Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 20 05:04:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et2_28584/10_2023/8et2_28584.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et2_28584/10_2023/8et2_28584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et2_28584/10_2023/8et2_28584.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et2_28584/10_2023/8et2_28584.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et2_28584/10_2023/8et2_28584.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et2_28584/10_2023/8et2_28584.pdb" } resolution = 4.96 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= 0.004 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 27672 2.51 5 N 7752 2.21 5 O 8016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "C TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "E TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 163": "OE1" <-> "OE2" Residue "F TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 163": "OE1" <-> "OE2" Residue "G TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 163": "OE1" <-> "OE2" Residue "H TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 163": "OE1" <-> "OE2" Residue "I TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 163": "OE1" <-> "OE2" Residue "J TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 163": "OE1" <-> "OE2" Residue "K TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 163": "OE1" <-> "OE2" Residue "L TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 163": "OE1" <-> "OE2" Residue "M TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 163": "OE1" <-> "OE2" Residue "N TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 163": "OE1" <-> "OE2" Residue "O TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 163": "OE1" <-> "OE2" Residue "P TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 163": "OE1" <-> "OE2" Residue "Q TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 163": "OE1" <-> "OE2" Residue "R TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 163": "OE1" <-> "OE2" Residue "S TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 163": "OE1" <-> "OE2" Residue "T TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 163": "OE1" <-> "OE2" Residue "U TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 163": "OE1" <-> "OE2" Residue "V TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 163": "OE1" <-> "OE2" Residue "W TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 163": "OE1" <-> "OE2" Residue "X TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 43584 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "B" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "C" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "D" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "E" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "F" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "G" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "H" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "I" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "J" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "K" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "L" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "M" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "N" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "O" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "P" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "Q" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "R" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "S" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "T" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "U" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "V" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "W" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Chain: "X" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 Time building chain proxies: 20.62, per 1000 atoms: 0.47 Number of scatterers: 43584 At special positions: 0 Unit cell: (273.9, 273.9, 73.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 8016 8.00 N 7752 7.00 C 27672 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: 15.38 Conformation dependent library (CDL) restraints added in 6.1 seconds 10416 Ramachandran restraints generated. 5208 Oldfield, 0 Emsley, 5208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9984 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 144 sheets defined 14.5% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.76 Creating SS restraints... Processing helix chain 'A' and resid 4 through 17 removed outlier: 3.846A pdb=" N THR A 9 " --> pdb=" O PHE A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 135 removed outlier: 4.049A pdb=" N ALA A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 152 Processing helix chain 'B' and resid 4 through 17 removed outlier: 3.847A pdb=" N THR B 9 " --> pdb=" O PHE B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 135 removed outlier: 4.050A pdb=" N ALA B 131 " --> pdb=" O GLN B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 152 Processing helix chain 'C' and resid 4 through 17 removed outlier: 3.847A pdb=" N THR C 9 " --> pdb=" O PHE C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 135 removed outlier: 4.049A pdb=" N ALA C 131 " --> pdb=" O GLN C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 152 Processing helix chain 'D' and resid 4 through 17 removed outlier: 3.847A pdb=" N THR D 9 " --> pdb=" O PHE D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 135 removed outlier: 