Starting phenix.real_space_refine on Tue Jul 23 08:45:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsv_22460/07_2024/7jsv_22460.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsv_22460/07_2024/7jsv_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_22460/07_2024/7jsv_22460.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsv_22460/07_2024/7jsv_22460.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsv_22460/07_2024/7jsv_22460.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsv_22460/07_2024/7jsv_22460.cif" } 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 11.66, per 1000 atoms: 0.53 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: 9.03 Conformation dependent library (CDL) restraints added in 3.4 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... Secondary structure from input PDB file: 164 helices and 0 sheets defined 87.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 8 through 10 No H-bonds generated for 'chain 'A' and resid 8 through 10' Processing helix chain 'A' and resid 11 through 20 Processing helix chain 'A' and resid 23 through 45 Processing helix chain 'A' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 10 No H-bonds generated for 'chain 'B' and resid 8 through 10' Processing helix chain 'B' and resid 11 through 20 Processing helix chain 'B' and resid 23 through 45 Processing helix chain 'B' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 10 No H-bonds generated for 'chain 'C' and resid 8 through 10' Processing helix chain 'C' and resid 11 through 20 Processing helix chain 'C' and resid 23 through 45 Processing helix chain 'C' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE C 53 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 10 No H-bonds generated for 'chain 'D' and resid 8 through 10' Processing helix chain 'D' and resid 11 through 20 Processing helix chain 'D' and resid 23 through 45 Processing helix chain 'D' and resid 47 through 68 removed outlier: 4.470A pdb=" N PHE D 53 " --> pdb=" O PHE D 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 10 No H-bonds generated for 'chain 'E' and resid 8 through 10' Processing helix chain 'E' and resid 11 through 20 Processing helix chain 'E' and resid 23 through 45 Processing helix chain 'E' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE E 53 " --> pdb=" O PHE E 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 10 No H-bonds generated for 'chain 'F' and resid 8 through 10' Processing helix chain 'F' and resid 11 through 20 Processing helix chain 'F' and resid 23 through 45 Processing helix chain 'F' and resid 47 through 68 removed outlier: 4.470A pdb=" N PHE F 53 " --> pdb=" O PHE F 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 10 No H-bonds generated for 'chain 'G' and resid 8 through 10' Processing helix chain 'G' and resid 11 through 20 Processing helix chain 'G' and resid 23 through 45 Processing helix chain 'G' and resid 47 through 68 removed outlier: 4.470A pdb=" N PHE G 53 " --> pdb=" O PHE G 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 10 No H-bonds generated for 'chain 'H' and resid 8 through 10' Processing helix chain 'H' and resid 11 through 20 Processing helix chain 'H' and resid 23 through 45 Processing helix chain 'H' and resid 47 through 68 removed outlier: 4.470A pdb=" N PHE H 53 " --> pdb=" O PHE H 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA H 54 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 10 No H-bonds generated for 'chain 'I' and resid 8 through 10' Processing helix chain 'I' and resid 11 through 20 Processing helix chain 'I' and resid 23 through 45 Processing helix chain 'I' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE I 53 " --> pdb=" O PHE I 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA I 54 " --> pdb=" O LEU I 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 10 No H-bonds generated for 'chain 'J' and resid 8 through 10' Processing helix chain 'J' and resid 11 through 20 Processing helix chain 'J' and resid 23 through 45 Processing helix chain 'J' and resid 47 through 68 removed outlier: 4.470A pdb=" N PHE J 53 " --> pdb=" O PHE J 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA J 54 " --> pdb=" O LEU J 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 10 No H-bonds generated for 'chain 'K' and resid 8 through 10' Processing helix chain 'K' and resid 11 through 20 Processing helix chain 'K' and resid 23 through 45 Processing helix chain 'K' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE K 53 " --> pdb=" O PHE K 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA K 54 " --> pdb=" O LEU K 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 10 No H-bonds generated for 'chain 'L' and resid 8 through 10' Processing helix chain 'L' and resid 11 through 20 Processing helix chain 'L' and resid 23 through 45 Processing helix chain 'L' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE L 53 " --> pdb=" O PHE L 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA L 54 " --> pdb=" O LEU L 50 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 10 No H-bonds generated for 'chain 'M' and resid 8 through 10' Processing helix chain 'M' and resid 11 through 20 Processing helix chain 'M' and resid 23 through 45 Processing helix chain 'M' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE M 53 " --> pdb=" O PHE M 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA M 54 " --> pdb=" O LEU M 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 10 No H-bonds generated for 'chain 'N' and resid 8 through 10' Processing helix chain 'N' and resid 11 through 20 Processing helix chain 'N' and resid 23 through 45 Processing helix chain 'N' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE N 53 " --> pdb=" O PHE N 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA N 54 " --> pdb=" O LEU N 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 8 through 10 No H-bonds generated for 'chain 'O' and resid 8 through 10' Processing helix chain 'O' and resid 11 through 20 Processing helix chain 'O' and resid 23 through 45 Processing helix chain 'O' and resid 47 through 68 removed outlier: 4.470A pdb=" N PHE O 53 " --> pdb=" O PHE O 49 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA O 54 " --> pdb=" O LEU O 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 8 through 10 No H-bonds generated for 'chain 'P' and resid 8 through 10' Processing helix chain 'P' and resid 11 through 20 Processing helix chain 'P' and resid 23 through 45 Processing helix chain 'P' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE P 53 " --> pdb=" O PHE P 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA P 54 " --> pdb=" O LEU P 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 10 No H-bonds generated for 'chain 'Q' and resid 8 through 10' Processing helix chain 'Q' and resid 11 through 20 Processing helix chain 'Q' and resid 23 through 45 Processing helix chain 'Q' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE Q 53 " --> pdb=" O PHE Q 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA Q 54 " --> pdb=" O LEU Q 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 10 No H-bonds generated for 'chain 'R' and resid 8 through 10' Processing helix chain 'R' and resid 11 through 20 Processing helix chain 'R' and resid 23 through 45 Processing helix chain 'R' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE R 53 " --> pdb=" O PHE R 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA R 54 " --> pdb=" O LEU R 50 " (cutoff:3.500A) Processing helix chain 'S' and resid 8 through 10 No H-bonds generated for 'chain 'S' and resid 8 through 10' Processing helix chain 'S' and resid 11 through 20 Processing helix chain 'S' and resid 23 through 45 Processing helix chain 'S' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE S 53 " --> pdb=" O PHE S 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA S 54 " --> pdb=" O LEU S 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 10 No H-bonds generated for 'chain 'T' and resid 8 through 10' Processing helix chain 'T' and resid 11 through 20 Processing helix chain 'T' and resid 23 through 45 Processing helix chain 'T' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE T 53 " --> pdb=" O PHE T 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA T 54 " --> pdb=" O LEU T 50 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 10 No H-bonds generated for 'chain 'U' and resid 8 through 10' Processing helix chain 'U' and resid 11 through 20 Processing helix chain 'U' and resid 23 through 45 Processing helix chain 'U' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE U 53 " --> pdb=" O PHE U 49 