Starting phenix.real_space_refine on Mon Mar 25 04:14:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy2_32192/03_2024/7vy2_32192_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy2_32192/03_2024/7vy2_32192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy2_32192/03_2024/7vy2_32192.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy2_32192/03_2024/7vy2_32192.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy2_32192/03_2024/7vy2_32192_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy2_32192/03_2024/7vy2_32192_updated.pdb" } resolution = 2.75 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= 1.000 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 2 7.16 5 P 52 5.49 5 Mg 64 5.21 5 S 171 5.16 5 C 32638 2.51 5 N 6181 2.21 5 O 7184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 5": "OD1" <-> "OD2" Residue "K TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 229": "OE1" <-> "OE2" Residue "g TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "02 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "03 TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "06 TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "07 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "08 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "08 TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 46292 Number of models: 1 Model: "" Number of chains: 131 Chain: "L" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2233 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2437 Classifications: {'peptide': 306} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 293} Chain: "H" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1884 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 224} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 386 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} 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: "B" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "D" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "F" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: "G" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "I" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: "J" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "K" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: "N" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "O" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 453 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Q" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: "R" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 347 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 448 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'FME:plan-2': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "T" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "V" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 451 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'FME:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "W" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 347 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: "Z" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "1" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: "2" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "3" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: "4" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "5" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "6" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 332 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "7" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 415 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "8" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 296 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "X" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 478 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain: "U" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 353 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain: "l" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2233 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "m" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2437 Classifications: {'peptide': 306} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 293} Chain: "h" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1884 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 224} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "a" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 386 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} 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: "b" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "d" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "f" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: "g" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "i" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: "j" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "k" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: "n" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "o" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 453 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "q" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: "r" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 347 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "s" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 454 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "t" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "v" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'FME:plan-2': 1, 'FME:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "w" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 347 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "y" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'FME:plan-2': 1, 'FME:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "z" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "01" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: "02" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "03" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: "04" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "05" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "06" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 332 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "07" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 415 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "08" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 296 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "x" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 456 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 54} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "u" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 71 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 12} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "L" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 482 Unusual residues: {'BCL': 2, 'BPH': 1, 'LMT': 2, 'PGV': 4, 'U10': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 104 Planarities with less than four sites: {'PGV:plan-3': 3, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 51 Chain: "M" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 535 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'CDL': 1, 'LMT': 4, 'PGV': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 185 Unusual residues: {'LMT': 1, 'PGV': 3, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 138 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'BCL': 1, 'U10': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 1, 'PGV': 1, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 143 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 210 Unusual residues: {'BCL': 1, 'CDL': 1, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 161 Unusual residues: {'BCL': 1, 'LMT': 1, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 151 Unusual residues: {'BCL': 1, 'CDL': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 57 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-1': 1} Unresolved non-hydrogen planarities: 6 Chain: "Z" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "2" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'BCL': 1, 'SPO': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "3" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 170 Unusual residues: {'BCL': 1, 'LMT': 2, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "4" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 141 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "6" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 60 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 151 Unusual residues: {'CDL': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 9 Chain: "U" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 102 Unusual residues: {'LMT': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "l" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 345 Unusual residues: {'BCL': 1, 'BPH': 1, 'PGV': 4, 'U10': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 104 Planarities with less than four sites: {'PGV:plan-3': 3, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 55 Chain: "m" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 634 Unusual residues: {' FE': 1, 'BCL': 3, 'BPH': 1, 'CDL': 2, 'LMT': 2, 'PGV': 2, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 2, 'CDL:plan-1': 1, 'U10:plan-10': 1} Unresolved non-hydrogen planarities: 12 Chain: "h" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 234 Unusual residues: {'CDL': 1, 'LMT': 2, 'PGV': 2, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "a" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 3 Chain: "b" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'BCL': 1, 'U10': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 27 Chain: "e" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 274 Unusual residues: {'BCL': 1, 'PGV': 2, 'PTY': 1, 'SPO': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "g" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "i" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 127 Unusual residues: {'BCL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 10 Chain: "j" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 149 Unusual residues: {'BCL': 1, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "n" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "o" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "q" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 166 Unusual residues: {'BCL': 1, 'LMT': 1, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "s" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 205 Unusual residues: {'BCL': 1, 'LMT': 2, 'SPO': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 5 Chain: "t" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "w" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "y" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 211 Unusual residues: {'BCL': 1, 'CDL': 1, 'LDA': 1, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'CDL:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "z" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "01" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "02" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "03" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 128 Unusual residues: {'BCL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "04" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "05" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "06" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "07" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "08" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "x" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'CDL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PGV:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 24.33, per 1000 atoms: 0.53 Number of scatterers: 46292 At special positions: 0 Unit cell: (220.58, 163.18, 106.6, 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 2 26.01 S 171 16.00 P 52 15.00 Mg 64 11.99 O 7184 8.00 N 6181 7.00 C 32638 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=60, symmetry=0 Number of additional bonds: simple=60, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.92 Conformation dependent library (CDL) restraints added in 7.0 seconds 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8434 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 192 helices and 10 sheets defined 65.1% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.99 Creating SS restraints... 