Starting phenix.real_space_refine on Sun Mar 10 14:42:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7g_8780/03_2024/5w7g_8780.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7g_8780/03_2024/5w7g_8780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7g_8780/03_2024/5w7g_8780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7g_8780/03_2024/5w7g_8780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7g_8780/03_2024/5w7g_8780.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7g_8780/03_2024/5w7g_8780.pdb" } resolution = 4.5 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= 0.059 sd= 0.149 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 504 5.49 5 S 189 5.16 5 C 32424 2.51 5 N 8946 2.21 5 O 11445 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 53508 Number of models: 1 Model: "" Number of chains: 44 Chain: "A" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1054 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "B" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "C" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1054 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "D" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "E" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1054 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "F" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "G" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1054 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "H" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "I" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1054 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "J" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "K" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1054 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "L" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "M" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1054 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "N" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "O" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1054 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "P" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "Q" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1054 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "R" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "S" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1054 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "T" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "U" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1054 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "V" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "W" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1054 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "X" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "Y" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1054 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "Z" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "a" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1054 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "b" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "c" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1054 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "d" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "e" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1054 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "f" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "g" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1054 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "h" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "i" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1054 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "j" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "k" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1054 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "l" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "m" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1054 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "n" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "o" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1054 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "p" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "q" Number of atoms: 5166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 5166 Classifications: {'DNA': 252} Link IDs: {'rna3p': 251} Chain: "r" Number of atoms: 5166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 5166 Classifications: {'DNA': 252} Link IDs: {'rna3p': 251} Time building chain proxies: 20.21, per 1000 atoms: 0.38 Number of scatterers: 53508 At special positions: 0 Unit cell: (155.4, 155.4, 154.35, 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 189 16.00 P 504 15.00 O 11445 8.00 N 8946 7.00 C 32424 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: 18.95 Conformation dependent library (CDL) restraints added in 6.1 seconds 10626 Ramachandran restraints generated. 5313 Oldfield, 0 Emsley, 5313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10290 Finding SS restraints... Secondary structure from input PDB file: 273 helices and 0 sheets defined 90.3% alpha, 0.0% beta 231 base pairs and 415 stacking pairs defined. Time for finding SS restraints: 14.15 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 Processing helix chain 'A' and resid 11 through 26 Processing helix chain 'A' and resid 30 through 67 Processing helix chain 'A' and resid 70 through 95 removed outlier: 4.533A pdb=" N ILE A 75 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY A 76 " --> pdb=" O GLU A 72 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A 77 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 111 Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 118 through 132 Processing helix chain 'B' and resid 10 through 25 removed outlier: 3.578A pdb=" N GLN B 18 " --> pdb=" O TYR B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 66 removed outlier: 4.298A pdb=" N THR B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 71 through 93 removed outlier: 3.714A pdb=" N LYS B 90 " --> pdb=" O TYR B 86 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 109 Processing helix chain 'B' and resid 109 through 114 Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'C' and resid 7 through 11 Processing helix chain 'C' and resid 11 through 26 Processing helix chain 'C' and resid 30 through 67 Processing helix chain 'C' and resid 70 through 95 removed outlier: 4.533A pdb=" N ILE C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLY C 76 " --> pdb=" O GLU C 72 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR C 77 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 111 Processing helix chain 'C' and resid 112 through 114 No H-bonds generated for 'chain 'C' and resid 112 through 114' Processing helix chain 'C' and resid 118 through 132 Processing helix chain 'D' and resid 10 through 25 removed outlier: 3.577A pdb=" N GLN D 18 " --> pdb=" O TYR D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 66 removed outlier: 4.298A pdb=" N THR D 35 " --> pdb=" O GLU D 31 " (cutoff:3.500A) Proline residue: D 50 - end of helix Processing helix chain 'D' and resid 71 through 93 removed outlier: 3.714A pdb=" N LYS D 90 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA D 91 " --> pdb=" O LEU D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 109 Processing helix chain 'D' and resid 109 through 114 Processing helix chain 'D' and resid 117 through 