Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 17 05:16:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsv_22460/08_2023/7jsv_22460_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsv_22460/08_2023/7jsv_22460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsv_22460/08_2023/7jsv_22460.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsv_22460/08_2023/7jsv_22460.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsv_22460/08_2023/7jsv_22460_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsv_22460/08_2023/7jsv_22460_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 41 5.49 5 S 205 5.16 5 C 14801 2.51 5 N 3075 2.21 5 O 4018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 22140 Number of models: 1 Model: "" Number of chains: 82 Chain: "A" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "B" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "C" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "D" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "E" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "F" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "G" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "H" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "I" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "J" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "K" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "L" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "M" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "N" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "O" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "P" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "Q" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "R" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "S" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "T" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "U" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "V" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "W" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "X" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "Y" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "Z" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "a" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "b" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "c" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "d" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "e" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "f" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "g" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "h" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "i" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "j" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "k" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "l" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "m" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "n" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "o" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.40, per 1000 atoms: 0.47 Number of scatterers: 22140 At special positions: 0 Unit cell: (98.28, 98.28, 170.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 205 16.00 P 41 15.00 O 4018 8.00 N 3075 7.00 C 14801 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: 8.30 Conformation dependent library (CDL) restraints added in 2.8 seconds 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4756 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 123 helices and 0 sheets defined 80.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS A 16 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 19 " --> pdb=" O LYS A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 44 Processing helix chain 'A' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY A 52 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A 57 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET A 64 " --> pdb=" O THR A 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS B 16 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE B 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 44 Processing helix chain 'B' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY B 52 " --> pdb=" O PHE B 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 57 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET B 64 " --> pdb=" O THR B 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS C 16 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE C 19 " --> pdb=" O LYS C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 44 Processing helix chain 'C' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY C 52 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C 57 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET C 64 " --> pdb=" O THR C 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS D 16 " --> pdb=" O ALA D 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE D 19 " --> pdb=" O LYS D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 44 Processing helix chain 'D' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY D 52 " --> pdb=" O PHE D 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER D 57 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET D 64 " --> pdb=" O THR D 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS E 16 " --> pdb=" O ALA E 13 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE E 19 " --> pdb=" O LYS E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 44 Processing helix chain 'E' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY E 52 " --> pdb=" O PHE E 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER E 57 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET E 64 " --> pdb=" O THR E 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS F 16 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE F 19 " --> pdb=" O