Starting phenix.real_space_refine on Sat Feb 24 16:14:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vot_32059/02_2024/7vot_32059_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vot_32059/02_2024/7vot_32059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vot_32059/02_2024/7vot_32059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vot_32059/02_2024/7vot_32059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vot_32059/02_2024/7vot_32059_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vot_32059/02_2024/7vot_32059_updated.pdb" } resolution = 2.9 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= 0.002 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 26 5.49 5 Mg 64 5.21 5 S 176 5.16 5 C 31648 2.51 5 N 6276 2.21 5 O 6792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 44984 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: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1955 Classifications: {'peptide': 258} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 234} 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: 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: "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: 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: "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: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "C" 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: "3" 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: "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: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "2" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 328 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} 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: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "0" 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: "X" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "Y" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 375 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} 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: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1955 Classifications: {'peptide': 258} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 234} 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: 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: "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: 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: "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: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "c" 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: "5" 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: "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: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "4" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 328 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} 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: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "b0" 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: "x" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "y" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 375 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "L" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 412 Unusual residues: {'BCL': 3, 'BPB': 1, 'PC1': 2, 'U10': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 75 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: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 326 Unusual residues: {'BCL': 1, 'BPB': 1, 'CDL': 1, 'FE2': 1, 'SPO': 1, 'U10': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 32 Chain: "H" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 139 Unusual residues: {'CDL': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 69 Chain: "A" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 220 Unusual residues: {'BCL': 1, 'PC1': 3, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 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: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 185 Unusual residues: {'BCL': 1, 'PC1': 2, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 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: "G" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "I" 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: "J" 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: "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: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "R" 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: "S" 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: "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: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 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: "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: 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: "Z" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "2" 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: "7" 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: "8" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "9" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'BCL': 1, 'SPO': 1} 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: "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: "l" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 412 Unusual residues: {'BCL': 3, 'BPB': 1, 'PC1': 2, 'U10': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 75 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: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 326 Unusual residues: {'BCL': 1, 'BPB': 1, 'CDL': 1, 'FE2': 1, 'SPO': 1, 'U10': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 32 Chain: "h" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 139 Unusual residues: {'CDL': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 69 Chain: "a" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 220 Unusual residues: {'BCL': 1, 'PC1': 3, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 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: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 185 Unusual residues: {'BCL': 1, 'PC1': 2, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "e" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 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: "g" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "i" 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: "j" 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: "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: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "r" 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: "s" 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: "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: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "v" Number of atoms: 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: "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: 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: "z" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "b1" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "4" 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: "6" 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: "b8" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "b9" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'BCL': 1, 'SPO': 1} 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: "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 Time building chain proxies: 24.35, per 1000 atoms: 0.54 Number of scatterers: 44984 At special positions: 0 Unit cell: (215.28, 140.4, 104, 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 176 16.00 P 26 15.00 Mg 64 11.99 O 6792 8.00 N 6276 7.00 C 31648 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: 19.66 Conformation dependent library (CDL) restraints added in 6.4 seconds 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8540 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 194 helices and 8 sheets defined 66.5% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.48 Creating SS restraints... Processing helix chain 'L' and resid 7 through 9 No H-bonds generated for 'chain 'L' and resid 7 through 9' Processing helix chain 'L' and resid 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: 3.638A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU L 131 " --> pdb=" O ALA L 127 " (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: 4.025A pdb=" N TYR L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 169 No H-bonds generated for 'chain 'L' and resid 167 through 169' Processing helix chain 'L' and resid 171 through 198 Processing helix chain 'L' and resid 209 through 220 Processing helix chain 'L' and resid 226 through 249 removed outlier: 3.627A pdb=" N HIS L 230 " --> pdb=" O THR L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 267 removed outlier: 3.728A pdb=" N TRP L 263 " --> pdb=" O TRP L 259 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN L 264 " --> pdb=" O VAL L 260 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TRP L 265 " --> pdb=" O ASP L 261 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TRP L 266 " --> pdb=" O TRP L 262 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL L 267 " --> pdb=" O TRP L 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 259 through 267' Processing helix chain 'M' and resid 37 through 42 removed outlier: 4.321A pdb=" N PHE M 42 " --> pdb=" O LEU M 38 " (cutoff:3.500A) 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 113 through 140 Processing helix chain 'M' and resid 145 through 161 removed outlier: 3.663A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU M 156 " --> pdb=" O SER M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 168 Processing helix chain 'M' and resid 171 through 173 No H-bonds generated for 'chain 'M' and resid 171 through 173' Processing helix chain 'M' and resid 179 through 192 removed outlier: 3.622A pdb=" N LEU M 183 " --> pdb=" O ILE M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 198 No H-bonds generated for 'chain 'M' and resid 196 through 198' Processing helix chain 'M' and resid 200 through 229 removed outlier: 4.619A pdb=" N ARG M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) removed outlier: 5.676A 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 removed outlier: 3.620A pdb=" N TRP M 252 " --> pdb=" O ALA M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 289 removed outlier: 3.885A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE M 282 " --> pdb=" O LEU M 278 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER M 287 " --> pdb=" O GLY M 283 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLY M 288 " --> pdb=" O ILE M 284 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR M 289 " --> pdb=" O LEU M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 301 Processing helix chain 'H' and resid 12 through 37 removed outlier: 4.067A 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: 3.917A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 243 removed outlier: 3.978A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 247 No H-bonds generated for 'chain 'H' and resid 245 through 247' Processing helix chain 'H' and resid 251 through 255 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 removed outlier: 3.580A pdb=" N ALA A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 45 Processing helix chain 'D' and resid 2 through 10 removed outlier: 4.202A 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 2 through 10 removed outlier: 3.874A pdb=" N TYR F 5 " --> pdb=" O SER F 2 " (cutoff:3.500A) 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 10 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 