Starting phenix.real_space_refine on Mon Mar 25 00:00:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vor_32058/03_2024/7vor_32058_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vor_32058/03_2024/7vor_32058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vor_32058/03_2024/7vor_32058.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vor_32058/03_2024/7vor_32058.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vor_32058/03_2024/7vor_32058_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vor_32058/03_2024/7vor_32058_updated.pdb" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 24 5.49 5 Mg 64 5.21 5 S 174 5.16 5 C 31612 2.51 5 N 6300 2.21 5 O 6804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b9 TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 44980 Number of models: 1 Model: "" Number of chains: 128 Chain: "L" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2232 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2445 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 294} Chain: "H" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1973 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 236} Chain: "A" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "B" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "D" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "E" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "F" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "G" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "I" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "J" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "K" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "N" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "O" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "P" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Q" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "R" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "S" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "T" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "U" 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: "V" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "W" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "C" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "3" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 437 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "Z" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "1" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 392 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "2" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 309 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "7" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 403 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "8" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "9" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "0" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "X" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 529 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "Y" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 361 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "l" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2232 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "m" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2445 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 294} Chain: "h" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1973 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 236} Chain: "a" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "b" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "d" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "e" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "f" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "g" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "i" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "j" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "k" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "n" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "o" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "p" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "q" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "r" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "s" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "t" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "u" 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: "v" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "w" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "c" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "5" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 437 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "z" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "b1" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 392 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "4" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 309 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "6" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 403 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "b8" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "b9" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "b0" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "x" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 529 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "y" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 361 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "L" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 354 Unusual residues: {'BCL': 2, 'BPH': 1, 'PC1': 2, 'U10': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 36 Chain: "M" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 360 Unusual residues: {'BCL': 2, 'BPH': 1, 'CDL': 1, 'FE2': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "A" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 222 Unusual residues: {'BCL': 1, 'PC1': 3, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 Chain: "B" 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: "D" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 147 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "E" 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: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 129 Unusual residues: {'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 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: 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: "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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 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: 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: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "U" 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: "V" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 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: "C" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "3" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 135 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "2" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "7" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 122 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "9" 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: "0" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 354 Unusual residues: {'BCL': 2, 'BPH': 1, 'PC1': 2, 'U10': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 36 Chain: "m" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 360 Unusual residues: {'BCL': 2, 'BPH': 1, 'CDL': 1, 'FE2': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "h" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "a" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 222 Unusual residues: {'BCL': 1, 'PC1': 3, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 Chain: "b" 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: "d" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 147 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "e" 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: "f" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 129 Unusual residues: {'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 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: 