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 33 through 56 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 84 through 111 Processing helix chain 'L' and resid 116 through 132 removed outlier: 3.622A 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 162 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 247 removed outlier: 3.777A pdb=" N HIS L 230 " --> pdb=" O THR L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 267 removed outlier: 3.670A pdb=" N TRP L 266 " --> pdb=" O TRP L 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 28 No H-bonds generated for 'chain 'M' and resid 26 through 28' Processing helix chain 'M' and resid 37 through 41 Processing helix chain 'M' and resid 55 through 77 Processing helix chain 'M' and resid 82 through 87 Processing helix chain 'M' and resid 99 through 101 No H-bonds generated for 'chain 'M' and resid 99 through 101' 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 161 removed outlier: 3.792A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 168 Processing helix chain 'M' and resid 171 through 173 No H-bonds generated for 'chain 'M' and resid 171 through 173' Processing helix chain 'M' and resid 179 through 192 removed outlier: 3.558A pdb=" N LEU M 183 " --> pdb=" O ILE M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 198 No H-bonds generated for 'chain 'M' and resid 196 through 198' Processing helix chain 'M' and resid 200 through 225 Processing helix chain 'M' and resid 227 through 229 No H-bonds generated for 'chain 'M' and resid 227 through 229' Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 243 through 256 removed outlier: 3.595A pdb=" N TRP M 252 " --> pdb=" O ALA M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 286 removed outlier: 3.911A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 301 Processing helix chain 'H' and resid 12 through 35 Processing helix chain 'H' and resid 104 through 107 No H-bonds generated for 'chain 'H' and resid 104 through 107' Processing helix chain 'H' and resid 110 through 112 No H-bonds generated for 'chain 'H' and resid 110 through 112' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 210 through 215 removed outlier: 3.828A pdb=" N PHE H 213 " --> pdb=" O SER H 210 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 243 removed outlier: 3.628A pdb=" N GLY H 240 " --> pdb=" O TYR H 236 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 247 No H-bonds generated for 'chain 'H' and resid 245 through 247' Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 13 through 37 removed outlier: 4.226A pdb=" N VAL A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 44 Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 13 through 37 removed outlier: 3.545A pdb=" N VAL D 18 " --> pdb=" O ARG D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'E' and resid 13 through 44 Processing helix chain 'F' and resid 4 through 9 Processing helix chain 'F' and resid 13 through 37 Processing helix chain 'F' and resid 43 through 50 Processing helix chain 'G' and resid 13 through 44 removed outlier: 3.514A pdb=" N GLN G 17 " --> pdb=" O ASP G 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 9 Processing helix chain 'I' and resid 13 through 37 Processing helix chain 'I' and resid 43 through 51 Processing helix chain 'J' and resid 13 through 44 Processing helix chain 'K' and resid 3 through 9 Processing helix chain 'K' and resid 13 through 37 Processing helix chain 'K' and resid 39 through 41 No H-bonds generated for 'chain 'K' and resid 39 through 41' Processing helix chain 'K' and resid 43 through 50 Processing helix chain 'N' and resid 13 through 44 Processing helix chain 'O' and resid 4 through 9 Processing helix chain 'O' and resid 13 through 37 Processing helix chain 'O' and resid 39 through 41 No H-bonds generated for 'chain 'O' and resid 39 through 41' Processing helix chain 'O' and resid 43 through 51 Processing helix chain 'P' and resid 15 through 44 Processing helix chain 'Q' and resid 5 through 9 Processing helix chain 'Q' and resid 13 through 37 removed outlier: 3.521A pdb=" N VAL Q 18 " --> pdb=" O ARG Q 14 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 50 Processing helix chain 'R' and resid 13 through 44 Processing helix chain 'S' and resid 4 through 9 Processing helix chain 'S' and resid 13 through 37 Processing helix chain 'S' and resid 43 through 50 Processing helix chain 'T' and resid 14 through 44 Processing helix chain 'V' and resid 4 through 10 Processing helix chain 'V' and resid 13 through 37 Processing helix chain 'V' and resid 43 through 50 Processing helix chain 'W' and resid 13 through 44 Processing helix chain 'Y' and resid 4 through 7 removed outlier: 3.540A pdb=" N ILE Y 7 " --> pdb=" O PHE Y 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 4 through 7' Processing helix chain 'Y' and resid 13 through 37 Processing helix chain 'Y' and resid 39 through 41 No H-bonds generated for 'chain 'Y' and resid 39 through 41' Processing helix chain 'Y' and resid 43 through 50 Processing helix chain 'Z' and resid 13 through 44 Processing helix chain '1' and resid 4 through 9 removed outlier: 3.814A pdb=" N TRP 1 8 " --> pdb=" O TYR 1 5 " (cutoff:3.500A) Processing helix chain '1' and resid 13 through 37 removed outlier: 3.680A pdb=" N VAL 1 18 " --> pdb=" O ARG 1 14 " (cutoff:3.500A) Processing helix chain '1' and resid 43 through 51 Processing helix chain '2' and resid 13 through 44 Processing helix chain '3' and resid 5 through 10 Processing helix chain '3' and resid 13 through 37 Processing helix chain '3' and resid 43 through 51 Processing helix chain '4' and resid 13 through 44 Processing helix chain '5' and resid 4 through 8 Processing helix chain '5' and resid 13 through 37 Processing helix chain '5' and resid 43 through 50 Processing helix chain '6' and resid 13 through 44 Processing helix chain '7' and resid 5 through 10 removed outlier: 3.776A pdb=" N TRP 7 8 " --> pdb=" O TYR 7 5 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE 7 10 " --> pdb=" O ILE 7 7 " (cutoff:3.500A) Processing helix chain '7' and resid 13 through 37 Processing helix chain '7' and resid 43 through 50 Processing helix chain '8' and resid 13 through 44 Processing helix chain 'X' and resid 15 through 53 Processing helix chain 'U' and resid 6 through 29 Processing helix chain 'U' and resid 32 through 48 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 33 through 56 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 84 through 111 Processing helix chain 'l' and resid 116 through 132 Processing helix chain 'l' and resid 134 through 138 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 153 through 164 removed outlier: 4.187A pdb=" N TYR l 164 " --> pdb=" O THR l 160 " (cutoff:3.500A) Processing helix chain 'l' and resid 167 through 169 No H-bonds generated for 'chain 'l' and resid 167 through 169' Processing helix chain 'l' and resid 171 through 198 Processing helix chain 'l' and resid 209 through 220 Processing helix chain 'l' and resid 226 through 249 removed outlier: 3.847A pdb=" N HIS l 230 " --> pdb=" O THR l 226 " (cutoff:3.500A) Processing helix chain 'l' and resid 259 through 267 removed outlier: 3.703A pdb=" N TRP l 265 " --> pdb=" O TRP l 262 " (cutoff:3.500A) Processing helix chain 'm' and resid 37 through 40 No H-bonds generated for 'chain 'm' and resid 37 through 40' Processing helix chain 'm' and resid 54 through 77 Processing helix chain 'm' and resid 82 through 87 Processing helix chain 'm' and resid 99 through 101 No H-bonds generated for 'chain 'm' and resid 99 through 101' 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 161 removed outlier: 3.665A pdb=" N ALA m 153 " --> pdb=" O ALA m 149 " (cutoff:3.500A) Processing helix chain 'm' and resid 163 through 168 Processing helix chain 'm' and resid 171 through 173 No H-bonds generated for 'chain 'm' and resid 171 through 173' Processing helix chain 'm' and resid 179 through 192 removed outlier: 3.741A pdb=" N LEU m 183 " --> pdb=" O ILE m 179 " (cutoff:3.500A) Processing helix chain 'm' and resid 196 through 198 No H-bonds generated for 'chain 'm' and resid 196 through 198' Processing helix chain 'm' and resid 200 through 225 Processing helix chain 'm' and resid 227 through 229 No H-bonds generated for 'chain 'm' and resid 227 through 229' Processing helix chain 'm' and resid 234 through 239 Processing helix chain 'm' and resid 243 through 256 Processing helix chain 'm' and resid 264 through 286 removed outlier: 3.856A pdb=" N VAL m 276 " --> pdb=" O MET m 272 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR m 277 " --> pdb=" O ALA m 273 " (cutoff:3.500A) Processing helix chain 'm' and resid 294 through 301 Processing helix chain 'h' and resid 12 through 36 removed outlier: 3.596A pdb=" N MET h 36 " --> pdb=" O GLN h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 104 through 107 No H-bonds generated for 'chain 'h' and resid 104 through 107' Processing helix chain 'h' and resid 110 through 112 No H-bonds generated for 'chain 'h' and resid 110 through 112' Processing helix chain 'h' and resid 193 through 195 No H-bonds generated for 'chain 'h' and resid 193 through 195' Processing helix chain 'h' and resid 210 through 212 No H-bonds generated for 'chain 'h' and resid 210 through 212' Processing helix chain 'h' and resid 227 through 243 removed outlier: 3.916A pdb=" N LEU h 241 " --> pdb=" O VAL h 237 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET h 242 " --> pdb=" O ALA h 238 " (cutoff:3.500A) Processing helix chain 'a' and resid 3 through 9 Processing helix chain 'a' and resid 13 through 37 removed outlier: 4.597A pdb=" N VAL a 18 " --> pdb=" O ARG a 14 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 44 Processing helix chain 'd' and resid 3 through 9 Processing helix chain 'd' and resid 13 through 37 removed outlier: 4.241A pdb=" N VAL d 18 " --> pdb=" O ARG d 14 " (cutoff:3.500A) Processing helix chain 'd' and resid 43 through 50 Processing helix chain 'e' and resid 13 through 44 Processing helix chain 'f' and resid 3 through 9 Processing helix chain 'f' and resid 13 through 37 Processing helix chain 'f' and resid 43 through 50 Processing helix chain 'g' and resid 13 through 44 Processing helix chain 'i' and resid 5 through 9 Processing helix chain 'i' and resid 13 through 37 Processing helix chain 'i' and resid 43 through 51 Processing helix chain 'j' and resid 13 through 44 Processing helix chain 'k' and resid 3 through 9 Processing helix chain 'k' and resid 13 through 37 Processing helix chain 'k' and resid 43 through 50 Processing helix chain 'n' and resid 13 through 44 Processing helix chain 'o' and resid 3 through 10 Processing helix chain 'o' and resid 13 through 37 Processing helix chain 'o' and resid 43 through 50 Processing helix chain 'p' and resid 15 through 44 Processing helix chain 'q' and resid 5 through 9 Processing helix chain 'q' and resid 13 through 37 Processing helix chain 'q' and resid 43 through 50 Processing helix chain 'r' and resid 13 through 44 Processing helix chain 's' and resid 5 through 9 Processing helix chain 's' and resid 13 through 37 Processing helix chain 's' and resid 43 through 50 Processing helix chain 't' and resid 13 through 44 Processing helix chain 'v' and resid 4 through 9 removed outlier: 3.842A pdb=" N ILE v 7 " --> pdb=" O PHE v 4 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP v 8 " --> pdb=" O TYR v 5 " (cutoff:3.500A) Processing helix chain 'v' and resid 13 through 37 Processing helix chain 'v' and resid 43 through 50 Processing helix chain 'w' and resid 13 through 44 removed outlier: 4.213A pdb=" N VAL w 22 " --> pdb=" O GLU w 18 " (cutoff:3.500A) Processing helix chain 'y' and resid 3 through 10 removed outlier: 3.813A pdb=" N LYS y 6 " --> pdb=" O LYS y 3 " (cutoff:3.500A) Processing helix chain 'y' and resid 13 through 37 Processing helix chain 'y' and resid 43 through 50 Processing helix chain 'z' and resid 13 through 44 Processing helix chain '01' and resid 4 through 9 