130 Processing helix chain 'E' and resid 7 through 11 Processing helix chain 'E' and resid 11 through 26 Processing helix chain 'E' and resid 30 through 67 Processing helix chain 'E' and resid 70 through 95 removed outlier: 4.533A pdb=" N ILE E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLY E 76 " --> pdb=" O GLU E 72 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR E 77 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 111 Processing helix chain 'E' and resid 112 through 114 No H-bonds generated for 'chain 'E' and resid 112 through 114' Processing helix chain 'E' and resid 118 through 132 Processing helix chain 'F' and resid 10 through 25 removed outlier: 3.577A pdb=" N GLN F 18 " --> pdb=" O TYR F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 66 removed outlier: 4.298A pdb=" N THR F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) Proline residue: F 50 - end of helix Processing helix chain 'F' and resid 71 through 93 removed outlier: 3.714A pdb=" N LYS F 90 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA F 91 " --> pdb=" O LEU F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 109 Processing helix chain 'F' and resid 109 through 114 Processing helix chain 'F' and resid 117 through 130 Processing helix chain 'G' and resid 7 through 11 Processing helix chain 'G' and resid 11 through 26 Processing helix chain 'G' and resid 30 through 67 Processing helix chain 'G' and resid 70 through 95 removed outlier: 4.533A pdb=" N ILE G 75 " --> pdb=" O THR G 71 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLY G 76 " --> pdb=" O GLU G 72 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR G 77 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 111 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 118 through 132 Processing helix chain 'H' and resid 10 through 25 removed outlier: 3.578A pdb=" N GLN H 18 " --> pdb=" O TYR H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 66 removed outlier: 4.299A pdb=" N THR H 35 " --> pdb=" O GLU H 31 " (cutoff:3.500A) Proline residue: H 50 - end of helix Processing helix chain 'H' and resid 71 through 93 removed outlier: 3.714A pdb=" N LYS H 90 " --> pdb=" O TYR H 86 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA H 91 " --> pdb=" O LEU H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 109 Processing helix chain 'H' and resid 109 through 114 Processing helix chain 'H' and resid 117 through 130 Processing helix chain 'I' and resid 7 through 11 Processing helix chain 'I' and resid 11 through 26 Processing helix chain 'I' and resid 30 through 67 Processing helix chain 'I' and resid 70 through 95 removed outlier: 4.533A pdb=" N ILE I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLY I 76 " --> pdb=" O GLU I 72 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR I 77 " --> pdb=" O ASP I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 111 Processing helix chain 'I' and resid 112 through 114 No H-bonds generated for 'chain 'I' and resid 112 through 114' Processing helix chain 'I' and resid 118 through 132 Processing helix chain 'J' and resid 10 through 25 removed outlier: 3.577A pdb=" N GLN J 18 " --> pdb=" O TYR J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 66 removed outlier: 4.299A pdb=" N THR J 35 " --> pdb=" O GLU J 31 " (cutoff:3.500A) Proline residue: J 50 - end of helix Processing helix chain 'J' and resid 71 through 93 removed outlier: 3.713A pdb=" N LYS J 90 " --> pdb=" O TYR J 86 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA J 91 " --> pdb=" O LEU J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 109 Processing helix chain 'J' and resid 109 through 114 Processing helix chain 'J' and resid 117 through 130 Processing helix chain 'K' and resid 7 through 11 Processing helix chain 'K' and resid 11 through 26 Processing helix chain 'K' and resid 30 through 67 Processing helix chain 'K' and resid 70 through 95 removed outlier: 4.533A pdb=" N ILE K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLY K 76 " --> pdb=" O GLU K 72 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR K 77 " --> pdb=" O ASP K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 111 Processing helix chain 'K' and resid 112 through 114 No H-bonds generated for 'chain 'K' and resid 112 through 114' Processing helix chain 'K' and resid 118 through 132 Processing helix chain 'L' and resid 10 through 25 removed outlier: 3.578A pdb=" N GLN L 18 " --> pdb=" O TYR L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 66 removed outlier: 4.298A pdb=" N THR L 35 " --> pdb=" O GLU L 31 " (cutoff:3.500A) Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 71 through 93 removed outlier: 3.714A pdb=" N LYS L 90 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA L 91 " --> pdb=" O LEU L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 109 Processing helix chain 'L' and resid 109 through 114 Processing helix chain 'L' and resid 117 through 130 Processing helix chain 'M' and resid 7 through 11 Processing helix chain 'M' and resid 11 through 26 Processing helix chain 'M' and resid 30 through 67 Processing helix chain 'M' and resid 70 through 95 removed outlier: 4.534A pdb=" N ILE M 75 " --> pdb=" O THR M 71 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY M 76 " --> pdb=" O GLU M 72 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR M 77 " --> pdb=" O ASP M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 111 Processing helix chain 'M' and resid 112 through 114 No H-bonds generated for 'chain 'M' and resid 112 through 114' Processing helix chain 'M' and resid 118 through 132 Processing helix chain 'N' and resid 10 through 25 removed outlier: 3.577A pdb=" N GLN N 18 " --> pdb=" O TYR N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 66 removed outlier: 4.298A pdb=" N THR N 35 " --> pdb=" O GLU N 31 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 71 through 93 removed outlier: 3.713A pdb=" N LYS N 90 " --> pdb=" O TYR N 86 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA N 91 " --> pdb=" O LEU N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 109 Processing helix chain 'N' and resid 109 through 114 Processing helix chain 'N' and resid 117 through 130 Processing helix chain 'O' and resid 7 through 11 Processing helix chain 'O' and resid 11 through 26 Processing helix chain 'O' and resid 30 through 67 Processing helix chain 'O' and resid 70 through 95 removed outlier: 4.533A pdb=" N ILE O 75 " --> pdb=" O THR O 71 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLY O 76 " --> pdb=" O GLU O 72 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR O 77 " --> pdb=" O ASP O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 96 through 111 Processing helix chain 'O' and resid 112 through 114 No H-bonds generated for 'chain 'O' and resid 112 through 114' Processing helix chain 'O' and resid 118 through 132 Processing helix chain 'P' and resid 10 through 25 removed outlier: 3.577A pdb=" N GLN P 18 " --> pdb=" O TYR P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 66 removed outlier: 4.298A pdb=" N THR P 35 " --> pdb=" O GLU P 31 " (cutoff:3.500A) Proline residue: P 50 - end of helix Processing helix chain 'P' and resid 71 through 93 removed outlier: 3.713A pdb=" N LYS P 90 " --> pdb=" O TYR P 86 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 109 Processing helix chain 'P' and resid 109 through 114 Processing helix chain 'P' and resid 117 through 130 Processing helix chain 'Q' and resid 7 through 11 Processing helix chain 'Q' and resid 11 through 26 Processing helix chain 'Q' and resid 30 through 67 Processing helix chain 'Q' and resid 70 through 95 removed