Starting phenix.real_space_refine on Thu Dec 7 16:09:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7g_8780/12_2023/5w7g_8780.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7g_8780/12_2023/5w7g_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_8780/12_2023/5w7g_8780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7g_8780/12_2023/5w7g_8780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7g_8780/12_2023/5w7g_8780.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w7g_8780/12_2023/5w7g_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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 20.99, per 1000 atoms: 0.39 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: 19.69 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: 15.14 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: 18.99 Time building geometry restraints manager: 21.34 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: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 3.840 Check model and map are aligned: 0.590 Set scattering table: 0.400 Process input model: 121.120 Find NCS groups from input model: 2.670 Set up NCS constraints: 0.500 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: 0.020 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.060 ------------------------------------------------------------------------------- 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 : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1541 time to fit residues: 9.3433 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1248 Evaluate side-chains 59 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.083 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 outliers start: 1 outliers final: 1 residues processed: 58 average time/residue: 0.1237 time to fit residues: 7.6895 Evaluate side-chains 43 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.089 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0130 time to fit residues: 0.1351 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: 0.1425 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0526 ------------------------------------------------------------------------------- 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: 8.9990 chunk 335 optimal weight: 9.9990 chunk 522 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 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: 0.5078 moved from start: 0.8465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.115 55606 Z= 0.656 Angle : 1.172 14.679 77419 Z= 0.652 Chirality : 0.057 0.211 8589 Planarity : 0.008 0.037 8043 Dihedral : 18.471 59.986 11985 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 58.13 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.35 % 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: 0.32 (0.11), residues: 5313 helix: 0.34 (0.08), residues: 4221 sheet: None (None), residues: 0 loop : 0.29 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.005 TRP Q 23 HIS 0.006 0.003 HIS k 86 PHE 0.018 0.004 PHE V 127 TYR 0.079 0.005 TYR o 49 ARG 0.008 0.001 ARG H 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 45 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 45 average time/residue: 0.1165 time to fit residues: 5.7333 Evaluate side-chains 30 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.091 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1258 Evaluate side-chains 58 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 57 average time/residue: 0.1373 time to fit residues: 8.3495 Evaluate side-chains 43 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.085 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0250 time to fit residues: 0.1490 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: 0.1443 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0549 ------------------------------------------------------------------------------- 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: 0.1980 chunk 162 optimal weight: 9.9990 chunk 434 optimal weight: 9.9990 chunk 355 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 523 optimal weight: 0.9990 chunk 565 optimal weight: 20.0000 chunk 465 optimal weight: 0.0270 chunk 518 optimal weight: 30.0000 chunk 178 optimal weight: 7.9990 chunk 419 optimal weight: 9.9990 overall best weight: 3.4444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 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: 0.4979 moved from start: 1.0247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 55606 Z= 0.495 Angle : 1.019 11.408 77419 Z= 0.572 Chirality : 0.052 0.165 8589 Planarity : 0.008 0.077 8043 Dihedral : 17.974 59.194 11985 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 52.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.90 % Allowed : 5.86 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.11), residues: 5313 helix: -0.30 (0.07), residues: 4347 sheet: None (None), residues: 0 loop : -0.11 (0.22), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.008 TRP S 23 HIS 0.002 0.001 HIS F 52 PHE 0.018 0.003 PHE l 127 TYR 0.059 0.006 TYR B 16 ARG 0.010 0.001 ARG b 13 *********************** REFINEMENT MACRO_CYCLE 3 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 40 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 0.1057 time to fit residues: 4.6724 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1260 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 outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.1251 time to fit residues: 6.8691 Evaluate side-chains 40 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.084 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1167 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 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 : 0.114 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0568 ------------------------------------------------------------------------------- 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: 2.9990 chunk 393 optimal weight: 8.9990 chunk 271 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 chunk 249 optimal weight: 6.9990 chunk 351 optimal weight: 20.0000 chunk 524 optimal weight: 30.0000 chunk 555 optimal weight: 20.0000 chunk 274 optimal weight: 6.9990 chunk 497 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- 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: 0.4910 moved from start: 1.