Processing helix chain '01' and resid 13 through 37 Processing helix chain '01' and resid 43 through 50 Processing helix chain '02' and resid 13 through 44 removed outlier: 3.531A pdb=" N LEU02 29 " --> pdb=" O SER02 25 " (cutoff:3.500A) Processing helix chain '03' and resid 4 through 10 Processing helix chain '03' and resid 13 through 37 Processing helix chain '03' and resid 43 through 51 Processing helix chain '04' and resid 13 through 44 Processing helix chain '05' and resid 4 through 9 Processing helix chain '05' and resid 13 through 37 Processing helix chain '05' and resid 43 through 51 Processing helix chain '06' and resid 13 through 44 Processing helix chain '07' and resid 5 through 10 removed outlier: 3.887A pdb=" N TRP07 8 " --> pdb=" O TYR07 5 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE07 10 " --> pdb=" O ILE07 7 " (cutoff:3.500A) Processing helix chain '07' and resid 13 through 37 Processing helix chain '07' and resid 43 through 51 Processing helix chain '08' and resid 13 through 44 Processing helix chain 'x' and resid 15 through 54 removed outlier: 3.502A pdb=" N ARG x 20 " --> pdb=" O LYS x 16 " (cutoff:3.500A) Processing helix chain 'u' and resid 56 through 60 Processing sheet with id= A, first strand: chain 'L' and resid 24 through 26 removed outlier: 3.641A pdb=" N PHE L 24 " --> pdb=" O VAL L 31 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 62 through 65 Processing sheet with id= C, first strand: chain 'H' and resid 87 through 89 Processing sheet with id= D, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.646A pdb=" N GLU H 180 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE H 167 " --> pdb=" O PHE H 178 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE H 178 " --> pdb=" O ILE H 167 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 196 through 198 removed outlier: 7.496A pdb=" N VAL H 205 " --> pdb=" O PRO H 152 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ARG H 154 " --> pdb=" O VAL H 205 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY H 162 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'l' and resid 24 through 26 removed outlier: 3.681A pdb=" N PHE l 24 " --> pdb=" O VAL l 31 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'h' and resid 62 through 65 Processing sheet with id= H, first strand: chain 'h' and resid 87 through 89 Processing sheet with id= I, first strand: chain 'h' and resid 131 through 133 removed outlier: 6.788A pdb=" N GLU h 180 " --> pdb=" O VAL h 165 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE h 167 " --> pdb=" O PHE h 178 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE h 178 " --> pdb=" O ILE h 167 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'h' and resid 202 through 204 removed outlier: 3.774A pdb=" N GLY h 162 " --> pdb=" O VAL h 153 " (cutoff:3.500A) 2241 hydrogen bonds defined for protein. 6432 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.50 Time building geometry restraints manager: 21.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.37: 13568 1.37 - 1.54: 33452 1.54 - 1.71: 384 1.71 - 1.88: 332 1.88 - 2.05: 256 Bond restraints: 47992 Sorted by residual: bond pdb=" CA7 CDL m 410 " pdb=" OA8 CDL m 410 " ideal model delta sigma weight residual 1.334 1.458 -0.124 1.10e-02 8.26e+03 1.28e+02 bond pdb=" CA7 CDL y 102 " pdb=" OA8 CDL y 102 " ideal model delta sigma weight residual 1.334 1.458 -0.124 1.10e-02 8.26e+03 1.27e+02 bond pdb=" CA7 CDL h 805 " pdb=" OA8 CDL h 805 " ideal model delta sigma weight residual 1.334 1.457 -0.123 1.10e-02 8.26e+03 1.26e+02 bond pdb=" CA7 CDL X 101 " pdb=" OA8 CDL X 101 " ideal model delta sigma weight residual 1.334 1.456 -0.122 1.10e-02 8.26e+03 1.23e+02 bond pdb=" CA7 CDL K 401 " pdb=" OA8 CDL K 401 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.22e+02 ... (remaining 47987 not shown) Histogram of bond angle deviations from ideal: 83.17 - 102.38: 844 102.38 - 121.58: 54369 121.58 - 140.79: 10206 140.79 - 160.00: 74 160.00 - 179.20: 122 Bond angle restraints: 65615 Sorted by residual: angle pdb=" C1D BCL f 102 " pdb=" C2D BCL f 102 " pdb=" CMD BCL f 102 " ideal model delta sigma weight residual 125.57 140.61 -15.04 1.83e+00 2.99e-01 6.77e+01 angle pdb=" C1D BCL a 101 " pdb=" C2D BCL a 101 " pdb=" CMD BCL a 101 " ideal model delta sigma weight residual 125.57 140.05 -14.48 1.83e+00 2.99e-01 6.27e+01 angle pdb=" C1D BCL d 101 " pdb=" C2D BCL d 101 " pdb=" CMD BCL d 101 " ideal model delta sigma weight residual 125.57 139.82 -14.24 1.83e+00 2.99e-01 6.07e+01 angle pdb=" C1D BCL b 101 " pdb=" C2D BCL b 101 " pdb=" CMD BCL b 101 " ideal model delta sigma weight residual 125.57 139.76 -14.19 1.83e+00 2.99e-01 6.02e+01 angle pdb=" C1D BCL o 101 " pdb=" C2D BCL o 101 " pdb=" CMD BCL o 101 " ideal model delta sigma weight residual 125.57 139.76 -14.19 1.83e+00 2.99e-01 6.02e+01 ... (remaining 65610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 25320 35.98 - 71.96: 1307 71.96 - 107.94: 232 107.94 - 143.92: 67 143.92 - 179.89: 18 Dihedral angle restraints: 26944 sinusoidal: 13827 harmonic: 13117 Sorted by residual: dihedral pdb=" C1 BCL a 101 " pdb=" CGA BCL a 101 " pdb=" O2A BCL a 101 " pdb=" CBA BCL a 101 " ideal model delta sinusoidal sigma weight residual 180.00 73.33 106.67 1 6.00e+00 2.78e-02 3.43e+02 dihedral pdb=" C1 BCL M 401 " pdb=" C2 BCL M 401 " pdb=" C3 BCL M 401 " pdb=" C5 BCL M 401 " ideal model delta sinusoidal sigma weight residual -180.00 -0.29 -179.71 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL m 402 " pdb=" C2 BCL m 402 " pdb=" C3 BCL m 402 " pdb=" C5 BCL m 402 " ideal model delta sinusoidal sigma weight residual -180.00 -0.94 -179.06 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 26941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 5305 0.064 - 0.128: 895 0.128 - 0.192: 206 0.192 - 0.256: 41 0.256 - 0.320: 20 Chirality restraints: 6467 Sorted by residual: chirality pdb=" C3C BPH l 302 " pdb=" C2C BPH l 302 " pdb=" C4C BPH l 302 " pdb=" CAC BPH l 302 " both_signs ideal model delta sigma weight residual False 2.83 2.52 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" C05 PGV h 801 " pdb=" C04 PGV h 801 " pdb=" C06 PGV h 801 " pdb=" O05 PGV h 801 " both_signs ideal model delta sigma weight residual False 2.29 2.59 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C05 PGV q 102 " pdb=" C04 PGV q 102 " pdb=" C06 PGV q 102 " pdb=" O05 PGV q 102 " both_signs ideal model delta sigma weight residual False 2.29 2.59 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 6464 not shown) Planarity restraints: 7851 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL Z 101 " 0.371 3.00e-02 1.11e+03 3.06e-01 5.21e+02 pdb=" CBA BCL Z 101 " 0.157 3.00e-02 1.11e+03 pdb=" CGA BCL Z 101 " -0.083 3.00e-02 1.11e+03 pdb=" O1A BCL Z 101 " 0.094 3.00e-02 1.11e+03 pdb=" O2A BCL Z 101 " -0.539 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL a 101 " -0.347 3.00e-02 1.11e+03 2.92e-01 4.73e+02 pdb=" CBA BCL a 101 " -0.033 3.00e-02 1.11e+03 pdb=" CGA BCL a 101 " 0.062 3.00e-02 1.11e+03 pdb=" O1A BCL a 101 " -0.195 3.00e-02 1.11e+03 pdb=" O2A BCL a 101 " 0.512 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BCL 7 101 " -0.230 3.10e-02 1.04e+03 2.86e-01 4.27e+02 pdb=" C4C BCL 7 101 " -0.199 3.10e-02 1.04e+03 pdb=" CHC BCL 7 101 " -0.056 3.10e-02 1.04e+03 pdb=" CHD BCL 7 101 " -0.071 3.10e-02 1.04e+03 pdb=" NC BCL 7 101 " 0.556 3.10e-02 1.04e+03 ... (remaining 7848 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 298 2.53 - 3.13: 33115 3.13 - 3.72: 77205 3.72 - 4.31: 114144 4.31 - 4.90: 183351 Nonbonded interactions: 408113 Sorted by model distance: nonbonded pdb=" OE2 GLU m 234 " pdb="FE FE m 405 " model vdw 1.943 2.260 nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 404 " model vdw 1.964 2.260 nonbonded pdb=" CE1 HIS e 38 " pdb="MG BCL e 102 " model vdw 1.989 3.130 nonbonded pdb=" O ALA L 78 " pdb=" O3' LMT L 305 " model vdw 2.026 2.440 nonbonded pdb=" CE1 HIS E 38 " pdb="MG BCL E 101 " model vdw 2.103 3.130 ... (remaining 408108 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 '01' and ((resid 4 through 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain '03' and ((resid 4 through 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain '05' and ((resid 4 through 6 and (name N or name CA or name C or name O o \ r name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain '07' and (resid 4 through 10 or (resid 11 and (name N or name CA or name \ C or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or nam \ e CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain '1' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain '3' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain '5' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain '7' and (resid 4 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain 'D' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 54)) selection = (chain 'F' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'I' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'K' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'O' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'Q' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'S' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 53 or (resid 54 and (name N or name \ CA or name C or name O or name CB )))) selection = (chain 'V' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 53 or (resid 54 and (name N or name \ CA or name C or name O or name CB )))) selection = (chain 'Y' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'd' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 54)) selection = (chain 'f' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'i' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'k' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'o' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'q' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 's' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'v' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'y' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 and (name N or name \ CA or name C or name O or name CB )) or resid 15 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain '02' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or nam \ e CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '04' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or nam \ e CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '06' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or nam \ e CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '08' and resid 11 through 48) selection = (chain '2' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '4' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '6' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain '8' and resid 11 through 48) selection = (chain 'B' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'E' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'G' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'J' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'N' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'P' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'R' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'T' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'W' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'Z' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'b' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'e' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'g' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'j' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'n' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'p' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'r' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 't' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'w' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) selection = (chain 'z' and ((resid 11 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 48)) } ncs_group { reference = (chain 'A' and resid 1 through 45) selection = (chain 'a' and resid 1 through 45) } ncs_group { reference = (chain 'H' and (resid 1 through 248 or resid 801 or (resid 802 and (name C1 or n \ ame C1' or name C10 or name C11 or name C12 or name C1B or name C2 or name C2' o \ r name C2B or name C3 or name C3' or name C4 