Starting phenix.real_space_refine on Tue Mar 12 03:05:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrg_34972/03_2024/8hrg_34972.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrg_34972/03_2024/8hrg_34972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrg_34972/03_2024/8hrg_34972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrg_34972/03_2024/8hrg_34972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrg_34972/03_2024/8hrg_34972.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrg_34972/03_2024/8hrg_34972.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.179 sd= 1.000 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 168 5.16 5 C 38472 2.51 5 N 9996 2.21 5 O 12537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 49": "OE1" <-> "OE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 294": "OE1" <-> "OE2" Residue "D ASP 328": "OD1" <-> "OD2" Residue "D PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A ASP 328": "OD1" <-> "OD2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B ASP 328": "OD1" <-> "OD2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C ASP 328": "OD1" <-> "OD2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 49": "OE1" <-> "OE2" Residue "E PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 294": "OE1" <-> "OE2" Residue "E ASP 328": "OD1" <-> "OD2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 49": "OE1" <-> "OE2" Residue "F PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 294": "OE1" <-> "OE2" Residue "F ASP 328": "OD1" <-> "OD2" Residue "F PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 49": "OE1" <-> "OE2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 294": "OE1" <-> "OE2" Residue "G ASP 328": "OD1" <-> "OD2" Residue "G PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 49": "OE1" <-> "OE2" Residue "H PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 294": "OE1" <-> "OE2" Residue "H ASP 328": "OD1" <-> "OD2" Residue "H PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 49": "OE1" <-> "OE2" Residue "I PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 294": "OE1" <-> "OE2" Residue "I ASP 328": "OD1" <-> "OD2" Residue "I PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 49": "OE1" <-> "OE2" Residue "J PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 294": "OE1" <-> "OE2" Residue "J ASP 328": "OD1" <-> "OD2" Residue "J PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 49": "OE1" <-> "OE2" Residue "K PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 294": "OE1" <-> "OE2" Residue "K ASP 328": "OD1" <-> "OD2" Residue "K PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 49": "OE1" <-> "OE2" Residue "L PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 294": "OE1" <-> "OE2" Residue "L ASP 328": "OD1" <-> "OD2" Residue "L PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 49": "OE1" <-> "OE2" Residue "M PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 294": "OE1" <-> "OE2" Residue "M ASP 328": "OD1" <-> "OD2" Residue "M PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 49": "OE1" <-> "OE2" Residue "N PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 294": "OE1" <-> "OE2" Residue "N ASP 328": "OD1" <-> "OD2" Residue "N PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 49": "OE1" <-> "OE2" Residue "O PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 294": "OE1" <-> "OE2" Residue "O ASP 328": "OD1" <-> "OD2" Residue "O PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 49": "OE1" <-> "OE2" Residue "P PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 294": "OE1" <-> "OE2" Residue "P ASP 328": "OD1" <-> "OD2" Residue "P PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 49": "OE1" <-> "OE2" Residue "Q PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 294": "OE1" <-> "OE2" Residue "Q ASP 328": "OD1" <-> "OD2" Residue "Q PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 49": "OE1" <-> "OE2" Residue "R PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 294": "OE1" <-> "OE2" Residue "R ASP 328": "OD1" <-> "OD2" Residue "R PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 49": "OE1" <-> "OE2" Residue "S PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 294": "OE1" <-> "OE2" Residue "S ASP 328": "OD1" <-> "OD2" Residue "S PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 49": "OE1" <-> "OE2" Residue "T PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 294": "OE1" <-> "OE2" Residue "T ASP 328": "OD1" <-> "OD2" Residue "T PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 49": "OE1" <-> "OE2" Residue "U PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 294": "OE1" <-> "OE2" Residue "U ASP 328": "OD1" <-> "OD2" Residue "U PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 61173 Number of models: 1 Model: "" Number of chains: 21 Chain: "D" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2913 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Chain: "A" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2913 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Chain: "B" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2913 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Chain: "C" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2913 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Chain: "E" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2913 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Chain: "F" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2913 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Chain: "G" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2913 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Chain: "H" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2913 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Chain: "I" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2913 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Chain: "J" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2913 