outlier: 4.533A pdb=" N ILE Q 75 " --> pdb=" O THR Q 71 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY Q 76 " --> pdb=" O GLU Q 72 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR Q 77 " --> pdb=" O ASP Q 73 " (cutoff:3.500A) Processing helix chain 'Q' and resid 96 through 111 Processing helix chain 'Q' and resid 112 through 114 No H-bonds generated for 'chain 'Q' and resid 112 through 114' Processing helix chain 'Q' and resid 118 through 132 Processing helix chain 'R' and resid 10 through 25 removed outlier: 3.577A pdb=" N GLN R 18 " --> pdb=" O TYR R 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 66 removed outlier: 4.299A pdb=" N THR R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) Proline residue: R 50 - end of helix Processing helix chain 'R' and resid 71 through 93 removed outlier: 3.713A pdb=" N LYS R 90 " --> pdb=" O TYR R 86 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA R 91 " --> pdb=" O LEU R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 109 Processing helix chain 'R' and resid 109 through 114 Processing helix chain 'R' and resid 117 through 130 Processing helix chain 'S' and resid 7 through 11 Processing helix chain 'S' and resid 11 through 26 Processing helix chain 'S' and resid 30 through 67 Processing helix chain 'S' and resid 70 through 95 removed outlier: 4.533A pdb=" N ILE S 75 " --> pdb=" O THR S 71 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY S 76 " --> pdb=" O GLU S 72 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR S 77 " --> pdb=" O ASP S 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 96 through 111 Processing helix chain 'S' and resid 112 through 114 No H-bonds generated for 'chain 'S' and resid 112 through 114' Processing helix chain 'S' and resid 118 through 132 Processing helix chain 'T' and resid 10 through 25 removed outlier: 3.577A pdb=" N GLN T 18 " --> pdb=" O TYR T 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 66 removed outlier: 4.298A pdb=" N THR T 35 " --> pdb=" O GLU T 31 " (cutoff:3.500A) Proline residue: T 50 - end of helix Processing helix chain 'T' and resid 71 through 93 removed outlier: 3.714A pdb=" N LYS T 90 " --> pdb=" O TYR T 86 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA T 91 " --> pdb=" O LEU T 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 94 through 109 Processing helix chain 'T' and resid 109 through 114 Processing helix chain 'T' and resid 117 through 130 Processing helix chain 'U' and resid 7 through 11 Processing helix chain 'U' and resid 11 through 26 Processing helix chain 'U' and resid 30 through 67 Processing helix chain 'U' and resid 70 through 95 removed outlier: 4.533A pdb=" N ILE U 75 " --> pdb=" O THR U 71 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLY U 76 " --> pdb=" O GLU U 72 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR U 77 " --> pdb=" O ASP U 73 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 111 Processing helix chain 'U' and resid 112 through 114 No H-bonds generated for 'chain 'U' and resid 112 through 114' Processing helix chain 'U' and resid 118 through 132 Processing helix chain 'V' and resid 10 through 25 removed outlier: 3.578A pdb=" N GLN V 18 " --> pdb=" O TYR V 14 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 66 removed outlier: 4.298A pdb=" N THR V 35 " --> pdb=" O GLU V 31 " (cutoff:3.500A) Proline residue: V 50 - end of helix Processing helix chain 'V' and resid 71 through 93 removed outlier: 3.714A pdb=" N LYS V 90 " --> pdb=" O TYR V 86 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA V 91 " --> pdb=" O LEU V 87 " (cutoff:3.500A) Processing helix chain 'V' and resid 94 through 109 Processing helix chain 'V' and resid 109 through 114 Processing helix chain 'V' and resid 117 through 130 Processing helix chain 'W' and resid 7 through 11 Processing helix chain 'W' and resid 11 through 26 Processing helix chain 'W' and resid 30 through 67 Processing helix chain 'W' and resid 70 through 95 removed outlier: 4.533A pdb=" N ILE W 75 " --> pdb=" O THR W 71 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLY W 76 " --> pdb=" O GLU W 72 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR W 77 " --> pdb=" O ASP W 73 " (cutoff:3.500A) Processing helix chain 'W' and resid 96 through 111 Processing helix chain 'W' and resid 112 through 114 No H-bonds generated for 'chain 'W' and resid 112 through 114' Processing helix chain 'W' and resid 118 through 132 Processing helix chain 'X' and resid 10 through 25 removed outlier: 3.577A pdb=" N GLN X 18 " --> pdb=" O TYR X 14 " (cutoff:3.500A) Processing helix chain 'X' and resid 29 through 66 removed outlier: 4.299A pdb=" N THR X 35 " --> pdb=" O GLU X 31 " (cutoff:3.500A) Proline residue: X 50 - end of helix Processing helix chain 'X' and resid 71 through 93 removed outlier: 3.714A pdb=" N LYS X 90 " --> pdb=" O TYR X 86 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA X 91 " --> pdb=" O LEU X 87 " (cutoff:3.500A) Processing helix chain 'X' and resid 94 through 109 Processing helix chain 'X' and resid 109 through 114 Processing helix chain 'X' and resid 117 through 130 Processing helix chain 'Y' and resid 7 through 11 Processing helix chain 'Y' and resid 11 through 26 Processing helix chain 'Y' and resid 30 through 67 Processing helix chain 'Y' and resid 70 through 95 removed outlier: 4.533A pdb=" N ILE Y 75 " --> pdb=" O THR Y 71 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY Y 76 " --> pdb=" O GLU Y 72 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR Y 77 " --> pdb=" O ASP Y 73 " (cutoff:3.500A) Processing helix chain 'Y' and resid 96 through 111 Processing helix chain 'Y' and resid 112 through 114 No H-bonds generated for 'chain 'Y' and resid 112 through 114' Processing helix chain 'Y' and resid 118 through 132 Processing helix chain 'Z' and resid 10 through 25 removed outlier: 3.578A pdb=" N GLN Z 18 " --> pdb=" O TYR Z 14 " (cutoff:3.500A) Processing helix chain 'Z' and resid 29 through 66 removed outlier: 4.298A pdb=" N THR Z 35 " --> pdb=" O GLU Z 31 " (cutoff:3.500A) Proline residue: Z 50 - end of helix Processing helix chain 'Z' and resid 71 through 93 removed outlier: 3.713A pdb=" N LYS Z 90 " --> pdb=" O TYR Z 86 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA Z 91 " --> pdb=" O LEU Z 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 94 through 109 Processing helix chain 'Z' and resid 109 through 114 Processing helix chain 'Z' and resid 117 through 130 Processing helix chain 'a' and resid 7 through 11 Processing helix chain 'a' and resid 11 through 26 Processing helix chain 'a' and resid 30 through 67 Processing helix chain 'a' and resid 70 through 95 removed outlier: 4.534A pdb=" N ILE a 75 " --> pdb=" O THR a 71 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY a 76 " --> pdb=" O GLU a 72 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR a 77 " --> pdb=" O ASP a 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 96 through 111 Processing helix chain 'a' and resid 112 through 114 No H-bonds generated for 'chain 'a' and resid 112 through 114' Processing helix chain 'a' and resid 118 through 132 Processing helix chain 'b' and resid 10 through 25 removed outlier: 3.578A pdb=" N GLN b 18 " --> pdb=" O TYR b 14 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 66 removed outlier: 4.298A pdb=" N THR b 35 " --> pdb=" O GLU b 31 " (cutoff:3.500A) Proline residue: b 50 - end of helix Processing helix chain 'b' and resid 71 through 93 removed outlier: 3.713A pdb=" N LYS b 90 " --> pdb=" O TYR b 86 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA b 91 " --> pdb=" O LEU b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 