Starting phenix.real_space_refine (version: dev) on Wed Dec 21 21:27:05 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vor_32058/12_2022/7vor_32058_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vor_32058/12_2022/7vor_32058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vor_32058/12_2022/7vor_32058.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vor_32058/12_2022/7vor_32058.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vor_32058/12_2022/7vor_32058_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vor_32058/12_2022/7vor_32058_updated.pdb" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "G PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b9 TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 44980 Number of models: 1 Model: "" Number of chains: 128 Chain: "L" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2232 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2445 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 294} Chain: "H" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1973 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 236} Chain: "A" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "B" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "D" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "E" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "F" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "G" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "I" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "J" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "K" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "N" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "O" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "P" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Q" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "R" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "S" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "T" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "U" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "V" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "W" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "C" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "3" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 437 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "Z" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "1" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 392 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "2" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 309 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "7" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 403 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "8" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "9" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "0" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "X" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 529 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "Y" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 361 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "l" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2232 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "m" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2445 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 294} Chain: "h" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1973 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 236} Chain: "a" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "b" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "d" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "e" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "f" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "g" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "i" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "j" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "k" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "n" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "o" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "p" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "q" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "r" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "s" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "t" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "u" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "v" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "w" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "c" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "5" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 437 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "z" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "b1" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 392 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "4" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 309 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "6" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 403 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "b8" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "b9" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 460 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "b0" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "x" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 529 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "y" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 361 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "L" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 354 Unusual residues: {'BCL': 2, 'BPH': 1, 'PC1': 2, 'U10': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 36 Chain: "M" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 360 Unusual residues: {'BCL': 2, 'BPH': 1, 'CDL': 1, 'FE2': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "A" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 222 Unusual residues: {'BCL': 1, 