LYS F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 44 Processing helix chain 'F' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY F 52 " --> pdb=" O PHE F 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER F 57 " --> pdb=" O ALA F 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET F 64 " --> pdb=" O THR F 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS G 16 " --> pdb=" O ALA G 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE G 19 " --> pdb=" O LYS G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 44 Processing helix chain 'G' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY G 52 " --> pdb=" O PHE G 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER G 57 " --> pdb=" O ALA G 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET G 64 " --> pdb=" O THR G 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 19 removed outlier: 3.966A pdb=" N LYS H 16 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE H 19 " --> pdb=" O LYS H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 44 Processing helix chain 'H' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY H 52 " --> pdb=" O PHE H 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER H 57 " --> pdb=" O ALA H 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET H 64 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS I 16 " --> pdb=" O ALA I 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE I 19 " --> pdb=" O LYS I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 44 Processing helix chain 'I' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY I 52 " --> pdb=" O PHE I 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER I 57 " --> pdb=" O ALA I 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET I 64 " --> pdb=" O THR I 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS J 16 " --> pdb=" O ALA J 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE J 19 " --> pdb=" O LYS J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 44 Processing helix chain 'J' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY J 52 " --> pdb=" O PHE J 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER J 57 " --> pdb=" O ALA J 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET J 64 " --> pdb=" O THR J 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS K 16 " --> pdb=" O ALA K 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE K 19 " --> pdb=" O LYS K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 44 Processing helix chain 'K' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY K 52 " --> pdb=" O PHE K 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER K 57 " --> pdb=" O ALA K 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET K 64 " --> pdb=" O THR K 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS L 16 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE L 19 " --> pdb=" O LYS L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 44 Processing helix chain 'L' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY L 52 " --> pdb=" O PHE L 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER L 57 " --> pdb=" O ALA L 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET L 64 " --> pdb=" O THR L 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 19 removed outlier: 3.966A pdb=" N LYS M 16 " --> pdb=" O ALA M 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE M 19 " --> pdb=" O LYS M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 44 Processing helix chain 'M' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY M 52 " --> pdb=" O PHE M 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER M 57 " --> pdb=" O ALA M 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET M 64 " --> pdb=" O THR M 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS N 16 " --> pdb=" O ALA N 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE N 19 " --> pdb=" O LYS N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 44 Processing helix chain 'N' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY N 52 " --> pdb=" O PHE N 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER N 57 " --> pdb=" O ALA N 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET N 64 " --> pdb=" O THR N 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS O 16 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE O 19 " --> pdb=" O LYS O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 24 through 44 Processing helix chain 'O' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY O 52 " --> pdb=" O PHE O 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER O 57 " --> pdb=" O ALA O 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET O 64 " --> pdb=" O THR O 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS P 16 " --> pdb=" O ALA P 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE P 19 " --> pdb=" O LYS P 16 " (cutoff:3.500A) Processing helix chain 'P' and resid 24 through 44 Processing helix chain 'P' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY P 52 " --> pdb=" O PHE P 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER P 57 " --> pdb=" O ALA P 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET P 64 " --> pdb=" O THR P 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS Q 16 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE Q 19 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 44 Processing helix chain 'Q' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY Q 52 " --> pdb=" O PHE Q 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER Q 57 " --> pdb=" O ALA Q 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET Q 64 " --> pdb=" O THR Q 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS R 16 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE R 19 " --> pdb=" O LYS R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 44 Processing helix chain 