94 through 109 Processing helix chain 'b' and resid 109 through 114 Processing helix chain 'b' and resid 117 through 130 Processing helix chain 'c' and resid 7 through 11 Processing helix chain 'c' and resid 11 through 26 Processing helix chain 'c' and resid 30 through 67 Processing helix chain 'c' and resid 70 through 95 removed outlier: 4.533A pdb=" N ILE c 75 " --> pdb=" O THR c 71 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY c 76 " --> pdb=" O GLU c 72 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR c 77 " --> pdb=" O ASP c 73 " (cutoff:3.500A) Processing helix chain 'c' and resid 96 through 111 Processing helix chain 'c' and resid 112 through 114 No H-bonds generated for 'chain 'c' and resid 112 through 114' Processing helix chain 'c' and resid 118 through 132 Processing helix chain 'd' and resid 10 through 25 removed outlier: 3.578A pdb=" N GLN d 18 " --> pdb=" O TYR d 14 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 66 removed outlier: 4.298A pdb=" N THR d 35 " --> pdb=" O GLU d 31 " (cutoff:3.500A) Proline residue: d 50 - end of helix Processing helix chain 'd' and resid 71 through 93 removed outlier: 3.713A pdb=" N LYS d 90 " --> pdb=" O TYR d 86 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA d 91 " --> pdb=" O LEU d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 109 Processing helix chain 'd' and resid 109 through 114 Processing helix chain 'd' and resid 117 through 130 Processing helix chain 'e' and resid 7 through 11 Processing helix chain 'e' and resid 11 through 26 Processing helix chain 'e' and resid 30 through 67 Processing helix chain 'e' and resid 70 through 95 removed outlier: 4.533A pdb=" N ILE e 75 " --> pdb=" O THR e 71 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLY e 76 " --> pdb=" O GLU e 72 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR e 77 " --> pdb=" O ASP e 73 " (cutoff:3.500A) Processing helix chain 'e' and resid 96 through 111 Processing helix chain 'e' and resid 112 through 114 No H-bonds generated for 'chain 'e' and resid 112 through 114' Processing helix chain 'e' and resid 118 through 132 Processing helix chain 'f' and resid 10 through 25 removed outlier: 3.577A pdb=" N GLN f 18 " --> pdb=" O TYR f 14 " (cutoff:3.500A) Processing helix chain 'f' and resid 29 through 66 removed outlier: 4.299A pdb=" N THR f 35 " --> pdb=" O GLU f 31 " (cutoff:3.500A) Proline residue: f 50 - end of helix Processing helix chain 'f' and resid 71 through 93 removed outlier: 3.714A pdb=" N LYS f 90 " --> pdb=" O TYR f 86 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA f 91 " --> pdb=" O LEU f 87 " (cutoff:3.500A) Processing helix chain 'f' and resid 94 through 109 Processing helix chain 'f' and resid 109 through 114 Processing helix chain 'f' and resid 117 through 130 Processing helix chain 'g' and resid 7 through 11 Processing helix chain 'g' and resid 11 through 26 Processing helix chain 'g' and resid 30 through 67 Processing helix chain 'g' and resid 70 through 95 removed outlier: 4.533A pdb=" N ILE g 75 " --> pdb=" O THR g 71 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLY g 76 " --> pdb=" O GLU g 72 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR g 77 " --> pdb=" O ASP g 73 " (cutoff:3.500A) Processing helix chain 'g' and resid 96 through 111 Processing helix chain 'g' and resid 112 through 114 No H-bonds generated for 'chain 'g' and resid 112 through 114' Processing helix chain 'g' and resid 118 through 132 Processing helix chain 'h' and resid 10 through 25 removed outlier: 3.578A pdb=" N GLN h 18 " --> pdb=" O TYR h 14 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 66 removed outlier: 4.298A pdb=" N THR h 35 " --> pdb=" O GLU h 31 " (cutoff:3.500A) Proline residue: h 50 - end of helix Processing helix chain 'h' and resid 71 through 93 removed outlier: 3.714A pdb=" N LYS h 90 " --> pdb=" O TYR h 86 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA h 91 " --> pdb=" O LEU h 87 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 109 Processing helix chain 'h' and resid 109 through 114 Processing helix chain 'h' and resid 117 through 130 Processing helix chain 'i' and resid 7 through 11 Processing helix chain 'i' and resid 11 through 26 Processing helix chain 'i' and resid 30 through 67 Processing helix chain 'i' and resid 70 through 95 removed outlier: 4.534A pdb=" N ILE i 75 " --> pdb=" O THR i 71 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLY i 76 " --> pdb=" O GLU i 72 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR i 77 " --> pdb=" O ASP i 73 " (cutoff:3.500A) Processing helix chain 'i' and resid 96 through 111 Processing helix chain 'i' and resid 112 through 114 No H-bonds generated for 'chain 'i' and resid 112 through 114' Processing helix chain 'i' and resid 118 through 132 Processing helix chain 'j' and resid 10 through 25 removed outlier: 3.578A pdb=" N GLN j 18 " --> pdb=" O TYR j 14 " (cutoff:3.500A) Processing helix chain 'j' and resid 29 through 66 removed outlier: 4.298A pdb=" N THR j 35 " --> pdb=" O GLU j 31 " (cutoff:3.500A) Proline residue: j 50 - end of helix Processing helix chain 'j' and resid 71 through 93 removed outlier: 3.714A pdb=" N LYS j 90 " --> pdb=" O TYR j 86 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA j 91 " --> pdb=" O LEU j 87 " (cutoff:3.500A) Processing helix chain 'j' and resid 94 through 109 Processing helix chain 'j' and resid 109 through 114 Processing helix chain 'j' and resid 117 through 130 Processing helix chain 'k' and resid 7 through 11 Processing helix chain 'k' and resid 11 through 26 Processing helix chain 'k' and resid 30 through 67 Processing helix chain 'k' and resid 70 through 95 removed outlier: 4.533A pdb=" N ILE k 75 " --> pdb=" O THR k 71 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY k 76 " --> pdb=" O GLU k 72 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR k 77 " --> pdb=" O ASP k 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 96 through 111 Processing helix chain 'k' and resid 112 through 114 No H-bonds generated for 'chain 'k' and resid 112 through 114' Processing helix chain 'k' and resid 118 through 132 Processing helix chain 'l' and resid 10 through 25 removed outlier: 3.577A pdb=" N GLN l 18 " --> pdb=" O TYR l 14 " (cutoff:3.500A) Processing helix chain 'l' and resid 29 through 66 removed outlier: 4.299A pdb=" N THR l 35 " --> pdb=" O GLU l 31 " (cutoff:3.500A) Proline residue: l 50 - end of helix Processing helix chain 'l' and resid 71 through 93 removed outlier: 3.714A pdb=" N LYS l 90 " --> pdb=" O TYR l 86 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA l 91 " --> pdb=" O LEU l 87 " (cutoff:3.500A) Processing helix chain 'l' and resid 94 through 109 Processing helix chain 'l' and resid 109 through 114 Processing helix chain 'l' and resid 117 through 130 Processing helix chain 'm' and resid 7 through 11 Processing helix chain 'm' and resid 11 through 26 Processing helix chain 'm' and resid 30 through 67 Processing helix chain 'm' and resid 70 through 95 removed outlier: 4.533A pdb=" N ILE m 75 " --> pdb=" O THR m 71 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY m 76 " --> pdb=" O GLU m 72 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR m 77 " --> pdb=" O ASP m 73 " (cutoff:3.500A) Processing helix chain 'm' and resid 96 through 111 Processing helix chain 'm' and resid 112 through 114 No H-bonds generated for 'chain 'm' and resid 112 through 114' Processing helix chain 'm' and resid 118 through 132 Processing helix chain 'n' and resid 10 through 25 removed outlier: 3.577A pdb=" N GLN n 18 " --> pdb=" O TYR n 14 " (cutoff:3.500A) Processing helix