 39 SER Chi-restraints excluded: chain BE residue 24 LEU Chi-restraints excluded: chain BF residue 18 TYR Chi-restraints excluded: chain BH residue 7 MET Chi-restraints excluded: chain BI residue 21 THR Chi-restraints excluded: chain BI residue 39 SER Chi-restraints excluded: chain BT residue 24 LEU Chi-restraints excluded: chain BT residue 31 SER Chi-restraints excluded: chain BU residue 39 SER Chi-restraints excluded: chain C1 residue 135 ASN Chi-restraints excluded: chain C2 residue 49 VAL Chi-restraints excluded: chain C2 residue 74 ASP Chi-restraints excluded: chain H2 residue 159 ASP Chi-restraints excluded: chain L residue 213 ASN Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain M residue 315 GLU Chi-restraints excluded: chain ab residue 3 ARG Chi-restraints excluded: chain ab residue 6 LEU Chi-restraints excluded: chain ab residue 49 ASP Chi-restraints excluded: chain ac residue 49 ASP Chi-restraints excluded: chain ad residue 12 ARG Chi-restraints excluded: chain af residue 56 SER Chi-restraints excluded: chain ah residue 36 GLN Chi-restraints excluded: chain ak residue 39 SER Chi-restraints excluded: chain an residue 64 MET Chi-restraints excluded: chain ao residue 49 ASP Chi-restraints excluded: chain bc residue 13 ARG Chi-restraints excluded: chain bh residue 13 ARG Chi-restraints excluded: chain bi residue 24 LEU Chi-restraints excluded: chain bl residue 8 THR Chi-restraints excluded: chain bm residue 8 THR Chi-restraints excluded: chain bn residue 10 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 396 optimal weight: 0.8980 chunk 417 optimal weight: 2.9990 chunk 380 optimal weight: 3.9990 chunk 405 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 176 optimal weight: 8.9990 chunk 318 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 366 optimal weight: 0.7980 chunk 383 optimal weight: 7.9990 chunk 404 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AJ 35 GLN AX 35 GLN C1 157 GLN H2 10 ASN ad 50 GLN ah 50 GLN ai 50 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 58313 Z= 0.171 Angle : 1.726 24.105 80224 Z= 0.586 Chirality : 0.035 0.211 8178 Planarity : 0.004 0.074 9122 Dihedral : 16.832 179.785 18036 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.58 % Allowed : 13.30 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.98 (0.12), residues: 4858 helix: 3.44 (0.08), residues: 3231 sheet: -0.60 (0.89), residues: 28 loop : 1.04 (0.17), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 270 HIS 0.010 0.001 HIS L 153 PHE 0.024 0.001 PHEBO 15 TYR 0.015 0.001 TYR L 164 ARG 0.016 0.000 ARGbi 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 576 time to evaluate : 3.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 28 MET cc_start: 0.9275 (mmm) cc_final: 0.8890 (mmm) REVERT: AB 42 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8347 (tp) REVERT: AD 6 MET cc_start: 0.8042 (mtm) cc_final: 0.7632 (mtm) REVERT: AF 3 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6973 (ttm170) REVERT: AF 19 SER cc_start: 0.8841 (m) cc_final: 0.8638 (p) REVERT: AJ 9 ASP cc_start: 0.7889 (t0) cc_final: 0.7670 (t0) REVERT: AK 14 MET cc_start: 0.8822 (mmm) cc_final: 0.8336 (mmm) REVERT: AL 9 ASP cc_start: 0.7362 (t0) cc_final: 0.6926 (t70) REVERT: AN 15 SER cc_start: 0.8786 (t) cc_final: 0.8561 (t) REVERT: AQ 14 MET cc_start: 0.8700 (mmm) cc_final: 0.8439 (mmm) REVERT: AQ 43 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8175 (tttt) REVERT: AR 3 ARG cc_start: 0.7733 (mpp80) cc_final: 0.7515 (mtt90) REVERT: AT 8 THR cc_start: 0.8846 (p) cc_final: 0.8624 (p) REVERT: AU 9 ASP cc_start: 0.8126 (t0) cc_final: 0.7865 (t0) REVERT: AU 42 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8516 (tp) REVERT: AV 6 MET cc_start: 0.8689 (mtp) cc_final: 0.8480 (mtp) REVERT: AW 3 ARG cc_start: 0.8096 (mtp-110) cc_final: 0.7774 (mtp85) REVERT: BD 7 MET cc_start: 0.7551 (tpp) cc_final: 0.6992 (tpp) REVERT: BF 18 TYR cc_start: 0.6795 (OUTLIER) cc_final: 0.6513 (m-10) REVERT: BK 10 GLU cc_start: 0.7354 (tp30) cc_final: 0.7059 (tp30) REVERT: BL 14 ARG cc_start: 0.8052 (ttp-110) cc_final: 0.7833 (mtm-85) REVERT: BN 19 MET cc_start: 0.7618 (mmm) cc_final: 0.7309 (tpp) REVERT: BO 15 PHE cc_start: 0.8164 (t80) cc_final: 0.7856 (t80) REVERT: BP 11 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7778 (mt-10) REVERT: BQ 8 THR cc_start: 0.7746 (p) cc_final: 0.7505 (p) REVERT: BT 10 GLU cc_start: 0.7025 (tp30) cc_final: 0.6785 (tp30) REVERT: C 113 LYS cc_start: 0.8117 (mttp) cc_final: 0.7901 (mptm) REVERT: C 205 MET cc_start: 0.9272 (mmt) cc_final: 0.8867 (mmt) REVERT: C2 43 GLU cc_start: 0.7948 (pt0) cc_final: 0.7745 (mt-10) REVERT: C2 74 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7788 (m-30) REVERT: H2 108 GLU cc_start: 0.5939 (mm-30) cc_final: 0.5571 (tp30) REVERT: M 315 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7261 (pm20) REVERT: aa 14 MET cc_start: 0.6604 (ttp) cc_final: 0.6267 (ttt) REVERT: ac 11 ARG cc_start: 0.7614 (ptp-170) cc_final: 0.7139 (ptt90) REVERT: ad 12 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8127 (ptt180) REVERT: ah 12 ARG cc_start: 0.7107 (mtm110) cc_final: 0.6891 (mmp-170) REVERT: ah 36 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7972 (mp10) REVERT: ai 3 ARG cc_start: 0.7648 (ttp-170) cc_final: 0.7264 (ttp-170) REVERT: ai 49 ASP cc_start: 0.7766 (p0) cc_final: 0.7368 (p0) REVERT: ai 50 GLN cc_start: 0.8315 (mp-120) cc_final: 0.8007 (mp10) REVERT: aj 9 ASP cc_start: 0.8080 (t0) cc_final: 0.7717 (t0) REVERT: aj 11 ARG cc_start: 0.7326 (mtt-85) cc_final: 0.7016 (mtm-85) REVERT: aj 12 ARG cc_start: 0.7995 (mtt-85) cc_final: 0.6719 (ptt90) REVERT: ak 11 ARG cc_start: 0.7390 (mtp-110) cc_final: 0.7052 (mtm180) REVERT: am 12 ARG cc_start: 0.6941 (mmm160) cc_final: 0.6538 (mmm160) REVERT: an 64 MET cc_start: 0.3360 (OUTLIER) cc_final: 0.2659 (mtm) REVERT: be 13 ARG cc_start: 0.7330 (tpp80) cc_final: 0.6898 (mtp85) REVERT: bh 13 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7437 (mtt90) REVERT: bp 11 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6871 (mt-10) outliers start: 63 outliers final: 36 residues processed: 603 average time/residue: 1.6201 time to fit residues: 1205.7411 Evaluate side-chains 614 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 567 time to evaluate : 3.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 17 LEU Chi-restraints excluded: chain AB residue 42 LEU Chi-restraints excluded: chain AC residue 48 THR Chi-restraints excluded: chain AE residue 48 THR Chi-restraints excluded: chain AF residue 3 ARG Chi-restraints excluded: chain AK residue 15 SER Chi-restraints excluded: chain AK residue 48 THR Chi-restraints excluded: chain AO residue 15 SER Chi-restraints excluded: chain AQ residue 43 LYS Chi-restraints excluded: chain AU residue 42 LEU Chi-restraints excluded: chain AX residue 6 MET Chi-restraints excluded: chain BB residue 19 MET Chi-restraints excluded: chain BC residue 31 SER Chi-restraints excluded: chain BD residue 8 THR Chi-restraints excluded: chain