or name C4' or name C5 or name C5' \ or name C6 or name C6' or name C7 or name C8 or name C9 or name O1' or name O1B \ or name O2' or name O3' or name O5' or name O5B or name O6')))) selection = (chain 'h' and (resid 1 through 248 or resid 801 through 802)) } ncs_group { reference = (chain 'L' and (resid 1 through 281 or resid 301 through 304 or (resid 307 and ( \ name C01 or name C02 or name C03 or name C04 or name C05 or name C06 or name C1 \ or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C \ 3 or name C4 or name C5 or name C6 or name C7 or name C8 or name O01 or name O02 \ or name O03 or name O04 or name O05 or name O06 or name O11 or name O12 or name \ O13 or name O14 or name P )) or (resid 308 and (name C01 or name C02 or name C0 \ 3 or name C04 or name C05 or name C06 or name C1 or name C19 or name C2 or name \ C20 or name C21 or name C3 or name C4 or name O01 or name O02 or name O03 or nam \ e O04 or name O05 or name O06 or name O11 or name O12 or name O13 or name O14 or \ name P )))) selection = (chain 'l' and (resid 1 through 281 or resid 301 through 304 or resid 307 throug \ h 308)) } ncs_group { reference = (chain 'M' and (resid 1 through 306 or resid 401 through 402 or resid 408 throug \ h 411)) selection = (chain 'm' and (resid 1 through 306 or resid 401 through 402 or (resid 408 and ( \ name C1 or name C1' or name C10 or name C11 or name C12 or name C1B or name C2 o \ r name C2' or name C3 or name C3' or name C4 or name C4' or name C5 or name C5' \ or name C6 or name C6' or name C7 or name C8 or name C9 or name O1' or name O1B \ or name O2' or name O3' or name O5' or name O6')) or resid 409 through 411)) } ncs_group { reference = (chain 'X' and (resid 10 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 69 or (resid 102 and (name CB2 or \ name OB2 or name CB3 or name OB3 or name C1 or name C11 or name C12 or name C13 \ or name C14 or name C15 or name C16 or name CA2 or name CA3 or name CA4 or name \ CA5 or name O1 or name OA2 or name OA3 or name OA4 or name OA5 or name OA6 or na \ me OA7 or name OB4 or name OB5 or name PA1 or name PB2)))) selection = (chain 'x' and (resid 10 through 69 or resid 102)) } 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: 4.980 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: 0.050 Extract box with map and model: 21.550 Check model and map are aligned: 0.780 Set scattering table: 0.470 Process input model: 119.360 Find NCS groups from input model: 3.820 Set up NCS constraints: 0.360 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:14.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.019 0.183 47992 Z= 0.989 Angle : 1.910 18.686 65615 Z= 0.825 Chirality : 0.056 0.320 6467 Planarity : 0.018 0.306 7851 Dihedral : 21.907 179.895 18510 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.39 % Allowed : 6.92 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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: 1.62 (0.12), residues: 4376 helix: 1.75 (0.09), residues: 2932 sheet: -0.67 (0.65), residues: 62 loop : -0.25 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 157 HIS 0.010 0.002 HIS L 153 PHE 0.021 0.002 PHE O 23 TYR 0.018 0.002 TYR I 51 ARG 0.006 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 916 time to evaluate : 4.588 Fit side-chains REVERT: M 20 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6484 (mmm) REVERT: M 60 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7264 (mm) REVERT: M 214 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8951 (tt) REVERT: M 263 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7990 (tm-30) REVERT: M 306 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7895 (mp) REVERT: B 20 HIS cc_start: 0.6593 (t-90) cc_final: 0.6351 (t70) REVERT: I 54 VAL cc_start: 0.7018 (p) cc_final: 0.6663 (t) REVERT: O 20 GLN cc_start: 0.7015 (mt0) cc_final: 0.6805 (pt0) REVERT: S 15 ARG cc_start: 0.4970 (tmm160) cc_final: 0.4150 (mtt180) REVERT: T 17 GLN cc_start: 0.6710 (mm110) cc_final: 0.6509 (mt0) REVERT: V 4 PHE cc_start: 0.5817 (m-80) cc_final: 0.5448 (m-80) REVERT: V 9 MET cc_start: 0.3549 (ttp) cc_final: 0.3143 (tmm) REVERT: W 42 TYR cc_start: 0.5602 (t80) cc_final: 0.5345 (t80) REVERT: 1 9 MET cc_start: 0.4219 (mtt) cc_final: 0.3841 (mmm) REVERT: 3 9 MET cc_start: 0.2292 (mtp) cc_final: 0.2003 (tpt) REVERT: 3 11 PHE cc_start: 0.4131 (OUTLIER) cc_final: 0.3873 (m-80) REVERT: 3 25 PHE cc_start: 0.7473 (t80) cc_final: 0.7174 (t80) REVERT: 3 36 LEU cc_start: 0.8570 (mt) cc_final: 0.8343 (mp) REVERT: 5 10 ILE cc_start: 0.5479 (pt) cc_final: 0.5259 (pp) REVERT: 5 15 ARG cc_start: 0.4740 (ptp-110) cc_final: 0.4398 (ttp80) REVERT: 5 39 PRO cc_start: 0.5542 (Cg_endo) cc_final: 0.5158 (Cg_exo) REVERT: 8 24 MET cc_start: 0.5023 (mmm) cc_final: 0.4568 (mmt) REVERT: X 29 LYS cc_start: 0.7872 (mtpp) cc_final: 0.7663 (mtpp) REVERT: U 13 MET cc_start: 0.5149 (mmm) cc_final: 0.4889 (mmm) REVERT: l 72 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6352 (pp20) REVERT: m 236 GLU cc_start: 0.7556 (tp30) cc_final: 0.7321 (tp30) REVERT: m 263 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8075 (tt0) REVERT: v 17 PHE cc_start: 0.7317 (m-80) cc_final: 0.7026 (t80) REVERT: 05 39 PRO cc_start: 0.7059 (Cg_endo) cc_final: 0.6631 (Cg_exo) REVERT: 06 24 MET cc_start: 0.6736 (mmm) cc_final: 0.6276 (ptp) REVERT: 06 47 TRP cc_start: 0.6418 (p90) cc_final: 0.6047 (p90) outliers start: 126 outliers final: 48 residues processed: 991 average time/residue: 1.1654 time to fit residues: 1517.5656 Evaluate side-chains 806 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 750 time to evaluate : 4.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 232 GLU Chi-restraints excluded: chain M residue 263 GLU Chi-restraints excluded: chain M residue 306 LEU Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 175 MET Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 TYR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain 1 residue 12 ASP Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 1 residue 46 ILE Chi-restraints excluded: chain 3 residue 11 PHE Chi-restraints excluded: chain X residue 57 ILE Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 267 VAL Chi-restraints excluded: chain m residue 8 THR Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain m residue 263 GLU Chi-restraints excluded: chain h residue 175 MET Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain d residue 20 GLN Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain i residue 9 MET Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain r residue 25 SER Chi-restraints excluded: chain s residue 40 SER Chi-restraints excluded: chain s residue 47 SER Chi-restraints excluded: chain t residue 12 THR Chi-restraints excluded: chain y residue 3 LYS Chi-restraints excluded: chain 03 residue 29 VAL Chi-restraints excluded: chain 03 residue 37 SER Chi-restraints excluded: chain 06 residue 11 LEU Chi-restraints excluded: chain 07 residue 54 VAL Chi-restraints excluded: chain x residue 66 ASN Chi-restraints excluded: chain x residue 68 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 362 optimal weight: 0.9990 chunk 325 optimal weight: 0.5980 chunk 180 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 219 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 336 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 204 optimal weight: 10.0000 chunk 250 optimal weight: 0.9990 chunk 389 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 183 ASN M 301 HIS H 32 GLN H 52 ASN A 20 GLN A 42 ASN B 17 GLN E 38 HIS F 20 GLN G 15 GLN G 17 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN T 17 GLN W 17 GLN 2 15 GLN 5 20 GLN 6 15 GLN ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 20 GLN X 66 ASN l 199 ASN m 259 ASN ** m 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 199 GLN ** h 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 20 GLN e 20 HIS ** e 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN ** r 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 20 HIS v 20 GLN w 15 GLN w 17 GLN y 52 ASN 01 20 GLN 01 42 ASN 02 17 GLN 04 17 GLN 04 20 HIS x 60 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 47992 Z= 0.174 Angle : 0.746 14.662 65615 Z= 0.284 Chirality : 0.039 0.248 6467 Planarity : 0.003 0.047 7851 Dihedral : 19.927 179.397 10819 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.04 % Allowed : 14.14 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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: 1.97 (0.13), residues: 4376 helix: 2.01 (0.09), residues: 2934 sheet: -0.14 (0.75), residues: 46 loop : -0.10 (0.18), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP g 44 HIS 0.017 0.001 HIS N 20 PHE 0.025 0.001 PHE D 23 TYR 0.015 0.001 TYR06 23 ARG 0.004 0.000 ARG M 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 830 time to evaluate : 4.588 Fit side-chains REVERT: M 20 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6221 (mmm) REVERT: M 60 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7105 (mm) REVERT: M 138 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6515 (tp40) REVERT: S 15 ARG cc_start: 0.4927 (tmm160) cc_final: 0.4090 (mtt180) REVERT: S 45 GLU cc_start: 0.7232 (pt0) cc_final: 0.6975 (pt0) REVERT: T 29 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7978 (tp) REVERT: V 4 PHE cc_start: 0.5890 (m-80) cc_final: 0.5559 (m-80) REVERT: 1 9 MET cc_start: 0.4177 (mtt) cc_final: 0.3639 (mmm) REVERT: 1 23 PHE cc_start: 0.6519 (t80) cc_final: 0.6166 (t80) REVERT: 1 27 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6880 (mm) REVERT: 1 31 ILE cc_start: 0.7675 (mp) cc_final: 0.7275 (mt) REVERT: 5 10 ILE cc_start: 0.5685 (pt) cc_final: 0.5459 (mm) REVERT: 5 15 ARG cc_start: 0.4835 (ptp-110) cc_final: 0.4442 (ttp80) REVERT: 5 39 PRO cc_start: 0.5526 (Cg_endo) cc_final: 0.5198 (Cg_exo) REVERT: 8 24 MET cc_start: 0.4907 (mmm) cc_final: 0.4485 (mmt) REVERT: l 72 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6865 (pp20) REVERT: f 20 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7224 (pt0) REVERT: y 3 LYS cc_start: 0.4457 (OUTLIER) cc_final: 0.4200 (pmtt) REVERT: 01 8 TRP cc_start: 0.7346 (m100) cc_final: 0.6938 (m100) REVERT: 05 39 PRO cc_start: 0.6910 (Cg_endo) cc_final: 0.6355 (Cg_exo) REVERT: 06 24 MET cc_start: 0.6704 (mmm) cc_final: 0.6227 (ptp) REVERT: 06 47 TRP cc_start: 0.6269 (p90) cc_final: 0.5930 (p90) outliers start: 150 outliers final: 50 residues processed: 904 average time/residue: 1.1589 time to fit residues: 1384.3655 Evaluate side-chains 791 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 733 time to evaluate : 4.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 226 THR Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 138 GLN Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 232 GLU Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 TYR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain T residue 29 LEU Chi-restraints excluded: chain T residue 35 ILE Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain 1 residue 27 LEU Chi-restraints excluded: chain 1 residue 46 ILE Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 8 THR Chi-restraints excluded: chain h residue 175 MET Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain d residue 20 GLN Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 20 GLN Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain i residue 9 MET Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain n residue 43 ILE Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain t residue 12 THR Chi-restraints excluded: chain w residue 21 SER Chi-restraints excluded: chain y residue 3 LYS Chi-restraints excluded: chain y residue 10 ILE Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain 02 residue 39 LEU Chi-restraints excluded: chain 03 residue 37 SER Chi-restraints excluded: chain 04 residue 21 SER Chi-restraints excluded: chain 04 residue 36 VAL Chi-restraints excluded: chain x residue 68 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 216 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 324 optimal weight: 1.9990 chunk 265 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 390 optimal weight: 1.9990 chunk 421 optimal weight: 20.0000 chunk 347 optimal weight: 0.0670 chunk 387 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 313 optimal weight: 5.