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.114 55606 Z= 0.482 Angle : 0.972 8.651 77419 Z= 0.555 Chirality : 0.052 0.171 8589 Planarity : 0.008 0.087 8043 Dihedral : 17.732 59.990 11985 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 49.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % 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: -1.15 (0.11), residues: 5313 helix: -0.56 (0.07), residues: 4389 sheet: None (None), residues: 0 loop : -0.88 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRP E 89 HIS 0.005 0.002 HIS I 86 PHE 0.036 0.006 PHE n 110 TYR 0.024 0.004 TYR o 128 ARG 0.015 0.002 ARG U 57 *********************** REFINEMENT MACRO_CYCLE 4 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: 0 poor density : 44 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1009 time to fit residues: 4.9401 Evaluate side-chains 29 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.122 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1713 Evaluate side-chains 50 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1518 time to fit residues: 8.1108 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1176 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: 0.1525 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0593 ------------------------------------------------------------------------------- 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: 4.9990 chunk 8 optimal weight: 10.0000 chunk 413 optimal weight: 0.6980 chunk 229 optimal weight: 0.7980 chunk 474 optimal weight: 5.9990 chunk 384 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 283 optimal weight: 6.9990 chunk 498 optimal weight: 20.0000 chunk 140 optimal weight: 2.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- 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: 0.4870 moved from start: 1.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 55606 Z= 0.442 Angle : 0.959 8.781 77419 Z= 0.546 Chirality : 0.051 0.206 8589 Planarity : 0.009 0.087 8043 Dihedral : 17.646 59.876 11985 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 51.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % 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 : 0.00 % 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: -1.45 (0.11), residues: 5313 helix: -0.83 (0.07), residues: 4368 sheet: None (None), residues: 0 loop : -0.64 (0.23), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.007 TRP N 44 HIS 0.003 0.002 HIS W 86 PHE 0.026 0.006 PHE b 48 TYR 0.041 0.004 TYR j 16 ARG 0.013 0.002 ARG W 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1200 time to fit residues: 5.5001 Evaluate side-chains 33 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.090 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1269 Evaluate side-chains 48 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 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 outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1392 time to fit residues: 7.1415 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1171 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.124 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1512 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.115 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0581 ------------------------------------------------------------------------------- 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: 9.9990 chunk 500 optimal weight: 30.0000 chunk 109 optimal weight: 10.0000 chunk 326 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 556 optimal weight: 20.0000 chunk 461 optimal weight: 6.9990 chunk 257 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 184 optimal weight: 0.0870 chunk 292 optimal weight: 0.4980 overall best weight: 3.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 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 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: 0.4857 moved from start: 1.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 55606 Z= 0.442 Angle : 1.019 15.544 77419 Z= 0.559 Chirality : 0.053 0.229 8589 Planarity : 0.009 0.072 8043 Dihedral : 17.653 59.947 11985 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 50.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.45 % Allowed : 3.15 % Favored : 96.40 % 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: -1.74 (0.11), residues: 5313 helix: -0.87 (0.07), residues: 4368 sheet: None (None), residues: 0 loop : -1.65 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.005 TRP f 44 HIS 0.003 0.002 HIS d 52 PHE 0.044 0.006 PHE Z 48 TYR 0.026 0.004 TYR G 49 ARG 0.010 0.001 ARG T 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 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 : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1295 time to fit residues: 5.6528 Evaluate side-chains 29 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.093 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1267 Evaluate side-chains 47 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.1535 time to fit residues: 7.5320 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1177 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.115 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1501 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.115 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0574 ------------------------------------------------------------------------------- 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: 7.9990 chunk 406 optimal weight: 30.0000 chunk 314 optimal weight: 8.9990 chunk 468 optimal weight: 9.9990 chunk 310 optimal weight: 8.9990 chunk 554 optimal weight: 20.0000 chunk 346 optimal weight: 7.9990 chunk 337 optimal weight: 10.0000 chunk 255 optimal weight: 6.