10 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 10 Processing helix chain 'O' and resid 13 through 37 Processing helix chain 'O' and resid 43 through 50 Processing helix chain 'P' and resid 14 through 45 Processing helix chain 'Q' and resid 2 through 10 removed outlier: 3.590A pdb=" N TYR Q 5 " --> pdb=" O SER Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 37 Processing helix chain 'Q' and resid 43 through 50 removed outlier: 4.100A pdb=" N SER Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA Q 48 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) 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 10 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 51 Processing helix chain 'C' and resid 14 through 45 Processing helix chain '3' and resid 2 through 10 removed outlier: 4.306A pdb=" N TYR 3 5 " --> pdb=" O SER 3 2 " (cutoff:3.500A) Processing helix chain '3' and resid 13 through 37 Processing helix chain '3' and resid 43 through 51 Processing helix chain 'Z' and resid 14 through 45 Processing helix chain '1' and resid 6 through 10 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 10 Processing helix chain '7' and resid 13 through 37 Processing helix chain '7' and resid 43 through 46 No H-bonds generated for 'chain '7' and resid 43 through 46' Processing helix chain '8' and resid 14 through 45 Processing helix chain '9' and resid 4 through 10 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 19 through 54 Processing helix chain 'Y' and resid 6 through 28 Processing helix chain 'Y' and resid 32 through 47 Processing helix chain 'l' and resid 7 through 9 No H-bonds generated for 'chain 'l' and resid 7 through 9' Processing helix chain 'l' and resid 32 through 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: 3.638A pdb=" N ALA l 124 " --> pdb=" O ALA l 120 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU l 131 " --> pdb=" O ALA l 127 " (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: 4.026A pdb=" N TYR l 164 " --> pdb=" O THR l 160 " (cutoff:3.500A) Processing helix chain 'l' and resid 167 through 169 No H-bonds generated for 'chain 'l' and resid 167 through 169' Processing helix chain 'l' and resid 171 through 198 Processing helix chain 'l' and resid 209 through 220 Processing helix chain 'l' and resid 226 through 249 removed outlier: 3.627A pdb=" N HIS l 230 " --> pdb=" O THR l 226 " (cutoff:3.500A) Processing helix chain 'l' and resid 259 through 267 removed outlier: 3.728A pdb=" N TRP l 263 " --> pdb=" O TRP l 259 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN l 264 " --> pdb=" O VAL l 260 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TRP l 265 " --> pdb=" O ASP l 261 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TRP l 266 " --> pdb=" O TRP l 262 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL l 267 " --> pdb=" O TRP l 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 259 through 267' Processing helix chain 'm' and resid 37 through 42 removed outlier: 4.322A pdb=" N PHE m 42 " --> pdb=" O LEU m 38 " (cutoff:3.500A) 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 113 through 140 Processing helix chain 'm' and resid 145 through 161 removed outlier: 3.662A pdb=" N ALA m 153 " --> pdb=" O ALA m 149 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU m 156 " --> pdb=" O SER m 152 " (cutoff:3.500A) Processing helix chain 'm' and resid 163 through 168 Processing helix chain 'm' and resid 171 through 173 No H-bonds generated for 'chain 'm' and resid 171 through 173' Processing helix chain 'm' and resid 179 through 192 removed outlier: 3.622A pdb=" N LEU m 183 " --> pdb=" O ILE m 179 " (cutoff:3.500A) Processing helix chain 'm' and resid 196 through 198 No H-bonds generated for 'chain 'm' and resid 196 through 198' Processing helix chain 'm' and resid 200 through 229 removed outlier: 4.619A pdb=" N ARG m 228 " --> pdb=" O LEU m 224 " (cutoff:3.500A) removed outlier: 5.675A 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 removed outlier: 3.620A pdb=" N TRP m 252 " --> pdb=" O ALA m 248 " (cutoff:3.500A) Processing helix chain 'm' and resid 264 through 289 removed outlier: 3.885A pdb=" N VAL m 276 " --> pdb=" O MET m 272 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR m 277 " --> pdb=" O ALA m 273 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE m 282 " --> pdb=" O LEU m 278 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER m 287 " --> pdb=" O GLY m 283 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLY m 288 " --> pdb=" O ILE m 284 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR m 289 " --> pdb=" O LEU m 285 " (cutoff:3.500A) Processing helix chain 'm' and resid 294 through 301 Processing helix chain 'h' and resid 12 through 37 removed outlier: 4.066A 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: 3.917A pdb=" N ALA h 214 " --> pdb=" O ASP h 211 " (cutoff:3.500A) Processing helix chain 'h' and resid 227 through 243 removed outlier: 3.977A pdb=" N LEU h 241 " --> pdb=" O VAL h 237 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N MET h 242 " --> pdb=" O ALA h 238 " (cutoff:3.500A) Processing helix chain 'h' and resid 245 through 247 No H-bonds generated for 'chain 'h' and resid 245 through 247' Processing helix chain 'h' and resid 251 through 255 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 removed outlier: 3.580A pdb=" N ALA a 48 " --> pdb=" O LEU a 44 " (cutoff:3.500A) Processing helix chain 'b' and resid 14 through 45 Processing helix chain 'd' and resid 2 through 10 removed outlier: 4.202A 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 2 through 10 removed outlier: 3.874A pdb=" N TYR f 5 " --> pdb=" O SER f 2 " (cutoff:3.500A) 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 10 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 10 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 10 Processing helix chain 'o' and resid 13 through 37 Processing helix chain 'o' and resid 43 through 50 Processing helix chain 'p' and resid 14 through 45 Processing helix chain 'q' and resid 2 through 10 removed outlier: 3.591A pdb=" N TYR q 5 " --> pdb=" O SER q 2 " (cutoff:3.500A) Processing helix chain 'q' and resid 13 through 37 Processing helix chain 'q' and resid 43 through 50 removed outlier: 4.099A pdb=" N SER q 47 " --> pdb=" O TRP q 43 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA q 48 " --> pdb=" O LEU q 44 " (cutoff:3.500A) 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 10 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 51 Processing helix chain 'c' and resid 14 through 45 Processing helix chain '5' and resid 2 through 10 removed outlier: 4.306A pdb=" N TYR 5 5 " --> pdb=" O SER 5 2 " (cutoff:3.500A) Processing helix chain '5' and resid 13 through 37 Processing helix chain '5' and resid 43 through 51 Processing helix chain 'z' and resid 14 through 45 Processing helix chain 'b1' and resid 6 through 10 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 10 Processing helix chain '6' and resid 13 through 37 Processing helix chain '6' and resid 43 through 46 No H-bonds generated for 'chain '6' and resid 43 through 46' Processing helix chain 'b8' and resid 14 through 45 Processing helix chain 'b9' and resid 4 through 10 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 19 through 54 Processing helix chain 'y' and resid 6 through 28 Processing helix chain 'y' and resid 32 through 47 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: 6.680A pdb=" N GLU H 180 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE H 167 " --> pdb=" O PHE H 178 " (cutoff:3.500A) removed outlier: 6.620A 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: 3.789A 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: 6.680A pdb=" N GLU h 180 " --> pdb=" O VAL h 165 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE h 167 " --> pdb=" O PHE h 178 " (cutoff:3.500A) removed outlier: 6.620A 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: 3.788A pdb=" N GLY h 162 " --> pdb=" O VAL h 153 " (cutoff:3.500A) 2296 hydrogen bonds defined for protein. 6540 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.12 Time building geometry restraints manager: 21.09 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: 12008 1.35 - 1.56: 34042 1.56 - 1.76: 52 1.76 - 1.97: 342 1.97 - 2.17: 256 Bond restraints: 46700 Sorted by residual: bond pdb=" C3C BPB L 303 " pdb=" CAC BPB L 303 " ideal model delta sigma weight residual 1.334 1.551 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C3C BPB l 303 " pdb=" CAC BPB l 303 " ideal model delta sigma weight residual 1.334 1.551 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C3C BPB M 403 " pdb=" CAC BPB M 403 " ideal model delta sigma weight residual 1.334 1.546 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C3C BPB m 403 " pdb=" CAC BPB m 403 " ideal model delta sigma weight residual 1.334 1.546 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" OB3 CDL m 406 " pdb=" PB2 CDL m 406 " ideal model delta sigma weight residual 1.529 1.457 0.072 1.00e-02 1.00e+04 5.21e+01 ... (remaining 46695 not shown) Histogram of bond angle deviations from ideal: 84.90 - 100.45: 292 100.45 - 115.99: 29876 115.99 - 131.54: 33330 131.54 - 147.08: 512 147.08 - 162.63: 128 Bond angle restraints: 64138 Sorted by residual: angle pdb=" C51 CDL m 406 " pdb=" CB5 CDL m 406 " pdb=" OB6 CDL m 406 " ideal model delta sigma weight residual 111.33 120.72 -9.39 1.32e+00 5.72e-01 5.05e+01 angle pdb=" C51 CDL M 406 " pdb=" CB5 CDL M 406 " pdb=" OB6 CDL M 406 " ideal model delta sigma weight residual 111.33 120.72 -9.39 1.32e+00 5.72e-01 5.04e+01 angle pdb=" C11 CDL h 303 " pdb=" CA5 CDL h 303 " pdb=" OA6 CDL h 303 " ideal model delta sigma weight residual 111.33 120.21 -8.88 1.32e+00 5.72e-01 4.51e+01 angle pdb=" C11 CDL H 303 " pdb=" CA5 CDL H 303 " pdb=" OA6 CDL H 303 " ideal model delta sigma weight residual 111.33 120.21 -8.88 1.32e+00 5.72e-01 4.51e+01 angle pdb=" C11 CDL m 406 " pdb=" CA5 CDL m 406 " pdb=" OA6 CDL m 406 " ideal model delta sigma weight residual 111.33 120.07 -8.74 1.32e+00 5.72e-01 4.37e+01 ... (remaining 64133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 24388 35.97 - 71.94: 550 71.94 - 107.92: 70 107.92 - 143.89: 10 143.89 - 179.86: 4 Dihedral angle restraints: 25022 sinusoidal: 11736 harmonic: 13286 Sorted by residual: dihedral pdb=" C1 BCL G 101 " pdb=" C2 BCL G 101 " pdb=" C3 BCL G 101 " pdb=" C5 BCL G 101 " ideal model delta sinusoidal sigma weight residual 180.00 0.14 179.86 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL g 101 " pdb=" C2 BCL g 101 " pdb=" C3 BCL g 101 " pdb=" C5 BCL g 101 " ideal model delta sinusoidal sigma weight residual 180.00 0.19 179.81 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL 2 101 " pdb=" C2 BCL 2 101 " pdb=" C3 BCL 2 101 " pdb=" C5 BCL 2 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.54 -179.46 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 25019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4686 0.042 - 0.084: 1306 0.084 - 0.126: 203 0.126 - 0.168: 12 0.168 - 0.210: 9 Chirality restraints: 6216 Sorted by residual: chirality pdb=" C2C BPB m 403 " pdb=" C1C BPB m 403 " pdb=" C3C BPB m 403 " pdb=" CMC BPB m 403 " both_signs ideal model delta sigma weight residual False -2.78 -2.57 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C2C BPB M 403 " pdb=" C1C BPB M 403 " pdb=" C3C BPB M 403 " pdb=" CMC BPB M 403 " both_signs ideal model delta sigma weight residual False -2.78 -2.57 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ARG M 247 " pdb=" N ARG M 247 " pdb=" C ARG M 247 " pdb=" CB ARG M 247 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.59e-01 ... (remaining 6213 not shown) Planarity restraints: 