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: "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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 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: 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: "r" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "u" 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: "v" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 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: "c" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "5" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 135 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "z" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "b1" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "4" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "6" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 122 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "b9" 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: "b0" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "x" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 23.74, per 1000 atoms: 0.53 Number of scatterers: 44980 At special positions: 0 Unit cell: (225.68, 142.48, 107.12, 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 174 16.00 P 24 15.00 Mg 64 11.99 O 6804 8.00 N 6300 7.00 C 31612 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=64, symmetry=0 Number of additional bonds: simple=64, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.05 Conformation dependent library (CDL) restraints added in 7.0 seconds 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 192 helices and 8 sheets defined 65.3% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.26 Creating SS restraints... Processing helix chain 'L' and resid 6 through 9 Processing helix chain 'L' and resid 32 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 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'L' and resid 84 through 111 Processing helix chain 'L' and resid 116 through 132 removed outlier: 3.571A pdb=" N PHE L 123 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 139 Processing helix chain 'L' and resid 142 through 144 No H-bonds generated for 'chain 'L' and resid 142 through 144' Processing helix chain 'L' and resid 152 through 164 removed outlier: 3.981A 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 250 Processing helix chain 'L' and resid 259 through 267 removed outlier: 4.358A pdb=" N TRP L 265 " --> pdb=" O ASP L 261 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N TRP L 266 " --> pdb=" O TRP L 262 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL L 267 " --> pdb=" O TRP L 263 " (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 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 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 229 removed outlier: 4.788A pdb=" N ARG M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N PHE M 229 " --> pdb=" O ALA M 225 " (cutoff:3.500A) 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: 3.753A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 300 Processing helix chain 'H' and resid 12 through 37 removed outlier: 4.132A pdb=" N ARG H 37 " --> pdb=" O THR H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 69 No H-bonds generated for 'chain 'H' and resid 67 through 69' 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: 3.995A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 243 removed outlier: 3.840A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 258 Processing helix chain 'A' and resid 4 through 10 Processing helix chain 'A' and resid 13 through 37 Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'B' and resid 14 through 45 Processing helix chain 'D' and resid 2 through 10 removed outlier: 4.436A pdb=" N TYR D 5 " --> pdb=" O SER D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 37 Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'E' and resid 14 through 45 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 14 through 45 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 14 through 45 Processing helix chain 'K' and resid 4 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 14 through 45 Processing helix chain 'O' and resid 4 through 9 Processing helix chain 'O' and resid 13 through 37 Processing helix chain 'O' and resid 43 through 50 Processing helix chain 'P' and resid 14 through 45 Processing helix chain 'Q' and resid 4 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 14 through 45 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 45 Processing helix chain 'U' and resid 4 through 9 Processing helix chain 'U' and resid 13 through 37 Processing helix chain 'U' and resid 43 through 50 Processing helix chain 'V' and resid 14 through 45 Processing helix chain 'W' and resid 4 through 9 Processing helix chain 'W' and resid 13 through 37 Processing helix chain 'W' and resid 43 through 50 Processing helix chain 'C' and resid 14 through 45 Processing helix chain '3' and resid 5 through 9 Processing helix chain '3' and resid 13 through 37 Processing helix chain '3' and resid 43 through 50 Processing helix chain 'Z' and resid 14 through 45 Processing helix chain '1' and resid 13 through 37 Processing helix chain '1' and resid 43 through 50 Processing helix chain '2' and resid 14 through 45 Processing helix chain '7' and resid 4 through 9 Processing helix chain '7' and resid 13 through 37 Processing helix chain '8' and resid 14 through 45 Processing helix chain '9' and resid 4 through 9 Processing helix chain '9' and resid 13 through 37 Processing helix chain '9' and resid 43 through 50 Processing helix chain '0' and resid 14 through 45 Processing helix chain 'X' and resid 10 through 12 No H-bonds generated for 'chain 'X' and resid 10 through 12' Processing helix chain 'X' and resid 15 through 54 Processing helix chain 'Y' and resid 6 through 28 Processing helix chain 'Y' and resid 32 through 48 Processing helix chain 'l' and resid 6 through 9 Processing helix chain 'l' and resid 32 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 80 through 82 No H-bonds generated for 'chain 'l' and resid 80 through 82' Processing helix chain 'l' and resid 84 through 111 Processing helix chain 'l' and resid 116 through 132 removed outlier: 3.571A pdb=" N PHE l 123 " --> pdb=" O PHE l 119 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA l 124 " --> pdb=" O ALA l 120 " (cutoff:3.500A) Processing helix chain 'l' and resid 134 through 139 Processing helix chain 'l' and resid 142 through 144 No H-bonds generated for 'chain 'l' and resid 142 through 144' Processing helix chain 'l' and resid 152 through 164 removed outlier: 3.981A 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 250 Processing helix chain 'l' and resid 259 through 267 removed outlier: 4.358A pdb=" N TRP l 265 " --> pdb=" O ASP l 261 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N TRP l 266 " --> pdb=" O TRP l 262 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL l 267 " --> pdb=" O TRP l 263 " (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 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 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 229 removed outlier: 4.788A pdb=" N ARG m 228 " --> pdb=" O LEU m 224 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N PHE m 229 " --> pdb=" O ALA m 225 " (cutoff:3.500A) 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: 3.753A pdb=" N VAL m 276 " --> pdb=" O MET m 272 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR m 277 " --> pdb=" O ALA m 273 " (cutoff:3.500A) Processing helix chain 'm' and resid 294 through 300 Processing helix chain 'h' and resid 12 through 37 removed outlier: 4.132A pdb=" N ARG h 37 " --> pdb=" O THR h 33 " (cutoff:3.500A) Processing helix chain 'h' and resid 67 through 69 No H-bonds generated for 'chain 'h' and resid 67 through 69' 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: 3.995A pdb=" N ALA h 214 " --> pdb=" O ASP h 211 " (cutoff:3.500A) Processing helix chain 'h' and resid 227 through 243 removed outlier: 3.840A pdb=" N LEU h 241 " --> pdb=" O VAL h 237 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N MET h 242 " --> pdb=" O ALA h 238 " (cutoff:3.500A) Processing helix chain 'h' and resid 251 through 258 Processing helix chain 'a' and resid 4 through 10 Processing helix chain 'a' and resid 13 through 37 Processing helix chain 'a' and resid 43 through 50 