'R' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY R 52 " --> pdb=" O PHE R 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER R 57 " --> pdb=" O ALA R 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET R 64 " --> pdb=" O THR R 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS S 16 " --> pdb=" O ALA S 13 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE S 19 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 44 Processing helix chain 'S' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY S 52 " --> pdb=" O PHE S 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER S 57 " --> pdb=" O ALA S 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET S 64 " --> pdb=" O THR S 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 19 removed outlier: 3.966A pdb=" N LYS T 16 " --> pdb=" O ALA T 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE T 19 " --> pdb=" O LYS T 16 " (cutoff:3.500A) Processing helix chain 'T' and resid 24 through 44 Processing helix chain 'T' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY T 52 " --> pdb=" O PHE T 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER T 57 " --> pdb=" O ALA T 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET T 64 " --> pdb=" O THR T 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS U 16 " --> pdb=" O ALA U 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE U 19 " --> pdb=" O LYS U 16 " (cutoff:3.500A) Processing helix chain 'U' and resid 24 through 44 Processing helix chain 'U' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY U 52 " --> pdb=" O PHE U 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER U 57 " --> pdb=" O ALA U 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET U 64 " --> pdb=" O THR U 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS V 16 " --> pdb=" O ALA V 13 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE V 19 " --> pdb=" O LYS V 16 " (cutoff:3.500A) Processing helix chain 'V' and resid 24 through 44 Processing helix chain 'V' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY V 52 " --> pdb=" O PHE V 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER V 57 " --> pdb=" O ALA V 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET V 64 " --> pdb=" O THR V 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS W 16 " --> pdb=" O ALA W 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE W 19 " --> pdb=" O LYS W 16 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 44 Processing helix chain 'W' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY W 52 " --> pdb=" O PHE W 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER W 57 " --> pdb=" O ALA W 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET W 64 " --> pdb=" O THR W 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS X 16 " --> pdb=" O ALA X 13 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE X 19 " --> pdb=" O LYS X 16 " (cutoff:3.500A) Processing helix chain 'X' and resid 24 through 44 Processing helix chain 'X' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY X 52 " --> pdb=" O PHE X 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER X 57 " --> pdb=" O ALA X 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET X 64 " --> pdb=" O THR X 61 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS Y 16 " --> pdb=" O ALA Y 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE Y 19 " --> pdb=" O LYS Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 24 through 44 Processing helix chain 'Y' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY Y 52 " --> pdb=" O PHE Y 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER Y 57 " --> pdb=" O ALA Y 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET Y 64 " --> pdb=" O THR Y 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS Z 16 " --> pdb=" O ALA Z 13 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE Z 19 " --> pdb=" O LYS Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 24 through 44 Processing helix chain 'Z' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY Z 52 " --> pdb=" O PHE Z 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER Z 57 " --> pdb=" O ALA Z 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET Z 64 " --> pdb=" O THR Z 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS a 16 " --> pdb=" O ALA a 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE a 19 " --> pdb=" O LYS a 16 " (cutoff:3.500A) Processing helix chain 'a' and resid 24 through 44 Processing helix chain 'a' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY a 52 " --> pdb=" O PHE a 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER a 57 " --> pdb=" O ALA a 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET a 64 " --> pdb=" O THR a 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS b 16 " --> pdb=" O ALA b 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE b 19 " --> pdb=" O LYS b 16 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 44 Processing helix chain 'b' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY b 52 " --> pdb=" O PHE b 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER b 57 " --> pdb=" O ALA b 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET b 64 " --> pdb=" O THR b 61 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS c 16 " --> pdb=" O ALA c 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE c 19 " --> pdb=" O LYS c 16 " (cutoff:3.500A) Processing helix chain 'c' and resid 24 through 44 Processing helix chain 'c' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY c 52 " --> pdb=" O PHE c 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER c 57 " --> pdb=" O ALA c 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET c 64 " --> pdb=" O THR c 61 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 19 removed outlier: 3.966A pdb=" N LYS d 16 " --> pdb=" O ALA d 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE d 19 " --> pdb=" O LYS d 16 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 44 Processing helix chain 'd' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY d 52 " --> pdb=" O PHE d 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER d 57 " --> pdb=" O ALA d 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET d 64 " --> pdb=" O THR d 61 " (cutoff:3.500A) Processing helix chain 'e' and resid 9 through 19 removed outlier: 3.966A pdb=" N LYS e 16 " --> pdb=" O ALA e 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE e 19 " --> pdb=" O LYS e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 24 through 44 Processing helix chain 'e' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY e 52 " --> pdb=" O PHE e 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER e 57 " --> pdb=" O ALA e 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET e 64 " --> pdb=" O THR e 61 " (cutoff:3.500A) Processing helix chain 'f' and resid 9 through 19 removed outlier: 3.964A pdb=" N LYS f 16 " --> pdb=" O ALA f 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE f 19 " --> pdb=" O LYS f 16 " (cutoff:3.500A) Processing helix chain 'f' and resid 24 through 44 Processing helix chain 'f' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY f 52 " --> pdb=" O PHE f 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER f 57 " --> pdb=" O ALA f 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET f 64 " --> pdb=" O THR f 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS g 16 " --> pdb=" O ALA g 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE g 19 " --> pdb=" O LYS g 16 " (cutoff:3.500A) Processing helix chain 'g' and resid 24 through 44 Processing helix chain 'g' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY g 52 " --> pdb=" O PHE g 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER g 57 " --> pdb=" O ALA g 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET g 64 " --> pdb=" O THR g 61 " (cutoff:3.500A) Processing helix chain 'h' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS h 16 " --> pdb=" O ALA h 13 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE h 19 " --> pdb=" O LYS h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 24 through 44 Processing helix chain 'h' and resid 47 through 67 removed outlier: 3.949A pdb=" N GLY h 52 " --> pdb=" O PHE h 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER h 57 " --> pdb=" O ALA h 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET h 64 " --> pdb=" O THR h 61 " (cutoff:3.500A) Processing helix chain 'i' and resid 9 through 19 removed outlier: 3.966A pdb=" N LYS i 16 " --> pdb=" O ALA i 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE i 19 " --> pdb=" O LYS i 16 " (cutoff:3.500A) Processing helix chain 'i' and resid 24 through 44 Processing helix chain 'i' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY i 52 " --> pdb=" O PHE i 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER i 57 " --> pdb=" O ALA i 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET i 64 " --> pdb=" O THR i 61 " (cutoff:3.500A) Processing helix chain 'j' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS j 16 " --> pdb=" O ALA j 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE j 19 " --> pdb=" O LYS j 16 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 44 Processing helix chain 'j' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY j 52 " --> pdb=" O PHE j 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER j 57 " --> pdb=" O ALA j 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET j 64 " --> pdb=" O THR j 61 " (cutoff:3.500A) Processing helix chain 'k' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS k 16 " --> pdb=" O ALA k 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE k 19 " --> pdb=" O LYS k 16 " (cutoff:3.500A) Processing helix chain 'k' and resid 24 through 44 Processing helix chain 'k' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY k 52 " --> pdb=" O PHE k 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER k 57 " --> pdb=" O ALA k 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET k 64 " --> pdb=" O THR k 61 " (cutoff:3.500A) Processing helix chain 'l' and resid 9 through 19 removed outlier: 3.964A pdb=" N LYS l 16 " --> pdb=" O ALA l 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE l 19 " --> pdb=" O LYS l 16 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 44 Processing helix chain 'l' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY l 52 " --> pdb=" O PHE l 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER l 57 " --> pdb=" O ALA l 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET l 64 " --> pdb=" O THR l 61 " (cutoff:3.500A) Processing helix chain 'm' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS m 16 " --> pdb=" O ALA m 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE m 19 " --> pdb=" O LYS m 16 " (cutoff:3.500A) Processing helix chain 'm' and resid 24 through 44 Processing helix chain 'm' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY m 52 " --> pdb=" O PHE m 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER m 57 " --> pdb=" O ALA m 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET m 64 " --> pdb=" O THR m 61 " (cutoff:3.500A) Processing helix chain 'n' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS n 16 " --> pdb=" O ALA n 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE n 19 " --> pdb=" O LYS n 16 " (cutoff:3.500A) Processing helix chain 'n' and resid 24 through 44 Processing helix chain 'n' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY n 52 " --> pdb=" O PHE n 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER n 57 " --> pdb=" O ALA n 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET n 64 " --> pdb=" O THR n 61 " (cutoff:3.500A) Processing helix chain 'o' and resid 9 through 19 removed outlier: 3.965A pdb=" N LYS o 16 " --> pdb=" O ALA o 13 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE o 19 " --> pdb=" O LYS o 16 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 44 Processing helix chain 'o' and resid 47 through 67 removed outlier: 3.948A pdb=" N GLY o 52 " --> pdb=" O PHE o 49 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER o 57 " --> pdb=" O ALA o 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET o 64 " --> pdb=" O THR o 61 " (cutoff:3.500A) 1558 hydrogen bonds defined for protein. 