7888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2C BPB L 303 " -0.381 2.00e-02 2.50e+03 5.00e-01 3.13e+03 pdb=" C3C BPB L 303 " 0.502 2.00e-02 2.50e+03 pdb=" C4C BPB L 303 " -0.207 2.00e-02 2.50e+03 pdb=" CAC BPB L 303 " 0.678 2.00e-02 2.50e+03 pdb=" CBC BPB L 303 " -0.591 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2C BPB l 303 " 0.382 2.00e-02 2.50e+03 5.00e-01 3.12e+03 pdb=" C3C BPB l 303 " -0.502 2.00e-02 2.50e+03 pdb=" C4C BPB l 303 " 0.207 2.00e-02 2.50e+03 pdb=" CAC BPB l 303 " -0.678 2.00e-02 2.50e+03 pdb=" CBC BPB l 303 " 0.591 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2C BPB M 403 " -0.007 2.00e-02 2.50e+03 2.37e-01 7.03e+02 pdb=" C3C BPB M 403 " -0.333 2.00e-02 2.50e+03 pdb=" C4C BPB M 403 " 0.140 2.00e-02 2.50e+03 pdb=" CAC BPB M 403 " 0.356 2.00e-02 2.50e+03 pdb=" CBC BPB M 403 " -0.156 2.00e-02 2.50e+03 ... (remaining 7885 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1003 2.70 - 3.25: 42324 3.25 - 3.80: 77608 3.80 - 4.35: 105894 4.35 - 4.90: 171554 Nonbonded interactions: 398383 Sorted by model distance: nonbonded pdb=" NE2 HIS l 190 " pdb="FE FE2 m 401 " model vdw 2.147 3.080 nonbonded pdb=" NE2 HIS L 190 " pdb="FE FE2 M 401 " model vdw 2.147 3.080 nonbonded pdb=" OE1 GLU M 234 " pdb="FE FE2 M 401 " model vdw 2.150 3.000 nonbonded pdb=" OE1 GLU m 234 " pdb="FE FE2 m 401 " model vdw 2.151 3.000 nonbonded pdb=" NE2 HIS M 219 " pdb="FE FE2 M 401 " model vdw 2.158 3.080 ... (remaining 398378 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 10 through 49) selection = (chain '2' and resid 10 through 49) selection = (chain '4' and resid 10 through 49) selection = (chain '8' and resid 10 through 49) selection = (chain 'B' and resid 10 through 49) selection = (chain 'C' and resid 10 through 49) selection = (chain 'E' and resid 10 through 49) selection = (chain 'G' and resid 10 through 49) selection = (chain 'J' and resid 10 through 49) selection = (chain 'N' and resid 10 through 49) selection = (chain 'P' and resid 10 through 49) selection = (chain 'R' and resid 10 through 49) selection = (chain 'T' and resid 10 through 49) selection = (chain 'V' and resid 10 through 49) selection = (chain 'Z' and resid 10 through 49) selection = (chain 'b' and resid 10 through 49) selection = (chain 'b0' and resid 10 through 49) selection = (chain 'b8' and resid 10 through 49) selection = (chain 'c' and resid 10 through 49) selection = (chain 'e' and resid 10 through 49) selection = (chain 'g' and resid 10 through 49) selection = (chain 'j' and resid 10 through 49) selection = (chain 'n' and resid 10 through 49) selection = (chain 'p' and resid 10 through 49) selection = (chain 'r' and resid 10 through 49) selection = (chain 't' and resid 10 through 49) selection = (chain 'v' and resid 10 through 49) selection = (chain 'z' and resid 10 through 49) } ncs_group { reference = (chain '1' and resid 2 through 48) selection = (chain '3' and resid 2 through 48) selection = (chain '5' and resid 2 through 48) selection = (chain '6' and resid 2 through 48) selection = (chain '7' and resid 2 through 48) selection = (chain '9' and resid 2 through 48) selection = (chain 'A' and resid 2 through 48) selection = (chain 'D' and resid 2 through 48) selection = (chain 'F' and resid 2 through 48) selection = (chain 'I' and resid 2 through 48) selection = (chain 'K' and resid 2 through 48) selection = (chain 'O' and resid 2 through 48) selection = (chain 'Q' and resid 2 through 48) selection = (chain 'S' and resid 2 through 48) selection = (chain 'U' and resid 2 through 48) selection = (chain 'W' and resid 2 through 48) selection = (chain 'a' and resid 2 through 48) selection = (chain 'b1' and resid 2 through 48) selection = (chain 'b9' and resid 2 through 48) selection = (chain 'd' and resid 2 through 48) selection = (chain 'f' and resid 2 through 48) selection = (chain 'i' and resid 2 through 48) selection = (chain 'k' and resid 2 through 48) selection = (chain 'o' and resid 2 through 48) selection = (chain 'q' and resid 2 through 48) selection = (chain 's' and resid 2 through 48) selection = (chain 'u' and resid 2 through 48) selection = (chain 'w' and resid 2 through 48) } 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: 4.310 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: 0.030 Extract box with map and model: 17.150 Check model and map are aligned: 0.750 Set scattering table: 0.480 Process input model: 113.400 Find NCS groups from input model: 3.290 Set up NCS constraints: 0.300 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:12.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 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 : 0.006 0.217 46700 Z= 0.341 Angle : 0.796 16.237 64138 Z= 0.329 Chirality : 0.038 0.210 6216 Planarity : 0.009 0.500 7888 Dihedral : 15.277 179.859 16482 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.37 % Allowed : 3.31 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.64 (0.12), residues: 4462 helix: 2.48 (0.09), residues: 2912 sheet: -0.44 (0.84), residues: 48 loop : 0.42 (0.17), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 263 HIS 0.009 0.001 HIS l 153 PHE 0.016 0.001 PHE l 216 TYR 0.013 0.001 TYR a 41 ARG 0.003 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1167 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1153 time to evaluate : 4.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 21 THR cc_start: 0.8669 (m) cc_final: 0.8312 (t) REVERT: M 23 ASP cc_start: 0.6976 (t0) cc_final: 0.6668 (t70) REVERT: M 236 GLU cc_start: 0.5951 (pt0) cc_final: 0.5665 (pt0) REVERT: H 19 SER cc_start: 0.9267 (p) cc_final: 0.9065 (p) REVERT: H 93 SER cc_start: 0.8088 (t) cc_final: 0.7877 (p) REVERT: H 128 HIS cc_start: 0.6873 (m90) cc_final: 0.6612 (m170) REVERT: H 170 ASP cc_start: 0.7118 (t0) cc_final: 0.6761 (t70) REVERT: H 184 LYS cc_start: 0.7216 (mmtp) cc_final: 0.6794 (ttmm) REVERT: H 230 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7753 (mt-10) REVERT: D 5 TYR cc_start: 0.8496 (p90) cc_final: 0.8163 (p90) REVERT: G 9 TYR cc_start: 0.7180 (m-10) cc_final: 0.6975 (m-80) REVERT: K 5 TYR cc_start: 0.7624 (p90) cc_final: 0.7416 (p90) REVERT: K 26 LEU cc_start: 0.8881 (mt) cc_final: 0.8635 (mm) REVERT: O 30 MET cc_start: 0.8060 (ttm) cc_final: 0.7654 (ttm) REVERT: S 3 LYS cc_start: 0.8725 (mttt) cc_final: 0.8488 (mmtm) REVERT: W 8 TRP cc_start: 0.9042 (m100) cc_final: 0.8630 (m100) REVERT: C 25 MET cc_start: 0.8214 (mmm) cc_final: 0.8009 (mmm) REVERT: X 17 THR cc_start: 0.6661 (m) cc_final: 0.6447 (t) REVERT: X 53 ARG cc_start: 0.6628 (mtt-85) cc_final: 0.5483 (ptm160) REVERT: l 48 LEU cc_start: 0.8851 (mt) cc_final: 0.8536 (mt) REVERT: l 52 SER cc_start: 0.8681 (t) cc_final: 0.8446 (m) REVERT: m 23 ASP cc_start: 0.7084 (t0) cc_final: 0.6841 (t70) REVERT: m 36 SER cc_start: 0.8613 (t) cc_final: 0.8393 (t) REVERT: m 233 ARG cc_start: 0.7573 (mtm-85) cc_final: 0.7217 (ttp-110) REVERT: m 246 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7851 (mt-10) REVERT: m 272 MET cc_start: 0.8399 (tpp) cc_final: 0.8172 (tpp) REVERT: h 173 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7279 (mp0) REVERT: a 44 LEU cc_start: 0.8996 (mt) cc_final: 0.8714 (mt) REVERT: d 5 TYR cc_start: 0.8493 (p90) cc_final: 0.8120 (p90) REVERT: f 15 ARG cc_start: 0.6707 (mmt90) cc_final: 0.6187 (mtp-110) REVERT: g 9 TYR cc_start: 0.7139 (m-10) cc_final: 0.6919 (m-80) REVERT: k 6 LYS cc_start: 0.8096 (tptt) cc_final: 0.7879 (tptm) REVERT: k 26 LEU cc_start: 0.8923 (mt) cc_final: 0.8644 (mm) REVERT: k 41 TYR cc_start: 0.7328 (m-80) cc_final: 0.7051 (m-80) REVERT: n 28 LEU cc_start: 0.9095 (tp) cc_final: 0.8876 (tp) REVERT: 5 5 TYR cc_start: 0.7992 (p90) cc_final: 0.7370 (p90) REVERT: 4 16 GLN cc_start: 0.7429 (mt0) cc_final: 0.7116 (mm110) REVERT: 6 14 ARG cc_start: 0.6966 (ptm160) cc_final: 0.6558 (ttp-110) REVERT: 6 30 MET cc_start: 0.8144 (ttm) cc_final: 0.7660 (ttm) REVERT: x 28 MET cc_start: 0.7010 (ttm) cc_final: 0.6728 (tpt) REVERT: x 53 ARG cc_start: 0.6363 (mtt-85) cc_final: 0.5348 (ptm160) REVERT: y 6 GLU cc_start: 0.6869 (tp30) cc_final: 0.6561 (tp30) outliers start: 14 outliers final: 10 residues processed: 1160 average time/residue: 1.2695 time to fit residues: 1905.7542 Evaluate side-chains 864 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 854 time to evaluate : 4.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain b1 residue 29 VAL Chi-restraints excluded: chain b0 residue 40 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 368 optimal weight: 0.0980 chunk 330 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 341 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 254 optimal weight: 1.9990 chunk 395 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 199 ASN ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN D 20 GLN I 20 GLN N 18 GLN R 16 GLN V 18 GLN 3 20 GLN Z 18 GLN 7 20 GLN ** l 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 194 GLN i 20 GLN k 42 ASN k 52 ASN n 18 GLN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 52 ASN r 16 GLN s 20 GLN v 18 GLN z 16 GLN 6 20 GLN x 26 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 46700 Z= 0.270 Angle : 0.640 11.448 64138 Z= 0.277 Chirality : 0.038 0.158 6216 Planarity : 0.004 0.041 7888 Dihedral : 16.432 179.972 8473 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.31 % Allowed : 13.55 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.43 (0.12), residues: 4462 helix: 2.32 (0.08), residues: 2926 sheet: -0.55 (0.83), residues: 48 loop : 0.31 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP o 8 HIS 0.012 0.002 HIS z 21 PHE 0.027 0.002 PHE O 17 TYR 0.018 0.002 TYRb1 5 ARG 0.007 0.001 ARG H 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 941 time to evaluate : 4.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 21 THR cc_start: 0.8690 (m) cc_final: 0.8293 (t) REVERT: M 23 ASP cc_start: 0.7197 (t0) cc_final: 0.6781 (t0) REVERT: M 36 SER cc_start: 0.8498 (t) cc_final: 0.8272 (t) REVERT: M 218 MET cc_start: 0.8217 (mtp) cc_final: 0.7995 (mtm) REVERT: H 105 MET cc_start: 0.8034 (mtm) cc_final: 0.7771 (mtm) REVERT: H 170 ASP cc_start: 0.7247 (t0) cc_final: 0.6802 (t70) REVERT: H 184 LYS cc_start: 0.7185 (mmtp) cc_final: 0.6750 (ttmm) REVERT: D 5 TYR cc_start: 0.8432 (p90) cc_final: 0.8120 (p90) REVERT: F 15 ARG cc_start: 0.6698 (mmt90) cc_final: 0.6243 (mtp-110) REVERT: G 9 TYR cc_start: 0.7198 (m-10) cc_final: 0.6995 (m-80) REVERT: I 3 LYS cc_start: 0.8229 (mtpm) cc_final: 0.8019 (mtmm) REVERT: K 5 TYR cc_start: 0.7570 (p90) cc_final: 0.7261 (p90) REVERT: O 3 LYS cc_start: 0.7993 (ttmm) cc_final: 0.7475 (tptp) REVERT: O 17 PHE cc_start: 0.8656 (m-80) cc_final: 0.8442 (m-80) REVERT: O 30 MET cc_start: 0.8187 (ttm) cc_final: 0.7951 (ttm) REVERT: P 25 MET cc_start: 0.8495 (mmm) cc_final: 0.8230 (mmt) REVERT: S 3 LYS cc_start: 0.8796 (mttt) cc_final: 0.8563 (mmtm) REVERT: W 8 TRP cc_start: 0.9136 (m100) cc_final: 0.8774 (m100) REVERT: 2 43 TYR cc_start: 0.8025 (t80) cc_final: 0.7803 (t80) REVERT: X 28 MET cc_start: 0.6458 (tmm) cc_final: 0.6153 (tmm) REVERT: X 53 ARG cc_start: 0.6497 (mtt-85) cc_final: 0.5313 (ptm160) REVERT: m 21 THR cc_start: 0.8619 (m) cc_final: 0.8180 (t) REVERT: m 23 ASP cc_start: 0.7078 (t0) cc_final: 0.6735 (t0) REVERT: m 36 SER cc_start: 0.8630 (t) cc_final: 0.8367 (t) REVERT: m 218 MET cc_start: 0.8303 (mtp) cc_final: 0.8075 (mtm) REVERT: m 233 ARG cc_start: 0.7379 (mtm-85) cc_final: 0.6880 (ttp-110) REVERT: h 173 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7514 (mp0) REVERT: d 5 TYR cc_start: 0.8490 (p90) cc_final: 0.8265 (p90) REVERT: e 18 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8144 (mt0) REVERT: f 15 ARG cc_start: 0.6832 (mmt90) cc_final: 0.6339 (mtp-110) REVERT: i 3 LYS cc_start: 0.8318 (mtpm) cc_final: 0.8100 (mtmm) REVERT: i 5 TYR cc_start: 0.8206 (p90) cc_final: 0.7925 (p90) REVERT: j 32 SER cc_start: 0.8769 (p) cc_final: 0.8487 (m) REVERT: k 6 LYS cc_start: 0.8109 (tptt) cc_final: 0.7884 (tptm) REVERT: k 41 TYR cc_start: 0.7354 (m-80) cc_final: 0.7043 (m-80) REVERT: q 45 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: u 15 ARG cc_start: 0.7845 (mmt90) cc_final: 0.7496 (mtt90) REVERT: 5 5 TYR cc_start: 0.7845 (p90) cc_final: 0.7290 (p90) REVERT: x 53 ARG cc_start: 0.6452 (mtt-85) cc_final: 0.5391 (ptm160) REVERT: x 58 GLN cc_start: 0.7806 (mp10) cc_final: 0.7580 (mm-40) REVERT: y 36 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8498 (tp) outliers start: 126 outliers final: 50 residues processed: 993 average time/residue: 1.2163 time to fit residues: 1571.6941 Evaluate side-chains 903 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 850 time to evaluate : 4.