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN F 20 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 GLN O 20 GLN ** O 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN R 20 HIS T 15 GLN ** Z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 20 ASN m 81 ASN ** m 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 GLN ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN v 20 GLN 01 42 ASN 04 20 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 47992 Z= 0.273 Angle : 0.757 15.324 65615 Z= 0.300 Chirality : 0.040 0.255 6467 Planarity : 0.004 0.054 7851 Dihedral : 19.024 179.719 10771 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.74 % Allowed : 16.21 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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: 1.74 (0.13), residues: 4376 helix: 1.83 (0.09), residues: 2947 sheet: -0.21 (0.75), residues: 46 loop : -0.19 (0.18), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP g 44 HIS 0.014 0.002 HIS n 20 PHE 0.021 0.002 PHE F 23 TYR 0.017 0.002 TYR m 198 ARG 0.005 0.000 ARG M 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 761 time to evaluate : 4.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 210 ASP cc_start: 0.6972 (p0) cc_final: 0.6722 (p0) REVERT: M 20 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6202 (mmm) REVERT: M 60 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7115 (mm) REVERT: M 138 GLN cc_start: 0.7260 (OUTLIER) cc_final: 0.6578 (tp40) REVERT: G 14 GLU cc_start: 0.6923 (mp0) cc_final: 0.6459 (mp0) REVERT: S 15 ARG cc_start: 0.5115 (tmm160) cc_final: 0.4179 (mtt180) REVERT: T 19 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7778 (tt) REVERT: T 29 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8057 (tt) REVERT: V 4 PHE cc_start: 0.5917 (m-80) cc_final: 0.5584 (m-80) REVERT: W 42 TYR cc_start: 0.5266 (t80) cc_final: 0.4876 (t80) REVERT: 1 9 MET cc_start: 0.4091 (mtt) cc_final: 0.3522 (mmm) REVERT: 1 27 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6872 (mm) REVERT: 1 31 ILE cc_start: 0.7774 (mp) cc_final: 0.7353 (mt) REVERT: 2 27 LEU cc_start: 0.6302 (tt) cc_final: 0.5861 (tt) REVERT: 5 39 PRO cc_start: 0.5564 (Cg_endo) cc_final: 0.5212 (Cg_exo) REVERT: 8 24 MET cc_start: 0.4895 (mmm) cc_final: 0.4475 (mmt) REVERT: l 72 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6972 (pp20) REVERT: m 263 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8075 (tt0) REVERT: g 17 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7207 (tm-30) REVERT: o 15 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6888 (mtm180) REVERT: v 17 PHE cc_start: 0.7543 (OUTLIER) cc_final: 0.7224 (t80) REVERT: z 39 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7837 (tp) REVERT: 01 4 PHE cc_start: 0.7312 (m-80) cc_final: 0.7101 (m-80) REVERT: 01 8 TRP cc_start: 0.7347 (m100) cc_final: 0.7039 (m100) REVERT: 06 24 MET cc_start: 0.6656 (mmm) cc_final: 0.6160 (ptp) REVERT: 06 47 TRP cc_start: 0.6281 (p90) cc_final: 0.6021 (p90) outliers start: 176 outliers final: 85 residues processed: 850 average time/residue: 1.1162 time to fit residues: 1264.4498 Evaluate side-chains 826 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 729 time to evaluate : 4.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain L residue 226 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 138 GLN Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 232 GLU Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 TYR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 29 LEU Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain 1 residue 27 LEU Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 46 ILE Chi-restraints excluded: chain 3 residue 40 SER Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 48 PHE Chi-restraints excluded: chain 6 residue 36 VAL Chi-restraints excluded: chain X residue 17 THR Chi-restraints excluded: chain X residue 57 ILE Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain l residue 267 VAL Chi-restraints excluded: chain m residue 8 THR Chi-restraints excluded: chain m residue 263 GLU Chi-restraints excluded: chain h residue 175 MET Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 11 LEU Chi-restraints excluded: chain b residue 14 GLU Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain d residue 20 GLN Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain g residue 17 GLN Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain i residue 9 MET Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain j residue 17 GLN Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain n residue 43 ILE Chi-restraints excluded: chain o residue 15 ARG Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain s residue 27 LEU Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain t residue 12 THR Chi-restraints excluded: chain v residue 17 PHE Chi-restraints excluded: chain v residue 40 SER Chi-restraints excluded: chain w residue 21 SER Chi-restraints excluded: chain y residue 3 LYS Chi-restraints excluded: chain y residue 10 ILE Chi-restraints excluded: chain y residue 24 LEU Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain z residue 21 SER Chi-restraints excluded: chain z residue 29 LEU Chi-restraints excluded: chain z residue 31 SER Chi-restraints excluded: chain z residue 39 LEU Chi-restraints excluded: chain 02 residue 9 THR Chi-restraints excluded: chain 02 residue 39 LEU Chi-restraints excluded: chain 03 residue 30 MET Chi-restraints excluded: chain 03 residue 37 SER Chi-restraints excluded: chain 03 residue 52 ASN Chi-restraints excluded: chain 03 residue 54 VAL Chi-restraints excluded: chain 04 residue 21 SER Chi-restraints excluded: chain 04 residue 36 VAL Chi-restraints excluded: chain x residue 68 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 385 optimal weight: 4.9990 chunk 293 optimal weight: 0.0980 chunk 202 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 391 optimal weight: 4.9990 chunk 414 optimal weight: 1.9990 chunk 204 optimal weight: 10.0000 chunk 371 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** O 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN T 15 GLN 6 20 HIS ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN q 20 GLN v 20 GLN y 52 ASN 01 20 GLN 04 20 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 47992 Z= 0.181 Angle : 0.686 14.547 65615 Z= 0.271 Chirality : 0.037 0.225 6467 Planarity : 0.003 0.049 7851 Dihedral : 17.970 179.785 10768 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.42 % Allowed : 17.67 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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: 1.96 (0.13), residues: 4376 helix: 2.00 (0.09), residues: 2951 sheet: -0.15 (0.76), residues: 46 loop : -0.14 (0.18), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP g 44 HIS 0.017 0.001 HIS z 20 PHE 0.026 0.001 PHE L 216 TYR 0.017 0.001 TYR t 23 ARG 0.004 0.000 ARG M 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 794 time to evaluate : 5.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 243 PHE cc_start: 0.7461 (m-10) cc_final: 0.7080 (m-10) REVERT: M 138 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6476 (tp40) REVERT: E 6 LEU cc_start: 0.5571 (OUTLIER) cc_final: 0.5281 (pp) REVERT: G 14 GLU cc_start: 0.6835 (mp0) cc_final: 0.6583 (mp0) REVERT: Q 20 GLN cc_start: 0.7042 (mm110) cc_final: 0.6798 (tp40) REVERT: S 15 ARG cc_start: 0.5080 (tmm160) cc_final: 0.3935 (ttt180) REVERT: S 45 GLU cc_start: 0.7275 (pt0) cc_final: 0.7045 (pt0) REVERT: T 19 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7736 (tt) REVERT: V 4 PHE cc_start: 0.5980 (m-80) cc_final: 0.5658 (m-80) REVERT: Y 12 ASP cc_start: 0.6753 (t70) cc_final: 0.5643 (m-30) REVERT: 1 9 MET cc_start: 0.4087 (mtt) cc_final: 0.3572 (mmm) REVERT: 1 27 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6797 (mm) REVERT: 1 31 ILE cc_start: 0.7689 (mp) cc_final: 0.7305 (mt) REVERT: 2 27 LEU cc_start: 0.6328 (tt) cc_final: 0.5898 (tt) REVERT: 3 6 LYS cc_start: 0.6725 (mtpt) cc_final: 0.6479 (tptt) REVERT: 5 39 PRO cc_start: 0.5535 (Cg_endo) cc_final: 0.5199 (Cg_exo) REVERT: 8 24 MET cc_start: 0.4900 (mmm) cc_final: 0.4478 (mmt) REVERT: l 72 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6987 (pp20) REVERT: g 17 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7148 (tm-30) REVERT: g 36 VAL cc_start: 0.7273 (OUTLIER) cc_final: 0.6955 (t) REVERT: n 42 TYR cc_start: 0.8120 (t80) cc_final: 0.7907 (t80) REVERT: v 17 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.7210 (t80) REVERT: z 19 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6351 (tp) REVERT: 01 8 TRP cc_start: 0.7355 (m100) cc_final: 0.6919 (m100) REVERT: 06 24 MET cc_start: 0.6547 (mmm) cc_final: 0.6090 (ptp) outliers start: 164 outliers final: 66 residues processed: 881 average time/residue: 1.1438 time to fit residues: 1338.0269 Evaluate side-chains 812 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 737 time to evaluate : 5.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 138 GLN Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 232 GLU Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 TYR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain 1 residue 27 LEU Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 1 residue 46 ILE Chi-restraints excluded: chain 4 residue 9 THR Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 48 PHE Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain l residue 267 VAL Chi-restraints excluded: chain m residue 8 THR Chi-restraints excluded: chain h residue 175 MET Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain d residue 20 GLN Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain g residue 17 GLN Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain i residue 9 MET Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain j residue 17 GLN Chi-restraints excluded: chain j residue 39 LEU Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain s residue 27 LEU Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain s residue 47 SER Chi-restraints excluded: chain v residue 17 PHE Chi-restraints excluded: chain w residue 21 SER Chi-restraints excluded: chain y residue 3 LYS Chi-restraints excluded: chain y residue 10 ILE Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain z residue 19 LEU Chi-restraints excluded: chain z residue 21 SER Chi-restraints excluded: chain z residue 29 LEU Chi-restraints excluded: chain 04 residue 21 SER Chi-restraints excluded: chain 04 residue 36 VAL Chi-restraints excluded: chain 07 residue 32 HIS Chi-restraints excluded: chain x residue 68 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 345 optimal weight: 5.9990 chunk 235 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 308 optimal weight: 0.7980 chunk 171 optimal weight: 5.9990 chunk 353 optimal weight: 8.9990 chunk 286 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 211 optimal weight: 0.0770 chunk 372 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN R 17 GLN T 15 GLN ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 20 ASN ** h 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 GLN ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN q 20 GLN ** r 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 20 GLN y 52 ASN 01 42 ASN 04 20 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 47992 Z= 0.159 Angle : 0.661 15.651 65615 Z= 0.263 Chirality : 0.037 0.224 6467 Planarity : 0.003 0.054 7851 Dihedral : 17.281 179.777 10762 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.26 % Allowed : 19.07 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.13), residues: 4376 helix: 2.09 (0.09), residues: 2951 sheet: 0.02 (0.78), residues: 46 loop : -0.10 (0.18), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP g 44 HIS 0.017 0.001 HIS z 20 PHE 0.025 0.001 PHE L 216 TYR 0.025 0.001 TYR F 5 ARG 0.004 0.000 ARG j 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 821 time to evaluate : 5.