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Chain: "K" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2913 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Chain: "L" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2913 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Chain: "M" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2913 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Chain: "N" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2913 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Chain: "O" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2913 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Chain: "P" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2913 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Chain: "Q" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2913 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Chain: "R" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2913 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Chain: "S" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2913 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Chain: "T" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2913 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Chain: "U" Number of atoms: 2913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2913 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Time building chain proxies: 22.81, per 1000 atoms: 0.37 Number of scatterers: 61173 At special positions: 0 Unit cell: (124.6, 123.2, 316.4, 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 168 16.00 O 12537 8.00 N 9996 7.00 C 38472 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: 17.85 Conformation dependent library (CDL) restraints added in 8.0 seconds 15624 Ramachandran restraints generated. 7812 Oldfield, 0 Emsley, 7812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14616 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 105 sheets defined 13.1% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.57 Creating SS restraints... Processing helix chain 'D' and resid 91 through 100 Processing helix chain 'D' and resid 192 through 200 Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU D 287 " --> pdb=" O LEU D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 369 Processing helix chain 'A' and resid 91 through 100 Processing helix chain 'A' and resid 192 through 200 Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 369 Processing helix chain 'B' and resid 91 through 100 Processing helix chain 'B' and resid 192 through 200 Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU B 287 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 369 Processing helix chain 'C' and resid 91 through 100 Processing helix chain 'C' and resid 192 through 200 Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU C 287 " --> pdb=" O LEU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 369 Processing helix chain 'E' and resid 91 through 100 Processing helix chain 'E' and resid 192 through 200 Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU E 287 " --> pdb=" O LEU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 369 Processing helix chain 'F' and resid 91 through 100 Processing helix chain 'F' and resid 192 through 200 Processing helix chain 'F' and resid 205 through 209 Processing helix chain 'F' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU F 287 " --> pdb=" O LEU F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 369 Processing helix chain 'G' and resid 91 through 100 Processing helix chain 'G' and resid 192 through 200 Processing helix chain 'G' and resid 205 through 209 Processing helix chain 'G' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU G 287 " --> pdb=" O LEU G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 369 Processing helix chain 'H' and resid 91 through 100 Processing helix chain 'H' and resid 192 through 200 Processing helix chain 'H' and resid 205 through 209 Processing helix chain 'H' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU H 287 " --> pdb=" O LEU H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 358 through 369 Processing helix chain 'I' and resid 91 through 100 Processing helix chain 'I' and resid 192 through 200 Processing helix chain 'I' and resid 205 through 209 Processing helix chain 'I' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU I 287 " --> pdb=" O LEU I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 369 Processing helix chain 'J' and resid 91 through 100 Processing helix chain 'J' and resid 192 through 200 Processing helix chain 'J' and resid 205 through 209 Processing helix chain 'J' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU J 287 " --> pdb=" O LEU J 283 " (cutoff:3.500A) Processing helix chain 'J' and resid 358 through 369 Processing helix chain 'K' and resid 91 through 100 Processing helix chain 'K' and resid 192 through 200 Processing helix chain 'K' and resid 205 through 209 Processing helix chain 'K' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU K 287 " --> pdb=" O LEU K 283 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 369 Processing helix chain 'L' and resid 91 through 100 Processing helix chain 'L' and resid 192 through 200 Processing helix chain 'L' and resid 205 through 209 Processing helix chain 'L' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU L 287 " --> pdb=" O LEU L 283 " (cutoff:3.500A) Processing helix chain 'L' and resid 358 through 369 Processing helix chain 'M' and resid 91 through 100 Processing helix chain 'M' and resid 192 through 200 Processing helix chain 'M' and resid 205 through 209 Processing helix chain 'M' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU M 287 " --> pdb=" O LEU M 283 " (cutoff:3.500A) Processing helix chain 'M' and resid 358 through 369 Processing helix chain 'N' and resid 91 through 100 Processing helix chain 'N' and resid 192 through 200 Processing helix chain 'N' and resid 205 through 209 Processing helix chain 