chain 'n' and resid 29 through 66 removed outlier: 4.299A pdb=" N THR n 35 " --> pdb=" O GLU n 31 " (cutoff:3.500A) Proline residue: n 50 - end of helix Processing helix chain 'n' and resid 71 through 93 removed outlier: 3.714A pdb=" N LYS n 90 " --> pdb=" O TYR n 86 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA n 91 " --> pdb=" O LEU n 87 " (cutoff:3.500A) Processing helix chain 'n' and resid 94 through 109 Processing helix chain 'n' and resid 109 through 114 Processing helix chain 'n' and resid 117 through 130 Processing helix chain 'o' and resid 7 through 11 Processing helix chain 'o' and resid 11 through 26 Processing helix chain 'o' and resid 30 through 67 Processing helix chain 'o' and resid 70 through 95 removed outlier: 4.534A pdb=" N ILE o 75 " --> pdb=" O THR o 71 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLY o 76 " --> pdb=" O GLU o 72 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR o 77 " --> pdb=" O ASP o 73 " (cutoff:3.500A) Processing helix chain 'o' and resid 96 through 111 Processing helix chain 'o' and resid 112 through 114 No H-bonds generated for 'chain 'o' and resid 112 through 114' Processing helix chain 'o' and resid 118 through 132 Processing helix chain 'p' and resid 10 through 25 removed outlier: 3.578A pdb=" N GLN p 18 " --> pdb=" O TYR p 14 " (cutoff:3.500A) Processing helix chain 'p' and resid 29 through 66 removed outlier: 4.298A pdb=" N THR p 35 " --> pdb=" O GLU p 31 " (cutoff:3.500A) Proline residue: p 50 - end of helix Processing helix chain 'p' and resid 71 through 93 removed outlier: 3.714A pdb=" N LYS p 90 " --> pdb=" O TYR p 86 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA p 91 " --> pdb=" O LEU p 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 94 through 109 Processing helix chain 'p' and resid 109 through 114 Processing helix chain 'p' and resid 117 through 130 3592 hydrogen bonds defined for protein. 10776 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 462 hydrogen bonds 924 hydrogen bond angles 0 basepair planarities 231 basepair parallelities 415 stacking parallelities Total time for adding SS restraints: 17.72 Time building geometry restraints manager: 20.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 8805 1.32 - 1.44: 17282 1.44 - 1.57: 28113 1.57 - 1.69: 1049 1.69 - 1.82: 357 Bond restraints: 55606 Sorted by residual: bond pdb=" CG GLN H 15 " pdb=" CD GLN H 15 " ideal model delta sigma weight residual 1.516 1.419 0.097 2.50e-02 1.60e+03 1.51e+01 bond pdb=" CG GLN P 15 " pdb=" CD GLN P 15 " ideal model delta sigma weight residual 1.516 1.419 0.097 2.50e-02 1.60e+03 1.50e+01 bond pdb=" CG GLN F 15 " pdb=" CD GLN F 15 " ideal model delta sigma weight residual 1.516 1.419 0.097 2.50e-02 1.60e+03 1.49e+01 bond pdb=" CG GLN j 15 " pdb=" CD GLN j 15 " ideal model delta sigma weight residual 1.516 1.420 0.096 2.50e-02 1.60e+03 1.49e+01 bond pdb=" CG GLN p 15 " pdb=" CD GLN p 15 " ideal model delta sigma weight residual 1.516 1.420 0.096 2.50e-02 1.60e+03 1.48e+01 ... (remaining 55601 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.07: 3979 106.07 - 113.07: 29268 113.07 - 120.08: 19503 120.08 - 127.08: 23045 127.08 - 134.08: 1624 Bond angle restraints: 77419 Sorted by residual: angle pdb=" C ILE N 67 " pdb=" N PRO N 68 " pdb=" CA PRO N 68 " ideal model delta sigma weight residual 119.90 128.29 -8.39 1.02e+00 9.61e-01 6.77e+01 angle pdb=" C ILE n 67 " pdb=" N PRO n 68 " pdb=" CA PRO n 68 " ideal model delta sigma weight residual 119.90 128.26 -8.36 1.02e+00 9.61e-01 6.71e+01 angle pdb=" C ILE d 67 " pdb=" N PRO d 68 " pdb=" CA PRO d 68 " ideal model delta sigma weight residual 119.90 128.25 -8.35 1.02e+00 9.61e-01 6.70e+01 angle pdb=" C ILE f 67 " pdb=" N PRO f 68 " pdb=" CA PRO f 68 " ideal model delta sigma weight residual 119.90 128.24 -8.34 1.02e+00 9.61e-01 6.69e+01 angle pdb=" C ILE R 67 " pdb=" N PRO R 68 " pdb=" CA PRO R 68 " ideal model delta sigma weight residual 119.90 128.24 -8.34 1.02e+00 9.61e-01 6.69e+01 ... (remaining 77414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 28091 17.28 - 34.57: 3289 34.57 - 51.85: 1002 51.85 - 69.13: 351 69.13 - 86.41: 42 Dihedral angle restraints: 32775 sinusoidal: 16773 harmonic: 16002 Sorted by residual: dihedral pdb=" CA VAL k 131 " pdb=" C VAL k 131 " pdb=" N ILE k 132 " pdb=" CA ILE k 132 " ideal model delta harmonic sigma weight residual 180.00 -162.62 -17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA VAL g 131 " pdb=" C VAL g 131 " pdb=" N ILE g 132 " pdb=" CA ILE g 132 " ideal model delta harmonic sigma weight residual -180.00 -162.63 -17.37 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA VAL K 131 " pdb=" C VAL K 131 " pdb=" N ILE K 132 " pdb=" CA ILE K 132 " ideal model delta harmonic sigma weight residual -180.00 -162.65 -17.35 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 32772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 4419 0.049 - 0.097: 2738 0.097 - 0.146: 1060 0.146 - 0.194: 285 0.194 - 0.243: 87 Chirality restraints: 8589 Sorted by residual: chirality pdb=" CG LEU D 83 " pdb=" CB LEU D 83 " pdb=" CD1 LEU D 83 " pdb=" CD2 LEU D 83 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CG LEU T 83 " pdb=" CB LEU T 83 " pdb=" CD1 LEU T 83 " pdb=" CD2 LEU T 83 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CG LEU X 83 " pdb=" CB LEU X 83 " pdb=" CD1 LEU X 83 " pdb=" CD2 LEU X 83 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 8586 not shown) Planarity restraints: 8043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR d 132 " -0.029 2.00e-02 2.50e+03 5.83e-02 3.40e+01 pdb=" C TYR d 132 " 0.101 2.00e-02 2.50e+03 pdb=" O TYR d 132 " -0.036 2.00e-02 2.50e+03 pdb=" OXT TYR d 132 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR P 132 " 0.029 2.00e-02 2.50e+03 5.83e-02 3.40e+01 pdb=" C TYR P 132 " -0.101 2.00e-02 2.50e+03 pdb=" O TYR P 132 " 0.036 2.00e-02 2.50e+03 pdb=" OXT TYR P 132 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR Z 132 " -0.029 2.00e-02 2.50e+03 5.83e-02 3.40e+01 pdb=" C TYR Z 132 " 0.101 2.00e-02 2.50e+03 pdb=" O TYR Z 132 " -0.036 2.00e-02 2.50e+03 pdb=" OXT TYR Z 132 " -0.036 2.00e-02 2.50e+03 ... (remaining 8040 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 4018 2.71 - 3.26: 58324 3.26 - 3.81: 101956 3.81 - 4.35: 127583 4.35 - 4.90: 197955 Nonbonded interactions: 489836 Sorted by model distance: nonbonded pdb=" CD2 LEU G 22 " pdb=" CD2 LEU I 29 " model vdw 2.165 3.880 nonbonded pdb=" CD2 LEU O 22 " pdb=" CD2 LEU Q 29 " model vdw 2.165 3.880 nonbonded pdb=" CD2 LEU Y 22 " pdb=" CD2 LEU a 29 " model vdw 2.165 3.880 nonbonded pdb=" CD2 LEU c 22 " pdb=" CD2 LEU e 29 " model vdw 2.165 3.880 nonbonded pdb=" CD2 LEU a 22 " pdb=" CD2 LEU c 29 " model vdw 2.165 3.880 ... (remaining 489831 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' selection = chain 'm' selection = chain 'o' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'l' selection = chain 'n' selection = chain 'p' } ncs_group { reference = chain 'q' selection = chain 'r' } Set up NCS constraints Number of NCS constrained groups: 3 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' selection = chain 'm' selection = chain 'o' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'l' selection = chain 'n' selection = chain 'p' } pdb_interpretation.ncs_group { reference = chain 'q' selection = chain 'r' } Set refine NCS operators NCS operators will be refined. 