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA U 54 " --> pdb=" O LEU U 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 10 No H-bonds generated for 'chain 'V' and resid 8 through 10' Processing helix chain 'V' and resid 11 through 20 Processing helix chain 'V' and resid 23 through 45 Processing helix chain 'V' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE V 53 " --> pdb=" O PHE V 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA V 54 " --> pdb=" O LEU V 50 " (cutoff:3.500A) Processing helix chain 'W' and resid 8 through 10 No H-bonds generated for 'chain 'W' and resid 8 through 10' Processing helix chain 'W' and resid 11 through 20 Processing helix chain 'W' and resid 23 through 45 Processing helix chain 'W' and resid 47 through 68 removed outlier: 4.470A pdb=" N PHE W 53 " --> pdb=" O PHE W 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA W 54 " --> pdb=" O LEU W 50 " (cutoff:3.500A) Processing helix chain 'X' and resid 8 through 10 No H-bonds generated for 'chain 'X' and resid 8 through 10' Processing helix chain 'X' and resid 11 through 20 Processing helix chain 'X' and resid 23 through 45 Processing helix chain 'X' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE X 53 " --> pdb=" O PHE X 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA X 54 " --> pdb=" O LEU X 50 " (cutoff:3.500A) Processing helix chain 'Y' and resid 8 through 10 No H-bonds generated for 'chain 'Y' and resid 8 through 10' Processing helix chain 'Y' and resid 11 through 20 Processing helix chain 'Y' and resid 23 through 45 Processing helix chain 'Y' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE Y 53 " --> pdb=" O PHE Y 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA Y 54 " --> pdb=" O LEU Y 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 8 through 10 No H-bonds generated for 'chain 'Z' and resid 8 through 10' Processing helix chain 'Z' and resid 11 through 20 Processing helix chain 'Z' and resid 23 through 45 Processing helix chain 'Z' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE Z 53 " --> pdb=" O PHE Z 49 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA Z 54 " --> pdb=" O LEU Z 50 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 10 No H-bonds generated for 'chain 'a' and resid 8 through 10' Processing helix chain 'a' and resid 11 through 20 Processing helix chain 'a' and resid 23 through 45 Processing helix chain 'a' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE a 53 " --> pdb=" O PHE a 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA a 54 " --> pdb=" O LEU a 50 " (cutoff:3.500A) Processing helix chain 'b' and resid 8 through 10 No H-bonds generated for 'chain 'b' and resid 8 through 10' Processing helix chain 'b' and resid 11 through 20 Processing helix chain 'b' and resid 23 through 45 Processing helix chain 'b' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE b 53 " --> pdb=" O PHE b 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA b 54 " --> pdb=" O LEU b 50 " (cutoff:3.500A) Processing helix chain 'c' and resid 8 through 10 No H-bonds generated for 'chain 'c' and resid 8 through 10' Processing helix chain 'c' and resid 11 through 20 Processing helix chain 'c' and resid 23 through 45 Processing helix chain 'c' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE c 53 " --> pdb=" O PHE c 49 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA c 54 " --> pdb=" O LEU c 50 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 10 No H-bonds generated for 'chain 'd' and resid 8 through 10' Processing helix chain 'd' and resid 11 through 20 Processing helix chain 'd' and resid 23 through 45 Processing helix chain 'd' and resid 47 through 68 removed outlier: 4.468A pdb=" N PHE d 53 " --> pdb=" O PHE d 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA d 54 " --> pdb=" O LEU d 50 " (cutoff:3.500A) Processing helix chain 'e' and resid 8 through 10 No H-bonds generated for 'chain 'e' and resid 8 through 10' Processing helix chain 'e' and resid 11 through 20 Processing helix chain 'e' and resid 23 through 45 Processing helix chain 'e' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE e 53 " --> pdb=" O PHE e 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA e 54 " --> pdb=" O LEU e 50 " (cutoff:3.500A) Processing helix chain 'f' and resid 8 through 10 No H-bonds generated for 'chain 'f' and resid 8 through 10' Processing helix chain 'f' and resid 11 through 20 Processing helix chain 'f' and resid 23 through 45 Processing helix chain 'f' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE f 53 " --> pdb=" O PHE f 49 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA f 54 " --> pdb=" O LEU f 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 8 through 10 No H-bonds generated for 'chain 'g' and resid 8 through 10' Processing helix chain 'g' and resid 11 through 20 Processing helix chain 'g' and resid 23 through 45 Processing helix chain 'g' and resid 47 through 68 removed outlier: 4.470A pdb=" N PHE g 53 " --> pdb=" O PHE g 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA g 54 " --> pdb=" O LEU g 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 8 through 10 No H-bonds generated for 'chain 'h' and resid 8 through 10' Processing helix chain 'h' and resid 11 through 20 Processing helix chain 'h' and resid 23 through 45 Processing helix chain 'h' and resid 47 through 68 removed outlier: 4.470A pdb=" N PHE h 53 " --> pdb=" O PHE h 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA h 54 " --> pdb=" O LEU h 50 " (cutoff:3.500A) Processing helix chain 'i' and resid 8 through 10 No H-bonds generated for 'chain 'i' and resid 8 through 10' Processing helix chain 'i' and resid 11 through 20 Processing helix chain 'i' and resid 23 through 45 Processing helix chain 'i' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE i 53 " --> pdb=" O PHE i 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA i 54 " --> pdb=" O LEU i 50 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 10 No H-bonds generated for 'chain 'j' and resid 8 through 10' Processing helix chain 'j' and resid 11 through 20 Processing helix chain 'j' and resid 23 through 45 Processing helix chain 'j' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE j 53 " --> pdb=" O PHE j 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA j 54 " --> pdb=" O LEU j 50 " (cutoff:3.500A) Processing helix chain 'k' and resid 8 through 10 No H-bonds generated for 'chain 'k' and resid 8 through 10' Processing helix chain 'k' and resid 11 through 20 Processing helix chain 'k' and resid 23 through 45 Processing helix chain 'k' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE k 53 " --> pdb=" O PHE k 49 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA k 54 " --> pdb=" O LEU k 50 " (cutoff:3.500A) Processing helix chain 'l' and resid 8 through 10 No H-bonds generated for 'chain 'l' and resid 8 through 10' Processing helix chain 'l' and resid 11 through 20 Processing helix chain 'l' and resid 23 through 45 Processing helix chain 'l' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE l 53 " --> pdb=" O PHE l 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA l 54 " --> pdb=" O LEU l 50 " (cutoff:3.500A) Processing helix chain 'm' and resid 8 through 10 No H-bonds generated for 'chain 'm' and resid 8 through 10' Processing helix chain 'm' and resid 11 through 20 Processing helix chain 'm' and resid 23 through 45 Processing helix chain 'm' and resid 47 through 68 removed outlier: 4.470A pdb=" N PHE m 53 " --> pdb=" O PHE m 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA m 54 " --> pdb=" O LEU m 50 " (cutoff:3.500A) Processing helix chain 'n' and resid 8 through 10 No H-bonds generated for 'chain 'n' and resid 8 through 10' Processing helix chain 'n' and resid 11 through 20 Processing helix chain 'n' and resid 23 through 45 Processing helix chain 'n' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE n 53 " --> pdb=" O PHE n 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA n 54 " --> pdb=" O LEU n 50 " (cutoff:3.500A) Processing helix chain 'o' and resid 8 through 10 No H-bonds generated for 'chain 'o' and resid 8 through 10' Processing helix chain 'o' and resid 11 through 20 Processing helix chain 'o' and resid 23 through 45 Processing helix chain 'o' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE o 53 " --> pdb=" O PHE o 49 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA o 54 " --> pdb=" O LEU o 50 " (cutoff:3.500A) 1681 hydrogen bonds defined for protein. 