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 243 PHE cc_start: 0.7426 (m-10) cc_final: 0.7083 (m-10) REVERT: M 138 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6415 (tp40) REVERT: E 6 LEU cc_start: 0.5556 (OUTLIER) cc_final: 0.5231 (pp) REVERT: G 14 GLU cc_start: 0.6558 (mp0) cc_final: 0.6312 (mp0) REVERT: S 9 MET cc_start: 0.4244 (mtp) cc_final: 0.3840 (mtp) REVERT: S 15 ARG cc_start: 0.5007 (tmm160) cc_final: 0.3893 (ttt180) REVERT: S 45 GLU cc_start: 0.7263 (pt0) cc_final: 0.7012 (pt0) REVERT: T 19 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7666 (tt) REVERT: V 4 PHE cc_start: 0.5926 (m-80) cc_final: 0.5613 (m-80) REVERT: Y 12 ASP cc_start: 0.6722 (t70) cc_final: 0.5665 (m-30) REVERT: 1 9 MET cc_start: 0.4016 (mtt) cc_final: 0.3547 (mmm) REVERT: 1 27 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6861 (mm) REVERT: 2 27 LEU cc_start: 0.6310 (tt) cc_final: 0.5874 (tt) REVERT: 3 6 LYS cc_start: 0.6728 (mtpt) cc_final: 0.6405 (tptt) REVERT: 5 11 PHE cc_start: 0.3189 (OUTLIER) cc_final: 0.2856 (t80) REVERT: 5 39 PRO cc_start: 0.5522 (Cg_endo) cc_final: 0.5198 (Cg_exo) REVERT: 7 45 GLU cc_start: 0.5239 (mm-30) cc_final: 0.4696 (tp30) REVERT: 8 24 MET cc_start: 0.4886 (mmm) cc_final: 0.4456 (mmt) REVERT: f 20 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7511 (pt0) REVERT: g 36 VAL cc_start: 0.7210 (OUTLIER) cc_final: 0.6904 (t) REVERT: z 39 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7840 (tp) REVERT: 01 8 TRP cc_start: 0.7208 (m100) cc_final: 0.6861 (m100) REVERT: 05 24 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7035 (tt) REVERT: 06 24 MET cc_start: 0.6574 (mmm) cc_final: 0.6081 (ptp) REVERT: 06 47 TRP cc_start: 0.6065 (p90) cc_final: 0.5842 (p90) outliers start: 158 outliers final: 61 residues processed: 903 average time/residue: 1.1481 time to fit residues: 1374.8190 Evaluate side-chains 817 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 747 time to evaluate : 4.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 138 GLN Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 232 GLU Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 TYR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain 1 residue 27 LEU Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 46 ILE Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 48 PHE Chi-restraints excluded: chain 5 residue 11 PHE Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 8 THR Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain h residue 185 ASP Chi-restraints excluded: chain a residue 42 ASN Chi-restraints excluded: chain d residue 20 GLN Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 20 GLN Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain i residue 9 MET Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain j residue 17 GLN Chi-restraints excluded: chain j residue 39 LEU Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain r residue 6 LEU Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain y residue 3 LYS Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain z residue 21 SER Chi-restraints excluded: chain z residue 29 LEU Chi-restraints excluded: chain z residue 31 SER Chi-restraints excluded: chain z residue 39 LEU Chi-restraints excluded: chain 02 residue 39 LEU Chi-restraints excluded: chain 04 residue 36 VAL Chi-restraints excluded: chain 05 residue 24 LEU Chi-restraints excluded: chain 07 residue 32 HIS Chi-restraints excluded: chain x residue 68 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 139 optimal weight: 6.9990 chunk 373 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 243 optimal weight: 0.3980 chunk 102 optimal weight: 0.6980 chunk 415 optimal weight: 6.9990 chunk 344 optimal weight: 0.9980 chunk 192 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 GLN ** O 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN R 17 GLN T 15 GLN ** Z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 20 ASN m 81 ASN ** m 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 GLN ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN ** r 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 20 GLN y 52 ASN 01 42 ASN 04 20 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 47992 Z= 0.246 Angle : 0.740 15.963 65615 Z= 0.298 Chirality : 0.040 0.272 6467 Planarity : 0.004 0.057 7851 Dihedral : 17.566 179.802 10750 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.66 % Allowed : 19.85 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.12), residues: 4376 helix: 2.08 (0.09), residues: 2907 sheet: -0.15 (0.76), residues: 46 loop : 0.26 (0.17), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP g 44 HIS 0.016 0.002 HIS z 20 PHE 0.030 0.002 PHE x 38 TYR 0.018 0.002 TYR t 23 ARG 0.005 0.000 ARG j 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 765 time to evaluate : 4.670 Fit side-chains revert: symmetry clash REVERT: L 2 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8693 (mt) REVERT: L 243 PHE cc_start: 0.7520 (m-10) cc_final: 0.7116 (m-10) REVERT: M 138 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6545 (tp40) REVERT: M 263 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7872 (tm-30) REVERT: E 6 LEU cc_start: 0.5492 (OUTLIER) cc_final: 0.5183 (pp) REVERT: K 9 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6657 (mtm) REVERT: S 9 MET cc_start: 0.4229 (mtp) cc_final: 0.3840 (mtp) REVERT: S 15 ARG cc_start: 0.5109 (tmm160) cc_final: 0.3934 (ttt180) REVERT: T 19 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7662 (tt) REVERT: V 4 PHE cc_start: 0.5932 (m-80) cc_final: 0.5624 (m-80) REVERT: V 9 MET cc_start: 0.5032 (OUTLIER) cc_final: 0.4365 (tmm) REVERT: Y 12 ASP cc_start: 0.6797 (t70) cc_final: 0.5642 (m-30) REVERT: 1 9 MET cc_start: 0.4018 (mtt) cc_final: 0.3644 (mmm) REVERT: 1 27 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6783 (mm) REVERT: 1 31 ILE cc_start: 0.7798 (mp) cc_final: 0.7400 (mt) REVERT: 2 27 LEU cc_start: 0.6326 (tt) cc_final: 0.5895 (tt) REVERT: 4 38 HIS cc_start: 0.5509 (m90) cc_final: 0.5278 (m170) REVERT: 5 11 PHE cc_start: 0.3297 (OUTLIER) cc_final: 0.2927 (t80) REVERT: 5 39 PRO cc_start: 0.5572 (Cg_endo) cc_final: 0.5225 (Cg_exo) REVERT: 7 45 GLU cc_start: 0.5326 (mm-30) cc_final: 0.4732 (tp30) REVERT: 8 24 MET cc_start: 0.4861 (mmm) cc_final: 0.4463 (mmp) REVERT: l 72 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6953 (pm20) REVERT: f 20 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7552 (pt0) REVERT: g 17 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7167 (tm-30) REVERT: g 36 VAL cc_start: 0.7270 (OUTLIER) cc_final: 0.6946 (t) REVERT: n 14 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6692 (tm-30) REVERT: z 39 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7924 (tp) REVERT: 01 8 TRP cc_start: 0.7376 (m100) cc_final: 0.7020 (m100) REVERT: 05 24 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7061 (tt) REVERT: 06 24 MET cc_start: 0.6535 (mmm) cc_final: 0.6097 (ptp) outliers start: 173 outliers final: 84 residues processed: 861 average time/residue: 1.1596 time to fit residues: 1338.7692 Evaluate side-chains 837 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 737 time to evaluate : 4.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 226 THR Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 138 GLN Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 232 GLU Chi-restraints excluded: chain M residue 263 GLU Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 TYR Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 40 SER Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 29 LEU Chi-restraints excluded: chain V residue 9 MET Chi-restraints excluded: chain Z residue 18 GLU Chi-restraints excluded: chain 1 residue 27 LEU Chi-restraints excluded: chain 1 residue 36 LEU Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 1 residue 46 ILE Chi-restraints excluded: chain 2 residue 21 SER Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 5 residue 11 PHE Chi-restraints excluded: chain 6 residue 36 VAL Chi-restraints excluded: chain X residue 57 ILE Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain l residue 267 VAL Chi-restraints excluded: chain m residue 8 THR Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain a residue 42 ASN Chi-restraints excluded: chain b residue 11 LEU Chi-restraints excluded: chain b residue 14 GLU Chi-restraints excluded: chain d residue 20 GLN Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 20 GLN Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain g residue 17 GLN Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain i residue 9 MET Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain j residue 17 GLN Chi-restraints excluded: chain j residue 35 ILE Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain n residue 14 GLU Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain q residue 44 LEU Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain s residue 27 LEU Chi-restraints excluded: chain s residue 40 SER Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain s residue 47 SER Chi-restraints excluded: chain t residue 12 THR Chi-restraints excluded: chain t residue 25 SER Chi-restraints excluded: chain v residue 40 SER Chi-restraints excluded: chain w residue 21 SER Chi-restraints excluded: chain y residue 3 LYS Chi-restraints excluded: chain y residue 10 ILE Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain z residue 21 SER Chi-restraints excluded: chain z residue 29 LEU Chi-restraints excluded: chain z residue 31 SER Chi-restraints excluded: chain z residue 39 LEU Chi-restraints excluded: chain 02 residue 39 LEU Chi-restraints excluded: chain 03 residue 54 VAL Chi-restraints excluded: chain 04 residue 21 SER Chi-restraints excluded: chain 04 residue 36 VAL Chi-restraints excluded: chain 05 residue 24 LEU Chi-restraints excluded: chain 07 residue 45 GLU Chi-restraints excluded: chain x residue 68 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 400 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 303 optimal weight: 8.9990 chunk 234 optimal weight: 4.9990 chunk 349 optimal weight: 9.9990 chunk 231 optimal weight: 3.9990 chunk 413 optimal weight: 20.0000 chunk 258 optimal weight: 0.9980 chunk 252 optimal weight: 3.9990 chunk 190 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN O 20 GLN ** O 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN T 15 GLN ** Z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 20 ASN l 56 GLN ** m 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 301 HIS a 20 GLN ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN r 15 GLN v 20 GLN y 52 ASN 04 20 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 47992 Z= 0.353 Angle : 0.824 16.487 65615 Z= 0.334 Chirality : 0.043 0.336 6467 Planarity : 0.004 0.081 7851 Dihedral : 18.331 179.876 10748 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.85 % Allowed : 20.15 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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: 1.78 (0.12), residues: 4376 helix: 1.77 (0.09), residues: 2905 sheet: -0.35 (0.73), residues: 46 loop : 0.10 (0.17), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP y 8 HIS 0.014 0.002 HIS z 20 PHE 0.033 0.002 PHE L 216 TYR 0.019 0.002 TYR m 198 ARG 0.006 0.001 ARG M 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 759 time to evaluate : 5.090 Fit side-chains revert: symmetry clash REVERT: L 2 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8700 (mt) REVERT: M 138 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.6569 (tp40) REVERT: M 214 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8954 (tt) REVERT: M 263 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7898 (tm-30) REVERT: H 248 ARG cc_start: 0.6650 (OUTLIER) cc_final: 0.6337 (mmm-85) REVERT: E 6 LEU cc_start: 0.5481 (OUTLIER) cc_final: 0.5151 (pp) REVERT: G 14 GLU cc_start: 0.6703 (mp0) cc_final: 0.6496 (mp0) REVERT: K 9 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6802 (mtm) REVERT: P 15 GLN cc_start: 0.6134 (OUTLIER) cc_final: 0.4423 (pm20) REVERT: S 9 MET cc_start: 0.4201 (mtp) cc_final: 0.3792 (mtp) REVERT: S 15 ARG cc_start: 0.5142 (tmm160) cc_final: 0.3920 (ttt180) REVERT: T 19 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7618 (tt) REVERT: V 4 PHE cc_start: 0.5913 (m-80) cc_final: 0.5627 (m-80) REVERT: V 9 MET cc_start: 0.5070 (OUTLIER) cc_final: 0.4367 (tmm) REVERT: W 38 HIS cc_start: 0.6804 (OUTLIER) cc_final: 0.6467 (m90) REVERT: Y 12 ASP cc_start: 0.6814 (t70) cc_final: 0.5655 (m-30) REVERT: Z 13 ASP cc_start: 0.5804 (m-30) cc_final: 0.5585 (m-30) REVERT: 1 27 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6832 (mm) REVERT: 2 27 LEU cc_start: 0.6361 (tt) cc_final: 0.5921 (tt) REVERT: 5 11 PHE cc_start: 0.3348 (OUTLIER) cc_final: 0.2946 (t80) REVERT: 8 24 MET cc_start: 0.4959 (mmm) cc_final: 0.4490 (mmp) REVERT: f 20 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7381 (pt0) REVERT: g 17 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7226 (tm-30) REVERT: n 14 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6776 (tm-30) REVERT: 01 8 TRP cc_start: 0.7454 (m100) cc_final: 0.7153 (m100) REVERT: 05 24 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.7085 (tt) REVERT: 06 24 MET cc_start: 0.6718 (mmm) cc_final: 0.6144 (ptp) REVERT: 06 45 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.6422 (ptm160) outliers start: 180 outliers final: 98 residues processed: 848 average time/residue: 1.1445 time to fit residues: 1283.7763 Evaluate side-chains 852 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 736 time to evaluate : 4.