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN 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: 0.4934 moved from start: 1.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.196 55606 Z= 0.581 Angle : 1.113 14.728 77419 Z= 0.610 Chirality : 0.056 0.275 8589 Planarity : 0.008 0.076 8043 Dihedral : 17.699 59.946 11985 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 57.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 0.45 % Allowed : 4.05 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.11), residues: 5313 helix: -1.10 (0.07), residues: 4368 sheet: None (None), residues: 0 loop : -1.82 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.006 TRP F 72 HIS 0.003 0.001 HIS d 52 PHE 0.067 0.008 PHE n 48 TYR 0.034 0.005 TYR L 16 ARG 0.012 0.002 ARG X 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 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: 1 poor density : 35 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 35 average time/residue: 0.1020 time to fit residues: 3.9758 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1268 Evaluate side-chains 42 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.115 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: 42 average time/residue: 0.1560 time to fit residues: 6.9858 Evaluate side-chains 34 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.087 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1170 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.120 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1470 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0560 ------------------------------------------------------------------------------- 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: 6.9990 chunk 221 optimal weight: 8.9990 chunk 330 optimal weight: 8.9990 chunk 166 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 352 optimal weight: 5.9990 chunk 377 optimal weight: 8.9990 chunk 274 optimal weight: 30.0000 chunk 51 optimal weight: 4.9990 chunk 435 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 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: 0.4953 moved from start: 1.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 55606 Z= 0.436 Angle : 1.048 13.349 77419 Z= 0.574 Chirality : 0.051 0.199 8589 Planarity : 0.020 0.362 8043 Dihedral : 17.566 59.844 11985 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 52.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % 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: -1.83 (0.11), residues: 5313 helix: -0.93 (0.07), residues: 4368 sheet: None (None), residues: 0 loop : -1.68 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.007 TRP B 44 HIS 0.004 0.002 HIS d 52 PHE 0.043 0.006 PHE Z 48 TYR 0.042 0.005 TYR Q 16 ARG 0.020 0.003 ARG m 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0954 time to fit residues: 3.7492 Evaluate side-chains 23 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.089 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1265 Evaluate side-chains 42 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1626 time to fit residues: 7.2514 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1162 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.115 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1488 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0579 ------------------------------------------------------------------------------- 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: 40.0000 chunk 530 optimal weight: 0.6980 chunk 484 optimal weight: 0.9980 chunk 516 optimal weight: 0.6980 chunk 310 optimal weight: 9.9990 chunk 224 optimal weight: 20.0000 chunk 405 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 466 optimal weight: 6.9990 chunk 488 optimal weight: 10.0000 chunk 514 optimal weight: 20.0000 overall best weight: 2.6784 ------------------------------------------------------------------------------- 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: 0.4821 moved from start: 1.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 55606 Z= 0.417 Angle : 1.101 15.178 77419 Z= 0.608 Chirality : 0.054 0.250 8589 Planarity : 0.015 0.264 8043 Dihedral : 17.343 59.810 11985 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 47.