Processing helix chain 'b' and resid 14 through 45 Processing helix chain 'd' and resid 2 through 10 removed outlier: 4.436A pdb=" N TYR d 5 " --> pdb=" O SER d 2 " (cutoff:3.500A) Processing helix chain 'd' and resid 13 through 37 Processing helix chain 'd' and resid 43 through 50 Processing helix chain 'e' and resid 14 through 45 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 14 through 45 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 14 through 45 Processing helix chain 'k' and resid 4 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 14 through 45 Processing helix chain 'o' and resid 4 through 9 Processing helix chain 'o' and resid 13 through 37 Processing helix chain 'o' and resid 43 through 50 Processing helix chain 'p' and resid 14 through 45 Processing helix chain 'q' and resid 4 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 14 through 45 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 45 Processing helix chain 'u' and resid 4 through 9 Processing helix chain 'u' and resid 13 through 37 Processing helix chain 'u' and resid 43 through 50 Processing helix chain 'v' and resid 14 through 45 Processing helix chain 'w' and resid 4 through 9 Processing helix chain 'w' and resid 13 through 37 Processing helix chain 'w' and resid 43 through 50 Processing helix chain 'c' and resid 14 through 45 Processing helix chain '5' and resid 5 through 9 Processing helix chain '5' and resid 13 through 37 Processing helix chain '5' and resid 43 through 50 Processing helix chain 'z' and resid 14 through 45 Processing helix chain 'b1' and resid 13 through 37 Processing helix chain 'b1' and resid 43 through 50 Processing helix chain '4' and resid 14 through 45 Processing helix chain '6' and resid 4 through 9 Processing helix chain '6' and resid 13 through 37 Processing helix chain 'b8' and resid 14 through 45 Processing helix chain 'b9' and resid 4 through 9 Processing helix chain 'b9' and resid 13 through 37 Processing helix chain 'b9' and resid 43 through 50 Processing helix chain 'b0' and resid 14 through 45 Processing helix chain 'x' and resid 10 through 12 No H-bonds generated for 'chain 'x' and resid 10 through 12' Processing helix chain 'x' and resid 15 through 54 Processing helix chain 'y' and resid 6 through 28 Processing helix chain 'y' and resid 32 through 48 Processing sheet with id= A, first strand: chain 'H' and resid 62 through 65 Processing sheet with id= B, first strand: chain 'H' and resid 87 through 89 Processing sheet with id= C, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.805A pdb=" N GLU H 180 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE H 167 " --> pdb=" O PHE H 178 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N PHE H 178 " --> pdb=" O ILE H 167 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 202 through 204 removed outlier: 3.828A pdb=" N GLY H 162 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'h' and resid 62 through 65 Processing sheet with id= F, first strand: chain 'h' and resid 87 through 89 Processing sheet with id= G, first strand: chain 'h' and resid 131 through 133 removed outlier: 6.805A pdb=" N GLU h 180 " --> pdb=" O VAL h 165 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE h 167 " --> pdb=" O PHE h 178 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N PHE h 178 " --> pdb=" O ILE h 167 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'h' and resid 202 through 204 removed outlier: 3.828A pdb=" N GLY h 162 " --> pdb=" O VAL h 153 " (cutoff:3.500A) 2302 hydrogen bonds defined for protein. 6624 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: 14.30 Time building geometry restraints manager: 20.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.35: 11995 1.35 - 1.55: 34061 1.55 - 1.76: 50 1.76 - 1.97: 338 1.97 - 2.18: 256 Bond restraints: 46700 Sorted by residual: bond pdb=" OB3 CDL M 407 " pdb=" PB2 CDL M 407 " ideal model delta sigma weight residual 1.529 1.455 0.074 1.00e-02 1.00e+04 5.44e+01 bond pdb=" OB3 CDL m 407 " pdb=" PB2 CDL m 407 " ideal model delta sigma weight residual 1.529 1.456 0.073 1.00e-02 1.00e+04 5.34e+01 bond pdb=" OA3 CDL m 407 " pdb=" PA1 CDL m 407 " ideal model delta sigma weight residual 1.529 1.458 0.071 1.00e-02 1.00e+04 5.03e+01 bond pdb=" OA3 CDL M 407 " pdb=" PA1 CDL M 407 " ideal model delta sigma weight residual 1.529 1.458 0.071 1.00e-02 1.00e+04 5.03e+01 bond pdb=" OB3 CDL F 102 " pdb=" PB2 CDL F 102 " ideal model delta sigma weight residual 1.529 1.459 0.070 1.00e-02 1.00e+04 4.88e+01 ... (remaining 46695 not shown) Histogram of bond angle deviations from ideal: 84.75 - 100.47: 286 100.47 - 116.19: 30060 116.19 - 131.91: 33205 131.91 - 147.63: 477 147.63 - 163.36: 128 Bond angle restraints: 64156 Sorted by residual: angle pdb=" O12 PC1 A 104 " pdb=" P PC1 A 104 " pdb=" O14 PC1 A 104 " ideal model delta sigma weight residual 123.67 100.39 23.28 3.00e+00 1.11e-01 6.02e+01 angle pdb=" O12 PC1 a 104 " pdb=" P PC1 a 104 " pdb=" O14 PC1 a 104 " ideal model delta sigma weight residual 123.67 100.41 23.26 3.00e+00 1.11e-01 6.01e+01 angle pdb=" O12 PC1 h 301 " pdb=" P PC1 h 301 " pdb=" O14 PC1 h 301 " ideal model delta sigma weight residual 123.67 100.85 22.82 3.00e+00 1.11e-01 5.78e+01 angle pdb=" O12 PC1 H 301 " pdb=" P PC1 H 301 " pdb=" O14 PC1 H 301 " ideal model delta sigma weight residual 123.67 100.85 22.82 3.00e+00 1.11e-01 5.78e+01 angle pdb=" O12 PC1 D 101 " pdb=" P PC1 D 101 " pdb=" O14 PC1 D 101 " ideal model delta sigma weight residual 123.67 100.96 22.71 3.00e+00 1.11e-01 5.73e+01 ... (remaining 64151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.57: 24094 31.57 - 63.13: 826 63.13 - 94.70: 94 94.70 - 126.27: 32 126.27 - 157.84: 2 Dihedral angle restraints: 25048 sinusoidal: 11706 harmonic: 13342 Sorted by residual: dihedral pdb=" C27 U10 l 304 " pdb=" C28 U10 l 304 " pdb=" C29 U10 l 304 " pdb=" C31 U10 l 304 " ideal model delta sinusoidal sigma weight residual -178.28 -20.45 -157.84 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" C27 U10 L 304 " pdb=" C28 U10 L 304 " pdb=" C29 U10 L 304 " pdb=" C31 U10 L 304 " ideal model delta sinusoidal sigma weight residual -178.28 -20.48 -157.80 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" C3M U10 L 305 " pdb=" C3 U10 L 305 " pdb=" O3 U10 L 305 " pdb=" C4 U10 L 305 " ideal model delta sinusoidal sigma weight residual 244.38 125.33 119.05 1 2.00e+01 2.50e-03 3.57e+01 ... (remaining 25045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4890 0.048 - 0.096: 1162 0.096 - 0.143: 176 0.143 - 0.191: 6 0.191 - 0.239: 8 Chirality restraints: 6242 Sorted by residual: chirality pdb=" C2C BPH m 404 " pdb=" C1C BPH m 404 " pdb=" C3C BPH m 404 " pdb=" CMC BPH m 404 " both_signs ideal model delta sigma weight residual False -2.81 -2.57 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C2C BPH M 404 " pdb=" C1C BPH M 404 " pdb=" C3C BPH M 404 " pdb=" CMC BPH M 404 " both_signs ideal model delta sigma weight residual False -2.81 -2.57 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C3C BPH L 303 " pdb=" C2C BPH L 303 " pdb=" C4C BPH L 303 " pdb=" CAC BPH L 303 " both_signs ideal model delta sigma weight residual False 2.83 2.61 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 6239 not shown) Planarity restraints: 7898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BPH m 404 " 0.013 2.00e-02 2.50e+03 4.75e-02 5.07e+01 pdb=" C1D BPH m 404 " 0.015 2.00e-02 2.50e+03 pdb=" C2D BPH m 404 " -0.024 2.00e-02 2.50e+03 pdb=" C3D BPH m 404 " -0.042 2.00e-02 2.50e+03 pdb=" C4D BPH m 404 " -0.024 2.00e-02 2.50e+03 pdb=" CAD BPH m 404 " 0.106 2.00e-02 2.50e+03 pdb=" CHA BPH m 404 " -0.045 2.00e-02 2.50e+03 pdb=" CHD BPH m 404 " 0.044 2.00e-02 2.50e+03 pdb=" CMD BPH m 404 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BPH M 404 " -0.013 2.00e-02 2.50e+03 4.74e-02 5.05e+01 pdb=" C1D BPH M 404 " -0.014 2.00e-02 2.50e+03 pdb=" C2D BPH M 404 " 0.024 2.00e-02 2.50e+03 pdb=" C3D BPH M 404 " 0.042 2.00e-02 2.50e+03 pdb=" C4D BPH M 404 " 0.023 2.00e-02 2.50e+03 pdb=" CAD BPH M 404 " -0.106 2.00e-02 2.50e+03 pdb=" CHA BPH M 404 " 0.045 2.00e-02 2.50e+03 pdb=" CHD BPH M 404 " -0.044 2.00e-02 2.50e+03 pdb=" CMD BPH M 404 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BPH l 303 " 0.016 2.00e-02 2.50e+03 3.05e-02 2.10e+01 pdb=" C1D BPH l 303 " 0.007 2.00e-02 2.50e+03 pdb=" C2D BPH l 303 " -0.017 2.00e-02 2.50e+03 pdb=" C3D BPH l 303 " -0.034 2.00e-02 2.50e+03 pdb=" C4D BPH l 