Starting phenix.real_space_refine on Fri Dec 15 21:52:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4x_28858/12_2023/8f4x_28858.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4x_28858/12_2023/8f4x_28858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4x_28858/12_2023/8f4x_28858.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4x_28858/12_2023/8f4x_28858.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4x_28858/12_2023/8f4x_28858.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4x_28858/12_2023/8f4x_28858.pdb" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 20580 2.51 5 N 6120 2.21 5 O 6000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 3": "OE1" <-> "OE2" Residue "0 GLU 13": "OE1" <-> "OE2" Residue "0 GLU 31": "OE1" <-> "OE2" Residue "0 GLU 35": "OE1" <-> "OE2" Residue "0 PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 31": "OE1" <-> "OE2" Residue "1 GLU 36": "OE1" <-> "OE2" Residue "1 PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 61": "OE1" <-> "OE2" Residue "2 GLU 13": "OE1" <-> "OE2" Residue "2 GLU 19": "OE1" <-> "OE2" Residue "2 PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 19": "OE1" <-> "OE2" Residue "3 GLU 35": "OE1" <-> "OE2" Residue "3 GLU 36": "OE1" <-> "OE2" Residue "3 GLU 47": "OE1" <-> "OE2" Residue "4 GLU 2": "OE1" <-> "OE2" Residue "4 GLU 4": "OE1" <-> "OE2" Residue "4 GLU 13": "OE1" <-> "OE2" Residue "4 GLU 19": "OE1" <-> "OE2" Residue "4 GLU 36": "OE1" <-> "OE2" Residue "5 GLU 19": "OE1" <-> "OE2" Residue "5 GLU 31": "OE1" <-> "OE2" Residue "5 GLU 35": "OE1" <-> "OE2" Residue "5 PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 61": "OE1" <-> "OE2" Residue "5 PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 2": "OE1" <-> "OE2" Residue "6 GLU 3": "OE1" <-> "OE2" Residue "6 GLU 4": "OE1" <-> "OE2" Residue "6 ASP 24": "OD1" <-> "OD2" Residue "6 PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 4": "OE1" <-> "OE2" Residue "7 PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 50": "OE1" <-> "OE2" Residue "7 GLU 61": "OE1" <-> "OE2" Residue "8 GLU 2": "OE1" <-> "OE2" Residue "8 GLU 36": "OE1" <-> "OE2" Residue "8 PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 47": "OE1" <-> "OE2" Residue "9 GLU 3": "OE1" <-> "OE2" Residue "9 GLU 13": "OE1" <-> "OE2" Residue "9 GLU 35": "OE1" <-> "OE2" Residue "9 GLU 36": "OE1" <-> "OE2" Residue "9 PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2": "OE1" <-> "OE2" Residue "A GLU 3": "OE1" <-> "OE2" Residue "A GLU 13": "OE1" <-> "OE2" Residue "A GLU 19": "OE1" <-> "OE2" Residue "A GLU 36": "OE1" <-> "OE2" Residue "A PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 13": "OE1" <-> "OE2" Residue "B GLU 25": "OE1" <-> "OE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "C PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "D GLU 2": "OE1" <-> "OE2" Residue "D GLU 3": "OE1" <-> "OE2" Residue "D GLU 4": "OE1" <-> "OE2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "E GLU 3": "OE1" <-> "OE2" Residue "E GLU 4": "OE1" <-> "OE2" Residue "E GLU 13": "OE1" <-> "OE2" Residue "E GLU 31": "OE1" <-> "OE2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "F GLU 3": "OE1" <-> "OE2" Residue "F GLU 47": "OE1" <-> "OE2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "G GLU 19": "OE1" <-> "OE2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "H GLU 19": "OE1" <-> "OE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 61": "OE1" <-> "OE2" Residue "I GLU 13": "OE1" <-> "OE2" Residue "I GLU 25": "OE1" <-> "OE2" Residue "I GLU 31": "OE1" <-> "OE2" Residue "I GLU 36": "OE1" <-> "OE2" Residue "I PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 47": "OE1" <-> "OE2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "J GLU 4": "OE1" <-> "OE2" Residue "J GLU 25": "OE1" <-> "OE2" Residue "J GLU 31": "OE1" <-> "OE2" Residue "J GLU 47": "OE1" <-> "OE2" Residue "J GLU 50": "OE1" <-> "OE2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "K GLU 3": "OE1" <-> "OE2" Residue "K GLU 19": "OE1" <-> "OE2" Residue "K GLU 25": "OE1" <-> "OE2" Residue "K GLU 31": "OE1" <-> "OE2" Residue "K GLU 36": "OE1" <-> "OE2" Residue "K PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 47": "OE1" <-> "OE2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "L GLU 3": "OE1" <-> "OE2" Residue "L GLU 19": "OE1" <-> "OE2" Residue "L GLU 35": "OE1" <-> "OE2" Residue "L GLU 36": "OE1" <-> "OE2" Residue "L GLU 47": "OE1" <-> "OE2" Residue "M GLU 2": "OE1" <-> "OE2" Residue "M GLU 13": "OE1" <-> "OE2" Residue "M GLU 35": "OE1" <-> "OE2" Residue "M GLU 36": "OE1" <-> "OE2" Residue "M PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "M PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 3": "OE1" <-> "OE2" Residue "N GLU 13": "OE1" <-> "OE2" Residue "N PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 3": "OE1" <-> "OE2" Residue "O GLU 13": "OE1" <-> "OE2" Residue "O GLU 25": "OE1" <-> "OE2" Residue "O PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 61": "OE1" <-> "OE2" Residue "P GLU 3": "OE1" <-> "OE2" Residue "P GLU 13": "OE1" <-> "OE2" Residue "P GLU 25": "OE1" <-> "OE2" Residue "P GLU 31": "OE1" <-> "OE2" Residue "P PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 3": "OE1" <-> "OE2" Residue "Q GLU 13": "OE1" <-> "OE2" Residue "Q GLU 31": "OE1" <-> "OE2" Residue "Q PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 13": "OE1" <-> "OE2" Residue "R GLU 50": "OE1" <-> "OE2" Residue "R GLU 61": "OE1" <-> "OE2" Residue "S GLU 3": "OE1" <-> "OE2" Residue "S GLU 13": "OE1" <-> "OE2" Residue "S GLU 50": "OE1" <-> "OE2" Residue "S GLU 61": "OE1" <-> "OE2" Residue "T GLU 13": "OE1" <-> "OE2" Residue "T GLU 25": "OE1" <-> "OE2" Residue "T GLU 31": "OE1" <-> "OE2" Residue "T GLU 61": "OE1" <-> "OE2" Residue "T PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 3": "OE1" <-> "OE2" Residue "U GLU 4": "OE1" <-> "OE2" Residue "U GLU 13": "OE1" <-> "OE2" Residue "U GLU 19": "OE1" <-> "OE2" Residue "U GLU 35": "OE1" <-> "OE2" Residue "U PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 4": "OE1" <-> "OE2" Residue "V GLU 13": "OE1" <-> "OE2" Residue "V GLU 35": "OE1" <-> "OE2" Residue "V PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 61": "OE1" <-> "OE2" Residue "W GLU 2": "OE1" <-> "OE2" Residue "W GLU 3": "OE1" <-> "OE2" Residue "W GLU 25": "OE1" <-> "OE2" Residue "W GLU 35": "OE1" <-> "OE2" Residue "W PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 50": "OE1" <-> "OE2" Residue "X GLU 3": "OE1" <-> "OE2" Residue "X GLU 4": "OE1" <-> "OE2" Residue "X GLU 19": "OE1" <-> "OE2" Residue "X GLU 31": "OE1" <-> "OE2" Residue "X GLU 35": "OE1" <-> "OE2" Residue "X PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 47": "OE1" <-> "OE2" Residue "Y GLU 19": "OE1" <-> "OE2" Residue "Y GLU 31": "OE1" <-> "OE2" Residue "Y GLU 36": "OE1" <-> "OE2" Residue "Y GLU 61": "OE1" <-> "OE2" Residue "Z GLU 25": "OE1" <-> "OE2" Residue "Z GLU 31": "OE1" <-> "OE2" Residue "Z GLU 36": "OE1" <-> "OE2" Residue "Z GLU 61": "OE1" <-> "OE2" Residue "a GLU 3": "OE1" <-> "OE2" Residue "a GLU 19": "OE1" <-> "OE2" Residue "a GLU 25": "OE1" <-> "OE2" Residue "a ASP 38": "OD1" <-> "OD2" Residue "a PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 3": "OE1" <-> "OE2" Residue "b GLU 13": "OE1" <-> "OE2" Residue "b GLU 25": "OE1" <-> "OE2" Residue "b GLU 31": "OE1" <-> "OE2" Residue "b GLU 35": "OE1" <-> "OE2" Residue "b PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 3": "OE1" <-> "OE2" Residue "c GLU 4": "OE1" <-> "OE2" Residue "c GLU 13": "OE1" <-> "OE2" Residue "c PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 35": "OE1" <-> "OE2" Residue "d PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 50": "OE1" <-> "OE2" Residue "e GLU 3": "OE1" <-> "OE2" Residue "e GLU 4": "OE1" <-> "OE2" Residue "e GLU 25": "OE1" <-> "OE2" Residue "e GLU 35": "OE1" <-> "OE2" Residue "e PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 50": "OE1" <-> "OE2" Residue "f GLU 4": "OE1" <-> "OE2" Residue "f GLU 13": "OE1" <-> "OE2" Residue "f GLU 35": "OE1" <-> "OE2" Residue "f PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 47": "OE1" <-> "OE2" Residue "f GLU 61": "OE1" <-> "OE2" Residue "f PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 2": "OE1" <-> "OE2" Residue "g GLU 13": "OE1" <-> "OE2" Residue "g GLU 31": "OE1" <-> "OE2" Residue "g GLU 36": "OE1" <-> "OE2" Residue "g PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 61": "OE1" <-> "OE2" Residue "h GLU 4": "OE1" <-> "OE2" Residue "h GLU 13": "OE1" <-> "OE2" Residue "h GLU 25": "OE1" <-> "OE2" Residue "h GLU 35": "OE1" <-> "OE2" Residue "h PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 61": "OE1" <-> "OE2" Residue "i GLU 3": "OE1" <-> "OE2" Residue "i GLU 25": "OE1" <-> "OE2" Residue "i GLU 31": "OE1" <-> "OE2" Residue "i GLU 35": "OE1" <-> "OE2" Residue "i GLU 36": "OE1" <-> "OE2" Residue "i GLU 47": "OE1" <-> "OE2" Residue "j GLU 2": "OE1" <-> "OE2" Residue "j GLU 13": "OE1" <-> "OE2" Residue "j GLU 19": "OE1" <-> "OE2" Residue "j PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 50": "OE1" <-> "OE2" Residue "j GLU 61": "OE1" <-> "OE2" Residue "j PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 3": "OE1" <-> "OE2" Residue "k GLU 19": "OE1" <-> "OE2" Residue "k GLU 25": "OE1" <-> "OE2" Residue "k GLU 31": "OE1" <-> "OE2" Residue "k GLU 35": "OE1" <-> "OE2" Residue "k GLU 36": "OE1" <-> "OE2" Residue "k PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 3": "OE1" <-> "OE2" Residue "l GLU 13": "OE1" <-> "OE2" Residue "l GLU 19": "OE1" <-> "OE2" Residue "l GLU 35": "OE1" <-> "OE2" Residue "l PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 2": "OE1" <-> "OE2" Residue "m GLU 3": "OE1" <-> "OE2" Residue "m GLU 36": "OE1" <-> "OE2" Residue "m PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 2": "OE1" <-> "OE2" Residue "n GLU 13": "OE1" <-> "OE2" Residue "n GLU 19": "OE1" <-> "OE2" Residue "n GLU 25": "OE1" <-> "OE2" Residue "n GLU 31": "OE1" <-> "OE2" Residue "n PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 47": "OE1" <-> "OE2" Residue "n GLU 50": "OE1" <-> "OE2" Residue "o GLU 3": "OE1" <-> "OE2" Residue "o GLU 13": "OE1" <-> "OE2" Residue "o GLU 19": "OE1" <-> "OE2" Residue "o GLU 35": "OE1" <-> "OE2" Residue "o PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 3": "OE1" <-> "OE2" Residue "p GLU 13": "OE1" <-> "OE2" Residue "p GLU 31": "OE1" <-> "OE2" Residue "p GLU 47": "OE1" <-> "OE2" Residue "q GLU 2": "OE1" <-> "OE2" Residue "q GLU 31": "OE1" <-> "OE2" Residue "q GLU 35": "OE1" <-> "OE2" Residue "r GLU 3": "OE1" <-> "OE2" Residue "r GLU 19": "OE1" <-> "OE2" Residue "r GLU 25": "OE1" <-> "OE2" Residue "r GLU 35": "OE1" <-> "OE2" Residue "r GLU 61": "OE1" <-> "OE2" Residue "s GLU 2": "OE1" <-> "OE2" Residue "s PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 13": "OE1" <-> "OE2" Residue "t GLU 36": "OE1" <-> "OE2" Residue "t PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 50": "OE1" <-> "OE2" Residue "t GLU 61": "OE1" <-> "OE2" Residue "u GLU 2": "OE1" <-> "OE2" Residue "u GLU 13": "OE1" <-> "OE2" Residue "u GLU 19": "OE1" <-> "OE2" Residue "u GLU 25": "OE1" <-> "OE2" Residue "u GLU 35": "OE1" <-> "OE2" Residue "u GLU 36": "OE1" <-> "OE2" Residue "u PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 19": "OE1" <-> "OE2" Residue "v PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 61": "OE1" <-> "OE2" Residue "w GLU 3": "OE1" <-> "OE2" Residue "w GLU 13": "OE1" <-> "OE2" Residue "w GLU 31": "OE1" <-> "OE2" Residue "w PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 47": "OE1" <-> "OE2" Residue "w GLU 61": "OE1" <-> "OE2" Residue "x GLU 3": "OE1" <-> "OE2" Residue "x GLU 25": "OE1" <-> "OE2" Residue "x GLU 31": "OE1" <-> "OE2" Residue "x PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 32760 Number of models: 1 Model: "" Number of chains: 60 Chain: "0" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "1" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "2" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "3" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "4" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "5" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "6" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "7" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "8" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "9" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "A" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "B" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "C" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "D" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "F" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "G" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "H" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "I" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "J" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "K" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "L" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "M" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "N" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "O" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "P" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "Q" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "R" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "S" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "T" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "U" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "V" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "W" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "X" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "Y" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "Z" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "a" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "b" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "c" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "d" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "e" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "f" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "g" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "h" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "i" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "j" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "k" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "l" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "m" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "n" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "o" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "p" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "q" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "r" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "s" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "t" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "u" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "v" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "w" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "x" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Time building chain proxies: 15.55, per 1000 atoms: 0.47 Number of scatterers: 32760 At special positions: 0 Unit cell: (153.12, 151.96, 151.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 6000 8.00 N 6120 7.00 C 20580 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=0, symmetry=0 Time building additional restraints: 11.55 Conformation dependent library (CDL) restraints added in 5.3 seconds 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 0 sheets defined 89.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain '0' and resid 1 through 20 Processing helix chain '0' and resid 22 through 37 Processing helix chain '0' and resid 39 through 50 removed outlier: 3.981A pdb=" N ALA 0 43 " --> pdb=" O PRO 0 39 " (cutoff:3.500A) Processing helix chain '0' and resid 53 through 65 Processing helix chain '1' and resid 2 through 20 Processing helix chain '1' and resid 22 through 37 Processing helix chain '1' and resid 39 through 50 removed outlier: 4.050A pdb=" N ALA 1 43 " --> pdb=" O PRO 1 39 " (cutoff:3.500A) Processing helix chain '1' and resid 53 through 65 Processing helix chain '2' and resid 2 through 20 Processing helix chain '2' and resid 22 through 37 Processing helix chain '2' and resid 39 through 51 removed outlier: 3.961A pdb=" N ALA 2 43 " --> pdb=" O PRO 2 39 " (cutoff:3.500A) Processing helix chain '2' and resid 53 through 65 Processing helix chain '3' and resid 2 through 21 removed outlier: 3.573A pdb=" N GLY 3 21 " --> pdb=" O LEU 3 17 " (cutoff:3.500A) Processing helix chain '3' and resid 22 through 36 removed outlier: 3.624A pdb=" N GLU 3 36 " --> pdb=" O ARG 3 32 " (cutoff:3.500A) Processing helix chain '3' and resid 39 through 50 removed outlier: 3.911A pdb=" N ALA 3 43 " --> pdb=" O PRO 3 39 " (cutoff:3.500A) Processing helix chain '3' and resid 53 through 65 Processing helix chain '4' and resid 2 through 21 removed outlier: 3.602A pdb=" N GLY 4 21 " --> pdb=" O LEU 4 17 " (cutoff:3.500A) Processing helix chain '4' and resid 22 through 36 removed outlier: 3.594A pdb=" N GLU 4 36 " --> pdb=" O ARG 4 32 " (cutoff:3.500A) Processing helix chain '4' and resid 39 through 50 removed outlier: 3.931A pdb=" N ALA 4 43 " --> pdb=" O PRO 4 39 " (cutoff:3.500A) Processing helix chain '4' and resid 53 through 65 Processing helix chain '5' and resid 2 through 20 removed outlier: 3.575A pdb=" N ALA 5 11 " --> pdb=" O ARG 5 7 " (cutoff:3.500A) Processing helix chain '5' and resid 22 through 37 Processing helix chain '5' and resid 39 through 50 removed outlier: 4.096A pdb=" N ALA 5 43 " --> pdb=" O PRO 5 39 " (cutoff:3.500A) Processing helix chain '5' and resid 53 through 65 Processing helix chain '6' and resid 2 through 20 Processing helix chain '6' and resid 22 through 36 Processing helix chain '6' and resid 39 through 50 removed outlier: 3.957A pdb=" N ALA 6 43 " --> pdb=" O PRO 6 39 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 65 Processing helix chain '7' and resid 2 through 20 Processing helix chain '7' and resid 22 through 36 Processing helix chain '7' and resid 39 through 52 removed outlier: 4.033A pdb=" N ALA 7 43 " --> pdb=" O PRO 7 39 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLY 7 52 " --> pdb=" O LEU 7 48 " (cutoff:3.500A) Processing helix chain '7' and resid 53 through 65 Processing helix chain '8' and resid 2 through 20 Processing helix chain '8' and resid 22 through 37 Processing helix chain '8' and resid 39 through 50 removed outlier: 4.066A pdb=" N ALA 8 43 " --> pdb=" O PRO 8 39 " (cutoff:3.500A) Processing helix chain '8' and resid 53 through 65 Processing helix chain '9' and resid 2 through 20 Processing helix chain '9' and resid 22 through 37 removed outlier: 3.526A pdb=" N GLU 9 36 " --> pdb=" O ARG 9 32 " (cutoff:3.500A) Processing helix chain '9' and resid 39 through 50 removed outlier: 3.971A pdb=" N ALA 9 43 " --> pdb=" O PRO 9 39 " (cutoff:3.500A) Processing helix chain '9' and resid 53 through 65 Processing helix chain 'A' and resid 2 through 20 Processing helix chain 'A' and resid 22 through 36 removed outlier: 3.556A pdb=" N GLU A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 50 removed outlier: 3.995A pdb=" N ALA A 43 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'B' and resid 2 through 20 Processing helix chain 'B' and resid 22 through 36 removed outlier: 3.669A pdb=" N GLU B 36 " --> pdb=" O ARG B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 50 removed outlier: 3.986A pdb=" N ALA B 43 " --> pdb=" O PRO B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'C' and resid 2 through 20 Processing helix chain 'C' and resid 22 through 36 Processing helix chain 'C' and resid 39 through 50 removed outlier: 3.979A pdb=" N ALA C 43 " --> pdb=" O PRO C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 65 Processing helix chain 'D' and resid 2 through 20 Processing helix chain 'D' and resid 22 through 36 removed outlier: 3.506A pdb=" N GLU D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 50 removed outlier: 3.973A pdb=" N ALA D 43 " --> pdb=" O PRO D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 65 removed outlier: 3.579A pdb=" N