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 226 THR Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 138 GLN Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 232 GLU Chi-restraints excluded: chain M residue 263 GLU Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 248 ARG Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 TYR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 40 SER Chi-restraints excluded: chain S residue 54 VAL Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 29 LEU Chi-restraints excluded: chain V residue 9 MET Chi-restraints excluded: chain W residue 38 HIS Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Z residue 18 GLU Chi-restraints excluded: chain 1 residue 27 LEU Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 1 residue 36 LEU Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 1 residue 46 ILE Chi-restraints excluded: chain 2 residue 21 SER Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 5 residue 11 PHE Chi-restraints excluded: chain 6 residue 36 VAL Chi-restraints excluded: chain X residue 57 ILE Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 137 VAL Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain l residue 267 VAL Chi-restraints excluded: chain m residue 8 THR Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain a residue 42 ASN Chi-restraints excluded: chain a residue 45 GLU Chi-restraints excluded: chain b residue 11 LEU Chi-restraints excluded: chain b residue 14 GLU Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain d residue 20 GLN Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 20 GLN Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain g residue 17 GLN Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain i residue 9 MET Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain j residue 17 GLN Chi-restraints excluded: chain j residue 35 ILE Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain n residue 14 GLU Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain q residue 44 LEU Chi-restraints excluded: chain r residue 6 LEU Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain s residue 27 LEU Chi-restraints excluded: chain s residue 40 SER Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain s residue 47 SER Chi-restraints excluded: chain t residue 12 THR Chi-restraints excluded: chain t residue 25 SER Chi-restraints excluded: chain v residue 40 SER Chi-restraints excluded: chain w residue 19 LEU Chi-restraints excluded: chain w residue 21 SER Chi-restraints excluded: chain y residue 3 LYS Chi-restraints excluded: chain y residue 10 ILE Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain z residue 21 SER Chi-restraints excluded: chain z residue 29 LEU Chi-restraints excluded: chain z residue 31 SER Chi-restraints excluded: chain z residue 39 LEU Chi-restraints excluded: chain 02 residue 39 LEU Chi-restraints excluded: chain 03 residue 30 MET Chi-restraints excluded: chain 03 residue 40 SER Chi-restraints excluded: chain 03 residue 54 VAL Chi-restraints excluded: chain 04 residue 21 SER Chi-restraints excluded: chain 04 residue 36 VAL Chi-restraints excluded: chain 05 residue 24 LEU Chi-restraints excluded: chain 06 residue 19 LEU Chi-restraints excluded: chain 06 residue 45 ARG Chi-restraints excluded: chain x residue 42 LEU Chi-restraints excluded: chain x residue 68 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 255 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 80 optimal weight: 0.0970 chunk 262 optimal weight: 0.6980 chunk 281 optimal weight: 1.9990 chunk 204 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 325 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 183 ASN O 20 GLN Q 20 GLN R 17 GLN T 15 GLN ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 20 ASN l 56 GLN ** m 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN r 15 GLN y 52 ASN 01 42 ASN 04 20 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 47992 Z= 0.165 Angle : 0.686 15.220 65615 Z= 0.278 Chirality : 0.038 0.251 6467 Planarity : 0.003 0.049 7851 Dihedral : 17.252 179.799 10748 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.58 % Allowed : 21.76 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.12), residues: 4376 helix: 2.15 (0.09), residues: 2896 sheet: -0.18 (0.76), residues: 46 loop : 0.23 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP y 8 HIS 0.009 0.001 HIS z 20 PHE 0.031 0.001 PHE x 38 TYR 0.020 0.001 TYR t 23 ARG 0.003 0.000 ARG x 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 770 time to evaluate : 4.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 138 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6419 (tp40) REVERT: M 182 HIS cc_start: 0.7580 (OUTLIER) cc_final: 0.7233 (p-80) REVERT: E 6 LEU cc_start: 0.5469 (OUTLIER) cc_final: 0.5168 (pp) REVERT: K 9 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6674 (mtm) REVERT: S 9 MET cc_start: 0.4235 (mtp) cc_final: 0.3841 (mtp) REVERT: S 15 ARG cc_start: 0.5050 (tmm160) cc_final: 0.4050 (ttm-80) REVERT: S 45 GLU cc_start: 0.7205 (pt0) cc_final: 0.6906 (pt0) REVERT: T 19 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7619 (tt) REVERT: V 4 PHE cc_start: 0.6106 (m-80) cc_final: 0.5739 (m-80) REVERT: V 9 MET cc_start: 0.5051 (OUTLIER) cc_final: 0.4283 (tmm) REVERT: W 38 HIS cc_start: 0.6807 (OUTLIER) cc_final: 0.6522 (m90) REVERT: 1 9 MET cc_start: 0.4658 (mmt) cc_final: 0.4436 (mmm) REVERT: 1 11 PHE cc_start: 0.5498 (m-10) cc_final: 0.5210 (m-80) REVERT: 1 27 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6772 (mm) REVERT: 1 31 ILE cc_start: 0.7663 (mp) cc_final: 0.7279 (mt) REVERT: 3 9 MET cc_start: 0.2883 (tpp) cc_final: 0.2675 (tpp) REVERT: 4 24 MET cc_start: 0.5531 (mmm) cc_final: 0.5083 (tpp) REVERT: 5 9 MET cc_start: 0.4973 (mtm) cc_final: 0.4469 (ttp) REVERT: 5 11 PHE cc_start: 0.3270 (OUTLIER) cc_final: 0.2971 (t80) REVERT: 5 39 PRO cc_start: 0.5503 (Cg_endo) cc_final: 0.5103 (Cg_exo) REVERT: 8 24 MET cc_start: 0.4950 (mmm) cc_final: 0.4454 (mmt) REVERT: m 263 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8008 (tt0) REVERT: f 20 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7308 (pt0) REVERT: g 36 VAL cc_start: 0.7230 (OUTLIER) cc_final: 0.6933 (t) REVERT: n 42 TYR cc_start: 0.8131 (t80) cc_final: 0.7907 (t80) REVERT: t 39 LEU cc_start: 0.8264 (tm) cc_final: 0.8059 (tp) REVERT: 01 8 TRP cc_start: 0.7370 (m100) cc_final: 0.7067 (m100) REVERT: 05 24 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7109 (tt) REVERT: 06 24 MET cc_start: 0.6624 (mmm) cc_final: 0.6150 (ptp) REVERT: 07 9 MET cc_start: 0.2472 (mpm) cc_final: 0.1424 (mmt) REVERT: 07 30 MET cc_start: 0.5198 (tpt) cc_final: 0.4976 (tpp) outliers start: 133 outliers final: 66 residues processed: 843 average time/residue: 1.1374 time to fit residues: 1271.8708 Evaluate side-chains 810 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 731 time to evaluate : 4.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 226 THR Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 138 GLN Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 232 GLU Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 TYR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain Q residue 7 ILE Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 29 LEU Chi-restraints excluded: chain V residue 9 MET Chi-restraints excluded: chain W residue 38 HIS Chi-restraints excluded: chain Y residue 11 PHE Chi-restraints excluded: chain Z residue 18 GLU Chi-restraints excluded: chain 1 residue 27 LEU Chi-restraints excluded: chain 1 residue 36 LEU Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 1 residue 46 ILE Chi-restraints excluded: chain 2 residue 21 SER Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 5 residue 11 PHE Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 137 VAL Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain l residue 267 VAL Chi-restraints excluded: chain m residue 8 THR Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain m residue 263 GLU Chi-restraints excluded: chain a residue 42 ASN Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain d residue 20 GLN Chi-restraints excluded: chain e residue 35 ILE Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 20 GLN Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain i residue 9 MET Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain j residue 17 GLN Chi-restraints excluded: chain j residue 35 ILE Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain q residue 44 LEU Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain s residue 40 SER Chi-restraints excluded: chain s residue 47 SER Chi-restraints excluded: chain t residue 25 SER Chi-restraints excluded: chain v residue 40 SER Chi-restraints excluded: chain y residue 3 LYS Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain z residue 21 SER Chi-restraints excluded: chain 03 residue 54 VAL Chi-restraints excluded: chain 04 residue 36 VAL Chi-restraints excluded: chain 05 residue 24 LEU Chi-restraints excluded: chain x residue 68 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 376 optimal weight: 10.0000 chunk 396 optimal weight: 7.9990 chunk 361 optimal weight: 5.9990 chunk 385 optimal weight: 9.9990 chunk 231 optimal weight: 4.9990 chunk 167 optimal weight: 9.9990 chunk 302 optimal weight: 10.0000 chunk 118 optimal weight: 0.9980 chunk 348 optimal weight: 5.9990 chunk 364 optimal weight: 1.9990 chunk 383 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN T 15 GLN ** Z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 15 GLN ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 56 GLN ** m 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 GLN ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 GLN r 15 GLN ** v 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 52 ASN 01 42 ASN 04 20 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 47992 Z= 0.401 Angle : 0.861 16.600 65615 Z= 0.351 Chirality : 0.045 0.370 6467 Planarity : 0.005 0.066 7851 Dihedral : 18.394 179.848 10748 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.93 % Allowed : 21.90 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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: 1.67 (0.12), residues: 4376 helix: 1.70 (0.09), residues: 2903 sheet: -0.37 (0.73), residues: 46 loop : 0.02 (0.17), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP06 44 HIS 0.013 0.002 HIS E 38 PHE 0.035 0.002 PHE L 216 TYR 0.033 0.002 TYR F 5 ARG 0.012 0.001 ARG M 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 739 time to evaluate : 4.664 Fit side-chains revert: symmetry clash REVERT: L 2 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8715 (mt) REVERT: M 138 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.6571 (tp40) REVERT: M 214 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8953 (tt) REVERT: M 263 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: E 6 LEU cc_start: 0.5558 (OUTLIER) cc_final: 0.5265 (pp) REVERT: F 20 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7698 (pt0) REVERT: F 35 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8301 (mm) REVERT: G 14 GLU cc_start: 0.6706 (mp0) cc_final: 0.6474 (mp0) REVERT: K 9 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6808 (mtm) REVERT: S 15 ARG cc_start: 0.5085 (tmm160) cc_final: 0.3958 (ttt180) REVERT: T 19 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7643 (tt) REVERT: V 4 PHE cc_start: 0.6109 (m-80) cc_final: 0.5765 (m-80) REVERT: V 9 MET cc_start: 0.5012 (OUTLIER) cc_final: 0.4451 (tmm) REVERT: W 38 HIS cc_start: 0.6784 (OUTLIER) cc_final: 0.6437 (m90) REVERT: 1 9 MET cc_start: 0.4557 (mmt) cc_final: 0.4271 (mmm) REVERT: 1 27 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6838 (mm) REVERT: 1 30 MET cc_start: 0.6644 (OUTLIER) cc_final: 0.5724 (tpt) REVERT: 1 46 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7271 (mp) REVERT: 2 27 LEU cc_start: 0.6315 (tt) cc_final: 0.5891 (tt) REVERT: 3 9 MET cc_start: 0.2886 (tpp) cc_final: 0.2670 (tpp) REVERT: 4 24 MET cc_start: 0.5551 (mmm) cc_final: 0.5194 (tpp) REVERT: 4 42 TYR cc_start: 0.5124 (OUTLIER) cc_final: 0.4562 (t80) REVERT: 5 11 PHE cc_start: 0.3399 (OUTLIER) cc_final: 0.3019 (t80) REVERT: 8 24 MET cc_start: 0.4985 (mmm) cc_final: 0.4615 (mmp) REVERT: f 20 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7373 (pt0) REVERT: y 9 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.6424 (mmm) REVERT: 01 8 TRP cc_start: 0.7467 (m100) cc_final: 0.7200 (m100) REVERT: 05 24 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.6982 (tt) REVERT: 06 17 GLN cc_start: 0.6382 (mm-40) cc_final: 0.5901 (mt0) REVERT: 06 24 MET cc_start: 0.6651 (mmm) cc_final: 0.6123 (ptp) REVERT: 06 45 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6426 (ptm160) outliers start: 146 outliers final: 81 residues processed: 821 average time/residue: 1.1119 time to fit residues: 1218.7010 Evaluate side-chains 821 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 720 time to evaluate : 3.