4.049A pdb=" N ALA D 131 " --> pdb=" O GLN D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 152 Processing helix chain 'E' and resid 4 through 17 removed outlier: 3.847A pdb=" N THR E 9 " --> pdb=" O PHE E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 135 removed outlier: 4.050A pdb=" N ALA E 131 " --> pdb=" O GLN E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 152 Processing helix chain 'F' and resid 4 through 17 removed outlier: 3.847A pdb=" N THR F 9 " --> pdb=" O PHE F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 135 removed outlier: 4.050A pdb=" N ALA F 131 " --> pdb=" O GLN F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 152 Processing helix chain 'G' and resid 4 through 17 removed outlier: 3.847A pdb=" N THR G 9 " --> pdb=" O PHE G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 135 removed outlier: 4.050A pdb=" N ALA G 131 " --> pdb=" O GLN G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 152 Processing helix chain 'H' and resid 4 through 17 removed outlier: 3.847A pdb=" N THR H 9 " --> pdb=" O PHE H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 135 removed outlier: 4.049A pdb=" N ALA H 131 " --> pdb=" O GLN H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 152 Processing helix chain 'I' and resid 4 through 17 removed outlier: 3.847A pdb=" N THR I 9 " --> pdb=" O PHE I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 135 removed outlier: 4.050A pdb=" N ALA I 131 " --> pdb=" O GLN I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 152 Processing helix chain 'J' and resid 4 through 17 removed outlier: 3.848A pdb=" N THR J 9 " --> pdb=" O PHE J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 135 removed outlier: 4.049A pdb=" N ALA J 131 " --> pdb=" O GLN J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 152 Processing helix chain 'K' and resid 4 through 17 removed outlier: 3.847A pdb=" N THR K 9 " --> pdb=" O PHE K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 135 removed outlier: 4.050A pdb=" N ALA K 131 " --> pdb=" O GLN K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 152 Processing helix chain 'L' and resid 4 through 17 removed outlier: 3.847A pdb=" N THR L 9 " --> pdb=" O PHE L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 135 removed outlier: 4.050A pdb=" N ALA L 131 " --> pdb=" O GLN L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 152 Processing helix chain 'M' and resid 4 through 17 removed outlier: 3.847A pdb=" N THR M 9 " --> pdb=" O PHE M 5 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 135 removed outlier: 4.050A pdb=" N ALA M 131 " --> pdb=" O GLN M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 152 Processing helix chain 'N' and resid 4 through 17 removed outlier: 3.847A pdb=" N THR N 9 " --> pdb=" O PHE N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 127 through 135 removed outlier: 4.050A pdb=" N ALA N 131 " --> pdb=" O GLN N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 152 Processing helix chain 'O' and resid 4 through 17 removed outlier: 3.847A pdb=" N THR O 9 " --> pdb=" O PHE O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 135 removed outlier: 4.049A pdb=" N ALA O 131 " --> pdb=" O GLN O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 144 through 152 Processing helix chain 'P' and resid 4 through 17 removed outlier: 3.847A pdb=" N THR P 9 " --> pdb=" O PHE P 5 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 135 removed outlier: 4.050A pdb=" N ALA P 131 " --> pdb=" O GLN P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 144 through 152 Processing helix chain 'Q' and resid 4 through 17 removed outlier: 3.847A pdb=" N THR Q 9 " --> pdb=" O PHE Q 5 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 135 removed outlier: 4.049A pdb=" N ALA Q 131 " --> pdb=" O GLN Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 152 Processing helix chain 'R' and resid 4 through 17 removed outlier: 3.846A pdb=" N THR R 9 " --> pdb=" O PHE R 5 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 135 removed outlier: 4.049A pdb=" N ALA R 131 " --> pdb=" O GLN R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 152 Processing helix chain 'S' and resid 4 through 17 removed outlier: 3.847A pdb=" N THR S 9 " --> pdb=" O PHE S 5 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 135 removed outlier: 4.049A pdb=" N ALA S 131 " --> pdb=" O GLN S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 144 through 152 Processing helix chain 'T' and resid 4 through 17 removed outlier: 3.847A pdb=" N THR T 9 " --> pdb=" O PHE T 5 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 135 removed outlier: 4.050A pdb=" N ALA T 131 " --> pdb=" O GLN T 127 " (cutoff:3.500A) Processing helix chain 'T' and resid 144 through 152 Processing helix chain 'U' and resid 4 through 17 removed outlier: 3.847A pdb=" N THR U 9 " --> pdb=" O PHE U 5 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 135 removed outlier: 4.049A pdb=" N ALA U 131 " --> pdb=" O GLN U 127 " (cutoff:3.500A) Processing helix chain 'U' and resid 144 through 152 Processing helix chain 'V' and resid 4 through 17 removed outlier: 3.847A pdb=" N THR V 9 " --> pdb=" O PHE V 5 " (cutoff:3.500A) Processing helix chain 'V' and resid 127 through 135 removed outlier: 4.050A pdb=" N ALA V 131 " --> pdb=" O GLN V 127 " (cutoff:3.500A) Processing helix chain 'V' and resid 144 through 152 Processing helix chain 'W' and resid 4 through 17 removed outlier: 3.847A pdb=" N THR W 9 " --> pdb=" O PHE W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 127 through 135 removed outlier: 