2091 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: 6.16 Time building geometry restraints manager: 8.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3239 1.30 - 1.43: 5576 1.43 - 1.55: 12956 1.55 - 1.67: 205 1.67 - 1.80: 451 Bond restraints: 22427 Sorted by residual: bond pdb=" CB PHE Z 53 " pdb=" CG PHE Z 53 " ideal model delta sigma weight residual 1.502 1.419 0.083 2.30e-02 1.89e+03 1.29e+01 bond pdb=" CB PHE d 53 " pdb=" CG PHE d 53 " ideal model delta sigma weight residual 1.502 1.420 0.082 2.30e-02 1.89e+03 1.29e+01 bond pdb=" CB PHE H 53 " pdb=" CG PHE H 53 " ideal model delta sigma weight residual 1.502 1.420 0.082 2.30e-02 1.89e+03 1.28e+01 bond pdb=" CB PHE n 53 " pdb=" CG PHE n 53 " ideal model delta sigma weight residual 1.502 1.420 0.082 2.30e-02 1.89e+03 1.28e+01 bond pdb=" CD GLU b 33 " pdb=" OE1 GLU b 33 " ideal model delta sigma weight residual 1.249 1.181 0.068 1.90e-02 2.77e+03 1.28e+01 ... (remaining 22422 not shown) Histogram of bond angle deviations from ideal: 95.95 - 103.52: 410 103.52 - 111.10: 8666 111.10 - 118.67: 9493 118.67 - 126.24: 10951 126.24 - 133.82: 205 Bond angle restraints: 29725 Sorted by residual: angle pdb=" N MET l 43 " pdb=" CA MET l 43 " pdb=" C MET l 43 " ideal model delta sigma weight residual 111.07 116.58 -5.51 1.07e+00 8.73e-01 2.65e+01 angle pdb=" N MET E 43 " pdb=" CA MET E 43 " pdb=" C MET E 43 " ideal model delta sigma weight residual 111.07 116.55 -5.48 1.07e+00 8.73e-01 2.62e+01 angle pdb=" N MET P 43 " pdb=" CA MET P 43 " pdb=" C MET P 43 " ideal model delta sigma weight residual 111.07 116.54 -5.47 1.07e+00 8.73e-01 2.62e+01 angle pdb=" N MET C 43 " pdb=" CA MET C 43 " pdb=" C MET C 43 " ideal model delta sigma weight residual 111.07 116.54 -5.47 1.07e+00 8.73e-01 2.61e+01 angle pdb=" N MET O 43 " pdb=" CA MET O 43 " pdb=" C MET O 43 " ideal model delta sigma weight residual 111.07 116.54 -5.47 1.07e+00 8.73e-01 2.61e+01 ... (remaining 29720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.86: 11374 11.86 - 23.71: 1049 23.71 - 35.57: 369 35.57 - 47.42: 123 47.42 - 59.28: 164 Dihedral angle restraints: 13079 sinusoidal: 5576 harmonic: 7503 Sorted by residual: dihedral pdb=" C THR k 18 " pdb=" N THR k 18 " pdb=" CA THR k 18 " pdb=" CB THR k 18 " ideal model delta harmonic sigma weight residual -122.00 -129.55 7.55 0 2.50e+00 1.60e-01 9.12e+00 dihedral pdb=" C THR V 18 " pdb=" N THR V 18 " pdb=" CA THR V 18 " pdb=" CB THR V 18 " ideal model delta harmonic sigma weight residual -122.00 -129.55 7.55 0 2.50e+00 1.60e-01 9.11e+00 dihedral pdb=" C THR i 18 " pdb=" N THR i 18 " pdb=" CA THR i 18 " pdb=" CB THR i 18 " ideal model delta harmonic sigma weight residual -122.00 -129.54 7.54 0 2.50e+00 1.60e-01 9.09e+00 ... (remaining 13076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1973 0.077 - 0.154: 1058 0.154 - 0.231: 254 0.231 - 0.308: 77 0.308 - 0.385: 41 Chirality restraints: 3403 Sorted by residual: chirality pdb=" CA THR V 18 " pdb=" N THR V 18 " pdb=" C THR V 18 " pdb=" CB THR V 18 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA THR k 18 " pdb=" N THR k 18 " pdb=" C THR k 18 " pdb=" CB THR k 18 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA THR B 18 " pdb=" N THR B 18 " pdb=" C THR B 18 " pdb=" CB THR B 18 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.69e+00 ... (remaining 3400 not shown) Planarity restraints: 3321 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR k 69 " -0.040 2.00e-02 2.50e+03 8.16e-02 6.66e+01 pdb=" C TYR k 69 " 0.141 2.00e-02 2.50e+03 pdb=" O TYR k 69 " -0.051 2.00e-02 2.50e+03 pdb=" OXT TYR k 69 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR e 69 " 0.040 2.00e-02 2.50e+03 8.15e-02 6.65e+01 pdb=" C TYR e 69 " -0.141 2.00e-02 2.50e+03 pdb=" O TYR e 69 " 0.051 2.00e-02 2.50e+03 pdb=" OXT TYR e 69 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR Y 69 " -0.040 2.00e-02 2.50e+03 8.15e-02 6.64e+01 pdb=" C TYR Y 69 " 0.141 2.00e-02 2.50e+03 pdb=" O TYR Y 69 " -0.051 2.00e-02 2.50e+03 pdb=" OXT TYR Y 69 " -0.050 2.00e-02 2.50e+03 ... (remaining 3318 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 9241 2.86 - 3.37: 23422 3.37 - 3.88: 36991 3.88 - 4.39: 46718 4.39 - 4.90: 72099 Nonbonded interactions: 188471 Sorted by model distance: nonbonded pdb=" O2 LHG O 101 " pdb=" O3 LHG O 101 " model vdw 2.348 2.432 nonbonded pdb=" O2 LHG K 101 " pdb=" O3 LHG K 101 " model vdw 2.348 2.432 nonbonded pdb=" O2 LHG V 101 " pdb=" O3 LHG V 101 " model vdw 2.348 2.432 nonbonded pdb=" O2 LHG U 101 " pdb=" O3 LHG U 101 " model vdw 2.348 2.432 nonbonded pdb=" O2 LHG o 101 " pdb=" O3 LHG o 101 " model vdw 2.348 2.432 ... (remaining 188466 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 '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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.730 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: 5.610 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 52.090 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.420 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 : 0.020 0.083 22427 Z= 1.241 Angle : 2.098 11.533 29725 Z= 1.152 Chirality : 0.103 0.385 3403 Planarity : 0.012 0.082 3321 Dihedral : 13.456 59.276 8323 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.00 % 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: 1.16 (0.15), residues: 2624 helix: 0.28 (0.09), residues: 2091 sheet: None (None), residues: 0 loop : 3.70 (0.28), residues: 533 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 999 time to evaluate : 2.626 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 999 average time/residue: 0.3248 time to fit residues: 507.1849 Evaluate side-chains 661 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 661 time to evaluate : 2.191 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 2.9990 chunk 186 optimal weight: 20.0000 chunk 103 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 192 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN J 22 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 22427 Z= 0.212 Angle : 0.638 10.181 29725 Z= 0.333 Chirality : 0.039 0.183 3403 Planarity : 0.006 0.022 3321 Dihedral : 14.865 77.676 4100 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer Outliers : 3.52 % 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: 1.12 (0.16), residues: 2624 helix: 0.25 (0.10), residues: 1640 sheet: None (None), residues: 0 loop : 2.06 (0.24), residues: 984 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 751 time to evaluate : 2.267 Fit side-chains revert: symmetry clash outliers start: 75 outliers final: 35 residues processed: 791 average time/residue: 0.2916 time to fit residues: 374.7114 Evaluate side-chains 658 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 623 time to evaluate : 2.422 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2120 time to fit residues: 16.9197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 185 optimal weight: 0.8980 chunk 152 optimal weight: 6.9990 chunk 61 optimal weight: 0.0870 chunk 223 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 76 optimal weight: 0.0270 chunk 179 optimal weight: 0.0970 overall best weight: 0.4014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 22427 Z= 0.167 Angle : 0.594 11.354 29725 Z= 0.297 Chirality : 0.038 0.183 3403 Planarity : 0.005 0.019 3321 Dihedral : 13.245 87.008 4100 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer Outliers : 1.88 % 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: -0.10 (0.14), residues: 2624 helix: -0.19 (0.11), residues: 1804 sheet: None (None), residues: 0 loop : 0.68 (0.20), residues: 820 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 676 time to evaluate : 2.429 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 16 residues processed: 694 average time/residue: 0.2895 time to fit residues: 325.2838 Evaluate side-chains 612 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 596 time to evaluate : 2.309 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1934 time to fit residues: 8.7748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 24 optimal weight: 20.0000 chunk 106 optimal weight: 7.9990 chunk 150 optimal weight: 30.0000 chunk 224 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.5750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 22427 Z= 0.286 Angle : 0.652 10.250 29725 Z= 0.328 Chirality : 0.040 0.185 3403 Planarity : 0.005 0.020 3321 Dihedral : 13.552 86.844 4100 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer Outliers : 2.91 % 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: -0.79 (0.14), residues: 2624 helix: -0.42 (0.11), residues: 1804 sheet: None (None), residues: 0 loop : -0.39 (0.18), residues: 820 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 654 time to evaluate : 2.573 Fit side-chains outliers start: 62 outliers final: 31 residues processed: 693 average time/residue: 0.2982 time to fit residues: 331.8219 Evaluate side-chains 612 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 581 time to evaluate : 2.234 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1938 time to fit residues: 14.3829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 30.0000 chunk 134 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 202 optimal weight: 7.9990 chunk 164 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 121 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** l 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.6243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 22427 Z= 0.194 Angle : 0.606 10.082 29725 Z= 0.299 Chirality : 0.038 0.198 3403 Planarity : 0.004 0.018 3321 Dihedral : 13.210 83.752 4100 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer Outliers : 1.50 % 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: -0.73 (0.14), residues: 2624 helix: -0.28 (0.11), residues: 1804 sheet: None (None), residues: 0 loop : -0.63 (0.18), residues: 820 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 639 time to evaluate : 2.439 Fit side-chains outliers start: 32 outliers final: 19 residues processed: 662 average time/residue: 0.3083 time to fit residues: 327.0096 Evaluate side-chains 597 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 578 time to evaluate : 2.538 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2373 time to fit residues: 11.1423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 0.7980 chunk 214 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 238 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN J 22 GLN d 22 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.6528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 22427 Z= 0.186 Angle : 0.624 12.155 29725 Z= 0.304 Chirality : 0.038 0.195 3403 Planarity : 0.004 0.016 3321 Dihedral : 13.062 78.630 4100 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer Outliers : 1.13 % 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: -0.71 (0.14), residues: 2624 helix: -0.24 (0.11), residues: 1804 sheet: None (None), residues: 0 loop : -0.66 (0.18), residues: 820 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 629 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 16 residues processed: 639 average time/residue: 0.3127 time to fit residues: 321.6828 Evaluate side-chains 602 