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain F residue 2 SER Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 2 residue 32 SER Chi-restraints excluded: chain 7 residue 1 MET Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 0 residue 26 SER Chi-restraints excluded: chain 0 residue 40 LEU Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain l residue 99 SER Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 18 GLN Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain n residue 32 SER Chi-restraints excluded: chain p residue 32 SER Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain q residue 45 GLU Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain v residue 22 SER Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain w residue 37 SER Chi-restraints excluded: chain b1 residue 20 GLN Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain 4 residue 28 LEU Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b0 residue 26 SER Chi-restraints excluded: chain y residue 36 LEU Chi-restraints excluded: chain y residue 52 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 220 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 329 optimal weight: 2.9990 chunk 269 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 396 optimal weight: 8.9990 chunk 428 optimal weight: 4.9990 chunk 353 optimal weight: 0.9990 chunk 393 optimal weight: 0.0670 chunk 135 optimal weight: 0.9980 chunk 318 optimal weight: 3.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 199 ASN ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN I 20 GLN N 18 GLN 3 20 GLN Z 18 GLN 7 20 GLN X 26 GLN Y 51 ASN l 199 ASN ** m 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 194 GLN i 20 GLN k 52 ASN n 16 GLN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 16 GLN 4 18 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 46700 Z= 0.208 Angle : 0.604 11.482 64138 Z= 0.259 Chirality : 0.037 0.175 6216 Planarity : 0.003 0.041 7888 Dihedral : 15.978 179.960 8462 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.68 % Allowed : 15.73 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.51 (0.12), residues: 4462 helix: 2.37 (0.08), residues: 2934 sheet: -0.50 (0.82), residues: 48 loop : 0.36 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 48 HIS 0.015 0.001 HIS Z 21 PHE 0.035 0.001 PHE o 17 TYR 0.017 0.001 TYR 2 24 ARG 0.006 0.000 ARG M 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 936 time to evaluate : 4.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 21 THR cc_start: 0.8567 (m) cc_final: 0.8148 (t) REVERT: M 23 ASP cc_start: 0.7179 (t0) cc_final: 0.6824 (t0) REVERT: M 36 SER cc_start: 0.8488 (t) cc_final: 0.8277 (t) REVERT: M 122 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8288 (ttt) REVERT: H 170 ASP cc_start: 0.7433 (t0) cc_final: 0.7011 (t70) REVERT: H 184 LYS cc_start: 0.7149 (mmtp) cc_final: 0.6677 (ttmm) REVERT: A 9 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7764 (mmm) REVERT: D 5 TYR cc_start: 0.8519 (p90) cc_final: 0.8089 (p90) REVERT: F 15 ARG cc_start: 0.6726 (mmt90) cc_final: 0.6298 (mtp-110) REVERT: F 46 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7917 (pt) REVERT: K 5 TYR cc_start: 0.7799 (p90) cc_final: 0.7489 (p90) REVERT: O 3 LYS cc_start: 0.7905 (ttmm) cc_final: 0.7442 (tptp) REVERT: O 30 MET cc_start: 0.8258 (ttm) cc_final: 0.8032 (ttm) REVERT: P 13 THR cc_start: 0.7331 (m) cc_final: 0.6884 (p) REVERT: P 25 MET cc_start: 0.8434 (mmm) cc_final: 0.8176 (mmt) REVERT: S 3 LYS cc_start: 0.8826 (mttt) cc_final: 0.8550 (mmtm) REVERT: 3 7 ILE cc_start: 0.8687 (tp) cc_final: 0.8442 (pt) REVERT: X 17 THR cc_start: 0.6575 (m) cc_final: 0.6080 (t) REVERT: X 28 MET cc_start: 0.6338 (tmm) cc_final: 0.6054 (tmm) REVERT: X 53 ARG cc_start: 0.6623 (mtt-85) cc_final: 0.5403 (ptm160) REVERT: l 20 ASN cc_start: 0.8072 (p0) cc_final: 0.7824 (p0) REVERT: m 21 THR cc_start: 0.8498 (m) cc_final: 0.8081 (t) REVERT: m 23 ASP cc_start: 0.7056 (t0) cc_final: 0.6745 (t0) REVERT: m 36 SER cc_start: 0.8602 (t) cc_final: 0.8361 (t) REVERT: m 122 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8253 (ttt) REVERT: m 218 MET cc_start: 0.8225 (mtp) cc_final: 0.7933 (mtm) REVERT: m 233 ARG cc_start: 0.7266 (mtm-85) cc_final: 0.6969 (ttp-110) REVERT: h 173 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7533 (mp0) REVERT: a 44 LEU cc_start: 0.8824 (mt) cc_final: 0.8599 (mt) REVERT: d 5 TYR cc_start: 0.8526 (p90) cc_final: 0.8168 (p90) REVERT: f 15 ARG cc_start: 0.6831 (mmt90) cc_final: 0.6355 (mtp-110) REVERT: i 5 TYR cc_start: 0.8207 (p90) cc_final: 0.7953 (p90) REVERT: j 32 SER cc_start: 0.8754 (p) cc_final: 0.8467 (m) REVERT: k 9 MET cc_start: 0.7758 (tpp) cc_final: 0.7312 (mtm) REVERT: k 42 ASN cc_start: 0.7690 (t0) cc_final: 0.7466 (t160) REVERT: q 45 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: r 7 LEU cc_start: 0.4998 (OUTLIER) cc_final: 0.4698 (tp) REVERT: s 14 ARG cc_start: 0.8245 (mtm110) cc_final: 0.7830 (mtm180) REVERT: u 15 ARG cc_start: 0.7804 (mmt90) cc_final: 0.7494 (mtt90) REVERT: v 14 ASP cc_start: 0.7496 (t70) cc_final: 0.7031 (t0) REVERT: c 9 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.6917 (m-80) REVERT: 5 5 TYR cc_start: 0.7876 (p90) cc_final: 0.7370 (p90) REVERT: x 28 MET cc_start: 0.6517 (tmt) cc_final: 0.6097 (tpt) REVERT: x 53 ARG cc_start: 0.6358 (mtt-85) cc_final: 0.5322 (ptm160) outliers start: 140 outliers final: 61 residues processed: 1004 average time/residue: 1.1901 time to fit residues: 1564.0901 Evaluate side-chains 928 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 860 time to evaluate : 4.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 122 MET Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 262 MET Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain S residue 37 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain U residue 3 LYS Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain 3 residue 27 LEU Chi-restraints excluded: chain 1 residue 20 GLN Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 2 residue 32 SER Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 0 residue 26 SER Chi-restraints excluded: chain 0 residue 40 LEU Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain l residue 48 LEU Chi-restraints excluded: chain l residue 99 SER Chi-restraints excluded: chain m residue 122 MET Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain h residue 196 VAL Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain n residue 32 SER Chi-restraints excluded: chain o residue 47 SER Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain q residue 45 GLU Chi-restraints excluded: chain r residue 7 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain v residue 22 SER Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain w residue 37 SER Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain b1 residue 4 PHE Chi-restraints excluded: chain 4 residue 28 LEU Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b9 residue 2 SER Chi-restraints excluded: chain b0 residue 26 SER Chi-restraints excluded: chain b0 residue 40 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 391 optimal weight: 0.7980 chunk 298 optimal weight: 3.9990 chunk 205 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 189 optimal weight: 6.9990 chunk 266 optimal weight: 0.9980 chunk 398 optimal weight: 5.9990 chunk 421 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 377 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 ASN N 18 GLN 3 20 GLN Z 18 GLN 7 20 GLN Y 51 ASN ** m 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 194 GLN i 20 GLN ** k 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 52 ASN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 20 GLN 4 18 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 46700 Z= 0.217 Angle : 0.615 11.401 64138 Z= 0.264 Chirality : 0.037 0.139 6216 Planarity : 0.003 0.044 7888 Dihedral : 15.810 179.994 8462 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 4.12 % Allowed : 17.52 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.50 (0.12), residues: 4462 helix: 2.37 (0.08), residues: 2928 sheet: -0.50 (0.82), residues: 48 loop : 0.33 (0.17), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 48 HIS 0.017 0.001 HIS Z 21 PHE 0.030 0.001 PHE O 17 TYR 0.021 0.001 TYR O 5 ARG 0.008 0.000 ARG M 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 926 time to evaluate : 4.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 21 THR cc_start: 0.8578 (m) cc_final: 0.8101 (t) REVERT: M 23 ASP cc_start: 0.7173 (t0) cc_final: 0.6753 (t0) REVERT: M 36 SER cc_start: 0.8513 (t) cc_final: 0.8303 (t) REVERT: M 122 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8261 (ttt) REVERT: H 79 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6738 (mt-10) REVERT: H 175 MET cc_start: 0.7949 (ptp) cc_final: 0.7740 (ptp) REVERT: D 5 TYR cc_start: 0.8532 (p90) cc_final: 0.8149 (p90) REVERT: F 15 ARG cc_start: 0.6719 (mmt90) cc_final: 0.6351 (mtp-110) REVERT: I 3 LYS cc_start: 0.8239 (mtpm) cc_final: 0.7884 (tppp) REVERT: I 5 TYR cc_start: 0.8227 (p90) cc_final: 0.7882 (p90) REVERT: K 3 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7631 (tptm) REVERT: K 5 TYR cc_start: 0.7995 (p90) cc_final: 0.7632 (p90) REVERT: K 46 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7833 (mt) REVERT: O 3 LYS cc_start: 0.7690 (ttmm) cc_final: 0.7279 (tptt) REVERT: O 5 TYR cc_start: 0.8321 (p90) cc_final: 0.8013 (p90) REVERT: P 25 MET cc_start: 0.8409 (mmm) cc_final: 0.8121 (mmt) REVERT: S 3 LYS cc_start: 0.8852 (mttt) cc_final: 0.8568 (mmtm) REVERT: S 17 PHE cc_start: 0.8205 (m-80) cc_final: 0.7966 (m-10) REVERT: T 14 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.7132 (t0) REVERT: 3 3 LYS cc_start: 0.7838 (mmmt) cc_final: 0.7455 (ttmm) REVERT: 3 7 ILE cc_start: 0.8743 (tp) cc_final: 0.8538 (pt) REVERT: 9 45 GLU cc_start: 0.7522 (tt0) cc_final: 0.7285 (tt0) REVERT: X 17 THR cc_start: 0.6487 (m) cc_final: 0.6012 (t) REVERT: X 28 MET cc_start: 0.6389 (tmm) cc_final: 0.6096 (tmm) REVERT: X 53 ARG cc_start: 0.6502 (mtt-85) cc_final: 0.5337 (ptm160) REVERT: Y 6 GLU cc_start: 0.6826 (tp30) cc_final: 0.6619 (tp30) REVERT: Y 51 ASN cc_start: 0.6512 (OUTLIER) cc_final: 0.5847 (m110) REVERT: Y 52 SER cc_start: 0.6940 (OUTLIER) cc_final: 0.6660 (m) REVERT: l 20 ASN cc_start: 0.8099 (p0) cc_final: 0.7877 (p0) REVERT: m 23 ASP cc_start: 0.6988 (t0) cc_final: 0.6616 (t0) REVERT: m 36 SER cc_start: 0.8538 (t) cc_final: 0.8311 (t) REVERT: m 122 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8238 (ttt) REVERT: h 173 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7562 (mp0) REVERT: a 44 LEU cc_start: 0.8820 (mt) cc_final: 0.8606 (mt) REVERT: d 5 TYR cc_start: 0.8530 (p90) cc_final: 0.8210 (p90) REVERT: f 15 ARG cc_start: 0.6797 (mmt90) cc_final: 0.6363 (mtp-110) REVERT: f 46 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7966 (pt) REVERT: i 3 LYS cc_start: 0.8304 (mtpm) cc_final: 0.7937 (tppp) REVERT: i 5 TYR cc_start: 0.8190 (p90) cc_final: 0.7893 (p90) REVERT: j 32 SER cc_start: 0.8747 (p) cc_final: 0.8511 (m) REVERT: k 6 LYS cc_start: 0.8058 (tptt) cc_final: 0.7655 (tptm) REVERT: o 5 TYR cc_start: 0.8202 (p90) cc_final: 0.7891 (p90) REVERT: o 33 LEU cc_start: 0.8577 (tp) cc_final: 0.8344 (tm) REVERT: q 45 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7379 (tp30) REVERT: r 7 LEU cc_start: 0.4850 (OUTLIER) cc_final: 0.4634 (tp) REVERT: s 3 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8187 (mttm) REVERT: u 15 ARG cc_start: 0.7733 (mmt90) cc_final: 0.7473 (mtt90) REVERT: v 14 ASP cc_start: 0.7559 (t70) cc_final: 0.7097 (t0) REVERT: c 9 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.6913 (m-80) REVERT: 5 5 TYR cc_start: 0.7867 (p90) cc_final: 0.7386 (p90) REVERT: b1 4 PHE cc_start: 0.6266 (OUTLIER) cc_final: 0.5881 (m-80) REVERT: b1 20 GLN cc_start: 0.7589 (tp-100) cc_final: 0.7381 (tp40) REVERT: b1 37 SER cc_start: 0.8886 (OUTLIER) cc_final: 0.8646 (p) REVERT: b8 15 GLU cc_start: 0.7628 (mp0) cc_final: 0.7422 (pm20) REVERT: x 28 MET cc_start: 0.6563 (OUTLIER) cc_final: 0.6104 (tpt) REVERT: x 53 ARG cc_start: 0.6341 (mtt-85) cc_final: 0.5281 (ptm160) REVERT: x 58 GLN cc_start: 0.7723 (mp10) cc_final: 0.7477 (mm-40) REVERT: y 36 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8285 (tm) outliers start: 157 outliers final: 74 residues processed: 994 average time/residue: 1.2493 time to fit residues: 1628.9620 Evaluate side-chains 949 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 858 time to evaluate : 4.