BD residue 39 SER Chi-restraints excluded: chain BE residue 24 LEU Chi-restraints excluded: chain BF residue 18 TYR Chi-restraints excluded: chain BH residue 7 MET Chi-restraints excluded: chain BI residue 21 THR Chi-restraints excluded: chain BI residue 39 SER Chi-restraints excluded: chain BT residue 24 LEU Chi-restraints excluded: chain BT residue 31 SER Chi-restraints excluded: chain BU residue 24 LEU Chi-restraints excluded: chain BU residue 39 SER Chi-restraints excluded: chain C1 residue 107 THR Chi-restraints excluded: chain C1 residue 135 ASN Chi-restraints excluded: chain C1 residue 154 SER Chi-restraints excluded: chain C2 residue 49 VAL Chi-restraints excluded: chain C2 residue 74 ASP Chi-restraints excluded: chain L residue 213 ASN Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain M residue 315 GLU Chi-restraints excluded: chain ab residue 3 ARG Chi-restraints excluded: chain ab residue 6 LEU Chi-restraints excluded: chain ab residue 49 ASP Chi-restraints excluded: chain ac residue 49 ASP Chi-restraints excluded: chain ad residue 12 ARG Chi-restraints excluded: chain af residue 56 SER Chi-restraints excluded: chain ah residue 36 GLN Chi-restraints excluded: chain ak residue 39 SER Chi-restraints excluded: chain an residue 64 MET Chi-restraints excluded: chain bc residue 13 ARG Chi-restraints excluded: chain bh residue 13 ARG Chi-restraints excluded: chain bi residue 24 LEU Chi-restraints excluded: chain bl residue 8 THR Chi-restraints excluded: chain bm residue 8 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 266 optimal weight: 2.9990 chunk 429 optimal weight: 5.9990 chunk 262 optimal weight: 7.9990 chunk 203 optimal weight: 0.7980 chunk 298 optimal weight: 7.9990 chunk 450 optimal weight: 8.9990 chunk 414 optimal weight: 1.9990 chunk 358 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 276 optimal weight: 0.8980 chunk 219 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 157 GLN H2 10 ASN aa 36 GLN ad 50 GLN ah 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 58313 Z= 0.198 Angle : 1.735 23.553 80224 Z= 0.590 Chirality : 0.036 0.217 8178 Planarity : 0.004 0.064 9122 Dihedral : 16.741 179.768 18034 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.48 % Allowed : 13.30 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.94 (0.12), residues: 4858 helix: 3.40 (0.08), residues: 3222 sheet: -0.64 (0.89), residues: 28 loop : 1.04 (0.17), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 270 HIS 0.011 0.001 HIS M 181 PHE 0.023 0.001 PHEBO 15 TYR 0.017 0.001 TYR L 164 ARG 0.014 0.000 ARGbi 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9716 Ramachandran restraints generated. 4858 Oldfield, 0 Emsley, 4858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 571 time to evaluate : 3.888 Fit side-chains revert: symmetry clash REVERT: AA 28 MET cc_start: 0.9283 (mmm) cc_final: 0.8894 (mmm) REVERT: AB 42 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8326 (tp) REVERT: AD 6 MET cc_start: 0.8035 (mtm) cc_final: 0.7635 (mtm) REVERT: AF 3 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6968 (ttm170) REVERT: AF 19 SER cc_start: 0.8853 (m) cc_final: 0.8644 (p) REVERT: AK 14 MET cc_start: 0.8829 (mmm) cc_final: 0.8350 (mmm) REVERT: AL 9 ASP cc_start: 0.7339 (t0) cc_final: 0.6899 (t70) REVERT: AN 15 SER cc_start: 0.8803 (t) cc_final: 0.8587 (t) REVERT: AQ 43 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8222 (tttt) REVERT: AR 3 ARG cc_start: 0.7725 (mpp80) cc_final: 0.7509 (mtt90) REVERT: AT 8 THR cc_start: 0.8877 (p) cc_final: 0.8656 (p) REVERT: AT 42 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8436 (tp) REVERT: AU 9 ASP cc_start: 0.8137 (t0) cc_final: 0.7868 (t0) REVERT: AU 42 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8510 (tp) REVERT: AV 6 MET cc_start: 0.8704 (mtp) cc_final: 0.8503 (mtp) REVERT: AW 3 ARG cc_start: 0.8088 (mtp-110) cc_final: 0.7755 (mtp85) REVERT: AX 45 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8404 (ttpt) REVERT: BD 7 MET cc_start: 0.7552 (tpp) cc_final: 0.6990 (tpp) REVERT: BF 18 TYR cc_start: 0.6802 (OUTLIER) cc_final: 0.6523 (m-10) REVERT: BG 11 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7703 (pt0) REVERT: BK 10 GLU cc_start: 0.7342 (tp30) cc_final: 0.7041 (tp30) REVERT: BL 14 ARG cc_start: 0.7972 (ttp-110) cc_final: 0.7772 (mtm-85) REVERT: BN 19 MET cc_start: 0.7647 (mmm) cc_final: 0.7327 (tpp) REVERT: BO 15 PHE cc_start: 0.8210 (t80) cc_final: 0.7908 (t80) REVERT: BP 11 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7771 (mt-10) REVERT: BQ 8 THR cc_start: 0.7819 (p) cc_final: 0.7557 (p) REVERT: BT 10 GLU cc_start: 0.7023 (tp30) cc_final: 0.6759 (tp30) REVERT: C 82 MET cc_start: 0.9071 (mmt) cc_final: 0.7806 (mmt) REVERT: C 113 LYS cc_start: 0.8152 (mttp) cc_final: 0.7945 (mptm) REVERT: C 205 MET cc_start: 0.9310 (mmt) cc_final: 0.9004 (mmt) REVERT: C2 43 GLU cc_start: 0.7950 (pt0) cc_final: 0.7738 (mt-10) REVERT: C2 74 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7783 (m-30) REVERT: H2 108 GLU cc_start: 0.5996 (mm-30) cc_final: 0.5608 (tp30) REVERT: M 315 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7273 (pm20) REVERT: aa 14 MET cc_start: 0.6713 (ttp) cc_final: 0.6435 (ttt) REVERT: ac 11 ARG cc_start: 0.7609 (ptp-170) cc_final: 0.7124 (ptt90) REVERT: ad 12 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8186 (ptt180) REVERT: ah 12 ARG cc_start: 0.7041 (mtm110) cc_final: 0.6818 (mmp-170) REVERT: ah 36 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7935 (mp10) REVERT: ai 3 ARG cc_start: 0.7641 (ttp-170) cc_final: 0.7283 (ttp-170) REVERT: ai 7 MET cc_start: 0.7916 (mtp) cc_final: 0.7691 (mtp) REVERT: aj 9 ASP cc_start: 0.8088 (t0) cc_final: 0.7795 (t0) REVERT: aj 11 ARG cc_start: 0.7427 (mtt-85) cc_final: 0.6965 (mtm-85) REVERT: aj 12 ARG cc_start: 0.8024 (mtt-85) cc_final: 0.6733 (ptt90) REVERT: ak 11 ARG cc_start: 0.7408 (mtp-110) cc_final: 0.7127 (mtm180) REVERT: am 12 ARG cc_start: 0.6963 (mmm160) cc_final: 0.6563 (mmm160) REVERT: an 64 MET cc_start: 0.3359 (OUTLIER) cc_final: 0.2658 (mtm) REVERT: be 13 ARG cc_start: 0.7335 (tpp80) cc_final: 0.6898 (mtp85) REVERT: bh 13 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7502 (mtt90) REVERT: bk 13 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7290 (ppt170) REVERT: bp 11 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6852 (mt-10) outliers start: 59 outliers final: 37 residues processed: 601 average time/residue: 1.6507 time to fit residues: 1220.7705 Evaluate side-chains 612 residues out of total 3999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 561 time to evaluate : 3.