'PC1': 3, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 147 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "E" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 129 Unusual residues: {'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "G" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'BCL': 1, 'SPO': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "3" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 135 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "2" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "7" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 122 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "9" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "0" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 354 Unusual residues: {'BCL': 2, 'BPH': 1, 'PC1': 2, 'U10': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 36 Chain: "m" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 360 Unusual residues: {'BCL': 2, 'BPH': 1, 'CDL': 1, 'FE2': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "h" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "a" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 222 Unusual residues: {'BCL': 1, 'PC1': 3, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 Chain: "b" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 147 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "e" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "f" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 129 Unusual residues: {'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "g" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "i" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "o" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "p" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "q" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'BCL': 1, 'SPO': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "r" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "t" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "v" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "5" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 135 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "z" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "b1" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "4" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "6" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 122 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "b9" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b0" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "x" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 24.45, per 1000 atoms: 0.54 Number of scatterers: 44980 At special positions: 0 Unit cell: (225.68, 142.48, 107.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 174 16.00 P 24 15.00 Mg 64 11.99 O 6804 8.00 N 6300 7.00 C 31612 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=64, symmetry=0 Number of additional bonds: simple=64, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.16 Conformation dependent library (CDL) restraints added in 5.1 seconds 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 192 helices and 8 sheets defined 65.3% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'L' and resid 6 through 9 Processing helix chain 'L' and resid 32 through 56 Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'L' and resid 84 through 111 Processing helix chain 'L' and resid 116 through 132 removed outlier: 3.571A pdb=" N PHE L 123 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 139 Processing helix chain 'L' and resid 142 through 144 No H-bonds generated for 'chain 'L' and resid 142 through 144' Processing helix chain 'L' and resid 152 through 164 removed outlier: 3.981A pdb=" N TYR L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 169 No H-bonds generated for 'chain 'L' and resid 167 through 169' Processing helix chain 'L' and resid 171 through 198 Processing helix chain 'L' and resid 209 through 220 Processing helix chain 'L' and resid 226 through 250 Processing helix chain 'L' and resid 259 through 267 removed outlier: 4.358A pdb=" N TRP L 265 " --> pdb=" O ASP L 261 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N TRP L 266 " --> pdb=" O TRP L 262 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL L 267 " --> pdb=" O TRP L 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 40 No H-bonds generated for 'chain 'M' and resid 37 through 40' Processing helix chain 'M' and resid 54 through 77 Processing helix chain 'M' and resid 82 through 87 Processing helix chain 'M' and resid 99 through 101 No H-bonds generated for 'chain 'M' and resid 99 through 101' Processing helix chain 'M' and resid 109 through 111 No H-bonds generated for 'chain 'M' and resid 109 through 111' Processing helix chain 'M' and resid 113 through 139 Processing helix chain 'M' and resid 145 through 161 Processing helix chain 'M' and resid 163 through 168 Processing helix chain 'M' and resid 171 through 173 No H-bonds generated for 'chain 'M' and resid 171 through 173' Processing helix chain 'M' and resid 179 through 192 Processing helix chain 'M' and resid 196 through 198 No H-bonds generated for 'chain 'M' and resid 196 through 198' Processing helix chain 'M' and resid 200 through 229 removed outlier: 4.788A pdb=" N ARG M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N PHE M 229 " --> pdb=" O ALA M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 243 through 256 Processing helix chain 'M' and resid 264 through 286 removed outlier: 3.753A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 300 Processing helix chain 'H' and resid 12 through 37 removed outlier: 4.132A pdb=" N ARG H 37 " --> pdb=" O THR H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 69 No H-bonds generated for 'chain 'H' and resid 67 through 69' Processing helix chain 'H' and resid 104 through 107 No H-bonds generated for 'chain 'H' and resid 104 through 107' Processing helix chain 'H' and resid 110 through 112 No H-bonds