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: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 3.910 Check model and map are aligned: 0.590 Set scattering table: 0.370 Process input model: 116.120 Find NCS groups from input model: 2.730 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4931 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 : 0.015 0.097 55606 Z= 0.949 Angle : 1.168 8.392 77419 Z= 0.824 Chirality : 0.071 0.243 8589 Planarity : 0.007 0.058 8043 Dihedral : 16.656 86.414 22485 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.45 % Allowed : 1.80 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.11), residues: 5313 helix: -0.20 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.37 (0.19), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.007 TRP K 23 HIS 0.007 0.002 HIS I 86 PHE 0.011 0.004 PHE R 127 TYR 0.058 0.009 TYR j 16 ARG 0.003 0.001 ARG a 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10626 Ramachandran restraints generated. 5313 Oldfield, 0 Emsley, 5313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10626 Ramachandran restraints generated. 5313 Oldfield, 0 Emsley, 5313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: -0.0415 (ttt) cc_final: -0.2224 (tmm) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1567 time to fit residues: 9.4883 Evaluate side-chains 31 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.089 Evaluate side-chains 59 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 PHE cc_start: 0.5203 (t80) cc_final: 0.4510 (t80) REVERT: B 124 ILE cc_start: 0.8229 (mm) cc_final: 0.8015 (mm) outliers start: 1 outliers final: 1 residues processed: 58 average time/residue: 0.1256 time to fit residues: 7.8124 Evaluate side-chains 43 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.083 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.110 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1405 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 485 optimal weight: 5.9990 chunk 435 optimal weight: 20.0000 chunk 241 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 293 optimal weight: 8.9990 chunk 232 optimal weight: 4.9990 chunk 450 optimal weight: 30.0000 chunk 174 optimal weight: 20.0000 chunk 274 optimal weight: 20.0000 chunk 335 optimal weight: 9.9990 chunk 522 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 86 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 105 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5084 moved from start: 0.8521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.116 55606 Z= 0.666 Angle : 1.171 13.710 77419 Z= 0.652 Chirality : 0.059 0.249 8589 Planarity : 0.008 0.043 8043 Dihedral : 18.560 59.859 11985 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 58.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.80 % Allowed : 5.41 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.11), residues: 5313 helix: 0.31 (0.08), residues: 4263 sheet: None (None), residues: 0 loop : 0.28 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP Q 23 HIS 0.008 0.003 HIS g 86 PHE 0.018 0.003 PHE d 127 TYR 0.085 0.005 TYR M 49 ARG 0.007 0.001 ARG V 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10362 Ramachandran restraints generated. 5181 Oldfield, 0 Emsley, 5181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10362 Ramachandran restraints generated. 5181 Oldfield, 0 Emsley, 5181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 36 ILE cc_start: 0.7990 (mt) cc_final: 0.7773 (mt) REVERT: o 107 THR cc_start: 0.5661 (m) cc_final: 0.4912 (m) REVERT: o 124 LEU cc_start: 0.5871 (mt) cc_final: 0.5090 (mt) outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 0.1093 time to fit residues: 5.2875 Evaluate side-chains 32 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.091 Evaluate side-chains 60 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: p 12 ASP cc_start: 0.4506 (OUTLIER) cc_final: 0.4148 (t70) REVERT: p 20 ILE cc_start: 0.7530 (mm) cc_final: 0.7034 (mt) REVERT: p 48 PHE cc_start: 0.5628 (t80) cc_final: 0.5151 (t80) REVERT: p 49 THR cc_start: 0.6693 (p) cc_final: 0.5536 (p) REVERT: p 72 TRP cc_start: 0.6517 (m-10) cc_final: 0.5884 (m-10) REVERT: p 120 THR cc_start: 0.6308 (p) cc_final: 0.5969 (p) outliers start: 3 outliers final: 1 residues processed: 59 average time/residue: 0.1333 time to fit residues: 8.3996 Evaluate side-chains 42 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.086 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.126 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1462 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 290 optimal weight: 0.3980 chunk 162 optimal weight: 4.9990 chunk 434 optimal weight: 10.0000 chunk 355 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 523 optimal weight: 10.0000 chunk 565 optimal weight: 20.0000 chunk 465 optimal weight: 30.0000 chunk 518 optimal weight: 30.0000 chunk 178 optimal weight: 9.9990 chunk 419 optimal weight: 0.0060 overall best weight: 4.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 104 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5016 moved from start: 1.0248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 55606 Z= 0.468 Angle : 1.010 11.715 77419 Z= 0.574 Chirality : 0.052 0.158 8589 Planarity : 0.008 0.077 8043 Dihedral : 17.985 58.939 11985 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 52.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.90 % Allowed : 4.05 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.11), residues: 5313 helix: -0.29 (0.07), residues: 4389 sheet: None (None), residues: 0 loop : -0.46 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.007 TRP S 23 HIS 0.006 0.003 HIS W 86 PHE 0.017 0.003 PHE L 78 TYR 0.056 0.005 TYR l 16 ARG 0.005 0.001 ARG J 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10114 Ramachandran restraints generated. 5057 Oldfield, 0 Emsley, 5057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10114 Ramachandran restraints generated. 5057 Oldfield, 0 Emsley, 5057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.6714 (m-30) cc_final: 0.6391 (t70) outliers start: 1 outliers final: 0 residues processed: 41 average time/residue: 0.1048 time to fit residues: 4.7410 Evaluate side-chains 29 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.089 Evaluate side-chains 52 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: l 82 LEU cc_start: 0.6892 (mt) cc_final: 0.6685 (mt) REVERT: l 124 ILE cc_start: 0.7716 (mm) cc_final: 0.6901 (mm) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.1172 time to fit residues: 6.4936 Evaluate side-chains 38 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.085 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.113 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1480 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 516 optimal weight: 1.9990 chunk 393 optimal weight: 7.9990 chunk 271 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 249 optimal weight: 9.9990 chunk 351 optimal weight: 6.9990 chunk 524 optimal weight: 30.0000 chunk 555 optimal weight: 10.0000 chunk 274 optimal weight: 5.9990 chunk 497 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5025 moved from start: 1.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.092 55606 Z= 0.508 Angle : 0.992 9.461 77419 Z= 0.560 Chirality : 0.053 0.209 8589 Planarity : 0.009 0.097 8043 Dihedral : 17.947 59.895 11985 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 54.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -1.18 (0.11), residues: 5313 helix: -0.52 (0.07), residues: 4389 sheet: None (None), residues: 0 loop : -1.26 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.005 TRP K 89 HIS 0.003 0.001 HIS Q 86 PHE 0.044 0.006 PHE D 48 TYR 0.029 0.004 TYR D 16 ARG 0.009 0.002 ARG a 9 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10114 Ramachandran restraints generated. 