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 17 LEU Chi-restraints excluded: chain AB residue 42 LEU Chi-restraints excluded: chain AC residue 48 THR Chi-restraints excluded: chain AE residue 48 THR Chi-restraints excluded: chain AF residue 3 ARG Chi-restraints excluded: chain AK residue 15 SER Chi-restraints excluded: chain AK residue 48 THR Chi-restraints excluded: chain AO residue 15 SER Chi-restraints excluded: chain AQ residue 43 LYS Chi-restraints excluded: chain AT residue 42 LEU Chi-restraints excluded: chain AU residue 42 LEU Chi-restraints excluded: chain AX residue 6 MET Chi-restraints excluded: chain AX residue 45 LYS Chi-restraints excluded: chain BB residue 19 MET Chi-restraints excluded: chain BC residue 31 SER Chi-restraints excluded: chain BD residue 8 THR Chi-restraints excluded: chain BD residue 39 SER Chi-restraints excluded: chain BE residue 24 LEU Chi-restraints excluded: chain BF residue 18 TYR Chi-restraints excluded: chain BI residue 21 THR Chi-restraints excluded: chain BI residue 39 SER Chi-restraints excluded: chain BT residue 24 LEU Chi-restraints excluded: chain BT residue 31 SER Chi-restraints excluded: chain BU residue 24 LEU Chi-restraints excluded: chain BU residue 39 SER Chi-restraints excluded: chain BW residue 7 MET Chi-restraints excluded: chain C1 residue 107 THR Chi-restraints excluded: chain C1 residue 135 ASN Chi-restraints excluded: chain C2 residue 49 VAL Chi-restraints excluded: chain C2 residue 74 ASP Chi-restraints excluded: chain H2 residue 159 ASP Chi-restraints excluded: chain L residue 213 ASN Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain M residue 315 GLU Chi-restraints excluded: chain ab residue 3 ARG Chi-restraints excluded: chain ab residue 6 LEU Chi-restraints excluded: chain ab residue 49 ASP Chi-restraints excluded: chain ac residue 49 ASP Chi-restraints excluded: chain ad residue 12 ARG Chi-restraints excluded: chain ad residue 39 SER Chi-restraints excluded: chain af residue 56 SER Chi-restraints excluded: chain ah residue 36 GLN Chi-restraints excluded: chain ak residue 39 SER Chi-restraints excluded: chain an residue 64 MET Chi-restraints excluded: chain bc residue 13 ARG Chi-restraints excluded: chain bh residue 13 ARG Chi-restraints excluded: chain bi residue 24 LEU Chi-restraints excluded: chain bk residue 13 ARG Chi-restraints excluded: chain bl residue 8 THR Chi-restraints excluded: chain bm residue 8 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 284 optimal weight: 3.9990 chunk 381 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 330 optimal weight: 0.2980 chunk 52 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 359 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 368 optimal weight: 0.0770 chunk 45 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 overall best weight: 1.4742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1 157 GLN H2 10 ASN M 311 GLN aa 36 GLN ad 50 GLN ah 50 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.102402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.075903 restraints weight = 92183.719| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.29 r_work: 0.2834 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 58313 Z= 0.197 Angle : 1.726 23.488 80224 Z= 0.587 Chirality : 0.036 0.217 8178 Planarity : 0.004 0.065 9122 Dihedral : 16.687 179.771 18034 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.45 % Allowed : 13.60 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.88 (0.12), residues: 4858 helix: 3.35 (0.08), residues: 3242 sheet: -0.64 (0.90), residues: 28 loop : 1.01 (0.17), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 270 HIS 0.011 0.001 HIS L 153 PHE 0.026 0.001 PHEBO 15 TYR 0.017 0.001 TYR L 164 ARG 0.014 0.000 ARGbi 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19013.61 seconds wall clock time: 329 minutes 28.88 seconds (19768.88 seconds total)