4.049A pdb=" N ALA W 131 " --> pdb=" O GLN W 127 " (cutoff:3.500A) Processing helix chain 'W' and resid 144 through 152 Processing helix chain 'X' and resid 4 through 17 removed outlier: 3.846A pdb=" N THR X 9 " --> pdb=" O PHE X 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 127 through 135 removed outlier: 4.050A pdb=" N ALA X 131 " --> pdb=" O GLN X 127 " (cutoff:3.500A) Processing helix chain 'X' and resid 144 through 152 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 44 removed outlier: 3.744A pdb=" N ARG A 44 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 50 " --> pdb=" O ARG A 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 95 removed outlier: 3.712A pdb=" N THR A 161 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 180 Processing sheet with id=AA6, first strand: chain 'A' and resid 211 through 213 Processing sheet with id=AA7, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AA8, first strand: chain 'B' and resid 43 through 44 removed outlier: 3.743A pdb=" N ARG B 44 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG B 50 " --> pdb=" O ARG B 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 84 through 95 removed outlier: 3.712A pdb=" N THR B 161 " --> pdb=" O ASN B 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AB2, first strand: chain 'B' and resid 170 through 180 Processing sheet with id=AB3, first strand: chain 'B' and resid 211 through 213 Processing sheet with id=AB4, first strand: chain 'C' and resid 23 through 24 Processing sheet with id=AB5, first strand: chain 'C' and resid 43 through 44 removed outlier: 3.745A pdb=" N ARG C 44 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG C 50 " --> pdb=" O ARG C 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 84 through 95 removed outlier: 3.710A pdb=" N THR C 161 " --> pdb=" O ASN C 123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 98 through 99 Processing sheet with id=AB8, first strand: chain 'C' and resid 170 through 180 Processing sheet with id=AB9, first strand: chain 'C' and resid 211 through 213 Processing sheet with id=AC1, first strand: chain 'D' and resid 23 through 24 Processing sheet with id=AC2, first strand: chain 'D' and resid 43 through 44 removed outlier: 3.745A pdb=" N ARG D 44 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG D 50 " --> pdb=" O ARG D 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR D 161 " --> pdb=" O ASN D 123 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 98 through 99 Processing sheet with id=AC5, first strand: chain 'D' and resid 170 through 180 Processing sheet with id=AC6, first strand: chain 'D' and resid 211 through 213 Processing sheet with id=AC7, first strand: chain 'E' and resid 23 through 24 Processing sheet with id=AC8, first strand: chain 'E' and resid 43 through 44 removed outlier: 3.744A pdb=" N ARG E 44 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG E 50 " --> pdb=" O ARG E 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 84 through 95 removed outlier: 3.712A pdb=" N THR E 161 " --> pdb=" O ASN E 123 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 98 through 99 Processing sheet with id=AD2, first strand: chain 'E' and resid 170 through 180 Processing sheet with id=AD3, first strand: chain 'E' and resid 211 through 213 Processing sheet with id=AD4, first strand: chain 'F' and resid 23 through 24 Processing sheet with id=AD5, first strand: chain 'F' and resid 43 through 44 removed outlier: 3.744A pdb=" N ARG F 44 " --> pdb=" O ARG F 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG F 50 " --> pdb=" O ARG F 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'F' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR F 161 " --> pdb=" O ASN F 123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 98 through 99 Processing sheet with id=AD8, first strand: chain 'F' and resid 170 through 180 Processing sheet with id=AD9, first strand: chain 'F' and resid 211 through 213 Processing sheet with id=AE1, first strand: chain 'G' and resid 23 through 24 Processing sheet with id=AE2, first strand: chain 'G' and resid 43 through 44 removed outlier: 3.744A pdb=" N ARG G 44 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG G 50 " --> pdb=" O ARG G 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'G' and resid 84 through 95 removed outlier: 3.712A pdb=" N THR G 161 " --> pdb=" O ASN G 123 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 98 through 99 Processing sheet with id=AE5, first strand: chain 'G' and resid 170 through 180 Processing sheet with id=AE6, first strand: chain 'G' and resid 211 through 213 Processing sheet with id=AE7, first strand: chain 'H' and resid 23 through 24 Processing sheet with id=AE8, first strand: chain 'H' and resid 43 through 44 removed outlier: 3.743A pdb=" N ARG H 44 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG H 50 " --> pdb=" O ARG H 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'H' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR H 161 " --> pdb=" O ASN H 123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 98 through 99 Processing sheet with id=AF2, first strand: chain 'H' and resid 170 through 180 Processing sheet with id=AF3, first strand: chain 'H' and resid 211 through 213 Processing sheet with id=AF4, first strand: chain 'I' and resid 23 through 24 Processing sheet with id=AF5, first strand: chain 'I' and resid 43 through 44 removed outlier: 3.743A pdb=" N ARG I 44 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG I 50 " --> pdb=" O ARG I 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'I' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR I 161 " --> pdb=" O ASN I 123 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 98 through 99 Processing sheet with id=AF8, first strand: chain 'I' and resid 170 through 180 Processing sheet with id=AF9, first strand: chain 'I' and resid 211 through 213 Processing sheet with id=AG1, first strand: chain 'J' and resid 23 through 24 Processing sheet with id=AG2, first strand: chain 'J' and resid 43 through 44 removed outlier: 3.745A pdb=" N ARG J 44 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG J 50 " --> pdb=" O ARG J 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'J' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR J 161 " --> pdb=" O ASN J 123 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 98 through 99 Processing sheet with id=AG5, first strand: chain 'J' and resid 170 through 180 Processing sheet with id=AG6, first strand: chain 'J' and resid 211 through 213 Processing sheet with id=AG7, first strand: chain 'K' and resid 23 through 24 Processing sheet with id=AG8, first strand: chain 'K' and resid 43 through 44 removed outlier: 3.744A pdb=" N ARG K 44 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG K 50 " --> pdb=" O ARG K 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'K' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR K 161 " --> pdb=" O ASN K 123 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 98 through 99 Processing sheet with id=AH2, first strand: chain 'K' and resid 170 through 180 Processing sheet with id=AH3, first strand: chain 'K' and resid 211 through 213 Processing sheet with id=AH4, first strand: chain 'L' and resid 23 through 24 Processing sheet with id=AH5, first strand: chain 'L' and resid 43 through 44 removed outlier: 3.745A pdb=" N ARG L 44 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG L 50 " --> pdb=" O ARG L 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'L' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR L 161 " --> pdb=" O ASN L 123 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 98 through 99 Processing sheet with id=AH8, first strand: chain 'L' and resid 170 through 180 Processing sheet with id=AH9, first strand: chain 'L' and resid 211 through 213 Processing sheet with id=AI1, first strand: chain 'M' and resid 23 through 24 Processing sheet with id=AI2, first strand: chain 'M' and resid 43 through 44 removed outlier: 3.744A pdb=" N ARG M 44 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG M 50 " --> pdb=" O ARG M 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'M' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR M 161 " --> pdb=" O ASN M 123 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 98 through 99 Processing sheet with id=AI5, first strand: chain 'M' and resid 170 through 180 Processing sheet with id=AI6, first strand: chain 'M' and resid 211 through 213 Processing sheet with id=AI7, first strand: chain 'N' and resid 23 through 24 Processing sheet with id=AI8, first strand: chain 'N' and resid 43 through 44 removed outlier: 3.745A pdb=" N ARG N 44 " --> pdb=" O ARG N 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG N 50 " --> pdb=" O ARG N 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain 'N' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR N 161 " --> pdb=" O ASN N 123 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'N' and resid 98 through 99 Processing sheet with id=AJ2, first strand: chain 'N' and resid 170 through 180 Processing sheet with id=AJ3, first strand: chain 'N' and resid 211 through 213 Processing sheet with id=AJ4, first strand: chain 'O' and resid 23 through 24 Processing sheet with id=AJ5, first strand: chain 'O' and resid 43 through 44 removed outlier: 3.745A pdb=" N ARG O 44 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG O 50 " --> pdb=" O ARG O 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ5 Processing sheet with id=AJ6, first strand: chain 'O' and resid 84 through 95 removed outlier: 3.712A pdb=" N THR O 161 " --> pdb=" O ASN O 123 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'O' and resid 98 through 99 Processing sheet with id=AJ8, first strand: chain 'O' and resid 170 through 180 Processing sheet with id=AJ9, first strand: chain 'O' and resid 211 through 213 Processing sheet with id=AK1, first strand: chain 'P' and resid 23 through 24 Processing sheet with id=AK2, first strand: chain 'P' and resid 43 through 44 removed outlier: 3.744A pdb=" N ARG P 44 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG P 50 " --> pdb=" O ARG P 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK2 Processing sheet with id=AK3, first strand: chain 'P' and resid 84 through 95 removed outlier: 3.712A pdb=" N THR P 161 " --> pdb=" O ASN P 123 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'P' and resid 98 through 99 Processing sheet with id=AK5, first strand: chain 'P' and resid 170 through 180 Processing sheet with id=AK6, first strand: chain 'P' and resid 211 through 213 Processing sheet with id=AK7, first strand: chain 'Q' and resid 23 through 24 Processing sheet with id=AK8, first strand: chain 'Q' and resid 43 through 44 removed outlier: 3.745A pdb=" N ARG Q 44 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG Q 50 " --> pdb=" O ARG Q 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK8 Processing sheet with id=AK9, first strand: chain 'Q' and resid 84 through 95 removed outlier: 3.710A pdb=" N THR Q 161 " --> pdb=" O ASN Q 123 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'Q' and resid 98 through 99 Processing