5057 Oldfield, 0 Emsley, 5057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10114 Ramachandran restraints generated. 5057 Oldfield, 0 Emsley, 5057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.7866 (mt) cc_final: 0.7629 (mp) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0934 time to fit residues: 4.0748 Evaluate side-chains 32 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.090 Evaluate side-chains 47 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: p 17 LYS cc_start: 0.8156 (mtmm) cc_final: 0.7836 (pttt) REVERT: p 72 TRP cc_start: 0.6154 (m-10) cc_final: 0.5796 (m-10) REVERT: p 124 ILE cc_start: 0.7700 (mm) cc_final: 0.7084 (mm) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1101 time to fit residues: 5.6247 Evaluate side-chains 39 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.092 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.112 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1459 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 462 optimal weight: 7.9990 chunk 315 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 413 optimal weight: 0.0470 chunk 229 optimal weight: 6.9990 chunk 474 optimal weight: 20.0000 chunk 384 optimal weight: 0.7980 chunk 0 optimal weight: 40.0000 chunk 283 optimal weight: 9.9990 chunk 498 optimal weight: 50.0000 chunk 140 optimal weight: 30.0000 overall best weight: 3.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4971 moved from start: 1.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 55606 Z= 0.485 Angle : 0.945 9.343 77419 Z= 0.537 Chirality : 0.050 0.212 8589 Planarity : 0.010 0.095 8043 Dihedral : 17.816 59.976 11985 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 52.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -1.21 (0.11), residues: 5313 helix: -0.54 (0.07), residues: 4389 sheet: None (None), residues: 0 loop : -1.31 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.005 TRP P 44 HIS 0.002 0.001 HIS A 86 PHE 0.049 0.006 PHE Z 48 TYR 0.039 0.004 TYR V 16 ARG 0.011 0.001 ARG J 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 MET cc_start: 0.7036 (mtt) cc_final: 0.6450 (mtt) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1058 time to fit residues: 4.6787 Evaluate side-chains 30 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.093 Evaluate side-chains 44 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: p 17 LYS cc_start: 0.8026 (mtmm) cc_final: 0.7578 (pttt) REVERT: p 72 TRP cc_start: 0.6269 (m-10) cc_final: 0.5714 (m-10) REVERT: p 74 MET cc_start: 0.5738 (mpp) cc_final: 0.4496 (mmm) REVERT: p 124 ILE cc_start: 0.7658 (mm) cc_final: 0.7255 (mm) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1293 time to fit residues: 6.1398 Evaluate side-chains 41 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.085 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.116 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1473 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 186 optimal weight: 20.0000 chunk 500 optimal weight: 40.0000 chunk 109 optimal weight: 8.9990 chunk 326 optimal weight: 30.0000 chunk 137 optimal weight: 3.9990 chunk 556 optimal weight: 20.0000 chunk 461 optimal weight: 7.9990 chunk 257 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 184 optimal weight: 0.3980 chunk 292 optimal weight: 1.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4982 moved from start: 1.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 55606 Z= 0.506 Angle : 0.993 11.494 77419 Z= 0.561 Chirality : 0.052 0.206 8589 Planarity : 0.011 0.116 8043 Dihedral : 17.829 59.988 11985 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 54.17 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.51 % Favored : 92.09 % Rotamer: Outliers : 0.45 % Allowed : 4.50 % Favored : 95.05 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -1.43 (0.11), residues: 5313 helix: -0.72 (0.07), residues: 4410 sheet: None (None), residues: 0 loop : -1.20 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP K 89 HIS 0.002 0.001 HIS F 52 PHE 0.056 0.007 PHE Z 48 TYR 0.040 0.004 TYR F 16 ARG 0.029 0.003 ARG O 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 MET cc_start: 0.6848 (mtt) cc_final: 0.6428 (mtt) outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.1175 time to fit residues: 4.8883 Evaluate side-chains 32 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.089 Evaluate side-chains 43 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: p 17 LYS cc_start: 0.8058 (mtmm) cc_final: 0.7666 (pttt) REVERT: p 74 MET cc_start: 0.5649 (mpp) cc_final: 0.4347 (mmm) REVERT: p 124 ILE cc_start: 0.7613 (mm) cc_final: 0.7278 (mm) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1382 time to fit residues: 6.3725 Evaluate side-chains 37 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.083 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.112 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1436 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 536 optimal weight: 30.0000 chunk 62 optimal weight: 8.9990 chunk 316 optimal weight: 5.9990 chunk 406 optimal weight: 6.9990 chunk 314 optimal weight: 6.9990 chunk 468 optimal weight: 0.0770 chunk 310 optimal weight: 0.5980 chunk 554 optimal weight: 10.0000 chunk 346 optimal weight: 0.0770 chunk 337 optimal weight: 1.9990 chunk 255 optimal weight: 7.9990 overall best weight: 1.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 105 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4829 moved from start: 1.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 55606 Z= 0.373 Angle : 0.923 12.096 77419 Z= 0.517 Chirality : 0.048 0.205 8589 Planarity : 0.007 0.053 8043 Dihedral : 17.406 58.825 11985 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 44.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.11), residues: 5313 helix: -0.38 (0.07), residues: 4389 sheet: None (None), residues: 0 loop : -1.11 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.005 TRP F 44 HIS 0.004 0.003 HIS F 52 PHE 0.052 0.008 PHE B 48 TYR 0.032 0.003 TYR i 49 ARG 0.008 0.001 ARG b 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1085 time to fit residues: 4.3508 Evaluate side-chains 29 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.090 Evaluate side-chains 45 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: p 72 TRP cc_start: 0.6519 (m-10) cc_final: 0.5570 (p-90) REVERT: p 74 MET cc_start: 0.5546 (mpp) cc_final: 0.4680 (mmm) REVERT: p 124 ILE cc_start: 0.7651 (mm) cc_final: 0.7309 (mm) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1481 time to fit residues: 7.1403 Evaluate side-chains 34 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.085 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.117 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1485 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 342 optimal weight: 9.9990 chunk 221 optimal weight: 8.9990 chunk 330 optimal weight: 0.8980 chunk 166 optimal weight: 8.9990 chunk 108 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 352 optimal weight: 30.0000 chunk 377 optimal weight: 30.0000 chunk 274 optimal weight: 6.9990 chunk 51 optimal weight: 0.0370 chunk 435 optimal weight: 0.9980 overall best weight: 2.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 40 GLN p 105 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4843 moved from start: 1.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 55606 Z= 0.385 Angle : 0.936 10.705 77419 Z= 0.516 Chirality : 0.048 0.166 8589 Planarity : 0.007 0.070 8043 Dihedral : 17.406 59.921 11985 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 46.