5043 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: 6.79 Time building geometry restraints manager: 9.71 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 - 16.60: 12423 16.60 - 33.19: 697 33.19 - 49.79: 287 49.79 - 66.39: 164 66.39 - 82.98: 41 Dihedral angle restraints: 13612 sinusoidal: 6109 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 13609 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: 8954 2.86 - 3.37: 23340 3.37 - 3.88: 37196 3.88 - 4.39: 46431 4.39 - 4.90: 72058 Nonbonded interactions: 187979 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 187974 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: 0.950 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: 0.760 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 57.370 Find NCS groups from input model: 4.600 Set up NCS constraints: 0.190 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.880 ------------------------------------------------------------------------------- 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= 1.236 Angle : 2.098 11.533 29725 Z= 1.152 Chirality : 0.103 0.385 3403 Planarity : 0.012 0.082 3321 Dihedral : 14.868 82.982 8856 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 % Allowed : 0.00 % Favored : 100.00 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.010 TRP Z 28 PHE 0.019 0.004 PHE b 51 TYR 0.041 0.011 TYR b 69 *********************** 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 : 2.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.7997 (mmm) cc_final: 0.7759 (tpp) REVERT: A 9 LYS cc_start: 0.8726 (tttt) cc_final: 0.8376 (tttt) REVERT: A 41 TYR cc_start: 0.8508 (t80) cc_final: 0.8184 (t80) REVERT: B 7 LEU cc_start: 0.8962 (mt) cc_final: 0.8567 (mt) REVERT: B 9 LYS cc_start: 0.9006 (tttt) cc_final: 0.8404 (ttpp) REVERT: B 23 SER cc_start: 0.8826 (p) cc_final: 0.8337 (t) REVERT: B 41 TYR cc_start: 0.8906 (t80) cc_final: 0.8544 (t80) REVERT: C 9 LYS cc_start: 0.8420 (tttt) cc_final: 0.7650 (ttpp) REVERT: D 9 LYS cc_start: 0.8852 (tttt) cc_final: 0.8227 (ttpp) REVERT: D 18 THR cc_start: 0.9005 (m) cc_final: 0.8788 (p) REVERT: D 41 TYR cc_start: 0.8904 (t80) cc_final: 0.8519 (t80) REVERT: E 7 LEU cc_start: 0.8976 (mt) cc_final: 0.8773 (mp) REVERT: E 9 LYS cc_start: 0.8519 (tttt) cc_final: 0.8152 (ttpt) REVERT: E 23 SER cc_start: 0.9263 (p) cc_final: 0.8908 (t) REVERT: F 23 SER cc_start: 0.8621 (p) cc_final: 0.8329 (t) REVERT: G 21 LYS cc_start: 0.8117 (tttt) cc_final: 0.7638 (tptt) REVERT: G 23 SER cc_start: 0.9259 (p) cc_final: 0.8951 (p) REVERT: G 41 TYR cc_start: 0.8469 (t80) cc_final: 0.8060 (t80) REVERT: G 64 MET cc_start: 0.8707 (mmt) cc_final: 0.8458 (mmm) REVERT: I 21 LYS cc_start: 0.8205 (tttt) cc_final: 0.7592 (tppt) REVERT: J 42 MET cc_start: 0.9147 (tmm) cc_final: 0.8851 (tmm) REVERT: K 9 LYS cc_start: 0.7983 (tttt) cc_final: 0.7473 (tptt) REVERT: L 9 LYS cc_start: 0.8466 (tttt) cc_final: 0.8191 (ttpt) REVERT: L 65 SER cc_start: 0.9454 (t) cc_final: 0.9057 (p) REVERT: M 9 LYS cc_start: 0.7617 (tttt) cc_final: 0.7083 (ttpt) REVERT: N 9 LYS cc_start: 0.8296 (tttt) cc_final: 0.8049 (ttmt) REVERT: O 9 LYS cc_start: 0.8764 (tttt) cc_final: 0.8528 (ttmm) REVERT: O 21 LYS cc_start: 0.7695 (tttt) cc_final: 0.7319 (tptm) REVERT: P 23 SER cc_start: 0.7849 (p) cc_final: 0.7526 (p) REVERT: P 65 SER cc_start: 0.8938 (t) cc_final: 0.8515 (p) REVERT: Q 40 MET cc_start: 0.9117 (mmm) cc_final: 0.8802 (mmt) REVERT: Q 42 MET cc_start: 0.8879 (tmm) cc_final: 0.8485 (tmm) REVERT: R 12 ASP cc_start: 0.7719 (m-30) cc_final: 0.7366 (m-30) REVERT: R 16 LYS cc_start: 0.8682 (tttt) cc_final: 0.8445 (ttpt) REVERT: S 9 LYS cc_start: 0.7838 (tttt) cc_final: 0.7634 (ttpp) REVERT: S 12 ASP cc_start: 0.7660 (m-30) cc_final: 0.7357 (m-30) REVERT: S 46 ASN cc_start: 0.8507 (t0) cc_final: 0.8289 (t0) REVERT: T 23 SER cc_start: 0.8875 (p) cc_final: 0.8591 (t) REVERT: U 8 MET cc_start: 0.7231 (mmm) cc_final: 0.6731 (tpp) REVERT: U 9 LYS cc_start: 0.7891 (tttt) cc_final: 0.7680 (ttpp) REVERT: U 41 TYR cc_start: 0.7928 (t80) cc_final: 0.7496 (t80) REVERT: V 9 LYS cc_start: 0.8531 (tttt) cc_final: 0.8290 (ttmt) REVERT: V 39 ILE cc_start: 0.9518 (tp) cc_final: 0.9312 (tp) REVERT: Y 23 SER cc_start: 0.8995 (p) cc_final: 0.8707 (t) REVERT: Y 64 MET cc_start: 0.8349 (mmt) cc_final: 0.7985 (mmm) REVERT: Z 53 PHE cc_start: 0.8513 (t80) cc_final: 0.7744 (t80) REVERT: a 46 ASN cc_start: 0.8863 (t0) cc_final: 0.8567 (t0) REVERT: c 12 ASP cc_start: 0.7717 (m-30) cc_final: 0.7508 (m-30) REVERT: d 8 MET cc_start: 0.7600 (mmm) cc_final: 0.7253 (mmt) REVERT: e 8 MET cc_start: 0.7530 (mmm) cc_final: 0.7330 (mmp) REVERT: f 9 LYS cc_start: 0.8279 (tttt) cc_final: 0.8075 (tppt) REVERT: g 9 LYS cc_start: 0.8460 (tttt) cc_final: 0.8158 (ptmt) REVERT: h 50 LEU cc_start: 0.9062 (mt) cc_final: 0.8796 (mt) REVERT: i 9 LYS cc_start: 0.8399 (tttt) cc_final: 0.7802 (tptt) REVERT: i 41 TYR cc_start: 0.8488 (t80) cc_final: 0.8212 (t80) REVERT: i 65 SER cc_start: 0.9179 (t) cc_final: 0.8961 (p) REVERT: j 28 TRP cc_start: 0.8069 (m-10) cc_final: 0.7805 (m-10) REVERT: j 64 MET cc_start: 0.7877 (mmt) cc_final: 0.7582 (mmp) REVERT: k 12 ASP cc_start: 0.8234 (m-30) cc_final: 0.7967 (m-30) REVERT: k 64 MET cc_start: 0.8456 (mmt) cc_final: 0.8236 (mmm) REVERT: l 42 MET cc_start: 0.8858 (tmm) cc_final: 0.8316 (tmm) REVERT: m 41 TYR cc_start: 0.7675 (t80) cc_final: 0.7404 (t80) REVERT: o 49 PHE cc_start: 0.8349 (m-80) cc_final: 0.8113 (m-10) outliers start: 0 outliers final: 0 residues processed: 999 average time/residue: 0.3120 time to fit residues: 487.7996 Evaluate side-chains 682 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 682 time to evaluate : 2.417 ------------------------------------------------------------------------------- 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: 0.9990 chunk 63 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 192 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 223 optimal weight: 6.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22427 Z= 0.214 Angle : 0.632 9.135 29725 Z= 0.334 Chirality : 0.041 0.208 3403 Planarity : 0.003 0.017 3321 Dihedral : 16.744 89.891 4633 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.89 % Allowed : 14.40 % Favored : 81.71 % 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: 2.44 (0.16), residues: 2624 helix: 1.28 (0.10), residues: 2091 sheet: None (None), residues: 0 loop : 3.66 (0.33), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP b 28 PHE 0.025 0.002 PHE C 49 TYR 0.018 0.002 TYR R 41 *********************** 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 821 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 738 time to evaluate : 2.247 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.8194 (mmm) cc_final: 0.7917 (tpp) REVERT: A 9 LYS cc_start: 0.8684 (tttt) cc_final: 0.8333 (tttm) REVERT: A 39 ILE cc_start: 0.9120 (tp) cc_final: 0.8893 (tp) REVERT: B 9 LYS cc_start: 0.8963 (tttt) cc_final: 0.8622 (ttpp) REVERT: C 9 LYS cc_start: 0.8429 (tttt) cc_final: 0.8047 (ttpp) REVERT: D 9 LYS cc_start: 0.8728 (tttt) cc_final: 0.8383 (ttpp) REVERT: E 55 ILE cc_start: 0.9060 (mm) cc_final: 0.8848 (mt) REVERT: F 64 MET cc_start: 0.8211 (mmm) cc_final: 0.7961 (mmm) REVERT: G 21 LYS cc_start: 0.8329 (tttt) cc_final: 0.7575 (tptt) REVERT: G 41 TYR cc_start: 0.8413 (t80) cc_final: 0.7868 (t80) REVERT: G 51 PHE cc_start: 0.9046 (m-80) cc_final: 0.8793 (m-80) REVERT: G 64 MET cc_start: 0.8890 (mmt) cc_final: 0.8585 (mmm) REVERT: H 8 MET cc_start: 0.7576 (tpp) cc_final: 0.7361 (tpp) REVERT: H 41 TYR cc_start: 0.8688 (t80) cc_final: 0.8076 (t80) REVERT: I 41 TYR cc_start: 0.8602 (t80) cc_final: 0.8218 (t80) REVERT: K 9 LYS cc_start: 0.8366 (tttt) cc_final: 0.8014 (tptt) REVERT: K 69 TYR cc_start: 0.6833 (m-80) cc_final: 0.6367 (m-80) REVERT: L 65 SER cc_start: 0.9358 (t) cc_final: 0.9050 (p) REVERT: N 65 SER cc_start: 0.9041 (t) cc_final: 0.8528 (p) REVERT: P 22 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7465 (mm-40) REVERT: P 41 TYR cc_start: 0.9119 (t80) cc_final: 0.8835 (t80) REVERT: P 62 ILE cc_start: 0.8806 (mm) cc_final: 0.8555 (mm) REVERT: P 65 SER cc_start: 0.8834 (t) cc_final: 0.8317 (p) REVERT: Q 41 TYR cc_start: 0.8989 (t80) cc_final: 0.8616 (t80) REVERT: R 8 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6890 (tpp) REVERT: R 64 MET cc_start: 0.8732 (mmm) cc_final: 0.8334 (mmm) REVERT: S 21 LYS cc_start: 0.8271 (tptm) cc_final: 0.7758 (tptm) REVERT: T 40 MET cc_start: 0.9059 (mmm) cc_final: 0.8826 (mmm) REVERT: U 40 MET cc_start: 0.7718 (mmm) cc_final: 0.7496 (mmt) REVERT: U 64 MET cc_start: 0.8240 (mmt) cc_final: 0.7889 (mmm) REVERT: U 65 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8475 (p) REVERT: X 8 MET cc_start: 0.7523 (tpp) cc_final: 0.7131 (tpp) REVERT: X 12 ASP cc_start: 0.7542 (p0) cc_final: 