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 122 MET Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 262 MET Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 79 GLU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain K residue 3 LYS Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain T residue 14 ASP Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain U residue 3 LYS Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain 3 residue 27 LEU Chi-restraints excluded: chain 1 residue 4 PHE Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 8 residue 7 LEU Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 9 residue 30 MET Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 0 residue 40 LEU Chi-restraints excluded: chain Y residue 51 ASN Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain l residue 48 LEU Chi-restraints excluded: chain l residue 99 SER Chi-restraints excluded: chain m residue 18 LEU Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 60 LEU Chi-restraints excluded: chain m residue 122 MET Chi-restraints excluded: chain m residue 182 HIS Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain h residue 48 THR Chi-restraints excluded: chain h residue 196 VAL Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain f residue 46 ILE Chi-restraints excluded: chain n residue 13 THR Chi-restraints excluded: chain n residue 32 SER Chi-restraints excluded: chain p residue 32 SER Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain q residue 45 GLU Chi-restraints excluded: chain r residue 7 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain s residue 3 LYS Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain v residue 22 SER Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain b1 residue 4 PHE Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain 4 residue 12 LEU Chi-restraints excluded: chain 4 residue 28 LEU Chi-restraints excluded: chain 4 residue 32 SER Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b9 residue 2 SER Chi-restraints excluded: chain b9 residue 37 SER Chi-restraints excluded: chain b0 residue 13 THR Chi-restraints excluded: chain x residue 28 MET Chi-restraints excluded: chain y residue 36 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 350 optimal weight: 5.9990 chunk 239 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 313 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 359 optimal weight: 4.9990 chunk 291 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 378 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 307 ASN ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 18 GLN 7 20 GLN Y 51 ASN ** l 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 199 ASN m 307 ASN h 194 GLN i 20 GLN ** k 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 42 ASN k 52 ASN o 20 GLN c 18 GLN ** z 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 18 GLN x 18 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.072 46700 Z= 0.529 Angle : 0.848 12.996 64138 Z= 0.356 Chirality : 0.046 0.210 6216 Planarity : 0.005 0.093 7888 Dihedral : 16.936 179.854 8462 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 5.07 % Allowed : 18.51 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.12), residues: 4462 helix: 1.64 (0.08), residues: 2930 sheet: -1.01 (0.78), residues: 48 loop : 0.09 (0.17), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP l 263 HIS 0.018 0.002 HIS Z 21 PHE 0.026 0.002 PHE x 47 TYR 0.024 0.002 TYR S 41 ARG 0.009 0.001 ARG M 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1101 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 908 time to evaluate : 4.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 21 THR cc_start: 0.8721 (m) cc_final: 0.8266 (t) REVERT: M 23 ASP cc_start: 0.7324 (t0) cc_final: 0.6949 (t0) REVERT: M 36 SER cc_start: 0.8600 (t) cc_final: 0.8345 (t) REVERT: A 9 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7371 (mmm) REVERT: F 15 ARG cc_start: 0.6981 (mmt90) cc_final: 0.6305 (ptt90) REVERT: G 30 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8774 (tp) REVERT: I 3 LYS cc_start: 0.8398 (mtpm) cc_final: 0.7990 (tppp) REVERT: I 5 TYR cc_start: 0.8193 (p90) cc_final: 0.7938 (p90) REVERT: K 41 TYR cc_start: 0.7752 (m-80) cc_final: 0.7304 (m-80) REVERT: O 3 LYS cc_start: 0.8008 (ttmm) cc_final: 0.7540 (tptt) REVERT: P 25 MET cc_start: 0.8554 (mmm) cc_final: 0.8337 (mmt) REVERT: Q 24 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9053 (mm) REVERT: S 3 LYS cc_start: 0.8940 (mttt) cc_final: 0.8678 (mmtm) REVERT: U 15 ARG cc_start: 0.7871 (mmt90) cc_final: 0.7191 (mtm110) REVERT: U 30 MET cc_start: 0.7418 (ttp) cc_final: 0.7151 (ttm) REVERT: V 14 ASP cc_start: 0.7500 (t0) cc_final: 0.7079 (t0) REVERT: 3 7 ILE cc_start: 0.8763 (tp) cc_final: 0.8520 (pt) REVERT: 2 25 MET cc_start: 0.7020 (mmm) cc_final: 0.6760 (mmm) REVERT: 9 45 GLU cc_start: 0.7480 (tt0) cc_final: 0.7269 (tt0) REVERT: X 17 THR cc_start: 0.6816 (m) cc_final: 0.6250 (t) REVERT: X 53 ARG cc_start: 0.6518 (mtt-85) cc_final: 0.5630 (ptm160) REVERT: Y 51 ASN cc_start: 0.6320 (OUTLIER) cc_final: 0.5943 (t0) REVERT: m 23 ASP cc_start: 0.7371 (t0) cc_final: 0.6897 (t0) REVERT: m 36 SER cc_start: 0.8639 (t) cc_final: 0.8385 (t) REVERT: h 173 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7634 (mp0) REVERT: b 18 GLN cc_start: 0.8580 (tt0) cc_final: 0.8333 (tt0) REVERT: e 18 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8077 (mt0) REVERT: f 15 ARG cc_start: 0.6958 (mmt90) cc_final: 0.6204 (ptt90) REVERT: g 30 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8748 (tp) REVERT: i 3 LYS cc_start: 0.8444 (mtpm) cc_final: 0.8074 (tppp) REVERT: i 5 TYR cc_start: 0.8242 (p90) cc_final: 0.7960 (p90) REVERT: j 32 SER cc_start: 0.8970 (p) cc_final: 0.8710 (m) REVERT: k 3 LYS cc_start: 0.8195 (tmtt) cc_final: 0.7963 (tptm) REVERT: k 41 TYR cc_start: 0.7704 (m-80) cc_final: 0.7225 (m-80) REVERT: n 28 LEU cc_start: 0.9200 (tt) cc_final: 0.8978 (tp) REVERT: o 6 LYS cc_start: 0.7888 (mtpt) cc_final: 0.7346 (mmpt) REVERT: s 3 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8221 (mttm) REVERT: s 46 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7733 (mp) REVERT: u 15 ARG cc_start: 0.7885 (mmt90) cc_final: 0.7507 (mtt90) REVERT: v 14 ASP cc_start: 0.7646 (t70) cc_final: 0.7151 (t0) REVERT: w 11 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8534 (m-10) REVERT: 5 5 TYR cc_start: 0.8053 (p90) cc_final: 0.7550 (p90) REVERT: b1 4 PHE cc_start: 0.6546 (OUTLIER) cc_final: 0.6115 (m-10) REVERT: x 53 ARG cc_start: 0.6477 (mtt-85) cc_final: 0.5570 (ptm160) REVERT: y 6 GLU cc_start: 0.6275 (OUTLIER) cc_final: 0.5951 (tp30) outliers start: 193 outliers final: 88 residues processed: 1002 average time/residue: 1.2770 time to fit residues: 1698.8525 Evaluate side-chains 956 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 857 time to evaluate : 4.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 110 LYS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 262 MET Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain S residue 37 SER Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain U residue 3 LYS Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain 3 residue 27 LEU Chi-restraints excluded: chain 1 residue 4 PHE Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 2 residue 32 SER Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 0 residue 40 LEU Chi-restraints excluded: chain X residue 60 ASN Chi-restraints excluded: chain Y residue 51 ASN Chi-restraints excluded: chain l residue 48 LEU Chi-restraints excluded: chain l residue 99 SER Chi-restraints excluded: chain l residue 241 VAL Chi-restraints excluded: chain l residue 251 THR Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 60 LEU Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain h residue 48 THR Chi-restraints excluded: chain h residue 196 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 18 GLN Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain i residue 38 THR Chi-restraints excluded: chain k residue 38 THR Chi-restraints excluded: chain n residue 32 SER Chi-restraints excluded: chain o residue 47 SER Chi-restraints excluded: chain p residue 20 LEU Chi-restraints excluded: chain p residue 32 SER Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain s residue 3 LYS Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 46 ILE Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain v residue 22 SER Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain w residue 11 PHE Chi-restraints excluded: chain w residue 37 SER Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain b1 residue 4 PHE Chi-restraints excluded: chain b1 residue 5 TYR Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain 4 residue 28 LEU Chi-restraints excluded: chain 4 residue 32 SER Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b8 residue 40 LEU Chi-restraints excluded: chain b9 residue 2 SER Chi-restraints excluded: chain b9 residue 37 SER Chi-restraints excluded: chain b0 residue 13 THR Chi-restraints excluded: chain b0 residue 26 SER Chi-restraints excluded: chain y residue 6 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 141 optimal weight: 1.9990 chunk 379 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 247 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 421 optimal weight: 0.7980 chunk 350 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 139 optimal weight: 0.6980 chunk 221 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 307 ASN K 20 GLN K 52 ASN S 20 GLN 7 20 GLN X 58 GLN Y 51 ASN ** l 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 307 ASN i 20 GLN k 20 GLN k 52 ASN n 16 GLN o 20 GLN q 20 GLN b1 20 GLN 4 18 GLN 6 20 GLN x 18 ASN x 58 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 46700 Z= 0.217 Angle : 0.657 11.217 64138 Z= 0.282 Chirality : 0.038 0.273 6216 Planarity : 0.004 0.060 7888 Dihedral : 16.209 179.984 8460 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.78 % Allowed : 21.38 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.12), residues: 4462 helix: 2.02 (0.09), residues: 2944 sheet: -0.74 (0.82), residues: 48 loop : 0.22 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP j 48 HIS 0.017 0.001 HIS Z 21 PHE 0.025 0.001 PHE 5 23 TYR 0.027 0.001 TYR O 5 ARG 0.011 0.000 ARG M 233 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 938 time to evaluate : 4.