303 " -0.015 2.00e-02 2.50e+03 pdb=" CAD BPH l 303 " 0.068 2.00e-02 2.50e+03 pdb=" CHA BPH l 303 " -0.027 2.00e-02 2.50e+03 pdb=" CHD BPH l 303 " 0.025 2.00e-02 2.50e+03 pdb=" CMD BPH l 303 " -0.021 2.00e-02 2.50e+03 ... (remaining 7895 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 900 2.69 - 3.24: 41380 3.24 - 3.80: 78657 3.80 - 4.35: 105602 4.35 - 4.90: 172873 Nonbonded interactions: 399412 Sorted by model distance: nonbonded pdb=" NE2 HIS l 190 " pdb="FE FE2 m 401 " model vdw 2.138 3.080 nonbonded pdb=" NE2 HIS L 190 " pdb="FE FE2 M 401 " model vdw 2.138 3.080 nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE2 M 401 " model vdw 2.147 3.000 nonbonded pdb=" OE2 GLU m 234 " pdb="FE FE2 m 401 " model vdw 2.147 3.000 nonbonded pdb=" NE2 HIS m 219 " pdb="FE FE2 m 401 " model vdw 2.163 3.080 ... (remaining 399407 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 '0' and resid 8 through 49) selection = (chain '8' and resid 8 through 49) selection = (chain 'B' and resid 8 through 49) selection = (chain 'C' and resid 8 through 49) selection = (chain 'E' and resid 8 through 49) selection = (chain 'G' and resid 8 through 49) selection = (chain 'J' and resid 8 through 49) selection = (chain 'N' and resid 8 through 49) selection = (chain 'P' and resid 8 through 49) selection = (chain 'R' and resid 8 through 49) selection = (chain 'T' and resid 8 through 49) selection = (chain 'V' and resid 8 through 49) selection = (chain 'Z' and resid 8 through 49) selection = (chain 'b' and resid 8 through 49) selection = (chain 'b0' and resid 8 through 49) selection = (chain 'b8' and resid 8 through 49) selection = (chain 'c' and resid 8 through 49) selection = (chain 'e' and resid 8 through 49) selection = (chain 'g' and resid 8 through 49) selection = (chain 'j' and resid 8 through 49) selection = (chain 'n' and resid 8 through 49) selection = (chain 'p' and resid 8 through 49) selection = (chain 'r' and resid 8 through 49) selection = (chain 't' and resid 8 through 49) selection = (chain 'v' and resid 8 through 49) selection = (chain 'z' and resid 8 through 49) } ncs_group { reference = (chain '1' and resid 8 through 48) selection = (chain '3' and resid 8 through 48) selection = (chain '5' and resid 8 through 48) selection = (chain '6' and resid 8 through 48) selection = (chain '7' and resid 8 through 48) selection = (chain 'I' and resid 8 through 48) selection = (chain 'K' and resid 8 through 48) selection = (chain 'O' and resid 8 through 48) selection = (chain 'U' and resid 8 through 48) selection = (chain 'W' and resid 8 through 48) selection = (chain 'b1' and resid 8 through 48) selection = (chain 'i' and resid 8 through 48) selection = (chain 'k' and resid 8 through 48) selection = (chain 'o' and resid 8 through 48) selection = (chain 'u' and resid 8 through 48) selection = (chain 'w' and resid 8 through 48) } ncs_group { reference = chain '2' selection = chain '4' } ncs_group { reference = (chain '9' and resid 1 through 55) selection = (chain 'A' and resid 1 through 55) selection = (chain 'D' and resid 1 through 55) selection = (chain 'F' and resid 1 through 55) selection = (chain 'Q' and resid 1 through 55) selection = (chain 'S' and resid 1 through 55) selection = (chain 'a' and resid 1 through 55) selection = (chain 'b9' and resid 1 through 55) selection = (chain 'd' and resid 1 through 55) selection = (chain 'f' and resid 1 through 55) selection = (chain 'q' and resid 1 through 55) selection = (chain 's' and resid 1 through 55) } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'X' selection = chain 'x' } ncs_group { reference = chain 'Y' selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.400 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: 16.420 Check model and map are aligned: 0.760 Set scattering table: 0.490 Process input model: 115.690 Find NCS groups from input model: 3.030 Set up NCS constraints: 0.400 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:12.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 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 : 0.007 0.077 46700 Z= 0.410 Angle : 0.959 23.281 64156 Z= 0.376 Chirality : 0.040 0.239 6242 Planarity : 0.004 0.047 7898 Dihedral : 15.584 157.836 16472 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.37 % Allowed : 3.04 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.88 (0.12), residues: 4482 helix: 2.64 (0.09), residues: 2976 sheet: -0.81 (0.74), residues: 48 loop : 0.50 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP l 263 HIS 0.009 0.001 HIS l 153 PHE 0.018 0.001 PHE h 20 TYR 0.013 0.001 TYR m 198 ARG 0.004 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 871 time to evaluate : 4.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 168 MET cc_start: 0.8870 (mmm) cc_final: 0.8598 (mmm) REVERT: M 216 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.8933 (t80) REVERT: H 134 MET cc_start: 0.7995 (ttp) cc_final: 0.7640 (ttp) REVERT: D 5 TYR cc_start: 0.9034 (p90) cc_final: 0.8715 (p90) REVERT: E 13 THR cc_start: 0.8286 (p) cc_final: 0.7939 (t) REVERT: F 15 ARG cc_start: 0.7509 (mtt-85) cc_final: 0.7095 (mtm110) REVERT: G 25 MET cc_start: 0.8809 (mmm) cc_final: 0.8522 (mmt) REVERT: O 11 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.7745 (m-80) REVERT: W 38 THR cc_start: 0.7978 (p) cc_final: 0.7613 (t) REVERT: C 25 MET cc_start: 0.7014 (mmm) cc_final: 0.6744 (tpp) REVERT: 8 25 MET cc_start: 0.8875 (mmm) cc_final: 0.8595 (mmm) REVERT: m 38 LEU cc_start: 0.9103 (tp) cc_final: 0.8896 (tp) REVERT: m 110 LYS cc_start: 0.7947 (mtmm) cc_final: 0.7745 (mptt) REVERT: m 168 MET cc_start: 0.8878 (mmm) cc_final: 0.8529 (mmm) REVERT: h 134 MET cc_start: 0.7972 (ttp) cc_final: 0.7604 (ttp) REVERT: d 5 TYR cc_start: 0.9035 (p90) cc_final: 0.8726 (p90) REVERT: e 13 THR cc_start: 0.8299 (p) cc_final: 0.7948 (t) REVERT: f 15 ARG cc_start: 0.7521 (mtt-85) cc_final: 0.7121 (mtm110) REVERT: g 25 MET cc_start: 0.8811 (mmm) cc_final: 0.8528 (mmt) REVERT: n 14 ASP cc_start: 0.7638 (t70) cc_final: 0.7375 (t0) REVERT: o 11 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.7639 (m-80) REVERT: c 25 MET cc_start: 0.6961 (mmm) cc_final: 0.6696 (tpp) REVERT: b8 25 MET cc_start: 0.8869 (mmm) cc_final: 0.8581 (mmm) outliers start: 14 outliers final: 1 residues processed: 883 average time/residue: 1.3508 time to fit residues: 1505.9690 Evaluate side-chains 694 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 690 time to evaluate : 4.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain o residue 11 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 366 optimal weight: 0.6980 chunk 328 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 chunk 112 optimal weight: 0.3980 chunk 221 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 340 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 394 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 GLN ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN F 20 GLN J 16 GLN N 16 GLN O 20 GLN Q 20 GLN ** V 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 20 GLN 9 52 ASN X 66 ASN ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 77 GLN ** m 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 GLN f 20 GLN j 16 GLN k 20 GLN n 16 GLN o 20 GLN q 20 GLN r 16 GLN ** v 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 GLN b9 52 ASN x 66 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 46700 Z= 0.268 Angle : 0.646 14.786 64156 Z= 0.265 Chirality : 0.038 0.151 6242 Planarity : 0.004 0.039 7898 Dihedral : 16.814 124.095 8438 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.43 % Allowed : 10.04 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.75 (0.12), residues: 4482 helix: 2.55 (0.09), residues: 2956 sheet: -0.73 (0.76), residues: 48 loop : 0.46 (0.17), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP M 252 HIS 0.010 0.001 HIS M 266 PHE 0.020 0.001 PHE h 20 TYR 0.016 0.001 TYR Q 41 ARG 0.005 0.000 ARG o 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 711 time to evaluate : 4.