sheet with id=AL2, first strand: chain 'Q' and resid 170 through 180 Processing sheet with id=AL3, first strand: chain 'Q' and resid 211 through 213 Processing sheet with id=AL4, first strand: chain 'R' and resid 23 through 24 Processing sheet with id=AL5, first strand: chain 'R' and resid 43 through 44 removed outlier: 3.745A pdb=" N ARG R 44 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG R 50 " --> pdb=" O ARG R 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL5 Processing sheet with id=AL6, first strand: chain 'R' and resid 84 through 95 removed outlier: 3.712A pdb=" N THR R 161 " --> pdb=" O ASN R 123 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'R' and resid 98 through 99 Processing sheet with id=AL8, first strand: chain 'R' and resid 170 through 180 Processing sheet with id=AL9, first strand: chain 'R' and resid 211 through 213 Processing sheet with id=AM1, first strand: chain 'S' and resid 23 through 24 Processing sheet with id=AM2, first strand: chain 'S' and resid 43 through 44 removed outlier: 3.744A pdb=" N ARG S 44 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG S 50 " --> pdb=" O ARG S 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM2 Processing sheet with id=AM3, first strand: chain 'S' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR S 161 " --> pdb=" O ASN S 123 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'S' and resid 98 through 99 Processing sheet with id=AM5, first strand: chain 'S' and resid 170 through 180 Processing sheet with id=AM6, first strand: chain 'S' and resid 211 through 213 Processing sheet with id=AM7, first strand: chain 'T' and resid 23 through 24 Processing sheet with id=AM8, first strand: chain 'T' and resid 43 through 44 removed outlier: 3.744A pdb=" N ARG T 44 " --> pdb=" O ARG T 50 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG T 50 " --> pdb=" O ARG T 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM8 Processing sheet with id=AM9, first strand: chain 'T' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR T 161 " --> pdb=" O ASN T 123 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'T' and resid 98 through 99 Processing sheet with id=AN2, first strand: chain 'T' and resid 170 through 180 Processing sheet with id=AN3, first strand: chain 'T' and resid 211 through 213 Processing sheet with id=AN4, first strand: chain 'U' and resid 23 through 24 Processing sheet with id=AN5, first strand: chain 'U' and resid 43 through 44 removed outlier: 3.745A pdb=" N ARG U 44 " --> pdb=" O ARG U 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG U 50 " --> pdb=" O ARG U 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN5 Processing sheet with id=AN6, first strand: chain 'U' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR U 161 " --> pdb=" O ASN U 123 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'U' and resid 98 through 99 Processing sheet with id=AN8, first strand: chain 'U' and resid 170 through 180 Processing sheet with id=AN9, first strand: chain 'U' and resid 211 through 213 Processing sheet with id=AO1, first strand: chain 'V' and resid 23 through 24 Processing sheet with id=AO2, first strand: chain 'V' and resid 43 through 44 removed outlier: 3.744A pdb=" N ARG V 44 " --> pdb=" O ARG V 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG V 50 " --> pdb=" O ARG V 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AO2 Processing sheet with id=AO3, first strand: chain 'V' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR V 161 " --> pdb=" O ASN V 123 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'V' and resid 98 through 99 Processing sheet with id=AO5, first strand: chain 'V' and resid 170 through 180 Processing sheet with id=AO6, first strand: chain 'V' and resid 211 through 213 Processing sheet with id=AO7, first strand: chain 'W' and resid 23 through 24 Processing sheet with id=AO8, first strand: chain 'W' and resid 43 through 44 removed outlier: 3.744A pdb=" N ARG W 44 " --> pdb=" O ARG W 50 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG W 50 " --> pdb=" O ARG W 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AO8 Processing sheet with id=AO9, first strand: chain 'W' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR W 161 " --> pdb=" O ASN W 123 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'W' and resid 98 through 99 Processing sheet with id=AP2, first strand: chain 'W' and resid 170 through 180 Processing sheet with id=AP3, first strand: chain 'W' and resid 211 through 213 Processing sheet with id=AP4, first strand: chain 'X' and resid 23 through 24 Processing sheet with id=AP5, first strand: chain 'X' and resid 43 through 44 removed outlier: 3.744A pdb=" N ARG X 44 " --> pdb=" O ARG X 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG X 50 " --> pdb=" O ARG X 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP5 Processing sheet with id=AP6, first strand: chain 'X' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR X 161 " --> pdb=" O ASN X 123 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'X' and resid 98 through 99 Processing sheet with id=AP8, first strand: chain 'X' and resid 170 through 180 Processing sheet with id=AP9, first strand: chain 'X' and resid 211 through 213 1272 hydrogen bonds defined for protein. 3312 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.81 Time building geometry restraints manager: 16.