generated for 'chain 'H' and resid 110 through 112' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 210 through 215 removed outlier: 3.995A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 243 removed outlier: 3.840A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 258 Processing helix chain 'A' and resid 4 through 10 Processing helix chain 'A' and resid 13 through 37 Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'B' and resid 14 through 45 Processing helix chain 'D' and resid 2 through 10 removed outlier: 4.436A pdb=" N TYR D 5 " --> pdb=" O SER D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 37 Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'E' and resid 14 through 45 Processing helix chain 'F' and resid 3 through 9 Processing helix chain 'F' and resid 13 through 37 Processing helix chain 'F' and resid 43 through 50 Processing helix chain 'G' and resid 14 through 45 Processing helix chain 'I' and resid 4 through 9 Processing helix chain 'I' and resid 13 through 37 Processing helix chain 'I' and resid 43 through 51 Processing helix chain 'J' and resid 14 through 45 Processing helix chain 'K' and resid 4 through 9 Processing helix chain 'K' and resid 13 through 37 Processing helix chain 'K' and resid 43 through 50 Processing helix chain 'N' and resid 14 through 45 Processing helix chain 'O' and resid 4 through 9 Processing helix chain 'O' and resid 13 through 37 Processing helix chain 'O' and resid 43 through 50 Processing helix chain 'P' and resid 14 through 45 Processing helix chain 'Q' and resid 4 through 9 Processing helix chain 'Q' and resid 13 through 37 Processing helix chain 'Q' and resid 43 through 50 Processing helix chain 'R' and resid 14 through 45 Processing helix chain 'S' and resid 4 through 9 Processing helix chain 'S' and resid 13 through 37 Processing helix chain 'S' and resid 43 through 50 Processing helix chain 'T' and resid 14 through 45 Processing helix chain 'U' and resid 4 through 9 Processing helix chain 'U' and resid 13 through 37 Processing helix chain 'U' and resid 43 through 50 Processing helix chain 'V' and resid 14 through 45 Processing helix chain 'W' and resid 4 through 9 Processing helix chain 'W' and resid 13 through 37 Processing helix chain 'W' and resid 43 through 50 Processing helix chain 'C' and resid 14 through 45 Processing helix chain '3' and resid 5 through 9 Processing helix chain '3' and resid 13 through 37 Processing helix chain '3' and resid 43 through 50 Processing helix chain 'Z' and resid 14 through 45 Processing helix chain '1' and resid 13 through 37 Processing helix chain '1' and resid 43 through 50 Processing helix chain '2' and resid 14 through 45 Processing helix chain '7' and resid 4 through 9 Processing helix chain '7' and resid 13 through 37 Processing helix chain '8' and resid 14 through 45 Processing helix chain '9' and resid 4 through 9 Processing helix chain '9' and resid 13 through 37 Processing helix chain '9' and resid 43 through 50 Processing helix chain '0' and resid 14 through 45 Processing helix chain 'X' and resid 10 through 12 No H-bonds generated for 'chain 'X' and resid 10 through 12' Processing helix chain 'X' and resid 15 through 54 Processing helix chain 'Y' and resid 6 through 28 Processing helix chain 'Y' and resid 32 through 48 Processing helix chain 'l' and resid 6 through 9 Processing helix chain 'l' and resid 32 through 56 Processing helix chain 'l' and resid 71 through 73 No H-bonds generated for 'chain 'l' and resid 71 through 73' Processing helix chain 'l' and resid 80 through 82 No H-bonds generated for 'chain 'l' and resid 80 through 82' Processing helix chain 'l' and resid 84 through 111 Processing helix chain 'l' and resid 116 through 132 removed outlier: 3.571A pdb=" N PHE l 123 " --> pdb=" O PHE l 119 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA l 124 " --> pdb=" O ALA l 120 " (cutoff:3.500A) Processing helix chain 'l' and resid 134 through 139 Processing helix chain 'l' and resid 142 through 144 No H-bonds generated for 'chain 'l' and resid 142 through 144' Processing helix chain 'l' and resid 152 through 164 removed outlier: 3.981A pdb=" N TYR l 164 " --> pdb=" O THR l 160 " (cutoff:3.500A) Processing helix chain 'l' and resid 167 through 169 No H-bonds generated for 'chain 'l' and resid 167 through 169' Processing helix chain 'l' and resid 171 through 198 Processing helix chain 'l' and resid 209 through 220 Processing helix chain 'l' and resid 226 through 250 Processing helix chain 'l' and resid 259 through 267 removed outlier: 4.358A pdb=" N TRP l 265 " --> pdb=" O ASP l 261 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N TRP l 266 " --> pdb=" O TRP l 262 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL l 267 " --> pdb=" O TRP l 263 " (cutoff:3.500A) Processing helix chain 'm' and resid 37 through 40 No H-bonds generated for 'chain 'm' and resid 37 through 40' Processing helix chain 'm' and resid 54 through 77 Processing helix chain 'm' and resid 82 through 87 Processing helix chain 'm' and resid 99 through 101 No H-bonds generated for 'chain 'm' and resid 99 through 101' Processing helix chain 'm' and resid 109 through 111 No H-bonds generated for 'chain 'm' and resid 109 through 111' Processing helix chain 'm' and resid 113 through 139 Processing helix chain 'm' and resid 145 through 161 Processing helix chain 'm' and resid 163 through 168 Processing helix chain 'm' and resid 171 through 173 No H-bonds generated for 'chain 'm' and resid 171 through 173' Processing helix chain 'm' and resid 179 through 192 Processing helix chain 'm' and resid 196 through 198 No H-bonds generated for 'chain 'm' and resid 196 through 198' Processing helix chain 'm' and resid 200 through 229 removed outlier: 4.788A pdb=" N ARG m 228 " --> pdb=" O LEU m 224 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N PHE m 229 " --> pdb=" O ALA m 225 " (cutoff:3.500A) Processing helix chain 'm' and resid 234 through 239 Processing helix chain 'm' and resid 243 through 256 Processing helix chain 'm' and resid 