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 205 GLU Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 226 THR Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 138 GLN Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 232 GLU Chi-restraints excluded: chain M residue 263 GLU Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 TYR Chi-restraints excluded: chain F residue 20 GLN Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain S residue 40 SER Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 29 LEU Chi-restraints excluded: chain V residue 9 MET Chi-restraints excluded: chain W residue 38 HIS Chi-restraints excluded: chain Y residue 11 PHE Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Z residue 18 GLU Chi-restraints excluded: chain 1 residue 27 LEU Chi-restraints excluded: chain 1 residue 30 MET Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 1 residue 36 LEU Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 1 residue 46 ILE Chi-restraints excluded: chain 2 residue 21 SER Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 31 SER Chi-restraints excluded: chain 4 residue 42 TYR Chi-restraints excluded: chain 5 residue 11 PHE Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 137 VAL Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain l residue 267 VAL Chi-restraints excluded: chain m residue 8 THR Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain a residue 42 ASN Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain d residue 20 GLN Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 20 GLN Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain i residue 9 MET Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain j residue 35 ILE Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain q residue 44 LEU Chi-restraints excluded: chain r residue 15 GLN Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain s residue 40 SER Chi-restraints excluded: chain s residue 47 SER Chi-restraints excluded: chain t residue 12 THR Chi-restraints excluded: chain t residue 25 SER Chi-restraints excluded: chain v residue 40 SER Chi-restraints excluded: chain w residue 21 SER Chi-restraints excluded: chain y residue 3 LYS Chi-restraints excluded: chain y residue 9 MET Chi-restraints excluded: chain y residue 10 ILE Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain z residue 19 LEU Chi-restraints excluded: chain z residue 21 SER Chi-restraints excluded: chain z residue 29 LEU Chi-restraints excluded: chain z residue 39 LEU Chi-restraints excluded: chain 02 residue 39 LEU Chi-restraints excluded: chain 03 residue 29 VAL Chi-restraints excluded: chain 03 residue 54 VAL Chi-restraints excluded: chain 04 residue 36 VAL Chi-restraints excluded: chain 05 residue 24 LEU Chi-restraints excluded: chain 06 residue 45 ARG Chi-restraints excluded: chain x residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 253 optimal weight: 0.7980 chunk 407 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 193 optimal weight: 0.9980 chunk 283 optimal weight: 2.9990 chunk 427 optimal weight: 2.9990 chunk 393 optimal weight: 0.9990 chunk 340 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 262 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN T 15 GLN ** Z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 20 ASN ** m 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 81 ASN ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 15 GLN y 52 ASN 04 20 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 47992 Z= 0.192 Angle : 0.727 15.325 65615 Z= 0.297 Chirality : 0.039 0.288 6467 Planarity : 0.004 0.064 7851 Dihedral : 17.629 179.823 10748 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.88 % Allowed : 23.22 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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: 1.99 (0.12), residues: 4376 helix: 1.96 (0.09), residues: 2895 sheet: -0.23 (0.75), residues: 46 loop : 0.12 (0.17), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP06 44 HIS 0.011 0.001 HIS z 20 PHE 0.035 0.001 PHE x 38 TYR 0.026 0.001 TYR F 5 ARG 0.014 0.000 ARG M 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 749 time to evaluate : 4.704 Fit side-chains revert: symmetry clash REVERT: M 138 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6480 (tp40) REVERT: M 182 HIS cc_start: 0.7584 (OUTLIER) cc_final: 0.7170 (p-80) REVERT: M 263 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7699 (tm-30) REVERT: D 9 MET cc_start: 0.6936 (mpp) cc_final: 0.6666 (mpp) REVERT: E 6 LEU cc_start: 0.5491 (OUTLIER) cc_final: 0.5191 (pp) REVERT: K 9 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6690 (mtm) REVERT: S 9 MET cc_start: 0.4384 (mtp) cc_final: 0.3957 (mtp) REVERT: S 15 ARG cc_start: 0.5039 (tmm160) cc_final: 0.3893 (ttt180) REVERT: S 45 GLU cc_start: 0.7278 (pt0) cc_final: 0.7024 (pt0) REVERT: T 19 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7630 (tt) REVERT: V 4 PHE cc_start: 0.6064 (m-80) cc_final: 0.5707 (m-80) REVERT: V 9 MET cc_start: 0.4983 (OUTLIER) cc_final: 0.4449 (tmm) REVERT: W 38 HIS cc_start: 0.6717 (OUTLIER) cc_final: 0.6345 (m90) REVERT: 1 27 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6785 (mm) REVERT: 1 31 ILE cc_start: 0.7724 (mp) cc_final: 0.7343 (mt) REVERT: 1 46 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7278 (mp) REVERT: 2 27 LEU cc_start: 0.6329 (tt) cc_final: 0.5897 (tt) REVERT: 3 29 VAL cc_start: 0.7877 (m) cc_final: 0.7641 (t) REVERT: 4 24 MET cc_start: 0.5527 (mmm) cc_final: 0.5179 (tpp) REVERT: 4 43 ILE cc_start: 0.6573 (mp) cc_final: 0.6015 (tp) REVERT: 5 11 PHE cc_start: 0.3265 (OUTLIER) cc_final: 0.2975 (t80) REVERT: 8 24 MET cc_start: 0.5061 (mmm) cc_final: 0.4422 (mmt) REVERT: f 20 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7299 (pt0) REVERT: g 36 VAL cc_start: 0.7326 (OUTLIER) cc_final: 0.7016 (t) REVERT: n 42 TYR cc_start: 0.8142 (t80) cc_final: 0.7940 (t80) REVERT: y 5 TYR cc_start: 0.6551 (p90) cc_final: 0.6320 (p90) REVERT: y 9 MET cc_start: 0.6563 (OUTLIER) cc_final: 0.6288 (mmm) REVERT: 01 8 TRP cc_start: 0.7398 (m100) cc_final: 0.7131 (m100) REVERT: 05 24 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6931 (tt) REVERT: 06 24 MET cc_start: 0.6604 (mmm) cc_final: 0.6109 (ptp) REVERT: 07 9 MET cc_start: 0.2372 (mpt) cc_final: 0.1733 (mmt) REVERT: 07 30 MET cc_start: 0.5459 (tpt) cc_final: 0.5181 (tpp) outliers start: 107 outliers final: 69 residues processed: 809 average time/residue: 1.1162 time to fit residues: 1206.8586 Evaluate side-chains 818 residues out of total 3755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 734 time to evaluate : 4.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 205 GLU Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 226 THR Chi-restraints excluded: chain L residue 235 LEU Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 20 MET Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 138 GLN Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 232 GLU Chi-restraints excluded: chain M residue 263 GLU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 TYR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain Q residue 7 ILE Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain S residue 40 SER Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain V residue 9 MET Chi-restraints excluded: chain W residue 38 HIS Chi-restraints excluded: chain Y residue 11 PHE Chi-restraints excluded: chain Z residue 18 GLU Chi-restraints excluded: chain 1 residue 27 LEU Chi-restraints excluded: chain 1 residue 36 LEU Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 1 residue 46 ILE Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 5 residue 11 PHE Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain l residue 15 THR Chi-restraints excluded: chain l residue 137 VAL Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain l residue 267 VAL Chi-restraints excluded: chain m residue 8 THR Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain h residue 185 ASP Chi-restraints excluded: chain a residue 42 ASN Chi-restraints excluded: chain d residue 20 GLN Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 20 GLN Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain g residue 36 VAL Chi-restraints excluded: chain i residue 9 MET Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain j residue 12 THR Chi-restraints excluded: chain j residue 35 ILE Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain n residue 11 LEU Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain s residue 40 SER Chi-restraints excluded: chain s residue 47 SER Chi-restraints excluded: chain t residue 12 THR Chi-restraints excluded: chain t residue 25 SER Chi-restraints excluded: chain v residue 40 SER Chi-restraints excluded: chain y residue 3 LYS Chi-restraints excluded: chain y residue 9 MET Chi-restraints excluded: chain y residue 10 ILE Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 40 SER Chi-restraints excluded: chain z residue 21 SER Chi-restraints excluded: chain z residue 29 LEU Chi-restraints excluded: chain 03 residue 54 VAL Chi-restraints excluded: chain 04 residue 36 VAL Chi-restraints excluded: chain 05 residue 24 LEU Chi-restraints excluded: chain 06 residue 45 ARG Chi-restraints excluded: chain x residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 270 optimal weight: 0.9980 chunk 362 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 313 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 340 optimal weight: 8.9990 chunk 142 optimal weight: 8.9990 chunk 350 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN T 15 GLN ** Z 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 20 ASN ** m 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 GLN ** n 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 15 GLN y 52 ASN 01 42 ASN 04 20 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.165616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.131872 restraints weight = 69401.963| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.47 r_work: 0.3303 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 47992 Z= 0.220 Angle : 0.738 15.472 65615 Z= 0.303 Chirality : 0.040 0.313 6467 Planarity : 0.004 0.053 7851 Dihedral : 17.471 179.810 10748 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.91 % Allowed : 23.57 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % 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: 1.99 (0.12), residues: 4376 helix: 1.96 (0.09), residues: 2895 sheet: -0.16 (0.76), residues: 46 loop : 0.13 (0.17), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP06 44 HIS 0.016 0.001 HIS N 20 PHE 0.034 0.001 PHE 3 25 TYR 0.024 0.001 TYR F 5 ARG 0.010 0.000 ARG M 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18791.26 seconds wall clock time: 332 minutes 35.24 seconds (19955.24 seconds total)