0.7162 (t0) REVERT: Z 41 TYR cc_start: 0.9047 (t80) cc_final: 0.8674 (t80) REVERT: a 10 SER cc_start: 0.9173 (p) cc_final: 0.8898 (t) REVERT: c 42 MET cc_start: 0.8647 (tmm) cc_final: 0.8062 (tmm) REVERT: d 15 VAL cc_start: 0.9062 (m) cc_final: 0.8856 (p) REVERT: e 40 MET cc_start: 0.7513 (tpp) cc_final: 0.7242 (tpp) REVERT: e 65 SER cc_start: 0.8893 (t) cc_final: 0.8431 (p) REVERT: g 42 MET cc_start: 0.8576 (tmm) cc_final: 0.7160 (tpt) REVERT: h 6 ASP cc_start: 0.4794 (p0) cc_final: 0.3947 (m-30) REVERT: h 41 TYR cc_start: 0.8645 (t80) cc_final: 0.8408 (t80) REVERT: h 49 PHE cc_start: 0.8774 (m-80) cc_final: 0.8415 (m-80) REVERT: i 9 LYS cc_start: 0.8349 (tttt) cc_final: 0.7951 (tptt) REVERT: j 27 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8285 (mtpp) REVERT: j 39 ILE cc_start: 0.9581 (tp) cc_final: 0.9199 (tp) REVERT: j 42 MET cc_start: 0.9080 (tmm) cc_final: 0.8532 (tmm) REVERT: k 64 MET cc_start: 0.8842 (mmt) cc_final: 0.8476 (mmm) REVERT: l 42 MET cc_start: 0.9161 (tmm) cc_final: 0.8738 (tmm) REVERT: l 56 ILE cc_start: 0.9465 (OUTLIER) cc_final: 0.9264 (tp) REVERT: m 41 TYR cc_start: 0.8490 (t80) cc_final: 0.8229 (t80) REVERT: m 64 MET cc_start: 0.8338 (mmt) cc_final: 0.8035 (mmt) REVERT: n 40 MET cc_start: 0.8200 (mmp) cc_final: 0.7652 (mmt) REVERT: o 9 LYS cc_start: 0.8418 (tttt) cc_final: 0.7986 (ttpt) outliers start: 83 outliers final: 39 residues processed: 771 average time/residue: 0.2910 time to fit residues: 361.5726 Evaluate side-chains 670 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 627 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain R residue 8 MET Chi-restraints excluded: chain T residue 8 MET Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 65 SER Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 65 SER Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain f residue 7 LEU Chi-restraints excluded: chain f residue 14 THR Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain j residue 27 LYS Chi-restraints excluded: chain j residue 34 VAL Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 56 ILE Chi-restraints excluded: chain l residue 57 SER Chi-restraints excluded: chain m residue 61 THR Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 34 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 241 optimal weight: 1.9990 chunk 199 optimal weight: 8.9990 chunk 221 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 179 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN ** l 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22427 Z= 0.228 Angle : 0.612 9.918 29725 Z= 0.317 Chirality : 0.041 0.185 3403 Planarity : 0.003 0.019 3321 Dihedral : 14.995 89.611 4633 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 4.69 % Allowed : 18.81 % Favored : 76.50 % 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: 2.46 (0.16), residues: 2624 helix: 1.57 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 2.33 (0.30), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 28 PHE 0.020 0.001 PHE C 49 TYR 0.016 0.001 TYR f 41 *********************** 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 753 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 653 time to evaluate : 2.222 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8970 (tttt) cc_final: 0.8751 (tttp) REVERT: A 33 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7296 (tm-30) REVERT: B 9 LYS cc_start: 0.8854 (tttt) cc_final: 0.8551 (ttpp) REVERT: C 46 ASN cc_start: 0.8283 (t0) cc_final: 0.8025 (t0) REVERT: C 64 MET cc_start: 0.9205 (tpp) cc_final: 0.8971 (mmt) REVERT: D 9 LYS cc_start: 0.8761 (tttt) cc_final: 0.8491 (ttpp) REVERT: D 12 ASP cc_start: 0.8892 (t0) cc_final: 0.8643 (t0) REVERT: G 21 LYS cc_start: 0.8460 (tttt) cc_final: 0.7810 (tptt) REVERT: G 41 TYR cc_start: 0.8471 (t80) cc_final: 0.8130 (t80) REVERT: G 64 MET cc_start: 0.8957 (mmt) cc_final: 0.8616 (mmm) REVERT: H 41 TYR cc_start: 0.8660 (t80) cc_final: 0.8191 (t80) REVERT: H 42 MET cc_start: 0.9277 (tmm) cc_final: 0.8972 (tmm) REVERT: K 9 LYS cc_start: 0.8587 (tttt) cc_final: 0.8363 (tptt) REVERT: L 41 TYR cc_start: 0.8868 (t80) cc_final: 0.8339 (t80) REVERT: N 62 ILE cc_start: 0.8744 (mm) cc_final: 0.8478 (mt) REVERT: N 65 SER cc_start: 0.9098 (t) cc_final: 0.8709 (p) REVERT: O 42 MET cc_start: 0.8921 (tmm) cc_final: 0.8048 (tmm) REVERT: O 43 MET cc_start: 0.8316 (mtm) cc_final: 0.7870 (mtp) REVERT: P 41 TYR cc_start: 0.9130 (t80) cc_final: 0.8789 (t80) REVERT: P 65 SER cc_start: 0.8837 (t) cc_final: 0.8637 (p) REVERT: Q 12 ASP cc_start: 0.8574 (m-30) cc_final: 0.8333 (t0) REVERT: R 5 THR cc_start: 0.7115 (p) cc_final: 0.6585 (t) REVERT: R 8 MET cc_start: 0.7051 (OUTLIER) cc_final: 0.6766 (tpp) REVERT: S 21 LYS cc_start: 0.8492 (tptm) cc_final: 0.8163 (tptm) REVERT: S 42 MET cc_start: 0.8785 (tmm) cc_final: 0.8488 (tmm) REVERT: T 42 MET cc_start: 0.8681 (ttp) cc_final: 0.8195 (tmm) REVERT: U 9 LYS cc_start: 0.8033 (ttpp) cc_final: 0.7686 (ttpt) REVERT: U 41 TYR cc_start: 0.8669 (t80) cc_final: 0.8380 (t80) REVERT: U 65 SER cc_start: 0.9084 (OUTLIER) cc_final: 0.8802 (p) REVERT: X 8 MET cc_start: 0.7230 (tpp) cc_final: 0.7023 (tpp) REVERT: X 40 MET cc_start: 0.8485 (mmm) cc_final: 0.8251 (mmm) REVERT: X 46 ASN cc_start: 0.8784 (t0) cc_final: 0.8459 (t0) REVERT: Z 33 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8093 (tm-30) REVERT: Z 41 TYR cc_start: 0.9028 (t80) cc_final: 0.8470 (t80) REVERT: a 41 TYR cc_start: 0.8933 (t80) cc_final: 0.8714 (t80) REVERT: b 22 GLN cc_start: 0.7810 (pm20) cc_final: 0.7387 (mt0) REVERT: c 64 MET cc_start: 0.8426 (mmt) cc_final: 0.7774 (mmm) REVERT: e 65 SER cc_start: 0.9181 (t) cc_final: 0.8727 (p) REVERT: f 6 ASP cc_start: 0.7269 (p0) cc_final: 0.5864 (m-30) REVERT: f 33 GLU cc_start: 0.5548 (mm-30) cc_final: 0.5280 (mm-30) REVERT: g 42 MET cc_start: 0.8453 (tmm) cc_final: 0.7154 (tpt) REVERT: h 15 VAL cc_start: 0.8866 (m) cc_final: 0.8476 (p) REVERT: h 21 LYS cc_start: 0.8143 (tttt) cc_final: 0.7901 (tptm) REVERT: h 49 PHE cc_start: 0.8783 (m-80) cc_final: 0.8382 (m-80) REVERT: i 8 MET cc_start: 0.7318 (tpp) cc_final: 0.7104 (tpp) REVERT: i 9 LYS cc_start: 0.8602 (tttt) cc_final: 0.8222 (tptt) REVERT: j 27 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8410 (mtpp) REVERT: j 39 ILE cc_start: 0.9569 (tp) cc_final: 0.9255 (tp) REVERT: j 42 MET cc_start: 0.8889 (tmm) cc_final: 0.8380 (tmm) REVERT: k 33 GLU cc_start: 0.7398 (tm-30) cc_final: 0.7180 (tm-30) REVERT: k 64 MET cc_start: 0.8928 (mmt) cc_final: 0.8673 (mmm) REVERT: l 50 LEU cc_start: 0.9283 (mt) cc_final: 0.8980 (mt) REVERT: m 64 MET cc_start: 0.8618 (mmt) cc_final: 0.8218 (mmt) REVERT: n 40 MET cc_start: 0.8189 (mmp) cc_final: 0.7938 (mmt) REVERT: o 9 LYS cc_start: 0.8713 (tttt) cc_final: 0.8335 (ttpp) outliers start: 100 outliers final: 71 residues processed: 710 average time/residue: 0.3095 time to fit residues: 356.6889 Evaluate side-chains 669 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 595 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 9 LYS Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 47 VAL Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain R residue 8 MET Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain T residue 8 MET Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 65 SER Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 34 VAL Chi-restraints excluded: chain Y residue 43 MET Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain a residue 9 LYS Chi-restraints excluded: chain a residue 12 ASP Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 60 ILE Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain e residue 61 THR Chi-restraints excluded: chain f residue 7 LEU Chi-restraints excluded: chain f residue 23 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain h residue 23 SER Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain i residue 34 VAL Chi-restraints excluded: chain j residue 27 LYS Chi-restraints excluded: chain j residue 34 VAL Chi-restraints excluded: chain j residue 65 SER Chi-restraints excluded: chain k residue 7 LEU Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain m residue 60 ILE Chi-restraints excluded: chain m residue 61 THR Chi-restraints excluded: chain n residue 29 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 150 optimal weight: 30.0000 chunk 224 optimal weight: 6.9990 chunk 237 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 212 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN ** l 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.5632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22427 Z= 0.207 Angle : 0.594 9.611 29725 Z= 0.302 Chirality : 0.040 0.165 3403 