264 through 286 removed outlier: 3.753A pdb=" N VAL m 276 " --> pdb=" O MET m 272 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR m 277 " --> pdb=" O ALA m 273 " (cutoff:3.500A) Processing helix chain 'm' and resid 294 through 300 Processing helix chain 'h' and resid 12 through 37 removed outlier: 4.132A pdb=" N ARG h 37 " --> pdb=" O THR h 33 " (cutoff:3.500A) Processing helix chain 'h' and resid 67 through 69 No H-bonds generated for 'chain 'h' and resid 67 through 69' Processing helix chain 'h' and resid 104 through 107 No H-bonds generated for 'chain 'h' and resid 104 through 107' Processing helix chain 'h' and resid 110 through 112 No H-bonds generated for 'chain 'h' and resid 110 through 112' Processing helix chain 'h' and resid 193 through 195 No H-bonds generated for 'chain 'h' and resid 193 through 195' Processing helix chain 'h' and resid 210 through 215 removed outlier: 3.995A pdb=" N ALA h 214 " --> pdb=" O ASP h 211 " (cutoff:3.500A) Processing helix chain 'h' and resid 227 through 243 removed outlier: 3.840A pdb=" N LEU h 241 " --> pdb=" O VAL h 237 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N MET h 242 " --> pdb=" O ALA h 238 " (cutoff:3.500A) Processing helix chain 'h' and resid 251 through 258 Processing helix chain 'a' and resid 4 through 10 Processing helix chain 'a' and resid 13 through 37 Processing helix chain 'a' and resid 43 through 50 Processing helix chain 'b' and resid 14 through 45 Processing helix chain 'd' and resid 2 through 10 removed outlier: 4.436A pdb=" N TYR d 5 " --> pdb=" O SER d 2 " (cutoff:3.500A) Processing helix chain 'd' and resid 13 through 37 Processing helix chain 'd' and resid 43 through 50 Processing helix chain 'e' and resid 14 through 45 Processing helix chain 'f' and resid 3 through 9 Processing helix chain 'f' and resid 13 through 37 Processing helix chain 'f' and resid 43 through 50 Processing helix chain 'g' and resid 14 through 45 Processing helix chain 'i' and resid 4 through 9 Processing helix chain 'i' and resid 13 through 37 Processing helix chain 'i' and resid 43 through 51 Processing helix chain 'j' and resid 14 through 45 Processing helix chain 'k' and resid 4 through 9 Processing helix chain 'k' and resid 13 through 37 Processing helix chain 'k' and resid 43 through 50 Processing helix chain 'n' and resid 14 through 45 Processing helix chain 'o' and resid 4 through 9 Processing helix chain 'o' and resid 13 through 37 Processing helix chain 'o' and resid 43 through 50 Processing helix chain 'p' and resid 14 through 45 Processing helix chain 'q' and resid 4 through 9 Processing helix chain 'q' and resid 13 through 37 Processing helix chain 'q' and resid 43 through 50 Processing helix chain 'r' and resid 14 through 45 Processing helix chain 's' and resid 4 through 9 Processing helix chain 's' and resid 13 through 37 Processing helix chain 's' and resid 43 through 50 Processing helix chain 't' and resid 14 through 45 Processing helix chain 'u' and resid 4 through 9 Processing helix chain 'u' and resid 13 through 37 Processing helix chain 'u' and resid 43 through 50 Processing helix chain 'v' and resid 14 through 45 Processing helix chain 'w' and resid 4 through 9 Processing helix chain 'w' and resid 13 through 37 Processing helix chain 'w' and resid 43 through 50 Processing helix chain 'c' and resid 14 through 45 Processing helix chain '5' and resid 5 through 9 Processing helix chain '5' and resid 13 through 37 Processing helix chain '5' and resid 43 through 50 Processing helix chain 'z' and resid 14 through 45 Processing helix chain 'b1' and resid 13 through 37 Processing helix chain 'b1' and resid 43 through 50 Processing helix chain '4' and resid 14 through 45 Processing helix chain '6' and resid 4 through 9 Processing helix chain '6' and resid 13 through 37 Processing helix chain 'b8' and resid 14 through 45 Processing helix chain 'b9' and resid 4 through 9 Processing helix chain 'b9' and resid 13 through 37 Processing helix chain 'b9' and resid 43 through 50 Processing helix chain 'b0' and resid 14 through 45 Processing helix chain 'x' and resid 10 through 12 No H-bonds generated for 'chain 'x' and resid 10 through 12' Processing helix chain 'x' and resid 15 through 54 Processing helix chain 'y' and resid 6 through 28 Processing helix chain 'y' and resid 32 through 48 Processing sheet with id= A, first strand: chain 'H' and resid 62 through 65 Processing sheet with id= B, first strand: chain 'H' and resid 87 through 89 Processing sheet with id= C, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.805A pdb=" N GLU H 180 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE H 167 " --> pdb=" O PHE H 178 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N PHE H 178 " --> pdb=" O ILE H 167 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 202 through 204 removed outlier: 3.828A pdb=" N GLY H 162 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'h' and resid 62 through 65 Processing sheet with id= F, first strand: chain 'h' and resid 87 through 89 Processing sheet with id= G, first strand: chain 'h' and resid 131 through 133 removed outlier: 6.805A pdb=" N GLU h 180 " --> pdb=" O VAL h 165 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE h 167 " --> pdb=" O PHE h 178 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N PHE h 178 " --> pdb=" O ILE h 167 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'h' and resid 202 through 204 removed outlier: 3.828A pdb=" N GLY h 162 " --> pdb=" O VAL h 153 " (cutoff:3.500A) 2302 hydrogen bonds defined for protein. 6624 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.29 Time building geometry restraints manager: 21.