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 21 THR cc_start: 0.8620 (m) cc_final: 0.8086 (t) REVERT: M 23 ASP cc_start: 0.7143 (t0) cc_final: 0.6810 (t0) REVERT: M 36 SER cc_start: 0.8584 (t) cc_final: 0.8337 (t) REVERT: F 15 ARG cc_start: 0.6911 (mmt90) cc_final: 0.6221 (ptt90) REVERT: I 3 LYS cc_start: 0.8320 (mtpm) cc_final: 0.7929 (tppp) REVERT: I 5 TYR cc_start: 0.8149 (p90) cc_final: 0.7814 (p90) REVERT: K 5 TYR cc_start: 0.7978 (p90) cc_final: 0.7707 (p90) REVERT: O 1 MET cc_start: 0.4217 (tmt) cc_final: 0.3962 (tmm) REVERT: O 3 LYS cc_start: 0.7790 (ttmm) cc_final: 0.7330 (tptt) REVERT: Q 12 ASP cc_start: 0.8121 (t70) cc_final: 0.7839 (t0) REVERT: Q 24 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8993 (mm) REVERT: S 3 LYS cc_start: 0.8927 (mttt) cc_final: 0.8673 (mmtm) REVERT: U 15 ARG cc_start: 0.7836 (mmt90) cc_final: 0.7171 (mtm110) REVERT: U 30 MET cc_start: 0.7308 (ttp) cc_final: 0.7048 (ttm) REVERT: C 9 TYR cc_start: 0.7843 (OUTLIER) cc_final: 0.7065 (m-10) REVERT: 3 3 LYS cc_start: 0.7768 (mmmt) cc_final: 0.7507 (ttmm) REVERT: 3 9 MET cc_start: 0.8323 (mmm) cc_final: 0.8083 (mpt) REVERT: 9 1 MET cc_start: 0.5717 (OUTLIER) cc_final: 0.5297 (tmt) REVERT: 9 45 GLU cc_start: 0.7445 (tt0) cc_final: 0.7240 (tt0) REVERT: X 17 THR cc_start: 0.6671 (m) cc_final: 0.6141 (t) REVERT: X 53 ARG cc_start: 0.6394 (mtt-85) cc_final: 0.5458 (ptm160) REVERT: Y 6 GLU cc_start: 0.6883 (tp30) cc_final: 0.6635 (pm20) REVERT: m 23 ASP cc_start: 0.7212 (t0) cc_final: 0.6640 (t0) REVERT: m 36 SER cc_start: 0.8577 (t) cc_final: 0.8329 (t) REVERT: m 233 ARG cc_start: 0.7215 (ttp-110) cc_final: 0.6988 (ttp-110) REVERT: a 44 LEU cc_start: 0.8893 (mt) cc_final: 0.8692 (mt) REVERT: e 18 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7995 (mt0) REVERT: f 6 LYS cc_start: 0.8601 (mmmt) cc_final: 0.8339 (mmmm) REVERT: f 15 ARG cc_start: 0.6857 (mmt90) cc_final: 0.6179 (ptt90) REVERT: i 3 LYS cc_start: 0.8346 (mtpm) cc_final: 0.7955 (tppp) REVERT: i 5 TYR cc_start: 0.8217 (p90) cc_final: 0.7861 (p90) REVERT: j 32 SER cc_start: 0.8827 (p) cc_final: 0.8592 (m) REVERT: k 3 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7900 (tptm) REVERT: o 45 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7068 (mm-30) REVERT: q 12 ASP cc_start: 0.8205 (t70) cc_final: 0.7958 (t0) REVERT: q 24 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8966 (mm) REVERT: s 3 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8216 (mttm) REVERT: s 14 ARG cc_start: 0.8197 (mtt90) cc_final: 0.7942 (mtm-85) REVERT: u 15 ARG cc_start: 0.7801 (mmt90) cc_final: 0.7476 (mtt90) REVERT: w 11 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8519 (m-10) REVERT: c 9 TYR cc_start: 0.7684 (OUTLIER) cc_final: 0.6912 (m-80) REVERT: 5 5 TYR cc_start: 0.7865 (p90) cc_final: 0.7443 (p90) REVERT: b1 4 PHE cc_start: 0.6398 (OUTLIER) cc_final: 0.6101 (m-10) REVERT: x 28 MET cc_start: 0.6592 (OUTLIER) cc_final: 0.6107 (tpt) REVERT: x 53 ARG cc_start: 0.6260 (mtt-85) cc_final: 0.5388 (ptm160) outliers start: 144 outliers final: 70 residues processed: 1008 average time/residue: 1.2191 time to fit residues: 1610.1226 Evaluate side-chains 968 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 886 time to evaluate : 4.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 262 MET Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain U residue 3 LYS Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain C residue 9 TYR Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 9 residue 1 MET Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 0 residue 40 LEU Chi-restraints excluded: chain X residue 60 ASN Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain l residue 48 LEU Chi-restraints excluded: chain l residue 99 SER Chi-restraints excluded: chain l residue 241 VAL Chi-restraints excluded: chain l residue 251 THR Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 60 LEU Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain h residue 48 THR Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 18 GLN Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain i residue 38 THR Chi-restraints excluded: chain k residue 3 LYS Chi-restraints excluded: chain n residue 32 SER Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain p residue 32 SER Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain s residue 3 LYS Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain v residue 22 SER Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain w residue 11 PHE Chi-restraints excluded: chain w residue 54 VAL Chi-restraints excluded: chain c residue 9 TYR Chi-restraints excluded: chain 5 residue 30 MET Chi-restraints excluded: chain b1 residue 4 PHE Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain 4 residue 12 LEU Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b9 residue 2 SER Chi-restraints excluded: chain b9 residue 37 SER Chi-restraints excluded: chain b0 residue 26 SER Chi-restraints excluded: chain x residue 28 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 406 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 308 optimal weight: 0.8980 chunk 238 optimal weight: 2.9990 chunk 355 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 chunk 420 optimal weight: 2.9990 chunk 262 optimal weight: 0.9980 chunk 256 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN K 20 GLN K 52 ASN N 16 GLN ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 ASN ** l 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 GLN k 20 GLN k 42 ASN k 52 ASN n 16 GLN o 20 GLN r 16 GLN b1 20 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 46700 Z= 0.243 Angle : 0.673 11.455 64138 Z= 0.289 Chirality : 0.039 0.310 6216 Planarity : 0.004 0.059 7888 Dihedral : 15.958 179.927 8460 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.91 % Allowed : 22.11 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.15 (0.12), residues: 4462 helix: 2.10 (0.09), residues: 2944 sheet: -0.65 (0.84), residues: 48 loop : 0.19 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP j 48 HIS 0.013 0.001 HIS z 21 PHE 0.025 0.001 PHE 5 23 TYR 0.028 0.001 TYR O 5 ARG 0.012 0.000 ARG M 233 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 925 time to evaluate : 5.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 21 THR cc_start: 0.8579 (m) cc_final: 0.8076 (t) REVERT: M 23 ASP cc_start: 0.7078 (t0) cc_final: 0.6753 (t0) REVERT: M 36 SER cc_start: 0.8534 (t) cc_final: 0.8295 (t) REVERT: M 122 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8283 (ttt) REVERT: H 226 THR cc_start: 0.8815 (p) cc_final: 0.8485 (t) REVERT: F 15 ARG cc_start: 0.6924 (mmt90) cc_final: 0.6222 (ptt90) REVERT: I 3 LYS cc_start: 0.8334 (mtpm) cc_final: 0.7974 (tppp) REVERT: I 5 TYR cc_start: 0.8107 (p90) cc_final: 0.7799 (p90) REVERT: K 5 TYR cc_start: 0.8034 (p90) cc_final: 0.7741 (p90) REVERT: O 3 LYS cc_start: 0.7733 (ttmm) cc_final: 0.7276 (tptt) REVERT: Q 12 ASP cc_start: 0.8191 (t70) cc_final: 0.7961 (t0) REVERT: Q 24 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8931 (mm) REVERT: S 3 LYS cc_start: 0.8939 (mttt) cc_final: 0.8661 (mmtm) REVERT: U 15 ARG cc_start: 0.7842 (mmt90) cc_final: 0.7258 (mtm110) REVERT: U 30 MET cc_start: 0.7364 (ttp) cc_final: 0.7119 (ttm) REVERT: 3 3 LYS cc_start: 0.7891 (mmmt) cc_final: 0.7630 (mmmt) REVERT: 2 15 GLU cc_start: 0.6500 (pm20) cc_final: 0.5811 (pm20) REVERT: 9 1 MET cc_start: 0.5889 (OUTLIER) cc_final: 0.5374 (tmt) REVERT: 9 45 GLU cc_start: 0.7435 (tt0) cc_final: 0.7227 (tt0) REVERT: X 17 THR cc_start: 0.6781 (m) cc_final: 0.6242 (t) REVERT: X 28 MET cc_start: 0.6613 (tmm) cc_final: 0.6228 (tpt) REVERT: X 53 ARG cc_start: 0.6385 (mtt-85) cc_final: 0.5504 (ptm160) REVERT: Y 6 GLU cc_start: 0.6921 (tp30) cc_final: 0.6654 (pm20) REVERT: m 23 ASP cc_start: 0.7143 (t0) cc_final: 0.6775 (t0) REVERT: m 36 SER cc_start: 0.8543 (t) cc_final: 0.8308 (t) REVERT: e 18 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.8034 (mt0) REVERT: f 6 LYS cc_start: 0.8569 (mmmt) cc_final: 0.8293 (mmmm) REVERT: f 15 ARG cc_start: 0.6945 (mmt90) cc_final: 0.6202 (ptt90) REVERT: i 3 LYS cc_start: 0.8345 (mtpm) cc_final: 0.7972 (tppp) REVERT: i 5 TYR cc_start: 0.8226 (p90) cc_final: 0.7915 (p90) REVERT: j 32 SER cc_start: 0.8873 (p) cc_final: 0.8624 (m) REVERT: o 3 LYS cc_start: 0.7435 (mtpp) cc_final: 0.7017 (ttmm) REVERT: o 5 TYR cc_start: 0.8177 (p90) cc_final: 0.7806 (p90) REVERT: o 45 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7051 (mm-30) REVERT: q 3 LYS cc_start: 0.8442 (mmmm) cc_final: 0.8168 (mmtt) REVERT: q 6 LYS cc_start: 0.8263 (tppp) cc_final: 0.7920 (mmmt) REVERT: q 12 ASP cc_start: 0.8201 (t70) cc_final: 0.7962 (t0) REVERT: q 24 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8898 (mm) REVERT: u 15 ARG cc_start: 0.7826 (mmt90) cc_final: 0.7495 (mtt90) REVERT: w 11 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8581 (m-10) REVERT: 5 3 LYS cc_start: 0.7612 (mmmt) cc_final: 0.7320 (ttmm) REVERT: 5 5 TYR cc_start: 0.8012 (p90) cc_final: 0.7535 (p90) REVERT: b1 4 PHE cc_start: 0.6238 (OUTLIER) cc_final: 0.5814 (m-10) REVERT: x 28 MET cc_start: 0.6693 (OUTLIER) cc_final: 0.6211 (tpt) REVERT: x 53 ARG cc_start: 0.6210 (mtt-85) cc_final: 0.5387 (ptm160) outliers start: 149 outliers final: 84 residues processed: 1002 average time/residue: 1.2091 time to fit residues: 1585.0378 Evaluate side-chains 984 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 891 time to evaluate : 4.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 122 MET Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 262 MET Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain U residue 3 LYS Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain 1 residue 4 PHE Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain 8 residue 40 LEU Chi-restraints excluded: chain 9 residue 1 MET Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 0 residue 18 GLN Chi-restraints excluded: chain X residue 60 ASN Chi-restraints excluded: chain Y residue 51 ASN Chi-restraints excluded: chain l residue 48 LEU Chi-restraints excluded: chain l residue 99 SER Chi-restraints excluded: chain l residue 241 VAL Chi-restraints excluded: chain l residue 251 THR Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 60 LEU Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain h residue 48 THR Chi-restraints excluded: chain h residue 196 VAL Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 18 GLN Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain i residue 37 SER Chi-restraints excluded: chain i residue 38 THR Chi-restraints excluded: chain k residue 38 THR Chi-restraints excluded: chain n residue 32 SER Chi-restraints excluded: chain o residue 20 GLN Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain p residue 32 SER Chi-restraints excluded: chain p residue 40 LEU Chi-restraints excluded: chain q residue 20 GLN Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain t residue 10 THR Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain u residue 29 VAL Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain w residue 11 PHE Chi-restraints excluded: chain w residue 37 SER Chi-restraints excluded: chain b1 residue 4 PHE Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain 4 residue 12 LEU Chi-restraints excluded: chain 4 residue 28 LEU Chi-restraints excluded: chain 4 residue 32 SER Chi-restraints excluded: chain 6 residue 30 MET Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b9 residue 2 SER Chi-restraints excluded: chain b9 residue 37 SER Chi-restraints excluded: chain b0 residue 26 SER Chi-restraints excluded: chain x residue 28 MET Chi-restraints excluded: chain x residue 60 ASN Chi-restraints excluded: chain y residue 52 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 259 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 250 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 267 optimal weight: 0.6980 chunk 286 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 330 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 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 ASN ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN N 16 GLN ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 ASN ** l 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 GLN ** k 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 52 ASN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 16 GLN b1 20 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 46700 Z= 0.217 Angle : 0.672 12.305 64138 Z= 0.291 Chirality : 0.039 0.316 6216 Planarity : 0.003 0.046 7888 Dihedral : 15.818 179.962 8460 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.47 % Allowed : 23.08 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.22 (0.12), residues: 4462 helix: 2.14 (0.09), residues: 2950 sheet: -0.61 (0.85), residues: 48 loop : 0.23 (0.18), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Z 29 HIS 0.013 0.001 HIS z 21 PHE 0.028 0.001 PHE 5 23 TYR 0.028 0.001 TYR O 5 ARG 0.010 0.000 ARG m 233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 924 time to evaluate : 4.