ARG D 57 " --> pdb=" O ASP D 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 21 removed outlier: 3.556A pdb=" N GLY E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 36 removed outlier: 3.547A pdb=" N GLU E 36 " --> pdb=" O ARG E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 50 removed outlier: 4.008A pdb=" N ALA E 43 " --> pdb=" O PRO E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 65 Processing helix chain 'F' and resid 2 through 20 Processing helix chain 'F' and resid 22 through 37 Processing helix chain 'F' and resid 39 through 50 removed outlier: 4.016A pdb=" N ALA F 43 " --> pdb=" O PRO F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 65 Processing helix chain 'G' and resid 2 through 21 removed outlier: 3.628A pdb=" N GLY G 21 " --> pdb=" O LEU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 37 Processing helix chain 'G' and resid 39 through 52 removed outlier: 4.060A pdb=" N ALA G 43 " --> pdb=" O PRO G 39 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY G 52 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 65 Processing helix chain 'H' and resid 2 through 20 Processing helix chain 'H' and resid 22 through 36 Processing helix chain 'H' and resid 39 through 50 removed outlier: 4.033A pdb=" N ALA H 43 " --> pdb=" O PRO H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 65 Processing helix chain 'I' and resid 2 through 20 Processing helix chain 'I' and resid 22 through 37 Processing helix chain 'I' and resid 39 through 51 removed outlier: 4.081A pdb=" N ALA I 43 " --> pdb=" O PRO I 39 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU I 50 " --> pdb=" O ARG I 46 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER I 51 " --> pdb=" O GLU I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 65 Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 22 through 37 Processing helix chain 'J' and resid 39 through 50 removed outlier: 3.984A pdb=" N ALA J 43 " --> pdb=" O PRO J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 65 Processing helix chain 'K' and resid 2 through 20 Processing helix chain 'K' and resid 22 through 37 Processing helix chain 'K' and resid 39 through 50 removed outlier: 4.038A pdb=" N ALA K 43 " --> pdb=" O PRO K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 65 Processing helix chain 'L' and resid 2 through 20 Processing helix chain 'L' and resid 22 through 37 Processing helix chain 'L' and resid 39 through 50 removed outlier: 3.995A pdb=" N ALA L 43 " --> pdb=" O PRO L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 65 Processing helix chain 'M' and resid 2 through 20 Processing helix chain 'M' and resid 22 through 37 Processing helix chain 'M' and resid 39 through 52 removed outlier: 4.113A pdb=" N ALA M 43 " --> pdb=" O PRO M 39 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 65 Processing helix chain 'N' and resid 2 through 20 removed outlier: 3.514A pdb=" N ALA N 11 " --> pdb=" O ARG N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 37 Processing helix chain 'N' and resid 39 through 50 removed outlier: 4.014A pdb=" N ALA N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 65 Processing helix chain 'O' and resid 2 through 20 Processing helix chain 'O' and resid 22 through 36 Processing helix chain 'O' and resid 39 through 50 removed outlier: 3.987A pdb=" N ALA O 43 " --> pdb=" O PRO O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 53 through 65 Processing helix chain 'P' and resid 2 through 20 Processing helix chain 'P' and resid 22 through 36 Processing helix chain 'P' and resid 39 through 50 removed outlier: 4.061A pdb=" N ALA P 43 " --> pdb=" O PRO P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 65 Processing helix chain 'Q' and resid 2 through 20 Processing helix chain 'Q' and resid 22 through 36 Processing helix chain 'Q' and resid 39 through 50 removed outlier: 4.029A pdb=" N ALA Q 43 " --> pdb=" O PRO Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 65 Processing helix chain 'R' and resid 2 through 20 Processing helix chain 'R' and resid 22 through 36 Processing helix chain 'R' and resid 39 through 52 removed outlier: 3.997A pdb=" N ALA R 43 " --> pdb=" O PRO R 39 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU R 47 " --> pdb=" O ALA R 43 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY R 52 " --> pdb=" O LEU R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 65 Processing helix chain 'S' and resid 2 through 20 Processing helix chain 'S' and resid 22 through 37 Processing helix chain 'S' and resid 39 through 50 removed outlier: 3.985A pdb=" N ALA S 43 " --> pdb=" O PRO S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 65 Processing helix chain 'T' and resid 2 through 20 Processing helix chain 'T' and resid 22 through 36 removed outlier: 3.786A pdb=" N GLU T 36 " --> pdb=" O ARG T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 50 removed outlier: 3.966A pdb=" N ALA T 43 " --> pdb=" O PRO T 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 53 through 65 Processing helix chain 'U' and resid 2 through 20 Processing helix chain 'U' and resid 22 through 36 removed outlier: 3.607A pdb=" N GLU U 36 " --> pdb=" O ARG U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 39 through 50 removed outlier: 4.034A pdb=" N ALA U 43 " --> pdb=" O PRO U 39 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 65 Processing helix chain 'V' and resid 2 through 20 Processing helix chain 'V' and resid 22 through 37 Processing helix chain 'V' and resid 39 through 50 removed outlier: 3.892A pdb=" N ALA V 43 " --> pdb=" O PRO V 39 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 65 Processing helix chain 'W' and resid 2 through 20 Processing helix chain 'W' and resid 22 through 36 removed outlier: 3.594A pdb=" N GLU W 36 " --> pdb=" O ARG W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 50 removed outlier: 3.993A pdb=" N ALA W 43 " --> pdb=" O PRO W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 65 Processing helix chain 'X' and resid 2 through 20 Processing helix chain 'X' and resid 22 through 37 Processing helix chain 'X' and resid 39 through 52 removed outlier: 4.063A pdb=" N ALA X 43 " --> pdb=" O PRO X 39 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY X 52 " --> pdb=" O LEU X 48 " (cutoff:3.500A) Processing helix chain 'X' and resid 53 through 65 Processing helix chain 'Y' and resid 2 through 20 Processing helix chain 'Y' and resid 22 through 37 Processing helix chain 'Y' and resid 39 through 52 removed outlier: 3.937A pdb=" N ALA Y 43 " --> pdb=" O PRO Y 39 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY Y 52 " --> pdb=" O LEU Y 48 " (cutoff:3.500A) Processing helix chain 'Y' and resid 53 through 65 Processing helix chain 'Z' and resid 2 through 