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.35: 11995 1.35 - 1.55: 34061 1.55 - 1.76: 50 1.76 - 1.97: 338 1.97 - 2.18: 256 Bond restraints: 46700 Sorted by residual: bond pdb=" OB3 CDL M 407 " pdb=" PB2 CDL M 407 " ideal model delta sigma weight residual 1.529 1.455 0.074 1.00e-02 1.00e+04 5.44e+01 bond pdb=" OB3 CDL m 407 " pdb=" PB2 CDL m 407 " ideal model delta sigma weight residual 1.529 1.456 0.073 1.00e-02 1.00e+04 5.34e+01 bond pdb=" OA3 CDL m 407 " pdb=" PA1 CDL m 407 " ideal model delta sigma weight residual 1.529 1.458 0.071 1.00e-02 1.00e+04 5.03e+01 bond pdb=" OA3 CDL M 407 " pdb=" PA1 CDL M 407 " ideal model delta sigma weight residual 1.529 1.458 0.071 1.00e-02 1.00e+04 5.03e+01 bond pdb=" OB3 CDL F 102 " pdb=" PB2 CDL F 102 " ideal model delta sigma weight residual 1.529 1.459 0.070 1.00e-02 1.00e+04 4.88e+01 ... (remaining 46695 not shown) Histogram of bond angle deviations from ideal: 84.75 - 100.47: 286 100.47 - 116.19: 30060 116.19 - 131.91: 33205 131.91 - 147.63: 477 147.63 - 163.36: 128 Bond angle restraints: 64156 Sorted by residual: angle pdb=" O12 PC1 A 104 " pdb=" P PC1 A 104 " pdb=" O14 PC1 A 104 " ideal model delta sigma weight residual 123.67 100.39 23.28 3.00e+00 1.11e-01 6.02e+01 angle pdb=" O12 PC1 a 104 " pdb=" P PC1 a 104 " pdb=" O14 PC1 a 104 " ideal model delta sigma weight residual 123.67 100.41 23.26 3.00e+00 1.11e-01 6.01e+01 angle pdb=" O12 PC1 h 301 " pdb=" P PC1 h 301 " pdb=" O14 PC1 h 301 " ideal model delta sigma weight residual 123.67 100.85 22.82 3.00e+00 1.11e-01 5.78e+01 angle pdb=" O12 PC1 H 301 " pdb=" P PC1 H 301 " pdb=" O14 PC1 H 301 " ideal model delta sigma weight residual 123.67 100.85 22.82 3.00e+00 1.11e-01 5.78e+01 angle pdb=" O12 PC1 D 101 " pdb=" P PC1 D 101 " pdb=" O14 PC1 D 101 " ideal model delta sigma weight residual 123.67 100.96 22.71 3.00e+00 1.11e-01 5.73e+01 ... (remaining 64151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.57: 23870 31.57 - 63.13: 666 63.13 - 94.70: 84 94.70 - 126.27: 30 126.27 - 157.84: 2 Dihedral angle restraints: 24652 sinusoidal: 11310 harmonic: 13342 Sorted by residual: dihedral pdb=" C27 U10 l 304 " pdb=" C28 U10 l 304 " pdb=" C29 U10 l 304 " pdb=" C31 U10 l 304 " ideal model delta sinusoidal sigma weight residual -178.28 -20.45 -157.84 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" C27 U10 L 304 " pdb=" C28 U10 L 304 " pdb=" C29 U10 L 304 " pdb=" C31 U10 L 304 " ideal model delta sinusoidal sigma weight residual -178.28 -20.48 -157.80 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" C3M U10 L 305 " pdb=" C3 U10 L 305 " pdb=" O3 U10 L 305 " pdb=" C4 U10 L 305 " ideal model delta sinusoidal sigma weight residual 244.38 125.33 119.05 1 2.00e+01 2.50e-03 3.57e+01 ... (remaining 24649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4890 0.048 - 0.096: 1162 0.096 - 0.143: 176 0.143 - 0.191: 6 0.191 - 0.239: 8 Chirality restraints: 6242 Sorted by residual: chirality pdb=" C2C BPH m 404 " pdb=" C1C BPH m 404 " pdb=" C3C BPH m 404 " pdb=" CMC BPH m 404 " both_signs ideal model delta sigma weight residual False -2.81 -2.57 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C2C BPH M 404 " pdb=" C1C BPH M 404 " pdb=" C3C BPH M 404 " pdb=" CMC BPH M 404 " both_signs ideal model delta sigma weight residual False -2.81 -2.57 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C3C BPH L 303 " pdb=" C2C BPH L 303 " pdb=" C4C BPH L 303 " pdb=" CAC BPH L 303 " both_signs ideal model delta sigma weight residual False 2.83 2.61 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 6239 not shown) Planarity restraints: 7898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BPH m 404 " 0.013 2.00e-02 2.50e+03 4.75e-02 5.07e+01 pdb=" C1D BPH m 404 " 0.015 2.00e-02 2.50e+03 pdb=" C2D BPH m 404 " -0.024 2.00e-02 2.50e+03 pdb=" C3D BPH m 404 " -0.042 2.00e-02 2.50e+03 pdb=" C4D BPH m 404 " -0.024 2.00e-02 2.50e+03 pdb=" CAD BPH m 404 " 0.106 2.00e-02 2.50e+03 pdb=" CHA BPH m 404 " -0.045 2.00e-02 2.50e+03 pdb=" CHD BPH m 404 " 0.044 2.00e-02 2.50e+03 pdb=" CMD BPH m 404 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BPH M 404 " -0.013 2.00e-02 2.50e+03 4.74e-02 5.05e+01 pdb=" C1D BPH M 404 " -0.014 2.00e-02 2.50e+03 pdb=" C2D BPH M 404 " 0.024 2.00e-02 2.50e+03 pdb=" C3D BPH M 404 " 0.042 2.00e-02 2.50e+03 pdb=" C4D BPH M 404 " 0.023 2.00e-02 2.50e+03 pdb=" CAD BPH M 404 " -0.106 2.00e-02 2.50e+03 pdb=" CHA BPH M 404 " 0.045 2.00e-02 2.50e+03 pdb=" CHD BPH M 404 " -0.044 2.00e-02 2.50e+03 pdb=" CMD BPH M 404 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BPH l 303 " 0.016 2.00e-02 2.50e+03 3.05e-02 2.10e+01 pdb=" C1D BPH l 303 " 0.007 2.00e-02 2.50e+03 pdb=" C2D BPH l 303 " -0.017 2.00e-02 2.50e+03 pdb=" C3D BPH l 303 " -0.034 2.00e-02 2.50e+03 pdb=" C4D BPH l 303 " -0.015 2.00e-02 2.50e+03 pdb=" CAD BPH l 303 " 0.068 2.00e-02 2.50e+03 pdb=" CHA BPH l 303 " -0.027 2.00e-02 2.50e+03 pdb=" CHD BPH l 303 " 0.025 2.00e-02 2.50e+03 pdb=" CMD BPH l 303 " -0.021 2.00e-02 2.50e+03 ... (remaining 7895 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 900 2.69 - 3.24: 41380 3.24 - 3.80: 78657 3.80 - 4.35: 105602 4.35 - 4.90: 172873 Nonbonded interactions: 399412 Sorted by model distance: nonbonded pdb=" NE2 HIS l 190 " pdb="FE FE2 m 401 " model vdw 2.138 3.080 nonbonded pdb=" NE2 HIS L 190 " pdb="FE FE2 M 401 " model vdw 2.138 3.080 nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE2 M 401 " model vdw 2.147 3.000 nonbonded pdb=" OE2 GLU m 234 " pdb="FE FE2 m 401 " model vdw 2.147 3.000 nonbonded pdb=" NE2 HIS m 219 " pdb="FE FE2 m 401 " model vdw 2.163 3.080 ... (remaining 399407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '0' and resid 8 through 49) selection = (chain '8' and resid 8 through 49) selection = (chain 'B' and resid 8 through 49) selection = (chain 'C' and resid 8 through 49) selection = (chain 'E' and resid 8 through 49) selection = (chain 'G' and resid 8 through 49) selection = (chain 'J' and resid 8 through 49) selection = (chain 'N' and resid 8 through 49) selection = (chain 'P' and resid 8 through 49) selection = (chain 'R' and resid 8 through 49) selection = (chain 'T' and resid 8 through 49) selection = (chain 'V' and resid 8 through 49) selection = (chain 'Z' and resid 8 through 49) selection = (chain 'b' and resid 8 through 49) selection = (chain 'b0' and resid 8 through 49) selection = (chain 'b8' and resid 8 through 49) selection = (chain 'c' and resid 8 