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -1.00 (0.11), residues: 5313 helix: -0.38 (0.08), residues: 4431 sheet: None (None), residues: 0 loop : -1.31 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.006 TRP V 44 HIS 0.004 0.001 HIS d 52 PHE 0.048 0.008 PHE B 48 TYR 0.040 0.004 TYR J 19 ARG 0.013 0.002 ARG F 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 31 PRO cc_start: 0.7870 (Cg_exo) cc_final: 0.7620 (Cg_endo) REVERT: C 34 MET cc_start: 0.6741 (mtm) cc_final: 0.6452 (mtt) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1075 time to fit residues: 4.2879 Evaluate side-chains 30 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.089 Evaluate side-chains 38 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: p 17 LYS cc_start: 0.8515 (mtmm) cc_final: 0.8127 (pttt) REVERT: p 72 TRP cc_start: 0.6527 (m-10) cc_final: 0.5588 (p-90) REVERT: p 74 MET cc_start: 0.5641 (mpp) cc_final: 0.4810 (mmm) REVERT: p 78 PHE cc_start: 0.5497 (t80) cc_final: 0.4811 (t80) REVERT: p 89 MET cc_start: 0.7255 (mtp) cc_final: 0.6673 (ttm) REVERT: p 123 LYS cc_start: 0.6007 (pttp) cc_final: 0.5132 (pttp) REVERT: p 124 ILE cc_start: 0.7817 (mm) cc_final: 0.7538 (mm) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1560 time to fit residues: 6.3251 Evaluate side-chains 32 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.085 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.113 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1480 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 504 optimal weight: 0.0980 chunk 530 optimal weight: 10.0000 chunk 484 optimal weight: 0.0270 chunk 516 optimal weight: 0.9990 chunk 310 optimal weight: 10.0000 chunk 224 optimal weight: 6.9990 chunk 405 optimal weight: 0.0670 chunk 158 optimal weight: 30.0000 chunk 466 optimal weight: 0.9990 chunk 488 optimal weight: 0.4980 chunk 514 optimal weight: 20.0000 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4670 moved from start: 1.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 55606 Z= 0.329 Angle : 0.851 8.470 77419 Z= 0.485 Chirality : 0.047 0.173 8589 Planarity : 0.007 0.062 8043 Dihedral : 17.076 59.437 11985 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 43.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -1.08 (0.11), residues: 5313 helix: -0.42 (0.07), residues: 4410 sheet: None (None), residues: 0 loop : -1.42 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.005 TRP P 44 HIS 0.007 0.003 HIS j 52 PHE 0.028 0.005 PHE H 110 TYR 0.024 0.003 TYR i 16 ARG 0.013 0.001 ARG Z 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 VAL cc_start: 0.9044 (t) cc_final: 0.8636 (t) REVERT: A 53 MET cc_start: 0.5646 (ppp) cc_final: 0.5035 (ptm) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1362 time to fit residues: 5.0336 Evaluate side-chains 25 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.123 Evaluate side-chains 39 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: p 74 MET cc_start: 0.5668 (mpp) cc_final: 0.5059 (mmm) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1662 time to fit residues: 6.9004 Evaluate side-chains 32 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.084 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.112 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1467 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 339 optimal weight: 5.9990 chunk 546 optimal weight: 5.9990 chunk 333 optimal weight: 8.9990 chunk 259 optimal weight: 4.9990 chunk 379 optimal weight: 0.0170 chunk 572 optimal weight: 20.0000 chunk 527 optimal weight: 5.9990 chunk 456 optimal weight: 0.0770 chunk 47 optimal weight: 20.0000 chunk 352 optimal weight: 10.0000 chunk 279 optimal weight: 4.9990 overall best weight: 3.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 HIS ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4702 moved from start: 1.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 55606 Z= 0.388 Angle : 0.972 15.185 77419 Z= 0.549 Chirality : 0.051 0.232 8589 Planarity : 0.008 0.062 8043 Dihedral : 17.141 56.596 11985 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 47.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % 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: -1.36 (0.11), residues: 5313 helix: -0.58 (0.07), residues: 4431 sheet: None (None), residues: 0 loop : -1.74 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.006 TRP o 23 HIS 0.002 0.001 HIS R 52 PHE 0.026 0.004 PHE H 110 TYR 0.028 0.004 TYR D 102 ARG 0.013 0.001 ARG h 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1178 time to fit residues: 3.7881 Evaluate side-chains 24 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.092 Evaluate side-chains 35 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: p 48 PHE cc_start: 0.5133 (m-80) cc_final: 0.4221 (m-80) REVERT: p 74 MET cc_start: 0.5657 (mpp) cc_final: 0.4994 (mmm) REVERT: p 89 MET cc_start: 0.6561 (mmm) cc_final: 0.5546 (mmt) REVERT: p 90 LYS cc_start: 0.6860 (mptt) cc_final: 0.6207 (pptt) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1619 time to fit residues: 6.0406 Evaluate side-chains 32 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.084 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.111 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1593 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 575 random chunks: chunk 362 optimal weight: 0.6980 chunk 485 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 420 optimal weight: 8.9990 chunk 67 optimal weight: 0.0980 chunk 126 optimal weight: 20.0000 chunk 456 optimal weight: 0.7980 chunk 191 optimal weight: 6.9990 chunk 469 optimal weight: 0.0970 chunk 57 optimal weight: 0.0870 chunk 84 optimal weight: 0.0670 overall best weight: 0.2094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.139813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.124488 restraints weight = 4297.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.127092 restraints weight = 3305.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.129026 restraints weight = 2627.033| |-----------------------------------------------------------------------------| r_work (final): 0.4133 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.132363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.123116 restraints weight = 3918.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.124715 restraints weight = 2959.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.125980 restraints weight = 2303.606| |-----------------------------------------------------------------------------| r_work (final): 0.4096 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.075131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.072302 restraints weight = 66104.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.073334 restraints weight = 26121.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.073926 restraints weight = 13201.834| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6040 moved from start: 1.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 55606 Z= 0.338 Angle : 0.954 11.605 77419 Z= 0.525 Chirality : 0.050 0.210 8589 Planarity : 0.007 0.060 8043 Dihedral : 16.946 58.070 11985 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 41.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: -1.00 (0.11), residues: 5313 helix: -0.31 (0.07), residues: 4284 sheet: None (None), residues: 0 loop : -1.56 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.006 TRP o 23 HIS 0.003 0.002 HIS B 52 PHE 0.025 0.004 PHE H 110 TYR 0.034 0.004 TYR d 102 ARG 0.016 0.001 ARG d 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4538.00 seconds wall clock time: 86 minutes 9.26 seconds (5169.26 seconds total)