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14299 1.34 - 1.46: 9038 1.46 - 1.58: 20823 1.58 - 1.70: 0 1.70 - 1.81: 240 Bond restraints: 44400 Sorted by residual: bond pdb=" CA VAL Q 165 " pdb=" CB VAL Q 165 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.08e-02 8.57e+03 1.71e+00 bond pdb=" CA VAL N 165 " pdb=" CB VAL N 165 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.08e-02 8.57e+03 1.69e+00 bond pdb=" CA VAL C 165 " pdb=" CB VAL C 165 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.08e-02 8.57e+03 1.63e+00 bond pdb=" CA VAL M 165 " pdb=" CB VAL M 165 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.08e-02 8.57e+03 1.61e+00 bond pdb=" CA VAL W 165 " pdb=" CB VAL W 165 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.08e-02 8.57e+03 1.61e+00 ... (remaining 44395 not shown) Histogram of bond angle deviations from ideal: 99.96 - 106.77: 870 106.77 - 113.59: 24202 113.59 - 120.40: 16099 120.40 - 127.21: 18157 127.21 - 134.03: 288 Bond angle restraints: 59616 Sorted by residual: angle pdb=" CA ARG H 33 " pdb=" CB ARG H 33 " pdb=" CG ARG H 33 " ideal model delta sigma weight residual 114.10 121.95 -7.85 2.00e+00 2.50e-01 1.54e+01 angle pdb=" CA ARG E 33 " pdb=" CB ARG E 33 " pdb=" CG ARG E 33 " ideal model delta sigma weight residual 114.10 121.94 -7.84 2.00e+00 2.50e-01 1.54e+01 angle pdb=" CA ARG V 33 " pdb=" CB ARG V 33 " pdb=" CG ARG V 33 " ideal model delta sigma weight residual 114.10 121.94 -7.84 2.00e+00 2.50e-01 1.54e+01 angle pdb=" CA ARG O 33 " pdb=" CB ARG O 33 " pdb=" CG ARG O 33 " ideal model delta sigma weight residual 114.10 121.93 -7.83 2.00e+00 2.50e-01 1.53e+01 angle pdb=" CA ARG S 33 " pdb=" CB ARG S 33 " pdb=" CG ARG S 33 " ideal model delta sigma weight residual 114.10 121.93 -7.83 2.00e+00 2.50e-01 1.53e+01 ... (remaining 59611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 23998 16.95 - 33.91: 2430 33.91 - 50.86: 380 50.86 - 67.82: 24 67.82 - 84.77: 48 Dihedral angle restraints: 26880 sinusoidal: 11496 harmonic: 15384 Sorted by residual: dihedral pdb=" CA ALA E 222 " pdb=" C ALA E 222 " pdb=" N GLY E 223 " pdb=" CA GLY E 223 " ideal model delta harmonic sigma weight residual -180.00 -154.41 -25.59 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA ALA U 222 " pdb=" C ALA U 222 " pdb=" N GLY U 223 " pdb=" CA GLY U 223 " ideal model delta harmonic sigma weight residual -180.00 -154.44 -25.56 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA ALA T 222 " pdb=" C ALA T 222 " pdb=" N GLY T 223 " pdb=" CA GLY T 223 " ideal model delta harmonic sigma weight residual -180.00 -154.44 -25.56 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 26877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3835 0.036 - 0.072: 1795 0.072 - 0.108: 675 0.108 - 0.144: 175 0.144 - 0.179: 96 Chirality restraints: 6576 Sorted by residual: chirality pdb=" CA ASN F 154 " pdb=" N ASN F 154 " pdb=" C ASN F 154 " pdb=" CB ASN F 154 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.05e-01 chirality pdb=" CA ASN T 154 " pdb=" N ASN T 154 " pdb=" C ASN T 154 " pdb=" CB ASN T 154 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" CA ASN C 154 " pdb=" N ASN C 154 " pdb=" C ASN C 154 " pdb=" CB ASN C 154 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.02e-01 ... (remaining 6573 not shown) Planarity restraints: 7584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 168 " 0.014 2.00e-02 2.50e+03 2.64e-02 6.98e+00 pdb=" C GLU F 168 " -0.046 2.00e-02 2.50e+03 pdb=" O GLU F 168 " 0.016 2.00e-02 2.50e+03 pdb=" N THR F 169 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU P 168 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.91e+00 pdb=" C GLU P 168 " 0.046 2.00e-02 2.50e+03 pdb=" O GLU P 168 " -0.016 2.00e-02 2.50e+03 pdb=" N THR P 169 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU Q 168 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C GLU Q 168 " 0.045 2.00e-02 2.50e+03 pdb=" O GLU Q 168 " -0.016 2.00e-02 2.50e+03 pdb=" N THR Q 169 " -0.016 2.00e-02 2.50e+03 ... (remaining 7581 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 308 2.48 - 3.09: 30468 3.09 - 3.69: 66955 3.69 - 4.30: 92308 4.30 - 4.90: 148193 Nonbonded interactions: 338232 Sorted by model distance: nonbonded pdb=" O GLN W 85 " pdb=" OG1 THR X 198 " model vdw 1.879 2.440 nonbonded pdb=" O MET T 16 " pdb=" OG SER U 27 " model vdw 1.910 2.440 nonbonded pdb=" O GLN L 85 " pdb=" OG1 THR M 198 " model vdw 1.958 2.440 nonbonded pdb=" O GLN T 85 " pdb=" OG1 THR U 198 " model vdw 1.968 2.440 nonbonded pdb=" O MET S 16 " pdb=" OG SER T 27 " model vdw 2.017 2.440 ... (remaining 338227 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 6.060 Check model and map are aligned: 0.640 Set scattering table: 0.360 Process input model: 98.130 Find NCS groups from input model: 2.780 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 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: 111.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5034 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 44400 Z= 0.243 Angle : 1.001 10.082 59616 Z= 0.558 Chirality : 0.050 0.179 6576 Planarity : 0.006 0.047 7584 Dihedral : 13.701 84.769 16896 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.73 % Favored : 88.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.10), residues: 5208 helix: -1.06 (0.19), residues: 696 sheet: -2.17 (0.11), residues: 2136 loop : -3.71 (0.10), residues: 2376 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10416 Ramachandran restraints generated. 5208 Oldfield, 0 Emsley, 5208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10416 Ramachandran restraints generated. 