through 49) selection = (chain 'e' and resid 8 through 49) selection = (chain 'g' and resid 8 through 49) selection = (chain 'j' and resid 8 through 49) selection = (chain 'n' and resid 8 through 49) selection = (chain 'p' and resid 8 through 49) selection = (chain 'r' and resid 8 through 49) selection = (chain 't' and resid 8 through 49) selection = (chain 'v' and resid 8 through 49) selection = (chain 'z' and resid 8 through 49) } ncs_group { reference = (chain '1' and resid 8 through 48) selection = (chain '3' and resid 8 through 48) selection = (chain '5' and resid 8 through 48) selection = (chain '6' and resid 8 through 48) selection = (chain '7' and resid 8 through 48) selection = (chain 'I' and resid 8 through 48) selection = (chain 'K' and resid 8 through 48) selection = (chain 'O' and resid 8 through 48) selection = (chain 'U' and resid 8 through 48) selection = (chain 'W' and resid 8 through 48) selection = (chain 'b1' and resid 8 through 48) selection = (chain 'i' and resid 8 through 48) selection = (chain 'k' and resid 8 through 48) selection = (chain 'o' and resid 8 through 48) selection = (chain 'u' and resid 8 through 48) selection = (chain 'w' and resid 8 through 48) } ncs_group { reference = chain '2' selection = chain '4' } ncs_group { reference = (chain '9' and resid 1 through 55) selection = (chain 'A' and resid 1 through 55) selection = (chain 'D' and resid 1 through 55) selection = (chain 'F' and resid 1 through 55) selection = (chain 'Q' and resid 1 through 55) selection = (chain 'S' and resid 1 through 55) selection = (chain 'a' and resid 1 through 55) selection = (chain 'b9' and resid 1 through 55) selection = (chain 'd' and resid 1 through 55) selection = (chain 'f' and resid 1 through 55) selection = (chain 'q' and resid 1 through 55) selection = (chain 's' and resid 1 through 55) } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'X' selection = chain 'x' } ncs_group { reference = chain 'Y' selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 24 5.49 5 Mg 64 5.21 5 S 174 5.16 5 C 31612 2.51 5 N 6300 2.21 5 O 6804 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 8.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 19.740 Check model and map are aligned: 0.700 Convert atoms to be neutral: 0.410 Process input model: 110.240 Find NCS groups from input model: 4.370 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.077 46700 Z= 0.410 Angle : 0.959 23.281 64156 Z= 0.376 Chirality : 0.040 0.239 6242 Planarity : 0.004 0.047 7898 Dihedral : 14.779 157.836 16076 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.12), residues: 4482 helix: 2.64 (0.09), residues: 2976 sheet: -0.81 (0.74), residues: 48 loop : 0.50 (0.17), residues: 1458 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 871 time to evaluate : 4.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 883 average time/residue: 1.3444 time to fit residues: 1517.7444 Evaluate side-chains 691 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 690 time to evaluate : 4.626 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.4301 time to fit residues: 6.5061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 366 optimal weight: 0.6980 chunk 328 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 221 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 340 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 394 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 GLN ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN F 20 GLN J 16 GLN N 16 GLN O 20 GLN Q 20 GLN ** V 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 20 GLN 9 52 ASN X 66 ASN ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 77 GLN ** m 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 GLN f 20 GLN j 16 GLN k 20 GLN n 16 GLN o 20 GLN q 20 GLN r 16 GLN ** v 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 GLN b9 52 ASN x 66 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 46700 Z= 0.322 Angle : 0.679 14.647 64156 Z= 0.279 Chirality : 0.040 0.151 6242 Planarity : 0.004 0.040 7898 Dihedral : 15.832 126.328 8034 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 3.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.12), residues: 4482 helix: 2.44 (0.09), residues: 2956 sheet: -0.78 (0.75), residues: 48 loop : 0.44 (0.17), residues: 1478 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 702 time to evaluate : 4.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 139 outliers final: 64 residues processed: 759 average time/residue: 1.3415 time to fit residues: 1297.3190 Evaluate side-chains 732 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 668 time to evaluate : 4.790 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 25 residues processed: 39 average time/residue: 0.6036 time to fit residues: 42.5038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 219 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 328 optimal weight: 0.4980 chunk 268 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 394 optimal weight: 9.9990 chunk 426 optimal weight: 1.9990 chunk 351 optimal weight: 10.0000 chunk 391 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 chunk 316 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN F 20 GLN K 20 GLN O 20 GLN R 16 GLN T 16 GLN 9 52 ASN ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 GLN k 20 GLN o 20 GLN t 16 GLN b9 52 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 46700 Z= 0.247 Angle : 0.636 14.897 64156 Z= 0.260 Chirality : 0.038 0.159 6242 Planarity : 0.003 0.037 7898 Dihedral : 15.422 121.835 8034 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer Outliers : 3.