20 Processing helix chain 'Z' and resid 22 through 36 removed outlier: 3.518A pdb=" N VAL Z 26 " --> pdb=" O ARG Z 22 " (cutoff:3.500A) Processing helix chain 'Z' and resid 39 through 50 removed outlier: 3.967A pdb=" N ALA Z 43 " --> pdb=" O PRO Z 39 " (cutoff:3.500A) Processing helix chain 'Z' and resid 53 through 65 Processing helix chain 'a' and resid 2 through 20 Processing helix chain 'a' and resid 22 through 36 removed outlier: 3.542A pdb=" N GLU a 36 " --> pdb=" O ARG a 32 " (cutoff:3.500A) Processing helix chain 'a' and resid 39 through 50 removed outlier: 3.982A pdb=" N ALA a 43 " --> pdb=" O PRO a 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 65 Processing helix chain 'b' and resid 2 through 20 Processing helix chain 'b' and resid 22 through 36 removed outlier: 3.760A pdb=" N GLU b 36 " --> pdb=" O ARG b 32 " (cutoff:3.500A) Processing helix chain 'b' and resid 39 through 50 removed outlier: 3.953A pdb=" N ALA b 43 " --> pdb=" O PRO b 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 53 through 65 Processing helix chain 'c' and resid 2 through 20 Processing helix chain 'c' and resid 22 through 36 removed outlier: 3.579A pdb=" N GLU c 36 " --> pdb=" O ARG c 32 " (cutoff:3.500A) Processing helix chain 'c' and resid 39 through 50 removed outlier: 3.890A pdb=" N ALA c 43 " --> pdb=" O PRO c 39 " (cutoff:3.500A) Processing helix chain 'c' and resid 53 through 65 Processing helix chain 'd' and resid 2 through 20 removed outlier: 3.650A pdb=" N ALA d 11 " --> pdb=" O ARG d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 22 through 36 removed outlier: 3.680A pdb=" N GLU d 36 " --> pdb=" O ARG d 32 " (cutoff:3.500A) Processing helix chain 'd' and resid 39 through 50 removed outlier: 4.059A pdb=" N ALA d 43 " --> pdb=" O PRO d 39 " (cutoff:3.500A) Processing helix chain 'd' and resid 53 through 65 Processing helix chain 'e' and resid 2 through 20 Processing helix chain 'e' and resid 22 through 36 removed outlier: 3.685A pdb=" N GLU e 36 " --> pdb=" O ARG e 32 " (cutoff:3.500A) Processing helix chain 'e' and resid 39 through 52 removed outlier: 3.933A pdb=" N ALA e 43 " --> pdb=" O PRO e 39 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY e 52 " --> pdb=" O LEU e 48 " (cutoff:3.500A) Processing helix chain 'e' and resid 53 through 65 Processing helix chain 'f' and resid 2 through 20 Processing helix chain 'f' and resid 22 through 37 removed outlier: 3.503A pdb=" N GLU f 36 " --> pdb=" O ARG f 32 " (cutoff:3.500A) Processing helix chain 'f' and resid 39 through 50 removed outlier: 3.859A pdb=" N ALA f 43 " --> pdb=" O PRO f 39 " (cutoff:3.500A) Processing helix chain 'f' and resid 53 through 65 Processing helix chain 'g' and resid 2 through 20 Processing helix chain 'g' and resid 22 through 36 removed outlier: 3.514A pdb=" N GLU g 36 " --> pdb=" O ARG g 32 " (cutoff:3.500A) Processing helix chain 'g' and resid 39 through 50 removed outlier: 3.977A pdb=" N ALA g 43 " --> pdb=" O PRO g 39 " (cutoff:3.500A) Processing helix chain 'g' and resid 53 through 65 Processing helix chain 'h' and resid 2 through 20 removed outlier: 3.511A pdb=" N ALA h 11 " --> pdb=" O ARG h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 36 removed outlier: 3.524A pdb=" N GLU h 36 " --> pdb=" O ARG h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 39 through 50 removed outlier: 3.873A pdb=" N ALA h 43 " --> pdb=" O PRO h 39 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU h 47 " --> pdb=" O ALA h 43 " (cutoff:3.500A) Processing helix chain 'h' and resid 53 through 65 Processing helix chain 'i' and resid 2 through 20 Processing helix chain 'i' and resid 22 through 36 removed outlier: 3.617A pdb=" N GLU i 36 " --> pdb=" O ARG i 32 " (cutoff:3.500A) Processing helix chain 'i' and resid 39 through 50 removed outlier: 4.009A pdb=" N ALA i 43 " --> pdb=" O PRO i 39 " (cutoff:3.500A) Processing helix chain 'i' and resid 53 through 65 Processing helix chain 'j' and resid 2 through 20 Processing helix chain 'j' and resid 22 through 36 Processing helix chain 'j' and resid 39 through 50 removed outlier: 3.936A pdb=" N ALA j 43 " --> pdb=" O PRO j 39 " (cutoff:3.500A) Processing helix chain 'j' and resid 53 through 65 Processing helix chain 'k' and resid 2 through 20 Processing helix chain 'k' and resid 22 through 36 Processing helix chain 'k' and resid 39 through 50 removed outlier: 3.941A pdb=" N ALA k 43 " --> pdb=" O PRO k 39 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 65 Processing helix chain 'l' and resid 2 through 20 Processing helix chain 'l' and resid 22 through 36 Processing helix chain 'l' and resid 39 through 50 removed outlier: 3.965A pdb=" N ALA l 43 " --> pdb=" O PRO l 39 " (cutoff:3.500A) Processing helix chain 'l' and resid 53 through 65 Processing helix chain 'm' and resid 2 through 20 Processing helix chain 'm' and resid 22 through 37 Processing helix chain 'm' and resid 39 through 52 removed outlier: 4.047A pdb=" N ALA m 43 " --> pdb=" O PRO m 39 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY m 52 " --> pdb=" O LEU m 48 " (cutoff:3.500A) Processing helix chain 'm' and resid 53 through 65 Processing helix chain 'n' and resid 2 through 20 Processing helix chain 'n' and resid 22 through 37 removed outlier: 3.525A pdb=" N GLU n 36 " --> pdb=" O ARG n 32 " (cutoff:3.500A) Processing helix chain 'n' and resid 39 through 50 removed outlier: 4.048A pdb=" N ALA n 43 " --> pdb=" O PRO n 39 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) Processing helix chain 'n' and resid 53 through 65 Processing helix chain 'o' and resid 2 through 20 Processing helix chain 'o' and resid 22 through 36 removed outlier: 3.657A pdb=" N GLU o 36 " --> pdb=" O ARG o 32 " (cutoff:3.500A) Processing helix chain 'o' and resid 39 through 50 removed outlier: 3.961A pdb=" N ALA o 43 " --> pdb=" O PRO o 39 " (cutoff:3.500A) Processing helix chain 'o' and resid 53 through 65 Processing helix chain 'p' and resid 2 through 21 removed outlier: 3.588A pdb=" N GLY p 21 " --> pdb=" O LEU p 17 " (cutoff:3.500A) Processing helix chain 'p' and resid 22 through 36 Processing helix chain 'p' and resid 39 through 50 removed outlier: 4.026A pdb=" N ALA p 43 " --> pdb=" O PRO p 39 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 65 Processing helix chain 'q' and resid 2 through 20 Processing helix chain 'q' and resid 22 through 36 removed outlier: 3.546A pdb=" N GLU q 36 " --> pdb=" O ARG q 32 " (cutoff:3.500A) Processing helix chain 'q' and resid 39 through 50 removed outlier: 4.010A pdb=" N ALA q 43 " --> pdb=" O PRO q 39 " (cutoff:3.500A) Processing helix chain 'q' and resid 53 through 65 Processing helix chain 'r' and resid 2 through 20 Processing helix chain 'r' and resid 22 through 36 removed outlier: 3.616A pdb=" N GLU r 36 " --> pdb=" O ARG r 32 " (cutoff:3.500A) Processing helix chain 'r' and resid 39 through 50 removed outlier: 4.016A pdb=" N ALA r 43 " --> pdb=" O PRO r 39 " (cutoff:3.500A) Processing helix chain 'r' and resid 53 through 65 Processing helix chain 's' and resid 2 through 21 removed outlier: 3.768A pdb=" N GLY s 21 " --> pdb=" O LEU s 17 " (cutoff:3.500A) Processing helix chain 's' and resid 22 through 36 Processing helix chain 's' and resid 39 through 50 removed outlier: 4.056A pdb=" N ALA s 43 " --> pdb=" O PRO s 39 " (cutoff:3.500A) Processing helix chain 's' and resid 53 through 65 Processing helix chain 't' and resid 2 through 20 Processing helix chain 't' and resid 22 through 37 Processing helix chain 't' and resid 39 through 50 removed outlier: 4.061A pdb=" N ALA t 43 " --> pdb=" O PRO t 39 " (cutoff:3.500A) Processing helix chain 't' and resid 53 through 65 Processing helix chain 'u' and resid 2 through 21 removed outlier: 3.574A pdb=" N GLY u 21 " --> pdb=" O LEU u 17 " (cutoff:3.500A) Processing helix chain 'u' and resid 22 through 36 Processing helix chain 'u' and resid 39 through 50 removed outlier: 4.031A pdb=" N ALA u 43 " --> pdb=" O PRO u 39 " (cutoff:3.500A) Processing helix chain 'u' and resid 53 through 65 Processing helix chain 'v' and resid 2 through 20 Processing helix chain 'v' and resid 22 through 36 Processing helix chain 'v' and resid 39 through 50 removed outlier: 4.048A pdb=" N ALA v 43 " --> pdb=" O PRO v 39 " (cutoff:3.500A) Processing helix chain 'v' and resid 53 through 66 Processing helix chain 'w' and resid 2 through 20 Processing helix chain 'w' and resid 22 through 36 Processing helix chain 'w' and resid 39 through 50 removed outlier: 4.117A pdb=" N ALA w 43 " --> pdb=" O PRO w 39 " (cutoff:3.500A) Processing helix chain 'w' and resid 53 through 65 removed outlier: 3.622A pdb=" N ARG w 57 " --> pdb=" O ASP w 53 " (cutoff:3.500A) Processing helix chain 'x' and resid 2 through 20 Processing helix chain 'x' and resid 22 through 37 removed outlier: 3.551A pdb=" N GLU x 36 " --> pdb=" O ARG x 32 " (cutoff:3.500A) Processing helix chain 'x' and resid 39 through 50 removed outlier: 4.048A pdb=" N ALA x 43 " --> pdb=" O PRO x 39 " (cutoff:3.500A) Processing helix chain 'x' and resid 53 through 65 2518 hydrogen bonds defined for protein. 7554 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: 10.14 Time building geometry restraints manager: 12.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11940 1.34 - 1.46: 3858 1.46 - 1.57: 17202 1.57 - 1.69: 0 1.69 - 1.80: 120 Bond restraints: 33120 Sorted by residual: bond pdb=" C ASP G 53 " pdb=" O ASP G 53 " ideal model delta sigma weight residual 1.248 1.237 0.011 1.26e-02 6.30e+03 8.03e-01 bond pdb=" C ASP b 53 " pdb=" O ASP b 53 " ideal model delta sigma weight residual 1.248 1.238 0.011 1.26e-02 6.30e+03 7.24e-01 bond pdb=" CA ASP R 38 " pdb=" CB ASP R 38 " ideal model delta sigma weight residual 1.519 1.534 -0.014 1.73e-02 3.34e+03 6.99e-01 bond pdb=" C ASP t 53 " pdb=" O ASP t 53 " ideal model delta sigma weight residual 1.248 1.238 0.010 1.26e-02 6.30e+03 6.86e-01 bond pdb=" N ARG i 22 " pdb=" CA ARG i 22 " ideal model delta sigma weight residual 1.464 1.455 0.009 1.07e-02 8.73e+03 6.56e-01 ... (remaining 33115 not shown) Histogram of bond angle deviations from ideal: 100.61 - 106.74: 816 106.74 - 112.87: 17216 112.87 - 119.00: 9327 119.00 - 125.13: 16921 125.13 - 131.26: 240 Bond angle restraints: 44520 Sorted by residual: angle pdb=" CA GLY R 52 " pdb=" C GLY R 52 " pdb=" N ASP R 53 " ideal model delta sigma weight residual 118.50 116.35 2.15 9.90e-01 1.02e+00 4.70e+00 angle pdb=" C LEU m 49 " pdb=" N GLU m 50 " pdb=" CA GLU m 50 " ideal model delta sigma weight residual 122.38 118.69 3.69 1.81e+00 3.05e-01 4.15e+00 angle pdb=" N GLY V 52 " pdb=" CA GLY V 52 " pdb=" C GLY V 52 " ideal model delta sigma weight residual 115.32 112.47 2.85 1.48e+00 4.57e-01 3.72e+00 angle pdb=" N GLY R 52 " pdb=" CA GLY R 52 " pdb=" C GLY R 52 " ideal model delta sigma weight residual 115.67 112.64 3.03 1.59e+00 3.96e-01 3.63e+00 angle pdb=" C LEU 2 49 " pdb=" N GLU 2 50 " pdb=" CA GLU 2 50 " ideal model delta sigma weight residual 122.38 118.98 3.40 1.81e+00 3.05e-01 3.52e+00 ... (remaining 44515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 18541 18.00 - 36.01: 1992 36.01 - 54.01: 285 54.01 - 72.01: 76 72.01 - 90.02: 106 Dihedral angle restraints: 21000 sinusoidal: 9360 harmonic: 11640 Sorted by residual: dihedral pdb=" CB GLU 3 47 " pdb=" CG GLU 3 47 " pdb=" CD GLU 3 47 " pdb=" OE1 GLU 3 47 " ideal model delta sinusoidal sigma weight residual 0.00 90.02 -90.02 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU F 36 " pdb=" CG GLU F 36 " pdb=" CD GLU F 36 " pdb=" OE1 GLU F 36 " ideal model delta sinusoidal sigma weight residual 0.00 89.91 -89.91 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 19 " pdb=" CG GLU A 19 " pdb=" CD GLU A 19 " pdb=" OE1 GLU A 19 " ideal model delta sinusoidal sigma weight residual 0.00 89.90 -89.90 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 3132 0.026 - 0.052: 1416 0.052 - 0.078: 356 0.078 - 0.105: 77 0.105 - 0.131: 59 Chirality restraints: 5040 Sorted by residual: chirality pdb=" CA PRO w 54 " pdb=" N PRO w 54 " pdb=" C PRO w 54 " pdb=" CB PRO w 54 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA PRO D 54 " pdb=" N PRO D 54 " pdb=" C PRO D 54 " pdb=" CB PRO D 54 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.55e-01 chirality pdb=" CA PRO v 23 " pdb=" N PRO v 23 " pdb=" C PRO v 23 " pdb=" CB PRO v 23 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.41e-01 ... (remaining 5037 not shown) Planarity restraints: 6000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP h 53 " 0.017 5.00e-02 4.00e+02 2.56e-02 1.04e+00 pdb=" N PRO h 54 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO h 54 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO h 54 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP K 53 " -0.017 5.00e-02 4.00e+02 2.55e-02 1.04e+00 pdb=" N PRO K 54 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO K 54 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO K 54 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP 3 53 " -0.016 5.00e-02 4.00e+02 2.46e-02 9.70e-01 pdb=" N PRO 3 54 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO 3 54 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO 3 54 " -0.014 5.00e-02 4.00e+02 ... (remaining 5997 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 5650 2.76 - 3.30: 32692 3.30 - 3.83: 53964 3.83 - 4.37: 59783 4.37 - 4.90: 104557 Nonbonded interactions: 256646 Sorted by model distance: nonbonded pdb=" NH1 ARG 6 22 " pdb=" OE2 GLU 6 25 " model vdw 2.226 2.520 nonbonded pdb=" N MET j 1 " pdb=" OE2 GLU j 4 " model vdw 