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 100 GLU cc_start: 0.7881 (pm20) cc_final: 0.7644 (pm20) REVERT: M 168 MET cc_start: 0.8828 (mmm) cc_final: 0.8586 (mmm) REVERT: H 43 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7288 (mm-30) REVERT: H 134 MET cc_start: 0.7978 (ttp) cc_final: 0.7599 (ttp) REVERT: A 30 MET cc_start: 0.8217 (ttt) cc_final: 0.7989 (ttp) REVERT: D 5 TYR cc_start: 0.9000 (p90) cc_final: 0.8735 (p90) REVERT: E 13 THR cc_start: 0.8281 (p) cc_final: 0.7928 (t) REVERT: F 15 ARG cc_start: 0.7456 (mtt-85) cc_final: 0.7096 (mtm110) REVERT: G 25 MET cc_start: 0.8770 (mmm) cc_final: 0.8553 (mmp) REVERT: I 6 LYS cc_start: 0.8978 (mtpp) cc_final: 0.8757 (mtpp) REVERT: O 11 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.7622 (m-80) REVERT: O 33 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8218 (tp) REVERT: C 25 MET cc_start: 0.7120 (mmm) cc_final: 0.6742 (tpp) REVERT: X 28 MET cc_start: 0.7611 (tpt) cc_final: 0.7315 (mmm) REVERT: X 61 GLN cc_start: 0.7623 (pt0) cc_final: 0.7392 (tt0) REVERT: m 38 LEU cc_start: 0.9136 (tp) cc_final: 0.8906 (tp) REVERT: m 100 GLU cc_start: 0.7884 (pm20) cc_final: 0.7646 (pm20) REVERT: m 110 LYS cc_start: 0.8031 (mtmm) cc_final: 0.7805 (mptt) REVERT: m 168 MET cc_start: 0.8823 (mmm) cc_final: 0.8586 (mmm) REVERT: h 43 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7236 (mm-30) REVERT: h 134 MET cc_start: 0.7992 (ttp) cc_final: 0.7606 (ttp) REVERT: a 30 MET cc_start: 0.8215 (ttt) cc_final: 0.7985 (ttp) REVERT: d 5 TYR cc_start: 0.8998 (p90) cc_final: 0.8734 (p90) REVERT: e 13 THR cc_start: 0.8292 (p) cc_final: 0.7729 (t) REVERT: e 15 GLU cc_start: 0.7719 (mp0) cc_final: 0.7419 (mp0) REVERT: f 15 ARG cc_start: 0.7461 (mtt-85) cc_final: 0.7094 (mtm110) REVERT: g 25 MET cc_start: 0.8771 (mmm) cc_final: 0.8547 (mmp) REVERT: i 6 LYS cc_start: 0.8977 (mtpp) cc_final: 0.8761 (mtpp) REVERT: o 11 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.7603 (m-80) REVERT: o 33 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8225 (tp) REVERT: c 25 MET cc_start: 0.7086 (mmm) cc_final: 0.6707 (tpp) REVERT: x 28 MET cc_start: 0.7594 (tpt) cc_final: 0.7280 (mmm) REVERT: x 61 GLN cc_start: 0.7599 (pt0) cc_final: 0.7389 (tt0) outliers start: 131 outliers final: 55 residues processed: 761 average time/residue: 1.3622 time to fit residues: 1310.1301 Evaluate side-chains 731 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 670 time to evaluate : 4.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain H residue 255 MET Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain W residue 40 SER Chi-restraints excluded: chain W residue 47 SER Chi-restraints excluded: chain 3 residue 47 SER Chi-restraints excluded: chain 7 residue 37 SER Chi-restraints excluded: chain X residue 60 ASN Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain m residue 54 SER Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain h residue 255 MET Chi-restraints excluded: chain a residue 3 LYS Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 26 SER Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 40 LEU Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain n residue 13 THR Chi-restraints excluded: chain n residue 36 ILE Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain o residue 37 SER Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 37 SER Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain w residue 47 SER Chi-restraints excluded: chain 5 residue 47 SER Chi-restraints excluded: chain 6 residue 37 SER Chi-restraints excluded: chain x residue 60 ASN Chi-restraints excluded: chain x residue 66 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 219 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 328 optimal weight: 1.9990 chunk 268 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 394 optimal weight: 8.9990 chunk 426 optimal weight: 3.9990 chunk 351 optimal weight: 8.9990 chunk 391 optimal weight: 0.0570 chunk 134 optimal weight: 9.9990 chunk 316 optimal weight: 0.9980 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN F 20 GLN K 20 GLN O 20 GLN R 16 GLN T 16 GLN 9 52 ASN ** X 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 GLN k 20 GLN r 16 GLN t 16 GLN b9 52 ASN ** x 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 46700 Z= 0.231 Angle : 0.625 14.757 64156 Z= 0.255 Chirality : 0.037 0.166 6242 Planarity : 0.003 0.038 7898 Dihedral : 16.361 121.756 8434 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.83 % Allowed : 11.45 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.70 (0.12), residues: 4482 helix: 2.51 (0.09), residues: 2972 sheet: -0.59 (0.78), residues: 48 loop : 0.42 (0.17), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 252 HIS 0.008 0.001 HIS l 153 PHE 0.019 0.001 PHE h 20 TYR 0.014 0.001 TYR A 41 ARG 0.004 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 686 time to evaluate : 4.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 139 MET cc_start: 0.9183 (mtp) cc_final: 0.8942 (mtm) REVERT: M 100 GLU cc_start: 0.7904 (pm20) cc_final: 0.7681 (pm20) REVERT: M 168 MET cc_start: 0.8805 (mmm) cc_final: 0.8601 (mmm) REVERT: H 43 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7295 (mm-30) REVERT: H 134 MET cc_start: 0.7962 (ttp) cc_final: 0.7550 (ttp) REVERT: A 30 MET cc_start: 0.8214 (ttt) cc_final: 0.7992 (ttp) REVERT: D 5 TYR cc_start: 0.8992 (p90) cc_final: 0.8699 (p90) REVERT: E 13 THR cc_start: 0.8332 (p) cc_final: 0.7789 (t) REVERT: E 15 GLU cc_start: 0.7738 (mp0) cc_final: 0.7438 (mp0) REVERT: F 15 ARG cc_start: 0.7457 (mtt-85) cc_final: 0.7104 (mtm110) REVERT: G 25 MET cc_start: 0.8762 (mmm) cc_final: 0.8539 (mmp) REVERT: I 6 LYS cc_start: 0.8893 (mtpp) cc_final: 0.8497 (mtmm) REVERT: O 11 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.7558 (m-80) REVERT: O 33 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8221 (tp) REVERT: T 46 ARG cc_start: 0.8139 (mtt180) cc_final: 0.7771 (mtt180) REVERT: V 25 MET cc_start: 0.8249 (tpp) cc_final: 0.7734 (mmm) REVERT: C 25 MET cc_start: 0.7112 (mmm) cc_final: 0.6720 (tpp) REVERT: 3 9 MET cc_start: 0.3859 (mmm) cc_final: 0.2774 (mmm) REVERT: X 28 MET cc_start: 0.7660 (tpt) cc_final: 0.7288 (mmm) REVERT: l 139 MET cc_start: 0.9172 (mtp) cc_final: 0.8937 (mtm) REVERT: m 38 LEU cc_start: 0.9148 (tp) cc_final: 0.8900 (tp) REVERT: m 100 GLU cc_start: 0.7916 (pm20) cc_final: 0.7699 (pm20) REVERT: m 110 LYS cc_start: 0.8059 (mtmm) cc_final: 0.7823 (mptt) REVERT: m 168 MET cc_start: 0.8807 (mmm) cc_final: 0.8603 (mmm) REVERT: m 216 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8862 (t80) REVERT: h 43 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7187 (mm-30) REVERT: h 134 MET cc_start: 0.7950 (ttp) cc_final: 0.7545 (ttp) REVERT: a 30 MET cc_start: 0.8212 (ttt) cc_final: 0.7993 (ttp) REVERT: d 5 TYR cc_start: 0.8992 (p90) cc_final: 0.8690 (p90) REVERT: e 13 THR cc_start: 0.8317 (p) cc_final: 0.7960 (t) REVERT: f 15 ARG cc_start: 0.7459 (mtt-85) cc_final: 0.7109 (mtm110) REVERT: g 25 MET cc_start: 0.8756 (mmm) cc_final: 0.8537 (mmp) REVERT: i 6 LYS cc_start: 0.8888 (mtpp) cc_final: 0.8501 (mtmm) REVERT: o 11 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.7602 (m-80) REVERT: o 33 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8239 (tp) REVERT: v 25 MET cc_start: 0.8245 (tpp) cc_final: 0.7864 (mmm) REVERT: c 25 MET cc_start: 0.7082 (mmm) cc_final: 0.6691 (tpp) REVERT: 5 9 MET cc_start: 0.3774 (mmm) cc_final: 0.2877 (mmm) REVERT: x 28 MET cc_start: 0.7677 (tpt) cc_final: 0.7331 (mmm) outliers start: 108 outliers final: 53 residues processed: 729 average time/residue: 1.3545 time to fit residues: 1247.2553 Evaluate side-chains 720 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 660 time to evaluate : 4.