Planarity : 0.002 0.018 3321 Dihedral : 14.526 89.280 4633 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 4.78 % Allowed : 20.36 % Favored : 74.86 % 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: 2.36 (0.16), residues: 2624 helix: 1.71 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 1.31 (0.29), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 28 PHE 0.019 0.001 PHE b 53 TYR 0.013 0.001 TYR e 41 *********************** 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 732 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 630 time to evaluate : 2.170 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7304 (tm-30) REVERT: B 12 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8086 (t0) REVERT: C 64 MET cc_start: 0.9319 (tpp) cc_final: 0.9026 (mmt) REVERT: D 9 LYS cc_start: 0.8814 (tttt) cc_final: 0.8497 (ttpp) REVERT: D 12 ASP cc_start: 0.8936 (t0) cc_final: 0.8719 (t0) REVERT: G 21 LYS cc_start: 0.8379 (tttt) cc_final: 0.7755 (tptt) REVERT: G 23 SER cc_start: 0.8744 (p) cc_final: 0.8484 (p) REVERT: G 41 TYR cc_start: 0.8512 (t80) cc_final: 0.8113 (t80) REVERT: G 64 MET cc_start: 0.9035 (mmt) cc_final: 0.8678 (mmm) REVERT: H 41 TYR cc_start: 0.8819 (t80) cc_final: 0.8357 (t80) REVERT: H 42 MET cc_start: 0.9248 (tmm) cc_final: 0.9043 (tmm) REVERT: L 41 TYR cc_start: 0.8828 (t80) cc_final: 0.8232 (t80) REVERT: M 62 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7848 (mt) REVERT: N 41 TYR cc_start: 0.8938 (t80) cc_final: 0.8737 (t80) REVERT: N 62 ILE cc_start: 0.8874 (mm) cc_final: 0.8645 (mm) REVERT: N 65 SER cc_start: 0.9047 (t) cc_final: 0.8656 (p) REVERT: P 41 TYR cc_start: 0.8976 (t80) cc_final: 0.8574 (t80) REVERT: P 62 ILE cc_start: 0.8838 (mm) cc_final: 0.8359 (mm) REVERT: Q 12 ASP cc_start: 0.8530 (m-30) cc_final: 0.8293 (t0) REVERT: S 64 MET cc_start: 0.8653 (tpp) cc_final: 0.8443 (mmt) REVERT: T 42 MET cc_start: 0.8683 (ttp) cc_final: 0.8227 (tmm) REVERT: U 8 MET cc_start: 0.7983 (mmm) cc_final: 0.7711 (tpp) REVERT: U 65 SER cc_start: 0.9072 (OUTLIER) cc_final: 0.8773 (p) REVERT: X 46 ASN cc_start: 0.8903 (t0) cc_final: 0.8452 (t0) REVERT: Y 8 MET cc_start: 0.8078 (tpp) cc_final: 0.7876 (tpp) REVERT: a 41 TYR cc_start: 0.8923 (t80) cc_final: 0.8639 (t80) REVERT: b 64 MET cc_start: 0.8216 (mmp) cc_final: 0.7782 (mmp) REVERT: c 9 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8348 (ptmt) REVERT: c 33 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7127 (tm-30) REVERT: c 64 MET cc_start: 0.8653 (mmt) cc_final: 0.8038 (mmm) REVERT: e 40 MET cc_start: 0.7809 (tpp) cc_final: 0.7536 (tpp) REVERT: e 65 SER cc_start: 0.9197 (t) cc_final: 0.8727 (p) REVERT: f 6 ASP cc_start: 0.7266 (p0) cc_final: 0.5979 (m-30) REVERT: f 33 GLU cc_start: 0.5418 (mm-30) cc_final: 0.5210 (mm-30) REVERT: h 15 VAL cc_start: 0.9038 (m) cc_final: 0.8713 (p) REVERT: h 21 LYS cc_start: 0.8179 (tttt) cc_final: 0.7961 (tptm) REVERT: h 49 PHE cc_start: 0.8815 (m-80) cc_final: 0.8367 (m-80) REVERT: i 9 LYS cc_start: 0.8663 (tttt) cc_final: 0.8305 (tptt) REVERT: j 27 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8477 (mtpp) REVERT: j 42 MET cc_start: 0.8962 (tmm) cc_final: 0.8353 (tmm) REVERT: j 55 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8710 (pt) REVERT: k 64 MET cc_start: 0.8955 (mmt) cc_final: 0.8571 (mmm) REVERT: l 50 LEU cc_start: 0.9291 (mt) cc_final: 0.8960 (mt) REVERT: n 8 MET cc_start: 0.6729 (tpt) cc_final: 0.5624 (ptt) REVERT: n 40 MET cc_start: 0.8232 (mmp) cc_final: 0.8004 (mmt) REVERT: n 43 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7566 (ttp) outliers start: 102 outliers final: 70 residues processed: 694 average time/residue: 0.2967 time to fit residues: 330.7156 Evaluate side-chains 649 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 572 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain U residue 65 SER Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Y residue 43 MET Chi-restraints excluded: chain Y residue 65 SER Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain a residue 9 LYS Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain c residue 9 LYS Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 10 SER Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain f residue 23 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 65 SER Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 34 VAL Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain j residue 27 LYS Chi-restraints excluded: chain j residue 34 VAL Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain k residue 7 LEU Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 55 ILE Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 60 ILE Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 43 MET Chi-restraints excluded: chain o residue 56 ILE 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: 4.9990 chunk 3 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 chunk 164 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 213 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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: 0.8178 moved from start: 0.5951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22427 Z= 0.329 Angle : 0.671 11.791 29725 Z= 0.342 Chirality : 0.043 0.177 3403 Planarity : 0.003 0.019 3321 Dihedral : 15.239 88.706 4633 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 5.63 % Allowed : 20.92 % Favored : 73.45 % 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: 2.16 (0.16), residues: 2624 helix: 1.54 (0.11), residues: 2173 sheet: None (None), residues: 0 loop : 1.31 (0.33), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 28 PHE 0.021 0.002 PHE R 53 TYR 0.014 0.002 TYR i 41 *********************** 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 733 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 613 time to evaluate : 2.204 Fit side-chains revert: symmetry clash REVERT: B 43 MET cc_start: 0.8785 (ttm) cc_final: 0.8442 (mtp) REVERT: C 40 MET cc_start: 0.8099 (mmm) cc_final: 0.7874 (mmm) REVERT: C 64 MET cc_start: 0.9271 (tpp) cc_final: 0.8856 (mmt) REVERT: D 9 LYS cc_start: 0.8910 (tttt) cc_final: 0.8557 (ttpp) REVERT: E 64 MET cc_start: 0.8979 (mmm) cc_final: 0.8725 (mmt) REVERT: G 21 LYS cc_start: 0.8565 (tttt) cc_final: 0.8016 (tptt) REVERT: G 23 SER cc_start: 0.8952 (p) cc_final: 0.8703 (p) REVERT: G 41 TYR cc_start: 0.8581 (t80) cc_final: 0.8066 (t80) REVERT: G 64 MET cc_start: 0.9001 (mmt) cc_final: 0.8657 (mmm) REVERT: H 41 TYR cc_start: 0.8995 (t80) cc_final: 0.8595 (t80) REVERT: H 43 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8119 (mtm) REVERT: I 41 TYR cc_start: 0.8875 (t80) cc_final: 0.8425 (t80) REVERT: I 42 MET cc_start: 0.9293 (tmm) cc_final: 0.9012 (tmm) REVERT: K 21 LYS cc_start: 0.8480 (tttt) cc_final: 0.8035 (tptp) REVERT: L 41 TYR cc_start: 0.8938 (t80) cc_final: 0.8357 (t80) REVERT: M 62 ILE cc_start: 0.8093 (mm) cc_final: 0.7875 (mt) REVERT: N 22 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7598 (mm-40) REVERT: N 62 ILE cc_start: 0.8860 (mm) cc_final: 0.8616 (mm) REVERT: N 65 SER cc_start: 0.9134 (t) cc_final: 0.8741 (p) REVERT: P 33 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8661 (tm-30) REVERT: Q 12 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8230 (t0) REVERT: U 41 TYR cc_start: 0.8732 (t80) cc_final: 0.8490 (t80) REVERT: U 64 MET cc_start: 0.8681 (mmt) cc_final: 0.8299 (mmt) REVERT: U 65 SER cc_start: 0.9136 (OUTLIER) cc_final: 0.8842 (p) REVERT: X 40 MET cc_start: 0.8806 (mmm) cc_final: 0.8500 (mmm) REVERT: X 46 ASN cc_start: 0.8967 (t0) cc_final: 0.8630 (t0) REVERT: Y 8 MET cc_start: 0.8296 (tpp) cc_final: 0.8075 (tpp) REVERT: Z 64 MET cc_start: 0.8916 (mmt) cc_final: 0.8704 (mmm) REVERT: a 9 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8668 (ttmm) REVERT: b 64 MET cc_start: 0.8233 (mmp) cc_final: 0.7866 (mmp) REVERT: c 8 MET cc_start: 0.8147 (tpp) cc_final: 0.7584 (tpp) REVERT: c 9 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8513 (ptmt) REVERT: e 40 MET cc_start: 0.7941 (tpp) cc_final: 0.7652 (tpp) REVERT: e 65 SER cc_start: 0.9231 (t) cc_final: 0.8791 (p) REVERT: f 6 ASP cc_start: 0.7394 (p0) cc_final: 0.6292 (m-30) REVERT: f 21 LYS cc_start: 0.7834 (tttt) cc_final: 0.7468 (tptm) REVERT: h 15 VAL cc_start: 0.8988 (m) cc_final: 0.8694 (p) REVERT: h 21 LYS cc_start: 0.8207 (tttt) cc_final: 0.7911 (tptm) REVERT: i 9 LYS cc_start: 0.8894 (tttt) cc_final: 0.8517 (tptt) REVERT: j 12 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.8001 (t0) REVERT: j 27 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8555 (mtpp) REVERT: j 42 MET cc_start: 0.8940 (tmm) cc_final: 0.8321 (tmm) REVERT: k 64 