2.275 2.520 nonbonded pdb=" N MET l 1 " pdb=" OE2 GLU l 4 " model vdw 2.286 2.520 nonbonded pdb=" OE1 GLU k 25 " pdb=" NH2 ARG k 28 " model vdw 2.295 2.520 nonbonded pdb=" O LEU 5 48 " pdb=" OG SER 5 51 " model vdw 2.302 2.440 ... (remaining 256641 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' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.710 Check model and map are aligned: 0.480 Set scattering table: 0.290 Process input model: 76.430 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.540 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 : 0.004 0.025 33120 Z= 0.250 Angle : 0.549 4.276 44520 Z= 0.355 Chirality : 0.033 0.131 5040 Planarity : 0.003 0.026 6000 Dihedral : 15.823 90.016 13320 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.12), residues: 3900 helix: 0.01 (0.08), residues: 3600 sheet: None (None), residues: 0 loop : 2.60 (0.24), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS T 8 PHE 0.015 0.002 PHE f 64 ARG 0.003 0.000 ARG p 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 3.926 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.6398 time to fit residues: 144.6212 Evaluate side-chains 81 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 3.855 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.3980 chunk 272 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 282 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 210 optimal weight: 0.8980 chunk 326 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 8 HIS 1 8 HIS 2 8 HIS 3 8 HIS 4 8 HIS 5 8 HIS 6 8 HIS 7 8 HIS 8 8 HIS 9 8 HIS A 8 HIS B 8 HIS C 8 HIS D 8 HIS E 8 HIS F 8 HIS G 8 HIS H 8 HIS I 8 HIS J 8 HIS K 8 HIS L 8 HIS M 8 HIS N 8 HIS O 8 HIS P 8 HIS Q 8 HIS R 8 HIS S 8 HIS T 8 HIS U 8 HIS V 8 HIS W 8 HIS X 8 HIS Y 8 HIS Z 8 HIS a 8 HIS b 8 HIS c 8 HIS d 8 HIS e 8 HIS f 8 HIS g 8 HIS h 8 HIS i 8 HIS j 8 HIS k 8 HIS l 8 HIS m 8 HIS n 8 HIS o 8 HIS p 8 HIS q 8 HIS r 8 HIS s 8 HIS t 8 HIS u 8 HIS v 8 HIS w 8 HIS x 8 HIS Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 33120 Z= 0.135 Angle : 0.411 5.984 44520 Z= 0.194 Chirality : 0.031 0.115 5040 Planarity : 0.004 0.030 6000 Dihedral : 3.653 28.775 4680 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Rotamer: Outliers : 0.58 % Allowed : 7.30 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.12), residues: 3900 helix: 2.01 (0.08), residues: 3660 sheet: None (None), residues: 0 loop : 3.87 (0.30), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS T 8 PHE 0.008 0.001 PHE G 42 ARG 0.007 0.000 ARG i 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 4.067 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 16 residues processed: 113 average time/residue: 0.3806 time to fit residues: 78.1010 Evaluate side-chains 101 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 3.938 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3105 time to fit residues: 14.2355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 272 optimal weight: 0.8980 chunk 222 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 327 optimal weight: 2.9990 chunk 353 optimal weight: 5.9990 chunk 291 optimal weight: 2.9990 chunk 324 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 262 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 33120 Z= 0.244 Angle : 0.429 4.187 44520 Z= 0.202 Chirality : 0.033 0.122 5040 Planarity : 0.004 0.033 6000 Dihedral : 3.602 26.250 4680 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 0.97 % Allowed : 9.24 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.91 (0.13), residues: 3900 helix: 2.54 (0.08), residues: 3660 sheet: None (None), residues: 0 loop : 3.43 (0.30), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 8 PHE 0.014 0.002 PHE L 64 ARG 0.005 0.000 ARG v 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 74 time to evaluate : 4.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 21 residues processed: 102 average time/residue: 0.3721 time to fit residues: 69.9170 Evaluate side-chains 94 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 73 time to evaluate : 4.141 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2954 time to fit residues: 17.0395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 5.9990 chunk 246 optimal weight: 2.9990 chunk 169 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 156 optimal weight: 10.0000 chunk 219 optimal weight: 5.9990 chunk 328 optimal weight: 0.8980 chunk 347 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 311 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 33120 Z= 0.349 Angle : 0.491 5.753 44520 Z= 0.231 Chirality : 0.036 0.129 5040 Planarity : 0.004 0.036 6000 Dihedral : 3.980 31.065 4680 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 1.55 % Allowed : 10.82 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.80 (0.12), residues: 3900 helix: 2.51 (0.08), residues: 3660 sheet: None (None), residues: 0 loop : 2.44 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 8 PHE 0.022 0.003 PHE 3 64 ARG 0.004 0.000 ARG X 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 68 time to evaluate : 3.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 33 residues processed: 109 average time/residue: 0.3816 time to fit residues: 75.0844 Evaluate side-chains 103 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 70 time to evaluate : 3.583 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2929 time to fit residues: 23.0696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 259 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 296 optimal weight: 0.8980 chunk 240 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 0.8980 chunk 312 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 33120 Z= 0.156 Angle : 0.375 6.899 44520 Z= 0.177 Chirality : 0.031 0.119 5040 Planarity : 0.004 0.035 6000 Dihedral : 3.476 26.833 4680 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Rotamer: Outliers : 0.73 % Allowed : 12.33 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.60 (0.12), residues: 3900 helix: 3.01 (0.08), residues: 3660 sheet: None (None), residues: 0 loop : 3.08 (0.33), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS r 8 PHE 0.010 0.001 PHE 3 64 ARG 0.004 0.000 ARG v 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 3.871 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 110 average time/residue: 0.3766 time to fit residues: 75.8621 Evaluate side-chains 90 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 3.790 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3203 time to fit residues: 14.0441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 0.0980 chunk 313 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 204 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 348 optimal weight: 5.9990 chunk 289 