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 21 THR cc_start: 0.8502 (m) cc_final: 0.7970 (t) REVERT: M 23 ASP cc_start: 0.7136 (t0) cc_final: 0.6874 (t70) REVERT: M 36 SER cc_start: 0.8523 (t) cc_final: 0.8287 (t) REVERT: M 122 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8263 (ttt) REVERT: M 168 MET cc_start: 0.7711 (mmm) cc_final: 0.7159 (mtm) REVERT: H 226 THR cc_start: 0.8798 (p) cc_final: 0.8444 (t) REVERT: F 15 ARG cc_start: 0.6929 (mmt90) cc_final: 0.6224 (ptt90) REVERT: I 3 LYS cc_start: 0.8329 (mtpm) cc_final: 0.7966 (tppp) REVERT: I 5 TYR cc_start: 0.8158 (p90) cc_final: 0.7804 (p90) REVERT: K 5 TYR cc_start: 0.7996 (p90) cc_final: 0.7730 (p90) REVERT: K 27 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8257 (tt) REVERT: O 3 LYS cc_start: 0.7764 (ttmm) cc_final: 0.7306 (tptt) REVERT: Q 12 ASP cc_start: 0.8160 (t70) cc_final: 0.7944 (t0) REVERT: Q 24 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8885 (mm) REVERT: S 3 LYS cc_start: 0.8946 (mttt) cc_final: 0.8676 (mmtm) REVERT: U 15 ARG cc_start: 0.7816 (mmt90) cc_final: 0.7216 (mtm110) REVERT: U 30 MET cc_start: 0.7349 (ttp) cc_final: 0.7115 (ttm) REVERT: W 6 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8391 (mtmm) REVERT: 3 3 LYS cc_start: 0.7896 (mmmt) cc_final: 0.7642 (ttmm) REVERT: 1 4 PHE cc_start: 0.5970 (OUTLIER) cc_final: 0.5426 (m-10) REVERT: 2 15 GLU cc_start: 0.6549 (pm20) cc_final: 0.5942 (pm20) REVERT: 9 1 MET cc_start: 0.5927 (OUTLIER) cc_final: 0.5392 (tmt) REVERT: 9 3 LYS cc_start: 0.8969 (mmmm) cc_final: 0.8709 (mmmt) REVERT: 9 45 GLU cc_start: 0.7410 (tt0) cc_final: 0.7194 (tt0) REVERT: X 17 THR cc_start: 0.6799 (m) cc_final: 0.6271 (t) REVERT: X 28 MET cc_start: 0.6610 (tmm) cc_final: 0.6138 (tpt) REVERT: X 53 ARG cc_start: 0.6420 (mtt-85) cc_final: 0.5531 (ptm160) REVERT: Y 6 GLU cc_start: 0.6964 (tp30) cc_final: 0.6697 (pm20) REVERT: m 23 ASP cc_start: 0.7145 (t0) cc_final: 0.6798 (t0) REVERT: m 36 SER cc_start: 0.8524 (t) cc_final: 0.8293 (t) REVERT: m 122 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8238 (ttt) REVERT: m 168 MET cc_start: 0.7724 (mmm) cc_final: 0.7161 (mtm) REVERT: h 195 MET cc_start: 0.7774 (mmm) cc_final: 0.7442 (mmm) REVERT: e 18 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.8027 (mt0) REVERT: e 26 SER cc_start: 0.8844 (m) cc_final: 0.8588 (p) REVERT: f 6 LYS cc_start: 0.8558 (mmmt) cc_final: 0.8275 (mmmm) REVERT: f 15 ARG cc_start: 0.6947 (mmt90) cc_final: 0.6206 (ptt90) REVERT: g 12 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7453 (mp) REVERT: i 3 LYS cc_start: 0.8328 (mtpm) cc_final: 0.7977 (tppp) REVERT: i 5 TYR cc_start: 0.8173 (p90) cc_final: 0.7904 (p90) REVERT: j 32 SER cc_start: 0.8809 (p) cc_final: 0.8563 (m) REVERT: n 28 LEU cc_start: 0.9103 (tt) cc_final: 0.8893 (tp) REVERT: o 3 LYS cc_start: 0.7402 (mtpp) cc_final: 0.6942 (ttmm) REVERT: o 5 TYR cc_start: 0.8182 (p90) cc_final: 0.7793 (p90) REVERT: o 45 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7074 (mm-30) REVERT: p 10 THR cc_start: 0.6388 (OUTLIER) cc_final: 0.6183 (p) REVERT: q 12 ASP cc_start: 0.8166 (t70) cc_final: 0.7815 (t0) REVERT: q 24 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8850 (mm) REVERT: u 15 ARG cc_start: 0.7818 (mmt90) cc_final: 0.7503 (mtt90) REVERT: 5 3 LYS cc_start: 0.7641 (mmmt) cc_final: 0.7368 (ttmm) REVERT: 5 5 TYR cc_start: 0.7997 (p90) cc_final: 0.7516 (p90) REVERT: b1 4 PHE cc_start: 0.6221 (OUTLIER) cc_final: 0.6005 (m-10) REVERT: x 28 MET cc_start: 0.6667 (OUTLIER) cc_final: 0.6201 (tpt) REVERT: x 53 ARG cc_start: 0.6209 (mtt-85) cc_final: 0.5381 (ptm160) outliers start: 132 outliers final: 85 residues processed: 984 average time/residue: 1.2156 time to fit residues: 1572.1596 Evaluate side-chains 989 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 890 time to evaluate : 4.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 122 MET Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 262 MET Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 6 LYS Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain 1 residue 4 PHE Chi-restraints excluded: chain 9 residue 1 MET Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 0 residue 18 GLN Chi-restraints excluded: chain X residue 60 ASN Chi-restraints excluded: chain l residue 48 LEU Chi-restraints excluded: chain l residue 99 SER Chi-restraints excluded: chain l residue 241 VAL Chi-restraints excluded: chain l residue 251 THR Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 60 LEU Chi-restraints excluded: chain m residue 122 MET Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain h residue 48 THR Chi-restraints excluded: chain h residue 196 VAL Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 18 GLN Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain i residue 38 THR Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain k residue 38 THR Chi-restraints excluded: chain n residue 32 SER Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain p residue 10 THR Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain p residue 32 SER Chi-restraints excluded: chain q residue 20 GLN Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 30 LEU Chi-restraints excluded: chain t residue 10 THR Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain u residue 29 VAL Chi-restraints excluded: chain v residue 22 SER Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain w residue 50 LYS Chi-restraints excluded: chain b1 residue 4 PHE Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain 4 residue 12 LEU Chi-restraints excluded: chain 4 residue 28 LEU Chi-restraints excluded: chain 4 residue 32 SER Chi-restraints excluded: chain 6 residue 30 MET Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b9 residue 2 SER Chi-restraints excluded: chain b9 residue 37 SER Chi-restraints excluded: chain b0 residue 26 SER Chi-restraints excluded: chain x residue 28 MET Chi-restraints excluded: chain x residue 60 ASN Chi-restraints excluded: chain y residue 52 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 382 optimal weight: 4.9990 chunk 402 optimal weight: 1.9990 chunk 367 optimal weight: 3.9990 chunk 391 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 307 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 353 optimal weight: 1.9990 chunk 370 optimal weight: 0.9980 chunk 390 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN K 20 GLN K 52 ASN ** N 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 26 GLN Y 51 ASN ** l 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 GLN j 16 GLN ** k 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 52 ASN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 20 GLN x 18 ASN x 58 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 46700 Z= 0.308 Angle : 0.730 12.539 64138 Z= 0.313 Chirality : 0.041 0.315 6216 Planarity : 0.004 0.079 7888 Dihedral : 15.998 179.932 8460 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.39 % Allowed : 23.29 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.02 (0.12), residues: 4462 helix: 1.97 (0.09), residues: 2938 sheet: -0.67 (0.84), residues: 48 loop : 0.21 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 29 HIS 0.015 0.002 HIS z 21 PHE 0.039 0.002 PHE K 23 TYR 0.029 0.002 TYR O 5 ARG 0.011 0.001 ARG m 233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 910 time to evaluate : 4.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 21 THR cc_start: 0.8577 (m) cc_final: 0.8045 (t) REVERT: M 23 ASP cc_start: 0.7143 (t0) cc_final: 0.6772 (t0) REVERT: M 36 SER cc_start: 0.8568 (t) cc_final: 0.8333 (t) REVERT: H 226 THR cc_start: 0.8812 (p) cc_final: 0.8454 (t) REVERT: F 9 MET cc_start: 0.8059 (mmm) cc_final: 0.7820 (mmp) REVERT: F 15 ARG cc_start: 0.6997 (mmt90) cc_final: 0.6247 (ptt90) REVERT: I 3 LYS cc_start: 0.8392 (mtpm) cc_final: 0.8046 (tppp) REVERT: I 5 TYR cc_start: 0.8169 (p90) cc_final: 0.7797 (p90) REVERT: K 5 TYR cc_start: 0.7885 (p90) cc_final: 0.7628 (p90) REVERT: K 27 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8271 (tt) REVERT: O 3 LYS cc_start: 0.7752 (ttmm) cc_final: 0.7297 (tptt) REVERT: Q 12 ASP cc_start: 0.8202 (t70) cc_final: 0.7975 (t0) REVERT: Q 24 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8933 (mm) REVERT: S 3 LYS cc_start: 0.8974 (mttt) cc_final: 0.8703 (mmtm) REVERT: U 15 ARG cc_start: 0.7840 (mmt90) cc_final: 0.7169 (mtm110) REVERT: U 30 MET cc_start: 0.7377 (ttp) cc_final: 0.7139 (ttm) REVERT: W 6 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8433 (mtmm) REVERT: C 25 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8157 (mmm) REVERT: 3 3 LYS cc_start: 0.7888 (mmmt) cc_final: 0.7645 (ttmm) REVERT: 1 4 PHE cc_start: 0.6002 (OUTLIER) cc_final: 0.5545 (m-10) REVERT: 1 26 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8651 (mp) REVERT: 1 37 SER cc_start: 0.9003 (p) cc_final: 0.8736 (p) REVERT: 2 15 GLU cc_start: 0.6767 (pm20) cc_final: 0.6376 (pm20) REVERT: 9 45 GLU cc_start: 0.7487 (tt0) cc_final: 0.7261 (tt0) REVERT: X 17 THR cc_start: 0.6870 (m) cc_final: 0.6322 (t) REVERT: X 28 MET cc_start: 0.6622 (tmm) cc_final: 0.6152 (tpt) REVERT: X 53 ARG cc_start: 0.6343 (mtt-85) cc_final: 0.5467 (ptm160) REVERT: Y 6 GLU cc_start: 0.7019 (tp30) cc_final: 0.6689 (pm20) REVERT: m 23 ASP cc_start: 0.7193 (t0) cc_final: 0.6835 (t0) REVERT: m 36 SER cc_start: 0.8562 (t) cc_final: 0.8329 (t) REVERT: h 195 MET cc_start: 0.7776 (mmm) cc_final: 0.7456 (mmm) REVERT: h 226 THR cc_start: 0.8843 (p) cc_final: 0.8401 (t) REVERT: e 18 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8020 (mt0) REVERT: f 15 ARG cc_start: 0.7002 (mmt90) cc_final: 0.6231 (ptt90) REVERT: g 12 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7471 (mp) REVERT: i 3 LYS cc_start: 0.8409 (mtpm) cc_final: 0.8062 (tppp) REVERT: i 5 TYR cc_start: 0.8239 (p90) cc_final: 0.7873 (p90) REVERT: j 32 SER cc_start: 0.8908 (p) cc_final: 0.8635 (m) REVERT: n 28 LEU cc_start: 0.9073 (tt) cc_final: 0.8846 (tp) REVERT: o 5 TYR cc_start: 0.8200 (p90) cc_final: 0.7879 (p90) REVERT: o 45 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7066 (mm-30) REVERT: q 24 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8898 (mm) REVERT: s 3 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8217 (mttm) REVERT: u 15 ARG cc_start: 0.7824 (mmt90) cc_final: 0.7498 (mtt90) REVERT: 5 3 LYS cc_start: 0.7681 (mmmt) cc_final: 0.7457 (ttmm) REVERT: 5 5 TYR cc_start: 0.8029 (p90) cc_final: 0.7591 (p90) REVERT: b1 4 PHE cc_start: 0.6231 (OUTLIER) cc_final: 0.6030 (m-10) REVERT: b8 16 GLN cc_start: 0.7203 (mt0) cc_final: 0.6930 (mt0) REVERT: x 28 MET cc_start: 0.6657 (OUTLIER) cc_final: 0.6188 (tpt) REVERT: x 53 ARG cc_start: 0.6248 (mtt-85) cc_final: 0.5389 (ptm160) outliers start: 129 outliers final: 89 residues processed: 975 average time/residue: 1.2065 time to fit residues: 1538.8150 Evaluate side-chains 984 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 882 time to evaluate : 4.