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain H residue 255 MET Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain O residue 6 LYS Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain 3 residue 47 SER Chi-restraints excluded: chain 7 residue 37 SER Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain m residue 54 SER Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain h residue 255 MET Chi-restraints excluded: chain a residue 3 LYS Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 26 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 40 LEU Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain k residue 9 MET Chi-restraints excluded: chain n residue 13 THR Chi-restraints excluded: chain n residue 36 ILE Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain o residue 6 LYS Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain s residue 16 VAL Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 37 SER Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain 6 residue 37 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 390 optimal weight: 7.9990 chunk 296 optimal weight: 0.8980 chunk 204 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 265 optimal weight: 0.9990 chunk 396 optimal weight: 5.9990 chunk 419 optimal weight: 2.9990 chunk 207 optimal weight: 0.0370 chunk 375 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN Q 20 GLN R 16 GLN T 16 GLN 8 18 GLN 9 52 ASN X 66 ASN ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 25 ASN ** m 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 GLN k 20 GLN q 20 GLN t 16 GLN b9 52 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 46700 Z= 0.196 Angle : 0.597 14.752 64156 Z= 0.244 Chirality : 0.037 0.160 6242 Planarity : 0.003 0.037 7898 Dihedral : 15.937 122.154 8434 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.17 % Allowed : 11.50 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.79 (0.12), residues: 4482 helix: 2.58 (0.09), residues: 2972 sheet: -0.46 (0.80), residues: 48 loop : 0.44 (0.17), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 252 HIS 0.008 0.001 HIS l 153 PHE 0.018 0.001 PHE H 20 TYR 0.016 0.001 TYR F 5 ARG 0.003 0.000 ARG a 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 706 time to evaluate : 4.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 100 GLU cc_start: 0.7888 (pm20) cc_final: 0.7658 (pm20) REVERT: M 168 MET cc_start: 0.8795 (mmm) cc_final: 0.8578 (mmm) REVERT: H 43 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7358 (mm-30) REVERT: H 134 MET cc_start: 0.7940 (ttp) cc_final: 0.7539 (ttp) REVERT: H 255 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6725 (mtp) REVERT: A 1 MET cc_start: 0.5388 (OUTLIER) cc_final: 0.3897 (mmt) REVERT: A 30 MET cc_start: 0.8202 (ttt) cc_final: 0.7972 (ttp) REVERT: D 5 TYR cc_start: 0.8970 (p90) cc_final: 0.8702 (p90) REVERT: E 13 THR cc_start: 0.8284 (p) cc_final: 0.7963 (t) REVERT: F 15 ARG cc_start: 0.7430 (mtt-85) cc_final: 0.7096 (mtm110) REVERT: G 25 MET cc_start: 0.8761 (mmm) cc_final: 0.8521 (mmp) REVERT: I 6 LYS cc_start: 0.8853 (mtpp) cc_final: 0.8416 (mtmm) REVERT: O 11 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.7687 (m-80) REVERT: C 25 MET cc_start: 0.7078 (mmm) cc_final: 0.6793 (tpp) REVERT: X 28 MET cc_start: 0.7666 (tpt) cc_final: 0.7303 (mmm) REVERT: X 61 GLN cc_start: 0.7762 (tt0) cc_final: 0.7476 (tt0) REVERT: m 100 GLU cc_start: 0.7892 (pm20) cc_final: 0.7668 (pm20) REVERT: m 168 MET cc_start: 0.8795 (mmm) cc_final: 0.8581 (mmm) REVERT: m 216 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8830 (t80) REVERT: h 43 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7178 (mm-30) REVERT: h 134 MET cc_start: 0.7929 (ttp) cc_final: 0.7537 (ttp) REVERT: h 255 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6734 (mtp) REVERT: a 30 MET cc_start: 0.8206 (ttt) cc_final: 0.7965 (ttp) REVERT: d 5 TYR cc_start: 0.8977 (p90) cc_final: 0.8737 (p90) REVERT: e 13 THR cc_start: 0.8327 (p) cc_final: 0.7742 (t) REVERT: e 15 GLU cc_start: 0.7727 (mp0) cc_final: 0.7465 (mp0) REVERT: f 15 ARG cc_start: 0.7425 (mtt-85) cc_final: 0.7086 (mtm110) REVERT: g 25 MET cc_start: 0.8750 (mmm) cc_final: 0.8519 (mmp) REVERT: i 6 LYS cc_start: 0.8849 (mtpp) cc_final: 0.8410 (mtmm) REVERT: o 11 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.7698 (m-80) REVERT: o 33 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8250 (tp) REVERT: c 25 MET cc_start: 0.7079 (mmm) cc_final: 0.6784 (tpp) REVERT: 5 9 MET cc_start: 0.4255 (mmm) cc_final: 0.3259 (mmm) REVERT: x 28 MET cc_start: 0.7675 (tpt) cc_final: 0.7310 (mmm) REVERT: x 61 GLN cc_start: 0.7755 (tt0) cc_final: 0.7464 (tt0) outliers start: 121 outliers final: 54 residues processed: 760 average time/residue: 1.3309 time to fit residues: 1282.9876 Evaluate side-chains 728 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 665 time to evaluate : 4.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain H residue 255 MET Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain W residue 40 SER Chi-restraints excluded: chain W residue 47 SER Chi-restraints excluded: chain X residue 60 ASN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain m residue 54 SER Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain h residue 242 MET Chi-restraints excluded: chain h residue 255 MET Chi-restraints excluded: chain a residue 3 LYS Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 26 SER Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 36 ILE Chi-restraints excluded: chain g residue 40 LEU Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain n residue 36 ILE Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 37 SER Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain w residue 47 SER Chi-restraints excluded: chain 5 residue 47 SER Chi-restraints excluded: chain x residue 60 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 349 optimal weight: 0.1980 chunk 238 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 312 optimal weight: 0.9980 chunk 173 optimal weight: 10.0000 chunk 357 optimal weight: 0.9990 chunk 289 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 chunk 376 optimal weight: 0.0000 chunk 105 optimal weight: 0.5980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN K 20 GLN N 16 GLN O 20 GLN P 16 GLN T 16 GLN 9 52 ASN ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 20 GLN n 16 GLN p 16 GLN t 16 GLN b9 52 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 46700 Z= 0.166 Angle : 0.581 14.690 64156 Z= 0.238 Chirality : 0.036 0.144 6242 Planarity : 0.003 0.037 7898 Dihedral : 15.645 122.274 8434 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.83 % Allowed : 12.66 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.83 (0.12), residues: 4482 helix: 2.61 (0.09), residues: 2988 sheet: -0.34 (0.82), residues: 48 loop : 0.41 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 3 8 HIS 0.007 0.001 HIS l 153 PHE 0.017 0.001 PHE h 20 TYR 0.019 0.001 TYR F 5 ARG 0.003 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 695 time to evaluate : 4.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 100 GLU cc_start: 0.7840 (pm20) cc_final: 0.7628 (pm20) REVERT: M 168 MET cc_start: 0.8774 (mmm) cc_final: 0.8558 (mmm) REVERT: M 182 HIS cc_start: 0.8816 (OUTLIER) cc_final: 0.8033 (p-80) REVERT: M 216 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8770 (t80) REVERT: H 43 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7292 (mm-30) REVERT: H 134 MET cc_start: 0.7916 (ttp) cc_final: 0.7562 (ttp) REVERT: H 255 MET cc_start: 0.6933 (OUTLIER) cc_final: 0.6709 (mtp) REVERT: A 1 MET cc_start: 0.5401 (OUTLIER) cc_final: 0.3641 (mmp) REVERT: A 30 MET cc_start: 0.8211 (ttt) cc_final: 0.7993 (ttt) REVERT: D 3 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8266 (mttp) REVERT: D 5 TYR cc_start: 0.8964 (p90) cc_final: 0.8502 (p90) REVERT: E 13 THR cc_start: 0.8305 (p) cc_final: 0.7780 (t) REVERT: E 14 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7542 (t70) REVERT: E 15 GLU cc_start: 0.7693 (mp0) cc_final: 0.7387 (mp0) REVERT: F 9 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.7879 (mpp) REVERT: F 15 ARG cc_start: 0.7415 (mtt-85) cc_final: 0.7076 (mtm110) REVERT: G 25 MET cc_start: 0.8750 (mmm) cc_final: 0.8511 (mmp) REVERT: I 6 LYS cc_start: 0.8801 (mtpp) cc_final: 0.8412 (mtmm) REVERT: O 11 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.7682 (m-80) REVERT: V 25 MET cc_start: 0.8269 (tpp) cc_final: 0.7576 (mmm) REVERT: C 25 MET cc_start: 0.7065 (mmm) cc_final: 0.6692 (tpp) REVERT: 3 9 MET cc_start: 0.4263 (mmm) cc_final: 0.3035 (mmm) REVERT: X 61 GLN cc_start: 0.7784 (tt0) cc_final: 0.7467 (tt0) REVERT: m 38 LEU cc_start: 0.9100 (tp) cc_final: 0.8834 (tp) REVERT: m 100 GLU cc_start: 0.7840 (pm20) cc_final: 0.7639 (pm20) REVERT: m 168 MET cc_start: 0.8776 (mmm) cc_final: 0.8561 (mmm) REVERT: m 182 HIS cc_start: 0.8811 (OUTLIER) cc_final: 0.8043 (p-80) REVERT: m 216 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8728 (t80) REVERT: h 43 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7130 (mm-30) REVERT: h 255 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.6718 (mtp) REVERT: a 30 MET cc_start: 0.8212 (ttt) cc_final: 0.7986 (ttp) REVERT: d 3 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8269 (mttp) REVERT: d 5 TYR cc_start: 0.8965 (p90) cc_final: 0.8531 (p90) REVERT: e 13 THR cc_start: 0.8293 (p) cc_final: 0.7813 (t) REVERT: e 14 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7565 (t70) REVERT: e 15 GLU cc_start: 0.7713 (mp0) cc_final: 0.7480 (mp0) REVERT: f 9 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7899 (mpp) REVERT: f 15 ARG cc_start: 0.7412 (mtt-85) cc_final: 0.7079 (mtm110) REVERT: g 25 MET cc_start: 0.8743 (mmm) cc_final: 0.8519 (mmp) REVERT: i 6 LYS cc_start: 0.8801 (mtpp) cc_final: 0.8418 (mtmm) REVERT: o 11 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.7693 (m-80) REVERT: v 25 MET cc_start: 0.8265 (tpp) cc_final: 0.7584 (mmm) REVERT: c 25 MET cc_start: 0.7031 (mmm) cc_final: 0.6657 (tpp) REVERT: x 61 GLN cc_start: 0.7812 (tt0) cc_final: 0.7500 (tt0) outliers start: 108 outliers final: 53 residues processed: 743 average time/residue: 1.3863 time to fit residues: 1314.3128 Evaluate side-chains 728 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 658 time to evaluate : 4.