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.12), residues: 4482 helix: 2.42 (0.09), residues: 2972 sheet: -0.62 (0.78), residues: 48 loop : 0.39 (0.17), residues: 1462 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 692 time to evaluate : 4.623 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 118 outliers final: 55 residues processed: 737 average time/residue: 1.3634 time to fit residues: 1281.8999 Evaluate side-chains 720 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 665 time to evaluate : 4.511 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 21 residues processed: 34 average time/residue: 0.6071 time to fit residues: 38.4929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 390 optimal weight: 8.9990 chunk 296 optimal weight: 0.6980 chunk 204 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 188 optimal weight: 8.9990 chunk 265 optimal weight: 0.9980 chunk 396 optimal weight: 8.9990 chunk 419 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 375 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN K 20 GLN Q 20 GLN T 16 GLN 8 18 GLN 9 52 ASN X 61 GLN ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 25 ASN ** m 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 GLN k 20 GLN o 20 GLN q 20 GLN t 16 GLN b9 52 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 46700 Z= 0.200 Angle : 0.608 14.922 64156 Z= 0.248 Chirality : 0.037 0.163 6242 Planarity : 0.003 0.038 7898 Dihedral : 15.114 122.195 8034 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.12), residues: 4482 helix: 2.53 (0.09), residues: 2972 sheet: -0.44 (0.80), residues: 48 loop : 0.42 (0.17), residues: 1462 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 696 time to evaluate : 4.391 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 113 outliers final: 52 residues processed: 745 average time/residue: 1.3615 time to fit residues: 1293.0842 Evaluate side-chains 710 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 658 time to evaluate : 4.467 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 26 residues processed: 28 average time/residue: 0.6134 time to fit residues: 33.2013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 349 optimal weight: 3.9990 chunk 238 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 312 optimal weight: 0.9990 chunk 173 optimal weight: 7.9990 chunk 357 optimal weight: 0.9990 chunk 289 optimal weight: 0.0010 chunk 0 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 chunk 376 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN K 20 GLN O 20 GLN P 16 GLN T 16 GLN 7 20 GLN 9 52 ASN ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 44 ASN b 16 GLN n 16 GLN p 16 GLN t 16 GLN 6 20 GLN b9 52 ASN x 61 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 46700 Z= 0.190 Angle : 0.600 14.767 64156 Z= 0.246 Chirality : 0.036 0.143 6242 Planarity : 0.003 0.037 7898 Dihedral : 14.878 122.193 8034 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.12), residues: 4482 helix: 2.51 (0.09), residues: 2988 sheet: -0.36 (0.81), residues: 48 loop : 0.36 (0.17), residues: 1446 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 695 time to evaluate : 4.750 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 55 residues processed: 741 average time/residue: 1.3828 time to fit residues: 1309.2079 Evaluate side-chains 717 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 662 time to evaluate : 4.689 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 27 residues processed: 29 average time/residue: 0.7124 time to fit residues: 37.1616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 141 optimal weight: 0.0980 chunk 377 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 246 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 419 optimal weight: 2.9990 chunk 348 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 138 optimal weight: 0.5980 chunk 220 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN N 16 GLN O 20 GLN Q 20 GLN T 16 GLN 9 52 ASN X 61 GLN ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 GLN k 20 GLN n 16 GLN o 20 GLN q 20 GLN t 16 GLN b9 52 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 46700 Z= 0.189 Angle : 0.601 14.692 64156 Z= 0.246 Chirality : 0.036 0.140 6242 Planarity : 0.003 0.039 7898 Dihedral : 14.739 122.110 8034 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer Outliers : 2.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.12), residues: 4482 helix: 2.53 (0.09), residues: 2990 sheet: -0.33 (0.82), residues: 48 loop : 0.38 (0.17), residues: 1444 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 679 time to evaluate : 4.684 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 55 residues processed: 729 average time/residue: 1.3279 time to fit residues: 1237.4811 Evaluate side-chains 718 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 663 time to evaluate : 4.499 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 33 residues processed: 22 average time/residue: 0.5645 time to fit residues: 25.9042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 404 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 306 optimal weight: 2.9990 chunk 237 optimal weight: 0.0570 chunk 353 optimal weight: 0.6980 chunk 234 optimal weight: 0.5980 chunk 418 optimal weight: 0.0870 chunk 261 optimal weight: 1.9990 chunk 255 optimal weight: 0.4980 chunk 193 optimal weight: 0.8980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN N 16 GLN O 20 GLN Q 20 GLN R 18 GLN T 16 GLN 9 52 ASN ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 20 GLN n 16 GLN o 20 GLN q 20 GLN r 16 GLN r 18 GLN t 16 GLN 6 20 GLN b9 52 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 46700 Z= 0.151 Angle : 0.583 14.708 64156 Z= 0.240 Chirality : 0.036 0.139 6242 Planarity : 0.003 0.039 7898 Dihedral : 14.489 122.532 8034 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.12), residues: 4482 helix: 2.62 (0.09), residues: 2988 sheet: -0.27 (0.83), residues: 48 loop : 0.37 (0.17), residues: 1446 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 704 time to evaluate : 4.702 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 43 residues processed: 743 average time/residue: 1.3872 time to fit residues: 1320.4855 Evaluate side-chains 702 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 659 time to evaluate : 4.626 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 35 residues processed: 8 average time/residue: 1.1319 time to fit residues: 17.7703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 258 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 265 optimal weight: 1.9990 chunk 284 optimal weight: 0.2980 chunk 206 optimal weight: 0.0770 chunk 38 optimal weight: 0.6980 chunk 328 optimal weight: 0.5980 overall best weight: 0.