MET cc_start: 0.8772 (mmt) cc_final: 0.8445 (mmm) REVERT: l 50 LEU cc_start: 0.9344 (mt) cc_final: 0.9038 (mt) REVERT: n 8 MET cc_start: 0.6588 (tpt) cc_final: 0.5692 (ptt) REVERT: n 42 MET cc_start: 0.8085 (tmm) cc_final: 0.7575 (tmm) outliers start: 120 outliers final: 91 residues processed: 694 average time/residue: 0.2902 time to fit residues: 323.3411 Evaluate side-chains 671 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 573 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 9 LYS Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 12 ASP Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 43 MET Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain U residue 65 SER Chi-restraints excluded: chain V residue 30 VAL Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain X residue 65 SER Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 65 SER Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain a residue 9 LYS Chi-restraints excluded: chain a residue 12 ASP Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 60 ILE Chi-restraints excluded: chain c residue 9 LYS Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 43 MET Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 10 SER Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain e residue 61 THR Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 65 SER Chi-restraints excluded: chain h residue 23 SER Chi-restraints excluded: chain h residue 44 THR Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 34 VAL Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain j residue 27 LYS Chi-restraints excluded: chain j residue 34 VAL Chi-restraints excluded: chain j residue 65 SER Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 30 VAL Chi-restraints excluded: chain l residue 39 ILE Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 60 ILE Chi-restraints excluded: chain m residue 61 THR Chi-restraints excluded: chain n residue 23 SER Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 56 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 238 optimal weight: 0.8980 chunk 197 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.8095 moved from start: 0.6221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22427 Z= 0.185 Angle : 0.606 10.439 29725 Z= 0.301 Chirality : 0.039 0.154 3403 Planarity : 0.002 0.017 3321 Dihedral : 14.667 89.650 4633 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 4.08 % Allowed : 23.55 % Favored : 72.37 % 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: 2.32 (0.17), residues: 2624 helix: 1.71 (0.11), residues: 2173 sheet: None (None), residues: 0 loop : 0.96 (0.33), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP T 28 PHE 0.018 0.001 PHE Z 19 TYR 0.014 0.001 TYR c 41 *********************** 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 701 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 614 time to evaluate : 2.360 Fit side-chains revert: symmetry clash REVERT: B 43 MET cc_start: 0.8810 (ttm) cc_final: 0.8360 (mtp) REVERT: D 9 LYS cc_start: 0.8809 (tttt) cc_final: 0.8460 (ttpp) REVERT: D 42 MET cc_start: 0.8265 (tmm) cc_final: 0.8064 (tmm) REVERT: E 21 LYS cc_start: 0.8992 (tptt) cc_final: 0.8635 (tptp) REVERT: F 9 LYS cc_start: 0.8696 (tppt) cc_final: 0.8491 (tppt) REVERT: G 21 LYS cc_start: 0.8404 (tttt) cc_final: 0.7789 (tptt) REVERT: G 23 SER cc_start: 0.8786 (p) cc_final: 0.8528 (p) REVERT: G 41 TYR cc_start: 0.8527 (t80) cc_final: 0.7937 (t80) REVERT: G 64 MET cc_start: 0.8974 (mmt) cc_final: 0.8710 (mmm) REVERT: H 41 TYR cc_start: 0.8931 (t80) cc_final: 0.8600 (t80) REVERT: H 43 MET cc_start: 0.8701 (ttm) cc_final: 0.8103 (mtm) REVERT: I 41 TYR cc_start: 0.8815 (t80) cc_final: 0.8475 (t80) REVERT: L 41 TYR cc_start: 0.8805 (t80) cc_final: 0.7863 (t80) REVERT: M 9 LYS cc_start: 0.8411 (ttpt) cc_final: 0.7852 (tptt) REVERT: M 12 ASP cc_start: 0.9069 (OUTLIER) cc_final: 0.8836 (t0) REVERT: N 22 GLN cc_start: 0.7537 (mm-40) cc_final: 0.7244 (mm-40) REVERT: N 62 ILE cc_start: 0.8910 (mm) cc_final: 0.8509 (mm) REVERT: N 65 SER cc_start: 0.8957 (t) cc_final: 0.8663 (p) REVERT: P 41 TYR cc_start: 0.9082 (t80) cc_final: 0.8686 (t80) REVERT: R 64 MET cc_start: 0.8428 (mmm) cc_final: 0.8041 (mmm) REVERT: T 42 MET cc_start: 0.8644 (ttp) cc_final: 0.8139 (tmm) REVERT: U 41 TYR cc_start: 0.8699 (t80) cc_final: 0.8473 (t80) REVERT: U 64 MET cc_start: 0.8521 (mmt) cc_final: 0.8112 (mmt) REVERT: U 65 SER cc_start: 0.9111 (OUTLIER) cc_final: 0.8819 (p) REVERT: W 40 MET cc_start: 0.8207 (mmt) cc_final: 0.7840 (tpp) REVERT: W 41 TYR cc_start: 0.8897 (t80) cc_final: 0.8593 (t80) REVERT: Z 40 MET cc_start: 0.8333 (mmm) cc_final: 0.7978 (mmm) REVERT: a 9 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8645 (ttmm) REVERT: b 64 MET cc_start: 0.8002 (mmp) cc_final: 0.7630 (mmp) REVERT: c 9 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8467 (ptmt) REVERT: c 64 MET cc_start: 0.8708 (mmt) cc_final: 0.8182 (mmm) REVERT: c 69 TYR cc_start: 0.7593 (m-80) cc_final: 0.7353 (m-80) REVERT: e 65 SER cc_start: 0.9159 (t) cc_final: 0.8771 (p) REVERT: f 21 LYS cc_start: 0.7835 (tttt) cc_final: 0.7389 (tptm) REVERT: g 42 MET cc_start: 0.8347 (tmm) cc_final: 0.7035 (tpt) REVERT: g 65 SER cc_start: 0.9092 (OUTLIER) cc_final: 0.8850 (m) REVERT: h 15 VAL cc_start: 0.8939 (m) cc_final: 0.8735 (p) REVERT: h 42 MET cc_start: 0.8743 (tmm) cc_final: 0.8541 (tmm) REVERT: i 9 LYS cc_start: 0.8807 (tttt) cc_final: 0.8443 (tptt) REVERT: j 12 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7977 (t0) REVERT: j 27 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8454 (mtpp) REVERT: j 42 MET cc_start: 0.8995 (tmm) cc_final: 0.8213 (tmm) REVERT: k 64 MET cc_start: 0.8854 (mmt) cc_final: 0.8361 (mmm) REVERT: l 50 LEU cc_start: 0.9293 (mt) cc_final: 0.9001 (mt) REVERT: n 8 MET cc_start: 0.6423 (tpt) cc_final: 0.5470 (ptt) outliers start: 87 outliers final: 59 residues processed: 672 average time/residue: 0.3166 time to fit residues: 346.0904 Evaluate side-chains 642 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 576 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain U residue 65 SER Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 65 SER Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain a residue 9 LYS Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain c residue 9 LYS Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain d residue 10 SER Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 65 SER Chi-restraints excluded: chain h residue 23 SER Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 34 VAL Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain j residue 27 LYS Chi-restraints excluded: chain k residue 7 LEU Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 39 ILE Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 60 ILE Chi-restraints excluded: chain n residue 29 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 200 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 237 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.8065 moved from start: 0.6489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22427 Z= 0.180 Angle : 0.617 10.887 29725 Z= 0.304 Chirality : 0.039 0.163 3403 Planarity : 0.002 0.019 3321 Dihedral : 14.398 89.940 4633 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.47 % Allowed : 25.61 % Favored : 70.92 % 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: 2.35 (0.17), residues: 2624 helix: 1.79 (0.11), residues: 2173 sheet: None (None), residues: 0 loop : 0.64 (0.32), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 28 PHE 0.023 0.001 PHE f 59 TYR 0.017 0.001 TYR c 41 *********************** 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 672 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 598 time to evaluate : 2.324 Fit side-chains REVERT: D 9 LYS cc_start: 0.8752 (tttt) cc_final: 0.8456 (ttpp) REVERT: E 21 LYS cc_start: 0.8928 (tptt) cc_final: 0.8608 (tptp) REVERT: F 64 MET cc_start: 0.8601 (mmm) cc_final: 0.8228 (mmt) REVERT: G 21 LYS cc_start: 0.8387 (tttt) cc_final: 0.7788 (tptt) REVERT: G 23 SER cc_start: 0.8772 (p) cc_final: 0.8468 (p) REVERT: G 41 TYR cc_start: 0.8509 (t80) cc_final: 0.8076 (t80) REVERT: G 64 MET cc_start: 0.9035 (mmt) cc_final: 0.8729 (mmm) REVERT: H 41 TYR cc_start: 0.8884 (t80) cc_final: 0.8553 (t80) REVERT: H 43 MET cc_start: 0.8745 (ttm) cc_final: 0.8302 (mtm) REVERT: I 41 TYR cc_start: 0.8720 (t80) cc_final: 0.8482 (t80) REVERT: L 41 TYR cc_start: 0.8795 (t80) cc_final: 0.7779 (t80) REVERT: L 42 MET cc_start: 0.8612 (tmm) cc_final: 0.8410 (tmm) REVERT: M 9 LYS cc_start: 0.8445 (ttpt) cc_final: 0.7808 (tptt) REVERT: M 12 ASP cc_start: 0.9058 (OUTLIER) cc_final: 0.8784 (t0) REVERT: N 65 SER cc_start: 0.9121 (t) cc_final: 0.8841 (p) REVERT: P 41 TYR cc_start: 0.8975 (t80) cc_final: 0.8707 (t80) REVERT: Q 8 MET cc_start: 0.8287 (mpp) cc_final: 0.7648 (mpp) REVERT: R 64 MET cc_start: 0.8391 (mmm) cc_final: 0.7993 (mmm) REVERT: S 42 MET cc_start: 0.8591 (tmm) cc_final: 0.8270 (tmm) REVERT: T 42 MET cc_start: 0.8677 (ttp) cc_final: 0.8232 (tmm) REVERT: U 41 TYR cc_start: 0.8616 (t80) cc_final: 0.8398 (t80) REVERT: U 64 MET cc_start: 0.8573 (mmt) cc_final: 0.8264 (mmt) REVERT: U 65 SER cc_start: 0.9067 (t) cc_final: 0.8805 (p) REVERT: W 41 TYR cc_start: 0.8860 (t80) cc_final: 0.8558 (t80) REVERT: X 40 MET cc_start: 0.8821 (mmm) cc_final: 0.8603 (mmm) REVERT: Y 8 MET cc_start: 0.8279 (tpp) cc_final: 0.8030 (tpp) REVERT: Z 64 MET cc_start: 0.8888 (mmt) cc_final: 0.8521 (mmm) REVERT: b 64 MET cc_start: 0.8022 (mmp) cc_final: 0.7678 (mmp) REVERT: c 9 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8335 (ptmt) REVERT: c 64 MET cc_start: 0.8677 (mmt) cc_final: 0.8187 (mmm) REVERT: e 65 SER cc_start: 0.9131 (t) cc_final: 0.8743 (p) REVERT: f 9 LYS cc_start: 0.8571 (tppt) cc_final: 0.8076 (ttmm) REVERT: f 21 LYS cc_start: 0.7812 (tttt) cc_final: 0.7412 (tptt) REVERT: g 65 SER cc_start: 0.9052 (OUTLIER) cc_final: 0.8807 (m) REVERT: i 9 LYS cc_start: 0.8710 (tttt) cc_final: 0.8442 (tptt) REVERT: j 27 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8425 (mtpp) REVERT: j 42 MET cc_start: 0.8931 (tmm) cc_final: 0.7980 (tmm) REVERT: j 55 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8637 (pt) REVERT: k 64 MET cc_start: 0.8945 (mmt) cc_final: 0.8417 (mmm) REVERT: l 42 MET cc_start: 0.8986 (tmm) cc_final: 0.8574 (tmm) REVERT: l 50 LEU cc_start: 0.9280 (mt) cc_final: 0.8975 (mt) REVERT: n 8 MET cc_start: 0.6400 (tpt) cc_final: 0.5612 (ptt) REVERT: n 42 MET cc_start: 0.7716 (tmm) cc_final: 0.7228 (tmm) outliers start: 74 outliers final: 53 residues processed: 649 average time/residue: 0.2835 time to fit residues: 295.7293 Evaluate side-chains 628 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 570 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 65 SER Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain c residue 9 LYS Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 65 SER Chi-restraints excluded: chain h residue 23 SER Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain j residue 27 LYS Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 65 SER Chi-restraints excluded: chain k residue 7 LEU Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 60 ILE Chi-restraints excluded: chain n residue 29 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 141 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 150 optimal weight: 30.0000 chunk 161 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 186 optimal weight: 20.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8035 moved from start: 0.6688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22427 Z= 0.177 Angle : 0.638 11.711 29725 Z= 0.310 Chirality : 0.038 0.166 3403 Planarity : 0.002 0.022 3321 Dihedral : 14.197 89.750 4633 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.19 % Allowed : 25.98 % Favored : 70.83 % 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: 2.38 (0.17), residues: 2624 helix: 1.86 (0.11), residues: 2173 sheet: None (None), residues: 0 loop : 0.35 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 28 PHE 0.016 0.001 PHE H 19 TYR 0.014 0.001 TYR X 41 *********************** 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 661 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 593 time to evaluate : 2.213 Fit side-chains REVERT: C 43 MET cc_start: 0.8027 (mmm) cc_final: 0.7695 (mmm) REVERT: D 9 LYS cc_start: 0.8731 (tttt) cc_final: 0.8446 (ttpp) REVERT: E 21 LYS cc_start: 0.8844 (tptt) cc_final: 0.8549 (tptp) REVERT: F 64 MET cc_start: 0.8545 (mmm) cc_final: 0.8195 (mmt) REVERT: G 21 LYS cc_start: 0.8343 (tttt) cc_final: 0.7771 (tptt) REVERT: G 23 SER cc_start: 0.8758 (p) cc_final: 0.8437 (p) REVERT: G 41 TYR cc_start: 0.8482 (t80) cc_final: 0.8145 (t80) REVERT: G 64 MET cc_start: 0.8990 (mmt) cc_final: 0.8735 (mmm) REVERT: H 16 LYS cc_start: 0.8916 (ttpp) cc_final: 0.8533 (ttpt) REVERT: H 41 TYR cc_start: 0.8867 (t80) cc_final: 0.8515 (t80) REVERT: H 43 MET cc_start: 0.8759 (ttm) cc_final: 0.8431 (mtt) REVERT: I 64 MET cc_start: 0.8657 (mmt) cc_final: 0.8354 (mmp) REVERT: L 41 TYR cc_start: 0.8799 (t80) cc_final: 0.7782 (t80) REVERT: L 42 MET cc_start: 0.8562 (tmm) cc_final: 0.8337 (tmm) REVERT: M 12 ASP cc_start: 0.9054 (OUTLIER) cc_final: 0.8823 (t0) REVERT: N 65 SER cc_start: 0.9115 (t) cc_final: 0.8863 (p) REVERT: O 41 TYR cc_start: 0.9145 (t80) cc_final: 0.8857 (t80) REVERT: Q 8 MET cc_start: 0.8317 (mpp) cc_final: 0.7697 (mpp) REVERT: R 40 MET cc_start: 0.8620 (tpp) cc_final: 0.8395 (tpp) REVERT: R 64 MET cc_start: 0.8390 (mmm) cc_final: 0.7955 (mmm) REVERT: S 42 MET cc_start: 0.8596 (tmm) cc_final: 0.8369 (tmm) REVERT: T 42 MET cc_start: 0.8552 (ttp) cc_final: 0.8142 (tmm) REVERT: U 41 TYR cc_start: 0.8529 (t80) cc_final: 0.8323 (t80) REVERT: U 65 SER cc_start: 0.9038 (t) cc_final: 0.8826 (p) REVERT: W 41 TYR cc_start: 0.8814 (t80) cc_final: 0.8525 (t80) REVERT: X 40 MET cc_start: 0.8812 (mmm) cc_final: 0.8596 (mmm) REVERT: Y 41 TYR cc_start: 0.8886 (t80) cc_final: 0.8678 (t80) REVERT: Z 40 MET cc_start: 0.8154 (mmm) cc_final: 0.7781 (mmm) REVERT: Z 41 TYR cc_start: 0.9043 (t80) cc_final: 0.8383 (t80) REVERT: Z 64 MET cc_start: 0.8900 (mmt) cc_final: 0.8665 (mmm) REVERT: b 64 MET cc_start: 0.8016 (mmp) cc_final: 0.7727 (mmp) REVERT: c 9 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8257 (ptmt) REVERT: c 64 MET cc_start: 0.8704 (mmt) cc_final: 0.8218 (mmm) REVERT: e 65 SER cc_start: 0.9142 (t) cc_final: 0.8762 (p) REVERT: f 9 LYS cc_start: 0.8516 (tppt) cc_final: 0.8220 (ttmm) REVERT: f 21 LYS cc_start: 0.7833 (tttt) cc_final: 0.7309 (tptt) REVERT: g 65 SER cc_start: 0.9003 (OUTLIER) cc_final: 0.8741 (m) REVERT: i 9 LYS cc_start: 0.8585 (tttt) cc_final: 0.8341 (tptt) REVERT: j 55 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8647 (pt) REVERT: k 64 MET cc_start: 0.8906 (mmt) cc_final: 0.8382 (mmm) REVERT: l 42 MET cc_start: 0.8902 (tmm) cc_final: 0.8506 (tmm) REVERT: l 50 LEU cc_start: 0.9257 (mt) cc_final: 0.8955 (mt) REVERT: n 8 MET cc_start: 0.6525 (tpt) cc_final: 0.5784 (ptt) REVERT: n 42 MET cc_start: 0.7611 (tmm) cc_final: 0.7257 (tmm) outliers start: 68 outliers final: 56 residues processed: 639 average time/residue: 0.2880 time to fit residues: 295.8373 Evaluate side-chains 626 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 566 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 65 SER Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 8 MET Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 65 SER Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain c residue 9 LYS Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 65 SER Chi-restraints excluded: chain h residue 23 SER Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 65 SER Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 55 ILE Chi-restraints excluded: chain n residue 29 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 215 optimal weight: 5.9990 chunk 227 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 220 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 199 optimal weight: 3.9990 chunk 208 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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: 0.8071 moved from start: 0.6735 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= 0.204 Angle : 0.681 12.861 29725 Z= 0.327 Chirality : 0.039 0.214 3403 Planarity : 0.002 0.020 3321 Dihedral : 14.261 88.491 4633 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.10 % Allowed : 26.22 % Favored : 70.68 % 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: 2.38 (0.17), residues: 2624 helix: 1.88 (0.11), residues: 2173 sheet: None (None), residues: 0 loop : 0.24 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP T 28 PHE 0.027 0.001 PHE f 59 TYR 0.018 0.001 TYR c 41 *********************** 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 641 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 575 time to evaluate : 2.191 Fit side-chains REVERT: C 43 MET cc_start: 0.8045 (mmm) cc_final: 0.7585 (mmm) REVERT: D 9 LYS cc_start: 0.8732 (tttt) cc_final: 0.8450 (ttpp) REVERT: D 64 MET cc_start: 0.9148 (mmt) cc_final: 0.8931 (mmm) REVERT: E 21 LYS cc_start: 0.8867 (tptt) cc_final: 0.8563 (tptp) REVERT: F 64 MET cc_start: 0.8579 (mmm) cc_final: 0.8191 (mmt) REVERT: G 21 LYS cc_start: 