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain H residue 242 MET Chi-restraints excluded: chain H residue 255 MET Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 3 LYS Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain W residue 40 SER Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain X residue 60 ASN Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 54 SER Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 105 MET Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain h residue 242 MET Chi-restraints excluded: chain h residue 255 MET Chi-restraints excluded: chain a residue 3 LYS Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain d residue 3 LYS Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 26 SER Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 40 LEU Chi-restraints excluded: chain i residue 30 MET Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain n residue 13 THR Chi-restraints excluded: chain n residue 36 ILE Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 37 SER Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain w residue 45 GLU Chi-restraints excluded: chain w residue 47 SER Chi-restraints excluded: chain 5 residue 47 SER Chi-restraints excluded: chain x residue 60 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 141 optimal weight: 0.0270 chunk 377 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 246 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 419 optimal weight: 2.9990 chunk 348 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 220 optimal weight: 0.8980 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN N 16 GLN O 20 GLN Q 20 GLN T 16 GLN 7 20 GLN 9 52 ASN ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 16 GLN q 20 GLN t 16 GLN 6 20 GLN b9 52 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 46700 Z= 0.202 Angle : 0.602 14.452 64156 Z= 0.247 Chirality : 0.037 0.139 6242 Planarity : 0.003 0.038 7898 Dihedral : 15.581 121.799 8434 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.09 % Allowed : 13.02 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.73 (0.12), residues: 4482 helix: 2.54 (0.09), residues: 2988 sheet: -0.35 (0.82), residues: 48 loop : 0.39 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP m 252 HIS 0.009 0.001 HIS l 153 PHE 0.018 0.001 PHE H 20 TYR 0.021 0.001 TYR F 5 ARG 0.003 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 679 time to evaluate : 4.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 72 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7684 (pt0) REVERT: L 139 MET cc_start: 0.9163 (mtp) cc_final: 0.8958 (mtm) REVERT: L 258 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8791 (mm110) REVERT: M 100 GLU cc_start: 0.7836 (pm20) cc_final: 0.7617 (pm20) REVERT: M 168 MET cc_start: 0.8788 (mmm) cc_final: 0.8553 (mmm) REVERT: M 182 HIS cc_start: 0.8924 (OUTLIER) cc_final: 0.8594 (p-80) REVERT: M 216 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8786 (t80) REVERT: H 43 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7319 (mm-30) REVERT: H 134 MET cc_start: 0.7928 (ttp) cc_final: 0.7558 (ttp) REVERT: H 255 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6712 (mtp) REVERT: A 1 MET cc_start: 0.5468 (OUTLIER) cc_final: 0.3422 (mmp) REVERT: A 30 MET cc_start: 0.8214 (ttt) cc_final: 0.7989 (ttt) REVERT: D 5 TYR cc_start: 0.8973 (p90) cc_final: 0.8454 (p90) REVERT: E 13 THR cc_start: 0.8286 (p) cc_final: 0.7768 (t) REVERT: E 14 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7532 (t70) REVERT: E 15 GLU cc_start: 0.7724 (mp0) cc_final: 0.7405 (mp0) REVERT: F 9 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.7897 (mpp) REVERT: F 15 ARG cc_start: 0.7422 (mtt-85) cc_final: 0.7115 (mtm110) REVERT: G 25 MET cc_start: 0.8767 (mmm) cc_final: 0.8537 (mmp) REVERT: I 6 LYS cc_start: 0.8793 (mtpp) cc_final: 0.8422 (mtmm) REVERT: O 11 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.7690 (m-80) REVERT: Q 5 TYR cc_start: 0.7589 (p90) cc_final: 0.7256 (p90) REVERT: V 25 MET cc_start: 0.8248 (tpp) cc_final: 0.7937 (mmm) REVERT: C 25 MET cc_start: 0.7110 (mmm) cc_final: 0.6702 (tpp) REVERT: X 28 MET cc_start: 0.7502 (mmm) cc_final: 0.7286 (mmm) REVERT: X 61 GLN cc_start: 0.7813 (tt0) cc_final: 0.7553 (tt0) REVERT: l 72 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7681 (pt0) REVERT: m 38 LEU cc_start: 0.9131 (tp) cc_final: 0.8875 (tp) REVERT: m 100 GLU cc_start: 0.7843 (pm20) cc_final: 0.7630 (pm20) REVERT: m 168 MET cc_start: 0.8788 (mmm) cc_final: 0.8555 (mmm) REVERT: m 182 HIS cc_start: 0.9028 (OUTLIER) cc_final: 0.8217 (p-80) REVERT: m 216 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8824 (t80) REVERT: h 43 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7137 (mm-30) REVERT: h 255 MET cc_start: 0.6919 (OUTLIER) cc_final: 0.6698 (mtp) REVERT: a 1 MET cc_start: 0.5568 (OUTLIER) cc_final: 0.3835 (mmt) REVERT: a 30 MET cc_start: 0.8213 (ttt) cc_final: 0.7991 (ttt) REVERT: d 5 TYR cc_start: 0.8978 (p90) cc_final: 0.8507 (p90) REVERT: e 13 THR cc_start: 0.8328 (p) cc_final: 0.8013 (t) REVERT: e 14 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7608 (t70) REVERT: f 9 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.7898 (mpp) REVERT: f 15 ARG cc_start: 0.7424 (mtt-85) cc_final: 0.7120 (mtm110) REVERT: g 25 MET cc_start: 0.8759 (mmm) cc_final: 0.8544 (mmp) REVERT: i 6 LYS cc_start: 0.8815 (mtpp) cc_final: 0.8414 (mtmm) REVERT: o 11 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.7724 (m-80) REVERT: q 5 TYR cc_start: 0.7618 (p90) cc_final: 0.7253 (p90) REVERT: v 25 MET cc_start: 0.8243 (tpp) cc_final: 0.7626 (mmm) REVERT: c 25 MET cc_start: 0.7079 (mmm) cc_final: 0.6668 (tpp) REVERT: 5 9 MET cc_start: 0.4152 (mmm) cc_final: 0.3487 (mpp) REVERT: x 28 MET cc_start: 0.7489 (mmm) cc_final: 0.7277 (mmm) REVERT: x 61 GLN cc_start: 0.7814 (tt0) cc_final: 0.7535 (tt0) outliers start: 118 outliers final: 65 residues processed: 728 average time/residue: 1.3618 time to fit residues: 1252.2709 Evaluate side-chains 741 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 657 time to evaluate : 4.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 258 GLN Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain H residue 242 MET Chi-restraints excluded: chain H residue 255 MET Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain W residue 40 SER Chi-restraints excluded: chain W residue 47 SER Chi-restraints excluded: chain 3 residue 45 GLU Chi-restraints excluded: chain X residue 60 ASN Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 54 SER Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 105 MET Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain h residue 242 MET Chi-restraints excluded: chain h residue 255 MET Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 3 LYS Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 26 SER Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 40 LEU Chi-restraints excluded: chain i residue 30 MET Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain n residue 13 THR Chi-restraints excluded: chain n residue 36 ILE Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 37 SER Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain w residue 47 SER Chi-restraints excluded: chain 5 residue 45 GLU Chi-restraints excluded: chain 5 residue 47 SER Chi-restraints excluded: chain x residue 60 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 404 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 306 optimal weight: 3.9990 chunk 237 optimal weight: 0.4980 chunk 353 optimal weight: 0.9980 chunk 234 optimal weight: 0.9980 chunk 418 optimal weight: 2.9990 chunk 261 optimal weight: 0.6980 chunk 255 optimal weight: 0.9980 chunk 193 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN N 16 GLN O 20 GLN Q 20 GLN R 18 GLN T 16 GLN 9 52 ASN ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 GLN n 16 GLN o 20 GLN q 20 GLN r 18 GLN t 16 GLN b9 52 ASN x 66 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 46700 Z= 0.204 Angle : 0.605 14.590 64156 Z= 0.249 Chirality : 0.037 0.139 6242 Planarity : 0.003 0.040 7898 Dihedral : 15.478 122.131 8434 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.09 % Allowed : 13.36 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.70 (0.12), residues: 4482 helix: 2.50 (0.09), residues: 2990 sheet: -0.33 (0.82), residues: 48 loop : 0.39 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 5 8 HIS 0.008 0.001 HIS L 153 PHE 0.018 0.001 PHE h 20 TYR 0.022 0.001 TYR f 5 ARG 0.003 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 675 time to evaluate : 4.