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 586 time to evaluate : 2.284 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2222 time to fit residues: 9.4637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 0.2980 chunk 26 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 237 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 144 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.6811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 22427 Z= 0.174 Angle : 0.643 11.578 29725 Z= 0.309 Chirality : 0.038 0.193 3403 Planarity : 0.004 0.018 3321 Dihedral : 12.884 71.978 4100 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer Outliers : 0.70 % 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: -0.50 (0.15), residues: 2624 helix: -0.13 (0.11), residues: 1804 sheet: None (None), residues: 0 loop : -0.46 (0.19), residues: 820 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 613 time to evaluate : 2.425 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 619 average time/residue: 0.3033 time to fit residues: 300.5679 Evaluate side-chains 582 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 573 time to evaluate : 2.316 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2511 time to fit residues: 7.0219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 150 optimal weight: 30.0000 chunk 161 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 186 optimal weight: 30.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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: 0.8060 moved from start: 0.6845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 22427 Z= 0.223 Angle : 0.676 12.463 29725 Z= 0.327 Chirality : 0.039 0.186 3403 Planarity : 0.004 0.018 3321 Dihedral : 13.133 61.535 4100 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer Outliers : 0.89 % 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: -0.63 (0.15), residues: 2624 helix: -0.20 (0.11), residues: 1804 sheet: None (None), residues: 0 loop : -0.59 (0.19), residues: 820 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 584 time to evaluate : 2.290 Fit side-chains outliers start: 19 outliers final: 15 residues processed: 592 average time/residue: 0.2984 time to fit residues: 284.5182 Evaluate side-chains 572 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 557 time to evaluate : 2.255 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1993 time to fit residues: 8.4844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 215 optimal weight: 8.9990 chunk 227 optimal weight: 0.6980 chunk 207 optimal weight: 0.8980 chunk 220 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 199 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7987 moved from start: 0.7164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 22427 Z= 0.184 Angle : 0.671 13.424 29725 Z= 0.323 Chirality : 0.038 0.168 3403 Planarity : 0.004 0.019 3321 Dihedral : 12.890 58.909 4100 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer Outliers : 0.47 % 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: -0.43 (0.15), residues: 2624 helix: -0.11 (0.11), residues: 1804 sheet: None (None), residues: 0 loop : -0.36 (0.20), residues: 820 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 598 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 601 average time/residue: 0.2968 time to fit residues: 287.1905 Evaluate side-chains 575 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 571 time to evaluate : 2.128 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2895 time to fit residues: 4.6272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 162 optimal weight: 30.0000 chunk 245 optimal weight: 0.9990 chunk 225 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 150 optimal weight: 30.0000 chunk 119 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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: 0.8017 moved from start: 0.7194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 22427 Z= 0.210 Angle : 0.701 13.604 29725 Z= 0.336 Chirality : 0.038 0.161 3403 Planarity : 0.004 0.026 3321 Dihedral : 12.868 59.788 4100 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer Outliers : 0.09 % 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: -0.78 (0.15), residues: 2624 helix: -0.20 (0.11), residues: 1845 sheet: None (None), residues: 0 loop : -0.98 (0.19), residues: 779 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 581 time to evaluate : 2.337 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 582 average time/residue: 0.3078 time to fit residues: 287.7636 Evaluate side-chains 564 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 563 time to evaluate : 2.305 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2429 time to fit residues: 3.4086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 195 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 200 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 171 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.123762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.109058 restraints weight = 30876.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.112119 restraints weight = 14687.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.113979 restraints weight = 8156.669| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.7330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 22427 Z= 0.200 Angle : 0.710 13.257 29725 Z= 0.338 Chirality : 0.038 0.161 3403 Planarity : 0.004 0.025 3321 Dihedral : 12.828 59.955 4100 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer Outliers : 0.05 % 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: -0.77 (0.15), residues: 2624 helix: -0.19 (0.11), residues: 1845 sheet: None (None), residues: 0 loop : -0.98 (0.19), residues: 779 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5246.85 seconds wall clock time: 96 minutes 17.06 seconds (5777.06 seconds total)