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 262 MET Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 6 LYS Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain 1 residue 4 PHE Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 0 residue 18 GLN Chi-restraints excluded: chain X residue 60 ASN Chi-restraints excluded: chain Y residue 51 ASN Chi-restraints excluded: chain l residue 48 LEU Chi-restraints excluded: chain l residue 99 SER Chi-restraints excluded: chain l residue 241 VAL Chi-restraints excluded: chain l residue 251 THR Chi-restraints excluded: chain m residue 52 LEU Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 60 LEU Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 262 MET Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain h residue 48 THR Chi-restraints excluded: chain h residue 196 VAL Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 18 GLN Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain i residue 37 SER Chi-restraints excluded: chain i residue 38 THR Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain k residue 38 THR Chi-restraints excluded: chain n residue 32 SER Chi-restraints excluded: chain o residue 33 LEU Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain p residue 10 THR Chi-restraints excluded: chain p residue 13 THR Chi-restraints excluded: chain p residue 32 SER Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain s residue 3 LYS Chi-restraints excluded: chain t residue 10 THR Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain u residue 29 VAL Chi-restraints excluded: chain v residue 22 SER Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain w residue 37 SER Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain b1 residue 4 PHE Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain 4 residue 28 LEU Chi-restraints excluded: chain 4 residue 30 LEU Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b9 residue 2 SER Chi-restraints excluded: chain b9 residue 37 SER Chi-restraints excluded: chain b0 residue 26 SER Chi-restraints excluded: chain x residue 28 MET Chi-restraints excluded: chain x residue 60 ASN Chi-restraints excluded: chain y residue 52 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 257 optimal weight: 2.9990 chunk 414 optimal weight: 0.9980 chunk 252 optimal weight: 0.6980 chunk 196 optimal weight: 2.9990 chunk 287 optimal weight: 0.5980 chunk 434 optimal weight: 2.9990 chunk 399 optimal weight: 3.9990 chunk 345 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 chunk 267 optimal weight: 0.7980 chunk 212 optimal weight: 0.0000 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 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 ASN ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN K 52 ASN ** Z 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 18 GLN ** 2 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 58 GLN ** l 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 GLN j 16 GLN ** k 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 52 ASN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 20 GLN x 18 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 46700 Z= 0.186 Angle : 0.667 13.341 64138 Z= 0.292 Chirality : 0.039 0.331 6216 Planarity : 0.003 0.066 7888 Dihedral : 15.632 179.999 8460 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.36 % Allowed : 24.68 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.20 (0.12), residues: 4462 helix: 2.08 (0.09), residues: 2982 sheet: -0.47 (0.88), residues: 48 loop : 0.28 (0.18), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP j 29 HIS 0.013 0.001 HIS z 21 PHE 0.034 0.001 PHE o 25 TYR 0.029 0.001 TYR 4 24 ARG 0.014 0.000 ARG m 233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8924 Ramachandran restraints generated. 4462 Oldfield, 0 Emsley, 4462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 932 time to evaluate : 4.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 21 THR cc_start: 0.8472 (m) cc_final: 0.7905 (t) REVERT: M 23 ASP cc_start: 0.6943 (t0) cc_final: 0.6597 (t0) REVERT: M 36 SER cc_start: 0.8499 (t) cc_final: 0.8264 (t) REVERT: M 168 MET cc_start: 0.7592 (mmm) cc_final: 0.6948 (mtm) REVERT: H 226 THR cc_start: 0.8770 (p) cc_final: 0.8410 (t) REVERT: A 22 VAL cc_start: 0.9201 (t) cc_final: 0.8988 (t) REVERT: E 26 SER cc_start: 0.8817 (m) cc_final: 0.8580 (p) REVERT: F 9 MET cc_start: 0.8136 (mmm) cc_final: 0.7918 (mmp) REVERT: F 15 ARG cc_start: 0.6939 (mmt90) cc_final: 0.6242 (ptt90) REVERT: I 3 LYS cc_start: 0.8367 (mtpm) cc_final: 0.8024 (tppp) REVERT: I 5 TYR cc_start: 0.8259 (p90) cc_final: 0.7838 (p90) REVERT: K 3 LYS cc_start: 0.7873 (tmtt) cc_final: 0.7616 (tptt) REVERT: K 5 TYR cc_start: 0.7848 (p90) cc_final: 0.7645 (p90) REVERT: K 27 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8216 (tt) REVERT: O 3 LYS cc_start: 0.7693 (ttmm) cc_final: 0.7256 (tptt) REVERT: Q 12 ASP cc_start: 0.8062 (t70) cc_final: 0.7787 (t0) REVERT: Q 24 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8894 (mm) REVERT: S 3 LYS cc_start: 0.8946 (mttt) cc_final: 0.8670 (mmtm) REVERT: U 15 ARG cc_start: 0.7793 (mmt90) cc_final: 0.7535 (mtt90) REVERT: U 30 MET cc_start: 0.7312 (ttp) cc_final: 0.7105 (ttm) REVERT: C 10 THR cc_start: 0.8416 (p) cc_final: 0.8178 (t) REVERT: 3 3 LYS cc_start: 0.7827 (mmmt) cc_final: 0.7529 (ttmm) REVERT: 1 4 PHE cc_start: 0.6045 (OUTLIER) cc_final: 0.5647 (m-10) REVERT: 1 5 TYR cc_start: 0.6862 (p90) cc_final: 0.5396 (p90) REVERT: 1 25 PHE cc_start: 0.8461 (t80) cc_final: 0.8055 (t80) REVERT: 1 37 SER cc_start: 0.8968 (p) cc_final: 0.8736 (p) REVERT: 9 3 LYS cc_start: 0.8937 (mmmm) cc_final: 0.8717 (mmmt) REVERT: 9 45 GLU cc_start: 0.7449 (tt0) cc_final: 0.7229 (tt0) REVERT: X 17 THR cc_start: 0.6772 (m) cc_final: 0.6240 (t) REVERT: X 28 MET cc_start: 0.6788 (OUTLIER) cc_final: 0.6263 (tpt) REVERT: X 53 ARG cc_start: 0.6293 (mtt-85) cc_final: 0.5425 (ptm160) REVERT: Y 6 GLU cc_start: 0.7008 (tp30) cc_final: 0.6544 (pm20) REVERT: m 23 ASP cc_start: 0.7175 (t0) cc_final: 0.6893 (t0) REVERT: m 36 SER cc_start: 0.8488 (t) cc_final: 0.8254 (t) REVERT: m 168 MET cc_start: 0.7616 (mmm) cc_final: 0.6958 (mtm) REVERT: h 193 MET cc_start: 0.7446 (mmt) cc_final: 0.7196 (mmm) REVERT: h 195 MET cc_start: 0.7709 (mmm) cc_final: 0.7379 (mmm) REVERT: h 226 THR cc_start: 0.8620 (p) cc_final: 0.8371 (t) REVERT: a 22 VAL cc_start: 0.9197 (t) cc_final: 0.8987 (t) REVERT: e 18 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.8022 (mt0) REVERT: e 26 SER cc_start: 0.8813 (m) cc_final: 0.8597 (p) REVERT: f 15 ARG cc_start: 0.6986 (mmt90) cc_final: 0.6227 (ptt90) REVERT: i 3 LYS cc_start: 0.8329 (mtpm) cc_final: 0.7891 (tppp) REVERT: i 5 TYR cc_start: 0.8220 (p90) cc_final: 0.7919 (p90) REVERT: j 32 SER cc_start: 0.8928 (p) cc_final: 0.8619 (m) REVERT: o 3 LYS cc_start: 0.7430 (mtpp) cc_final: 0.6915 (ttmm) REVERT: o 5 TYR cc_start: 0.8183 (p90) cc_final: 0.7783 (p90) REVERT: q 12 ASP cc_start: 0.8041 (t70) cc_final: 0.7778 (t0) REVERT: q 24 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8826 (mm) REVERT: u 15 ARG cc_start: 0.7808 (mmt90) cc_final: 0.7499 (mtt90) REVERT: w 11 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8496 (m-10) REVERT: 5 5 TYR cc_start: 0.7959 (p90) cc_final: 0.7567 (p90) REVERT: 5 9 MET cc_start: 0.8624 (mpp) cc_final: 0.8198 (mpt) REVERT: b1 25 PHE cc_start: 0.8454 (t80) cc_final: 0.8064 (t80) REVERT: b1 37 SER cc_start: 0.8925 (OUTLIER) cc_final: 0.8578 (p) REVERT: x 28 MET cc_start: 0.6624 (OUTLIER) cc_final: 0.6176 (tpt) REVERT: x 53 ARG cc_start: 0.6194 (mtt-85) cc_final: 0.5356 (ptm160) outliers start: 90 outliers final: 63 residues processed: 983 average time/residue: 1.2347 time to fit residues: 1599.5852 Evaluate side-chains 960 residues out of total 3808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 888 time to evaluate : 4.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 143 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain 1 residue 4 PHE Chi-restraints excluded: chain 2 residue 30 LEU Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain X residue 28 MET Chi-restraints excluded: chain l residue 48 LEU Chi-restraints excluded: chain l residue 99 SER Chi-restraints excluded: chain l residue 241 VAL Chi-restraints excluded: chain l residue 251 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain e residue 7 LEU Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain e residue 18 GLN Chi-restraints excluded: chain e residue 40 LEU Chi-restraints excluded: chain i residue 37 SER Chi-restraints excluded: chain i residue 38 THR Chi-restraints excluded: chain n residue 32 SER Chi-restraints excluded: chain p residue 10 THR Chi-restraints excluded: chain p residue 32 SER Chi-restraints excluded: chain q residue 20 GLN Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 30 LEU Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain u residue 29 VAL Chi-restraints excluded: chain v residue 22 SER Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain w residue 11 PHE Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain b1 residue 37 SER Chi-restraints excluded: chain 4 residue 28 LEU Chi-restraints excluded: chain 4 residue 30 LEU Chi-restraints excluded: chain b8 residue 20 LEU Chi-restraints excluded: chain b9 residue 2 SER Chi-restraints excluded: chain b9 residue 37 SER Chi-restraints excluded: chain b0 residue 26 SER Chi-restraints excluded: chain x residue 28 MET Chi-restraints excluded: chain x residue 60 ASN Chi-restraints excluded: chain y residue 52 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 274 optimal weight: 2.9990 chunk 368 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 318 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 346 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 355 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 GLN K 52 ASN P 18 GLN ** Z 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 18 GLN 2 21 HIS Y 51 ASN ** l 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 GLN ** k 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 52 ASN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 20 GLN x 26 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.137490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.112229 restraints weight = 64421.506| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.02 r_work: 0.3141 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 46700 Z= 0.259 Angle : 0.704 12.963 64138 Z= 0.307 Chirality : 0.040 0.314 6216 Planarity : 0.004 0.065 7888 Dihedral : 15.674 179.965 8460 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.42 % Allowed : 24.95 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.09 (0.12), residues: 4462 helix: 2.01 (0.09), residues: 2970 sheet: -0.58 (0.86), residues: 48 loop : 0.24 (0.18), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP J 29 HIS 0.014 0.001 HIS z 21 PHE 0.044 0.001 PHE K 23 TYR 0.029 0.002 TYR Q 5 ARG 0.015 0.001 ARG m 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20917.30 seconds wall clock time: 371 minutes 17.60 seconds (22277.60 seconds total)