optimal weight: 8.9990 chunk 161 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 33120 Z= 0.129 Angle : 0.366 8.551 44520 Z= 0.173 Chirality : 0.030 0.114 5040 Planarity : 0.004 0.035 6000 Dihedral : 3.048 20.155 4680 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 0.42 % Allowed : 13.30 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.03 (0.12), residues: 3900 helix: 3.27 (0.08), residues: 3660 sheet: None (None), residues: 0 loop : 3.56 (0.32), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS r 8 PHE 0.008 0.001 PHE L 64 ARG 0.004 0.000 ARG v 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 3.704 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 97 average time/residue: 0.3902 time to fit residues: 68.3263 Evaluate side-chains 83 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 4.863 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3205 time to fit residues: 10.9079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 198 optimal weight: 8.9990 chunk 254 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 293 optimal weight: 7.9990 chunk 194 optimal weight: 0.8980 chunk 346 optimal weight: 6.9990 chunk 217 optimal weight: 4.9990 chunk 211 optimal weight: 7.9990 chunk 160 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 33120 Z= 0.334 Angle : 0.493 7.983 44520 Z= 0.231 Chirality : 0.035 0.129 5040 Planarity : 0.004 0.043 6000 Dihedral : 3.520 23.613 4680 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Rotamer: Outliers : 0.70 % Allowed : 14.42 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.43 (0.12), residues: 3900 helix: 2.91 (0.08), residues: 3660 sheet: None (None), residues: 0 loop : 2.81 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS p 8 PHE 0.020 0.003 PHE D 64 ARG 0.003 0.000 ARG X 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 64 time to evaluate : 4.249 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 17 residues processed: 81 average time/residue: 0.4224 time to fit residues: 63.4777 Evaluate side-chains 81 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 64 time to evaluate : 4.284 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3309 time to fit residues: 16.0718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 236 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 272 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 33120 Z= 0.127 Angle : 0.373 8.770 44520 Z= 0.176 Chirality : 0.030 0.115 5040 Planarity : 0.004 0.036 6000 Dihedral : 3.045 18.633 4680 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 0.30 % Allowed : 14.58 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.07 (0.12), residues: 3900 helix: 3.30 (0.08), residues: 3660 sheet: None (None), residues: 0 loop : 3.42 (0.33), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS C 8 PHE 0.008 0.001 PHE 3 64 ARG 0.003 0.000 ARG v 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 4.213 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 83 average time/residue: 0.3984 time to fit residues: 61.2598 Evaluate side-chains 78 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 4.477 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3376 time to fit residues: 9.9121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 4.9990 chunk 332 optimal weight: 5.9990 chunk 303 optimal weight: 0.9990 chunk 323 optimal weight: 3.9990 chunk 194 optimal weight: 0.6980 chunk 140 optimal weight: 0.5980 chunk 253 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 292 optimal weight: 0.9990 chunk 305 optimal weight: 3.9990 chunk 322 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 33120 Z= 0.121 Angle : 0.377 7.256 44520 Z= 0.175 Chirality : 0.030 0.113 5040 Planarity : 0.004 0.035 6000 Dihedral : 2.746 15.628 4680 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 0.18 % Allowed : 15.00 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.32 (0.12), residues: 3900 helix: 3.45 (0.08), residues: 3660 sheet: None (None), residues: 0 loop : 3.70 (0.32), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS p 8 PHE 0.007 0.001 PHE q 64 ARG 0.003 0.000 ARG v 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 4.113 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 87 average time/residue: 0.4109 time to fit residues: 66.7691 Evaluate side-chains 79 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 4.134 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3251 time to fit residues: 8.0644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 0.1980 chunk 341 optimal weight: 0.4980 chunk 208 optimal weight: 0.9990 chunk 162 optimal weight: 7.9990 chunk 237 optimal weight: 2.9990 chunk 358 optimal weight: 2.9990 chunk 330 optimal weight: 1.9990 chunk 285 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 33120 Z= 0.144 Angle : 0.398 9.411 44520 Z= 0.183 Chirality : 0.031 0.115 5040 Planarity : 0.004 0.038 6000 Dihedral : 2.748 16.684 4680 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 0.24 % Allowed : 15.12 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.29 (0.12), residues: 3900 helix: 3.42 (0.08), residues: 3660 sheet: None (None), residues: 0 loop : 3.84 (0.33), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS p 8 PHE 0.008 0.001 PHE q 64 ARG 0.003 0.000 ARG v 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 3.816 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 79 average time/residue: 0.3789 time to fit residues: 55.5303 Evaluate side-chains 75 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 3.750 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3076 time to fit residues: 7.2016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 0.7980 chunk 304 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 263 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 286 optimal weight: 0.2980 chunk 119 optimal weight: 0.9990 chunk 293 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.086395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.074297 restraints weight = 105644.933| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 3.56 r_work: 0.3431 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 33120 Z= 0.121 Angle : 0.385 8.796 44520 Z= 0.177 Chirality : 0.030 0.113 5040 Planarity : 0.003 0.036 6000 Dihedral : 2.640 15.791 4680 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 0.15 % Allowed : 15.33 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.43 (0.12), residues: 3900 helix: 3.51 (0.08), residues: 3660 sheet: None (None), residues: 0 loop : 4.01 (0.33), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS p 8 PHE 0.007 0.001 PHE J 64 ARG 0.003 0.000 ARG v 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4291.54 seconds wall clock time: 79 minutes 27.73 seconds (4767.73 seconds total)