0.8402 (tttt) cc_final: 0.7899 (tptt) REVERT: G 23 SER cc_start: 0.8779 (p) cc_final: 0.8455 (p) REVERT: G 41 TYR cc_start: 0.8514 (t80) cc_final: 0.8080 (t80) REVERT: G 64 MET cc_start: 0.9026 (mmt) cc_final: 0.8762 (mmm) REVERT: H 16 LYS cc_start: 0.8921 (ttpp) cc_final: 0.8560 (ttpt) REVERT: H 41 TYR cc_start: 0.8908 (t80) cc_final: 0.8663 (t80) REVERT: H 43 MET cc_start: 0.8729 (ttm) cc_final: 0.8295 (mtm) REVERT: I 64 MET cc_start: 0.8691 (mmt) cc_final: 0.8393 (mmp) REVERT: K 41 TYR cc_start: 0.9022 (t80) cc_final: 0.8546 (t80) REVERT: L 41 TYR cc_start: 0.8809 (t80) cc_final: 0.7806 (t80) REVERT: M 12 ASP cc_start: 0.9066 (OUTLIER) cc_final: 0.8854 (t0) REVERT: N 62 ILE cc_start: 0.8404 (mm) cc_final: 0.8119 (mm) REVERT: N 65 SER cc_start: 0.9128 (t) cc_final: 0.8839 (p) REVERT: P 40 MET cc_start: 0.8685 (mmm) cc_final: 0.8265 (mmm) REVERT: Q 8 MET cc_start: 0.8391 (mpp) cc_final: 0.7719 (mpp) REVERT: R 42 MET cc_start: 0.8753 (tmm) cc_final: 0.8475 (tmm) REVERT: R 64 MET cc_start: 0.8412 (mmm) cc_final: 0.7945 (mmm) REVERT: S 42 MET cc_start: 0.8596 (tmm) cc_final: 0.8357 (tmm) REVERT: T 42 MET cc_start: 0.8631 (ttp) cc_final: 0.8137 (tmm) REVERT: U 41 TYR cc_start: 0.8594 (t80) cc_final: 0.8384 (t80) REVERT: W 41 TYR cc_start: 0.8867 (t80) cc_final: 0.8528 (t80) REVERT: X 40 MET cc_start: 0.8834 (mmm) cc_final: 0.8598 (mmm) REVERT: Y 8 MET cc_start: 0.8284 (tpp) cc_final: 0.7969 (tpp) REVERT: Z 40 MET cc_start: 0.8243 (mmm) cc_final: 0.7906 (mmm) REVERT: Z 64 MET cc_start: 0.8886 (mmt) cc_final: 0.8503 (mmm) REVERT: b 64 MET cc_start: 0.8070 (mmp) cc_final: 0.7815 (mmp) REVERT: c 9 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8303 (ptmt) REVERT: e 65 SER cc_start: 0.9164 (t) cc_final: 0.8771 (p) REVERT: f 9 LYS cc_start: 0.8536 (tppt) cc_final: 0.8223 (ttmm) REVERT: g 65 SER cc_start: 0.9003 (OUTLIER) cc_final: 0.8746 (m) REVERT: j 22 GLN cc_start: 0.8094 (mp10) cc_final: 0.7817 (mp10) REVERT: j 55 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8691 (pt) REVERT: k 64 MET cc_start: 0.8930 (mmt) cc_final: 0.8421 (mmm) REVERT: l 42 MET cc_start: 0.8900 (tmm) cc_final: 0.8485 (tmm) REVERT: l 50 LEU cc_start: 0.9245 (mt) cc_final: 0.8953 (mt) REVERT: n 8 MET cc_start: 0.6452 (tpt) cc_final: 0.5695 (ptt) outliers start: 66 outliers final: 54 residues processed: 622 average time/residue: 0.2830 time to fit residues: 283.7307 Evaluate side-chains 617 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 559 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 65 SER Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 8 MET Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 65 SER Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain c residue 9 LYS Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 65 SER Chi-restraints excluded: chain h residue 23 SER Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 65 SER Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 60 ILE Chi-restraints excluded: chain n residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 162 optimal weight: 40.0000 chunk 245 optimal weight: 0.8980 chunk 225 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 150 optimal weight: 30.0000 chunk 119 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8029 moved from start: 0.6915 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= 0.185 Angle : 0.703 15.030 29725 Z= 0.333 Chirality : 0.038 0.161 3403 Planarity : 0.002 0.025 3321 Dihedral : 14.146 88.284 4633 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.39 % Allowed : 26.59 % Favored : 71.01 % 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: 2.40 (0.16), residues: 2624 helix: 1.92 (0.11), residues: 2173 sheet: None (None), residues: 0 loop : 0.10 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Z 28 PHE 0.017 0.001 PHE Z 19 TYR 0.013 0.001 TYR Z 41 ********************** 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 635 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 584 time to evaluate : 2.113 Fit side-chains REVERT: C 43 MET cc_start: 0.8079 (mmm) cc_final: 0.7620 (mmm) REVERT: D 9 LYS cc_start: 0.8703 (tttt) cc_final: 0.8447 (ttpp) REVERT: E 21 LYS cc_start: 0.8800 (tptt) cc_final: 0.8533 (tptp) REVERT: F 64 MET cc_start: 0.8468 (mmm) cc_final: 0.8101 (mmt) REVERT: G 21 LYS cc_start: 0.8394 (tttt) cc_final: 0.7893 (tptt) REVERT: G 41 TYR cc_start: 0.8445 (t80) cc_final: 0.8150 (t80) REVERT: G 64 MET cc_start: 0.8999 (mmt) cc_final: 0.8729 (mmm) REVERT: H 16 LYS cc_start: 0.8928 (ttpp) cc_final: 0.8544 (ttpt) REVERT: H 41 TYR cc_start: 0.8863 (t80) cc_final: 0.8542 (t80) REVERT: H 43 MET cc_start: 0.8745 (ttm) cc_final: 0.8387 (mtt) REVERT: K 41 TYR cc_start: 0.8993 (t80) cc_final: 0.8582 (t80) REVERT: L 41 TYR cc_start: 0.8866 (t80) cc_final: 0.7952 (t80) REVERT: M 40 MET cc_start: 0.8710 (tpp) cc_final: 0.8067 (mmm) REVERT: N 62 ILE cc_start: 0.8359 (mm) cc_final: 0.8037 (mm) REVERT: N 65 SER cc_start: 0.9114 (t) cc_final: 0.8834 (p) REVERT: P 40 MET cc_start: 0.8653 (mmm) cc_final: 0.8231 (mmm) REVERT: Q 8 MET cc_start: 0.8390 (mpp) cc_final: 0.7780 (mpp) REVERT: Q 40 MET cc_start: 0.8417 (tpp) cc_final: 0.8027 (mmt) REVERT: R 40 MET cc_start: 0.8598 (tpp) cc_final: 0.8370 (tpp) REVERT: R 64 MET cc_start: 0.8397 (mmm) cc_final: 0.7901 (mmm) REVERT: S 26 VAL cc_start: 0.8693 (t) cc_final: 0.8434 (t) REVERT: S 33 GLU cc_start: 0.8287 (tm-30) cc_final: 0.8064 (tm-30) REVERT: S 42 MET cc_start: 0.8584 (tmm) cc_final: 0.8350 (tmm) REVERT: T 42 MET cc_start: 0.8566 (ttp) cc_final: 0.8083 (tmm) REVERT: W 41 TYR cc_start: 0.8822 (t80) cc_final: 0.8532 (t80) REVERT: X 40 MET cc_start: 0.8824 (mmm) cc_final: 0.8592 (mmm) REVERT: Y 8 MET cc_start: 0.8230 (tpp) cc_final: 0.7962 (tpp) REVERT: Z 40 MET cc_start: 0.8209 (mmm) cc_final: 0.7882 (mmm) REVERT: Z 41 TYR cc_start: 0.9071 (t80) cc_final: 0.8523 (t80) REVERT: Z 64 MET cc_start: 0.8865 (mmt) cc_final: 0.8422 (mmm) REVERT: b 40 MET cc_start: 0.9096 (mmp) cc_final: 0.8870 (mmp) REVERT: b 64 MET cc_start: 0.8004 (mmp) cc_final: 0.7741 (mmp) REVERT: c 9 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8253 (ptmt) REVERT: c 64 MET cc_start: 0.8675 (mmt) cc_final: 0.8188 (mmm) REVERT: e 65 SER cc_start: 0.9145 (t) cc_final: 0.8747 (p) REVERT: f 9 LYS cc_start: 0.8533 (tppt) cc_final: 0.8256 (ttmm) REVERT: j 22 GLN cc_start: 0.7924 (mp10) cc_final: 0.7639 (mp10) REVERT: j 42 MET cc_start: 0.8532 (tmm) cc_final: 0.8212 (tmm) REVERT: j 55 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8581 (pt) REVERT: k 64 MET cc_start: 0.8887 (mmt) cc_final: 0.8631 (mmm) REVERT: l 42 MET cc_start: 0.8863 (tmm) cc_final: 0.8493 (tmm) REVERT: l 50 LEU cc_start: 0.9226 (mt) cc_final: 0.8945 (mt) REVERT: n 8 MET cc_start: 0.6489 (tpt) cc_final: 0.5740 (ptt) outliers start: 51 outliers final: 44 residues processed: 619 average time/residue: 0.2831 time to fit residues: 282.1361 Evaluate side-chains 615 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 569 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 65 SER Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 8 MET Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain c residue 9 LYS Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 65 SER Chi-restraints excluded: chain h residue 23 SER Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 65 SER Chi-restraints excluded: chain k residue 7 LEU Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain n residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 30.0000 chunk 195 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 36 optimal weight: 0.0980 chunk 171 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.125087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.109060 restraints weight = 29537.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.112436 restraints weight = 13987.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.114438 restraints weight = 7808.638| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.7044 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= 0.182 Angle : 0.706 18.558 29725 Z= 0.335 Chirality : 0.038 0.164 3403 Planarity : 0.002 0.028 3321 Dihedral : 14.087 87.358 4633 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.49 % Allowed : 26.78 % Favored : 70.73 % 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: 2.43 (0.16), residues: 2624 helix: 1.97 (0.11), residues: 2173 sheet: None (None), residues: 0 loop : -0.07 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 28 PHE 0.023 0.001 PHE Y 19 TYR 0.017 0.001 TYR I 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5311.64 seconds wall clock time: 97 minutes 10.01 seconds (5830.01 seconds total)