5208 Oldfield, 0 Emsley, 5208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1641 time to fit residues: 5.1463 Evaluate side-chains 25 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.198 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 445 optimal weight: 0.2980 chunk 400 optimal weight: 3.9990 chunk 222 optimal weight: 0.0000 chunk 136 optimal weight: 4.9990 chunk 269 optimal weight: 0.7980 chunk 213 optimal weight: 0.0270 chunk 413 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 251 optimal weight: 7.9990 chunk 308 optimal weight: 5.9990 chunk 479 optimal weight: 30.0000 overall best weight: 1.0244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 181 GLN O 186 HIS O 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5039 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 44400 Z= 0.182 Angle : 0.726 7.245 59616 Z= 0.383 Chirality : 0.048 0.158 6576 Planarity : 0.005 0.044 7584 Dihedral : 7.045 23.673 5808 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 0.50 % Allowed : 6.44 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.11), residues: 5208 helix: -0.64 (0.19), residues: 744 sheet: -1.63 (0.13), residues: 1656 loop : -3.87 (0.09), residues: 2808 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 30 average time/residue: 0.1447 time to fit residues: 5.1418 Evaluate side-chains 21 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.202 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 266 optimal weight: 0.0040 chunk 148 optimal weight: 10.0000 chunk 399 optimal weight: 0.8980 chunk 326 optimal weight: 0.1980 chunk 132 optimal weight: 4.9990 chunk 480 optimal weight: 1.9990 chunk 518 optimal weight: 0.7980 chunk 427 optimal weight: 0.0470 chunk 476 optimal weight: 0.0770 chunk 163 optimal weight: 0.7980 chunk 385 optimal weight: 0.4980 overall best weight: 0.1648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4966 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 44400 Z= 0.153 Angle : 0.680 7.655 59616 Z= 0.358 Chirality : 0.047 0.149 6576 Planarity : 0.004 0.040 7584 Dihedral : 6.378 22.332 5808 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.50 % Allowed : 5.94 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.11), residues: 5208 helix: -0.51 (0.19), residues: 768 sheet: -1.80 (0.11), residues: 2232 loop : -3.88 (0.10), residues: 2208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 30 average time/residue: 0.1664 time to fit residues: 5.7831 Evaluate side-chains 22 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.220 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 0.0670 chunk 361 optimal weight: 0.0980 chunk 249 optimal weight: 0.0980 chunk 53 optimal weight: 10.0000 chunk 229 optimal weight: 0.4980 chunk 322 optimal weight: 0.5980 chunk 482 optimal weight: 2.9990 chunk 510 optimal weight: 0.4980 chunk 251 optimal weight: 0.0670 chunk 456 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 overall best weight: 0.1656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4907 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 44400 Z= 0.150 Angle : 0.672 7.493 59616 Z= 0.347 Chirality : 0.047 0.141 6576 Planarity : 0.004 0.039 7584 Dihedral : 6.230 21.952 5808 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 0.50 % Allowed : 3.96 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.11), residues: 5208 helix: -0.29 (0.19), residues: 768 sheet: -1.86 (0.10), residues: 2232 loop : -3.82 (0.10), residues: 2208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.1721 time to fit residues: 5.3983 Evaluate side-chains 21 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.196 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 425 optimal weight: 0.0970 chunk 289 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 380 optimal weight: 6.9990 chunk 210 optimal weight: 0.5980 chunk 435 optimal weight: 0.0020 chunk 352 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 260 optimal weight: 0.9990 chunk 458 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4931 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 44400 Z= 0.143 Angle : 0.653 7.579 59616 Z= 0.336 Chirality : 0.045 0.134 6576 Planarity : 0.004 0.039 7584 Dihedral : 5.991 21.068 5808 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.50 % Allowed : 6.44 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.11), residues: 5208 helix: -0.42 (0.19), residues: 768 sheet: -1.88 (0.10), residues: 2232 loop : -3.75 (0.10), residues: 2208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 28 average time/residue: 0.1790 time to fit residues: 5.7977 Evaluate side-chains 21 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.219 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 0.8980 chunk 459 optimal weight: 0.0010 chunk 100 optimal weight: 2.9990 chunk 299 optimal weight: 6.9990 chunk 125 optimal weight: 0.0370 chunk 510 optimal weight: 0.0670 chunk 424 optimal weight: 9.9990 chunk 236 optimal weight: 0.0470 chunk 42 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 268 optimal weight: 0.9980 overall best weight: 0.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4797 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 44400 Z= 0.159 Angle : 0.712 8.207 59616 Z= 0.366 Chirality : 0.046 0.167 6576 Planarity : 0.004 0.040 7584 Dihedral : 5.913 20.835 5808 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.11), residues: 5208 helix: -0.73 (0.19), residues: 768 sheet: -1.87 (0.10), residues: 2304 loop : -3.61 (0.11), residues: 2136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.2095 time to fit residues: 6.4311 Evaluate side-chains 24 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.214 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 0.0030 chunk 57 optimal weight: 1.9990 chunk 291 optimal weight: 9.9990 chunk 373 optimal weight: 0.8980 chunk 289 optimal weight: 0.0050 chunk 430 optimal weight: 0.5980 chunk 285 optimal weight: 0.3980 chunk 508 optimal weight: 4.9990 chunk 318 optimal weight: 5.9990 chunk 310 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 overall best weight: 0.