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.10), residues: 5313 helix: -1.13 (0.07), residues: 4410 sheet: None (None), residues: 0 loop : -2.31 (0.18), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.008 TRP j 72 HIS 0.003 0.002 HIS B 52 PHE 0.024 0.005 PHE f 48 TYR 0.041 0.004 TYR E 16 ARG 0.015 0.002 ARG h 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 31 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1176 time to fit residues: 4.0320 Evaluate side-chains 24 residues out of total 117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.089 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1261 Evaluate side-chains 38 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1500 time to fit residues: 6.1006 Evaluate side-chains 30 residues out of total 105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.085 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1173 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 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1502 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 675, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 771, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.2223 > 50: distance: 0 - 1: 26.399 distance: 1 - 2: 17.755 distance: 2 - 3: 20.145 distance: 4 - 5: 31.069 distance: 5 - 6: 14.734 distance: 5 - 8: 9.042 distance: 6 - 12: 11.041 distance: 7 - 34: 41.744 distance: 8 - 9: 21.016 distance: 9 - 10: 18.068 distance: 12 - 13: 28.604 distance: 13 - 14: 20.942 distance: 13 - 16: 11.044 distance: 14 - 15: 8.344 distance: 14 - 18: 3.909 distance: 15 - 45: 49.889 distance: 16 - 17: 32.088 distance: 18 - 19: 29.879 distance: 19 - 20: 23.333 distance: 19 - 22: 16.457 distance: 20 - 21: 6.786 distance: 20 - 27: 29.659 distance: 21 - 53: 23.680 distance: 22 - 23: 10.788 distance: 23 - 24: 5.008 distance: 24 - 25: 42.856 distance: 25 - 26: 17.948 distance: 27 - 28: 14.331 distance: 28 - 29: 25.237 distance: 28 - 31: 27.756 distance: 29 - 30: 20.176 distance: 29 - 34: 32.603 distance: 30 - 62: 37.889 distance: 31 - 32: 19.774 distance: 31 - 33: 46.997 distance: 34 - 35: 26.591 distance: 35 - 36: 26.776 distance: 35 - 38: 22.643 distance: 36 - 37: 36.376 distance: 36 - 45: 36.192 distance: 37 - 69: 26.099 distance: 41 - 42: 40.425 distance: 42 - 43: 25.631 distance: 42 - 44: 36.020 distance: 45 - 46: 29.691 distance: 46 - 47: 27.529 distance: 46 - 49: 24.526 distance: 47 - 48: 51.693 distance: 47 - 53: 25.150 distance: 48 - 77: 48.804 distance: 49 - 50: 49.376 distance: 50 - 51: 18.100 distance: 50 - 52: 57.023 distance: 53 - 54: 38.365 distance: 54 - 55: 31.305 distance: 55 - 56: 8.238 distance: 55 - 62: 27.382 distance: 56 - 85: 21.188 distance: 57 - 58: 22.563 distance: 58 - 59: 21.895 distance: 59 - 60: 21.592 distance: 62 - 63: 20.893 distance: 63 - 64: 28.188 distance: 63 - 66: 23.628 distance: 64 - 65: 3.450 distance: 64 - 69: 25.845 distance: 65 - 93: 25.892 distance: 66 - 67: 9.062 distance: 66 - 68: 15.012 distance: 69 - 70: 17.716 distance: 70 - 71: 26.341 distance: 70 - 73: 23.193 distance: 71 - 72: 4.493 distance: 71 - 77: 12.234 distance: 72 - 101: 24.187 distance: 73 - 74: 39.078 distance: 74 - 75: 18.616 distance: 74 - 76: 35.484 distance: 77 - 78: 33.353 distance: 78 - 79: 29.589 distance: 78 - 81: 25.081 distance: 79 - 80: 12.193 distance: 79 - 85: 20.154 distance: 80 - 110: 21.604 distance: 81 - 82: 28.886 distance: 82 - 83: 23.942 distance: 82 - 84: 8.334 distance: 85 - 86: 18.021 distance: 86 - 87: 31.921 distance: 86 - 89: 54.159 distance: 87 - 88: 13.245 distance: 87 - 93: 19.243 distance: 88 - 117: 45.194 distance: 89 - 91: 23.774 distance: 90 - 92: 37.207 distance: 93 - 94: 33.417 distance: 94 - 95: 30.603 distance: 94 - 97: 22.522 distance: 95 - 96: 26.397 distance: 95 - 101: 13.984 distance: 97 - 98: 27.101 distance: 98 - 99: 43.589 distance: 98 - 100: 25.063 distance: 102 - 103: 40.973 distance: 102 - 105: 12.008 distance: 103 - 104: 26.015 distance: 103 - 110: 33.492 distance: 105 - 106: 21.224 distance: 106 - 107: 41.185 distance: 107 - 108: 18.312 distance: 108 - 109: 36.212 distance: 110 - 111: 37.238 distance: 111 - 112: 43.748 distance: 111 - 114: 40.374 distance: 112 - 113: 39.855 distance: 112 - 117: 22.212 distance: 114 - 115: 31.247 distance: 114 - 116: 26.136 distance: 117 - 118: 11.418 distance: 118 - 119: 18.290 distance: 118 - 121: 11.969 distance: 119 - 120: 36.027 distance: 119 - 125: 49.999 distance: 121 - 122: 62.235 distance: 122 - 123: 15.230 distance: 122 - 124: 25.557 distance: 125 - 126: 24.515 distance: 126 - 127: 17.155 distance: 126 - 129: 17.687 distance: 127 - 134: 31.548 distance: 129 - 130: 17.177 distance: 130 - 131: 47.922 distance: 131 - 132: 39.475 distance: 134 - 135: 24.381 distance: 135 - 136: 24.689 distance: 135 - 138: 39.183 distance: 136 - 137: 9.922 distance: 136 - 141: 4.423 distance: 138 - 139: 41.002 distance: 138 - 140: 20.972 distance: 141 - 142: 27.241 distance: 143 - 144: 30.507 distance: 143 - 146: 25.680 distance: 144 - 170: 41.243 distance: 146 - 147: 33.880 distance: 147 - 148: 14.919 distance: 147 - 150: 26.581 distance: 148 - 149: 17.555 distance: 148 - 153: 30.716 distance: 150 - 151: 33.555 distance: 153 - 154: 11.718 distance: 154 - 155: 27.742 distance: 154 - 157: 11.951 distance: 155 - 156: 9.248 distance: 155 - 162: 15.334 distance: 157 - 158: 54.506 distance: 159 - 161: 33.213 distance: 162 - 163: 8.627 distance: 163 - 164: 22.341 distance: 163 - 166: 14.408 distance: 164 - 165: 20.564 distance: 164 - 170: 19.178 distance: 166 - 167: 20.340 distance: 167 - 168: 6.880 distance: 167 - 169: 3.119 distance: 170 - 171: 22.244 distance: 171 - 172: 25.633 distance: 171 - 174: 20.460 distance: 172 - 173: 16.909 distance: 172 - 182: 27.832 distance: 174 - 175: 15.596 distance: 175 - 176: 31.189 distance: 175 - 177: 5.842 distance: 176 - 178: 8.054 distance: 177 - 179: 5.375 distance: 178 - 180: 4.806 distance: 179 - 180: 38.172 distance: 180 - 181: 6.412 distance: 182 - 183: 20.257 distance: 183 - 184: 39.109 distance: 183 - 186: 40.602 distance: 184 - 190: 36.695 distance: 186 - 187: 8.566 distance: 186 - 188: 39.437 distance: 187 - 189: 7.607 distance: 190 - 191: 38.900 distance: 191 - 192: 31.759 distance: 192 - 193: 40.757 distance: 192 - 194: 18.963 distance: 194 - 195: 31.446 distance: 195 - 196: 30.373 distance: 195 - 198: 11.440 distance: 196 - 197: 42.055 distance: 198 - 199: 26.391 distance: 199 - 200: 34.237 distance: 199 - 201: 5.540 distance: 200 - 202: 3.882 distance: 201 - 203: 10.316 distance: 203 - 204: 30.548