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 72 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7687 (pt0) REVERT: M 100 GLU cc_start: 0.7831 (pm20) cc_final: 0.7607 (pm20) REVERT: M 168 MET cc_start: 0.8786 (mmm) cc_final: 0.8552 (mmm) REVERT: M 182 HIS cc_start: 0.8903 (OUTLIER) cc_final: 0.8518 (p-80) REVERT: M 216 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8809 (t80) REVERT: H 43 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7306 (mm-30) REVERT: H 255 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6693 (mtp) REVERT: A 1 MET cc_start: 0.5451 (OUTLIER) cc_final: 0.3404 (mmp) REVERT: A 30 MET cc_start: 0.8212 (ttt) cc_final: 0.7979 (ttt) REVERT: D 5 TYR cc_start: 0.8994 (p90) cc_final: 0.8517 (p90) REVERT: E 13 THR cc_start: 0.8272 (p) cc_final: 0.7764 (t) REVERT: E 14 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7561 (t70) REVERT: E 15 GLU cc_start: 0.7744 (mp0) cc_final: 0.7430 (mp0) REVERT: F 9 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.7922 (mpp) REVERT: F 15 ARG cc_start: 0.7392 (mtt-85) cc_final: 0.7106 (mtm110) REVERT: G 25 MET cc_start: 0.8753 (mmm) cc_final: 0.8531 (mmp) REVERT: I 6 LYS cc_start: 0.8760 (mtpp) cc_final: 0.8401 (mtmm) REVERT: K 15 ARG cc_start: 0.7560 (mtp85) cc_final: 0.6828 (ptt180) REVERT: O 11 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.7649 (m-80) REVERT: V 25 MET cc_start: 0.8211 (tpp) cc_final: 0.7628 (mmm) REVERT: C 25 MET cc_start: 0.7122 (mmm) cc_final: 0.6720 (tpp) REVERT: 3 9 MET cc_start: 0.4076 (mmm) cc_final: 0.3316 (mpp) REVERT: X 61 GLN cc_start: 0.7829 (tt0) cc_final: 0.7563 (tt0) REVERT: l 72 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7692 (pt0) REVERT: m 38 LEU cc_start: 0.9140 (tp) cc_final: 0.8875 (tp) REVERT: m 100 GLU cc_start: 0.7837 (pm20) cc_final: 0.7620 (pm20) REVERT: m 168 MET cc_start: 0.8787 (mmm) cc_final: 0.8554 (mmm) REVERT: m 216 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8819 (t80) REVERT: h 43 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7135 (mm-30) REVERT: h 255 MET cc_start: 0.6917 (OUTLIER) cc_final: 0.6699 (mtp) REVERT: a 1 MET cc_start: 0.5571 (OUTLIER) cc_final: 0.3846 (mmt) REVERT: a 30 MET cc_start: 0.8216 (ttt) cc_final: 0.7982 (ttt) REVERT: d 5 TYR cc_start: 0.8986 (p90) cc_final: 0.8560 (p90) REVERT: e 13 THR cc_start: 0.8346 (p) cc_final: 0.7862 (t) REVERT: e 14 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7639 (t70) REVERT: e 15 GLU cc_start: 0.7735 (mp0) cc_final: 0.7456 (mp0) REVERT: f 9 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7903 (mpp) REVERT: f 15 ARG cc_start: 0.7397 (mtt-85) cc_final: 0.7109 (mtm110) REVERT: g 25 MET cc_start: 0.8759 (mmm) cc_final: 0.8546 (mmp) REVERT: i 6 LYS cc_start: 0.8775 (mtpp) cc_final: 0.8406 (mtmm) REVERT: o 9 MET cc_start: 0.7881 (mtp) cc_final: 0.7352 (mmt) REVERT: o 11 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.7712 (m-80) REVERT: v 25 MET cc_start: 0.8213 (tpp) cc_final: 0.7622 (mmm) REVERT: c 25 MET cc_start: 0.7085 (mmm) cc_final: 0.6673 (tpp) REVERT: 5 9 MET cc_start: 0.4337 (mmm) cc_final: 0.3070 (mmm) REVERT: x 61 GLN cc_start: 0.7834 (tt0) cc_final: 0.7557 (tt0) outliers start: 118 outliers final: 69 residues processed: 734 average time/residue: 1.3643 time to fit residues: 1268.7870 Evaluate side-chains 740 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 654 time to evaluate : 4.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 54 SER Chi-restraints excluded: chain M residue 128 SER Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain H residue 242 MET Chi-restraints excluded: chain H residue 255 MET Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain O residue 11 PHE Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain W residue 40 SER Chi-restraints excluded: chain W residue 47 SER Chi-restraints excluded: chain 3 residue 47 SER Chi-restraints excluded: chain 7 residue 37 SER Chi-restraints excluded: chain X residue 60 ASN Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 72 GLU Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 54 SER Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain h residue 242 MET Chi-restraints excluded: chain h residue 255 MET Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 3 LYS Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain d residue 2 SER Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 26 SER Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain g residue 40 LEU Chi-restraints excluded: chain i residue 30 MET Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain n residue 13 THR Chi-restraints excluded: chain n residue 36 ILE Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain o residue 11 PHE Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 40 LEU Chi-restraints excluded: chain w residue 7 ILE Chi-restraints excluded: chain w residue 37 SER Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain w residue 47 SER Chi-restraints excluded: chain 5 residue 47 SER Chi-restraints excluded: chain 6 residue 37 SER Chi-restraints excluded: chain x residue 60 ASN Chi-restraints excluded: chain x residue 66 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.6728 > 50: distance: 3 - 22: 25.977 distance: 9 - 27: 18.480 distance: 14 - 35: 32.164 distance: 17 - 22: 22.627 distance: 18 - 42: 33.059 distance: 22 - 23: 10.770 distance: 23 - 24: 20.624 distance: 23 - 26: 39.789 distance: 24 - 25: 12.207 distance: 24 - 27: 6.645 distance: 25 - 47: 24.393 distance: 27 - 28: 16.916 distance: 28 - 29: 23.466 distance: 28 - 31: 15.799 distance: 29 - 30: 12.337 distance: 29 - 35: 30.128 distance: 30 - 57: 50.826 distance: 31 - 32: 8.459 distance: 31 - 33: 14.633 distance: 32 - 34: 30.737 distance: 35 - 36: 37.910 distance: 36 - 37: 23.719 distance: 36 - 39: 25.664 distance: 37 - 38: 16.427 distance: 37 - 42: 18.805 distance: 38 - 65: 25.369 distance: 39 - 40: 31.775 distance: 39 - 41: 32.329 distance: 42 - 43: 25.323 distance: 43 - 44: 25.039 distance: 43 - 46: 33.052 distance: 44 - 45: 30.128 distance: 44 - 47: 9.945 distance: 45 - 70: 24.074 distance: 47 - 48: 9.577 distance: 48 - 49: 26.302 distance: 48 - 51: 19.501 distance: 49 - 50: 25.758 distance: 49 - 57: 20.032 distance: 50 - 77: 35.434 distance: 51 - 52: 21.608 distance: 52 - 53: 32.790 distance: 52 - 54: 23.944 distance: 53 - 55: 28.639 distance: 54 - 56: 35.356 distance: 55 - 56: 29.669 distance: 56 - 191: 21.578 distance: 57 - 58: 10.657 distance: 58 - 59: 22.902 distance: 58 - 61: 37.428 distance: 59 - 60: 23.486 distance: 59 - 65: 10.981 distance: 60 - 89: 41.301 distance: 61 - 62: 37.164 distance: 62 - 63: 24.617 distance: 62 - 64: 47.078 distance: 65 - 66: 3.959 distance: 66 - 69: 17.951 distance: 67 - 68: 9.373 distance: 67 - 70: 20.938 distance: 68 - 97: 17.412 distance: 70 - 71: 30.780 distance: 71 - 72: 21.519 distance: 71 - 74: 11.109 distance: 72 - 73: 20.414 distance: 72 - 77: 31.685 distance: 74 - 75: 16.329 distance: 74 - 76: 15.962 distance: 77 - 78: 30.678 distance: 78 - 79: 3.568 distance: 78 - 81: 29.709 distance: 79 - 80: 24.947 distance: 79 - 89: 19.284 distance: 81 - 82: 13.313 distance: 82 - 83: 20.121 distance: 82 - 84: 19.051 distance: 83 - 85: 5.903 distance: 84 - 86: 6.048 distance: 85 - 87: 13.822 distance: 86 - 87: 11.418 distance: 87 - 88: 31.631 distance: 89 - 90: 9.442 distance: 90 - 91: 14.566 distance: 90 - 93: 22.973 distance: 91 - 92: 19.621 distance: 91 - 97: 17.164 distance: 93 - 94: 16.612 distance: 93 - 95: 29.620 distance: 94 - 96: 30.901