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 16 GLN O 20 GLN Q 20 GLN R 16 GLN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 16 GLN 9 52 ASN ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 44 ASN n 16 GLN o 20 GLN q 20 GLN r 16 GLN ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 16 GLN b9 52 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 46700 Z= 0.170 Angle : 0.594 14.415 64156 Z= 0.245 Chirality : 0.036 0.139 6242 Planarity : 0.003 0.037 7898 Dihedral : 14.408 121.895 8034 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer Outliers : 2.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.12), residues: 4482 helix: 2.61 (0.09), residues: 2990 sheet: -0.33 (0.81), residues: 48 loop : 0.39 (0.17), residues: 1444 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 670 time to evaluate : 4.642 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 48 residues processed: 719 average time/residue: 1.3658 time to fit residues: 1251.2015 Evaluate side-chains 709 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 661 time to evaluate : 4.695 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 35 residues processed: 13 average time/residue: 0.4958 time to fit residues: 17.3793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 380 optimal weight: 0.7980 chunk 400 optimal weight: 0.0570 chunk 365 optimal weight: 0.8980 chunk 389 optimal weight: 4.9990 chunk 234 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 306 optimal weight: 1.9990 chunk 119 optimal weight: 0.4980 chunk 352 optimal weight: 4.9990 chunk 368 optimal weight: 0.9990 chunk 388 optimal weight: 3.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 16 GLN O 20 GLN ** P 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN R 16 GLN T 16 GLN Z 21 HIS 9 52 ASN ** l 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 GLN n 16 GLN o 20 GLN q 20 GLN r 16 GLN t 16 GLN b9 52 ASN x 8 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 46700 Z= 0.186 Angle : 0.607 14.420 64156 Z= 0.250 Chirality : 0.036 0.143 6242 Planarity : 0.003 0.037 7898 Dihedral : 14.394 121.993 8034 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.12), residues: 4482 helix: 2.58 (0.09), residues: 2986 sheet: -0.32 (0.82), residues: 48 loop : 0.41 (0.17), residues: 1448 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 658 time to evaluate : 4.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 48 residues processed: 698 average time/residue: 1.3846 time to fit residues: 1230.8221 Evaluate side-chains 697 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 649 time to evaluate : 4.767 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 35 residues processed: 13 average time/residue: 0.8085 time to fit residues: 20.9205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 255 optimal weight: 0.6980 chunk 412 optimal weight: 0.6980 chunk 251 optimal weight: 0.6980 chunk 195 optimal weight: 0.9980 chunk 286 optimal weight: 2.9990 chunk 432 optimal weight: 0.9990 chunk 397 optimal weight: 10.0000 chunk 344 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 265 optimal weight: 0.9990 chunk 211 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN N 16 GLN O 20 GLN ** P 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN R 16 GLN 9 52 ASN l 60 ASN ** m 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 GLN k 20 GLN n 16 GLN o 20 GLN q 20 GLN r 16 GLN t 16 GLN b9 52 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 46700 Z= 0.206 Angle : 0.618 14.474 64156 Z= 0.255 Chirality : 0.037 0.139 6242 Planarity : 0.003 0.038 7898 Dihedral : 14.438 122.109 8034 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.12), residues: 4482 helix: 2.53 (0.09), residues: 2986 sheet: -0.35 (0.81), residues: 48 loop : 0.41 (0.17), residues: 1448 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8964 Ramachandran restraints generated. 4482 Oldfield, 0 Emsley, 4482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 659 time to evaluate : 4.928 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 41 residues processed: 704 average time/residue: 1.4076 time to fit residues: 1260.2526 Evaluate side-chains 688 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 647 time to evaluate : 4.598 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 37 residues processed: 5 average time/residue: 0.4737 time to fit residues: 9.7503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 273 optimal weight: 0.4980 chunk 366 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 317 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 344 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 354 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN B 16 GLN N 16 GLN O 20 GLN ** P 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN R 16 GLN 7 20 GLN 9 52 ASN ** m 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 44 ASN b 16 GLN n 16 GLN o 20 GLN q 20 GLN r 16 GLN z 21 HIS 6 20 GLN b9 52 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.149466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.110395 restraints weight = 53824.496| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.26 r_work: 0.2865 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 46700 Z= 0.197 Angle : 0.619 14.600 64156 Z= 0.257 Chirality : 0.037 0.145 6242 Planarity : 0.003 0.038 7898 Dihedral : 14.392 122.332 8034 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.12), residues: 4482 helix: 2.51 (0.09), residues: 2998 sheet: -0.34 (0.81), residues: 48 loop : 0.39 (0.17), residues: 1436 =============================================================================== Job complete usr+sys time: 17799.61 seconds wall clock time: 314 minutes 5.95 seconds (18845.95 seconds total)