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4789 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 44400 Z= 0.156 Angle : 0.681 7.985 59616 Z= 0.354 Chirality : 0.048 0.171 6576 Planarity : 0.004 0.040 7584 Dihedral : 5.810 20.703 5808 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 0.50 % Allowed : 1.98 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.10), residues: 5208 helix: -1.34 (0.18), residues: 768 sheet: -2.18 (0.10), residues: 2424 loop : -3.38 (0.11), residues: 2016 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 28 average time/residue: 0.2035 time to fit residues: 6.5262 Evaluate side-chains 22 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.220 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0538 time to fit residues: 0.3743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 7.9990 chunk 203 optimal weight: 8.9990 chunk 303 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 98 optimal weight: 0.2980 chunk 323 optimal weight: 0.8980 chunk 346 optimal weight: 0.1980 chunk 251 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 400 optimal weight: 0.0170 overall best weight: 1.4820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4992 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 44400 Z= 0.182 Angle : 0.676 8.210 59616 Z= 0.351 Chirality : 0.048 0.164 6576 Planarity : 0.004 0.042 7584 Dihedral : 5.870 20.809 5808 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.10), residues: 5208 helix: -1.25 (0.18), residues: 768 sheet: -2.06 (0.11), residues: 1968 loop : -3.31 (0.10), residues: 2472 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.2009 time to fit residues: 6.4194 Evaluate side-chains 20 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.201 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 462 optimal weight: 3.9990 chunk 487 optimal weight: 0.9990 chunk 444 optimal weight: 8.9990 chunk 474 optimal weight: 0.0970 chunk 285 optimal weight: 0.9990 chunk 206 optimal weight: 10.0000 chunk 372 optimal weight: 0.0010 chunk 145 optimal weight: 9.9990 chunk 428 optimal weight: 6.9990 chunk 448 optimal weight: 0.9980 chunk 472 optimal weight: 7.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4943 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 44400 Z= 0.150 Angle : 0.665 8.434 59616 Z= 0.345 Chirality : 0.047 0.166 6576 Planarity : 0.004 0.041 7584 Dihedral : 5.719 20.673 5808 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.10), residues: 5208 helix: -1.10 (0.18), residues: 720 sheet: -1.82 (0.12), residues: 1848 loop : -3.41 (0.09), residues: 2640 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1809 time to fit residues: 5.4658 Evaluate side-chains 20 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.229 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 0.0870 chunk 501 optimal weight: 0.7980 chunk 306 optimal weight: 6.9990 chunk 237 optimal weight: 6.9990 chunk 348 optimal weight: 0.5980 chunk 526 optimal weight: 20.0000 chunk 484 optimal weight: 3.9990 chunk 418 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 323 optimal weight: 0.0980 chunk 256 optimal weight: 0.0770 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 51 HIS ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4893 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 44400 Z= 0.151 Angle : 0.660 8.675 59616 Z= 0.341 Chirality : 0.047 0.162 6576 Planarity : 0.004 0.042 7584 Dihedral : 5.616 21.186 5808 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: -3.59 (0.10), residues: 5208 helix: -0.98 (0.18), residues: 768 sheet: -1.85 (0.11), residues: 1848 loop : -3.29 (0.09), residues: 2592 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1793 time to fit residues: 5.4199 Evaluate side-chains 22 residues out of total 202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.217 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 4.9990 chunk 446 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 386 optimal weight: 0.0470 chunk 61 optimal weight: 30.0000 chunk 116 optimal weight: 10.0000 chunk 419 optimal weight: 4.9990 chunk 175 optimal weight: 0.0050 chunk 430 optimal weight: 0.0670 chunk 53 optimal weight: 0.2980 chunk 77 optimal weight: 7.9990 overall best weight: 1.0832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.141220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.125133 restraints weight = 9911.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.126700 restraints weight = 7869.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.127867 restraints weight = 6611.413| |-----------------------------------------------------------------------------| r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4965 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 44400 Z= 0.157 Angle : 0.652 8.796 59616 Z= 0.337 Chirality : 0.046 0.164 6576 Planarity : 0.004 0.042 7584 Dihedral : 5.688 21.357 5808 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.10), residues: 5208 helix: -0.74 (0.18), residues: 768 sheet: -1.85 (0.11), residues: 1848 loop : -3.21 (0.10), residues: 2592 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4420.12 seconds wall clock time: 84 minutes 29.40 seconds (5069.40 seconds total)