'N' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU N 287 " --> pdb=" O LEU N 283 " (cutoff:3.500A) Processing helix chain 'N' and resid 358 through 369 Processing helix chain 'O' and resid 91 through 100 Processing helix chain 'O' and resid 192 through 200 Processing helix chain 'O' and resid 205 through 209 Processing helix chain 'O' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU O 287 " --> pdb=" O LEU O 283 " (cutoff:3.500A) Processing helix chain 'O' and resid 358 through 369 Processing helix chain 'P' and resid 91 through 100 Processing helix chain 'P' and resid 192 through 200 Processing helix chain 'P' and resid 205 through 209 Processing helix chain 'P' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU P 287 " --> pdb=" O LEU P 283 " (cutoff:3.500A) Processing helix chain 'P' and resid 358 through 369 Processing helix chain 'Q' and resid 91 through 100 Processing helix chain 'Q' and resid 192 through 200 Processing helix chain 'Q' and resid 205 through 209 Processing helix chain 'Q' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU Q 287 " --> pdb=" O LEU Q 283 " (cutoff:3.500A) Processing helix chain 'Q' and resid 358 through 369 Processing helix chain 'R' and resid 91 through 100 Processing helix chain 'R' and resid 192 through 200 Processing helix chain 'R' and resid 205 through 209 Processing helix chain 'R' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU R 287 " --> pdb=" O LEU R 283 " (cutoff:3.500A) Processing helix chain 'R' and resid 358 through 369 Processing helix chain 'S' and resid 91 through 100 Processing helix chain 'S' and resid 192 through 200 Processing helix chain 'S' and resid 205 through 209 Processing helix chain 'S' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU S 287 " --> pdb=" O LEU S 283 " (cutoff:3.500A) Processing helix chain 'S' and resid 358 through 369 Processing helix chain 'T' and resid 91 through 100 Processing helix chain 'T' and resid 192 through 200 Processing helix chain 'T' and resid 205 through 209 Processing helix chain 'T' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU T 287 " --> pdb=" O LEU T 283 " (cutoff:3.500A) Processing helix chain 'T' and resid 358 through 369 Processing helix chain 'U' and resid 91 through 100 Processing helix chain 'U' and resid 192 through 200 Processing helix chain 'U' and resid 205 through 209 Processing helix chain 'U' and resid 275 through 287 removed outlier: 3.780A pdb=" N LEU U 287 " --> pdb=" O LEU U 283 " (cutoff:3.500A) Processing helix chain 'U' and resid 358 through 369 Processing sheet with id= 1, first strand: chain 'D' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 27 current: chain 'D' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 68 through 75 current: chain 'D' and resid 143 through 159 removed outlier: 6.801A pdb=" N SER D 170 " --> pdb=" O ASN D 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA D 155 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR D 168 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL D 157 " --> pdb=" O ARG D 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG D 166 " --> pdb=" O VAL D 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 166 through 173 current: chain 'D' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 260 through 268 current: chain 'D' and resid 331 through 337 Processing sheet with id= 2, first strand: chain 'D' and resid 40 through 43 removed outlier: 4.182A pdb=" N SER D 64 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR D 43 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN D 62 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'D' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS D 86 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'D' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG D 307 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE D 213 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR D 222 " --> pdb=" O ILE D 213 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY D 253 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 25 through 27 current: chain 'A' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 75 current: chain 'A' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER A 170 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA A 155 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR A 168 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL A 157 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG A 166 " --> pdb=" O VAL A 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 166 through 173 current: chain 'A' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 260 through 268 current: chain 'A' and resid 331 through 337 Processing sheet with id= 7, first strand: chain 'A' and resid 40 through 43 removed outlier: 4.182A pdb=" N SER A 64 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR A 43 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN A 62 " --> pdb=" O THR A 43 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS A 86 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG A 307 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE A 213 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR A 222 " --> pdb=" O ILE A 213 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY A 253 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'B' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 25 through 27 current: chain 'B' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 75 current: chain 'B' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER B 170 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA B 155 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR B 168 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL B 157 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ARG B 166 " --> pdb=" O VAL B 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 166 through 173 current: chain 'B' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 260 through 268 current: chain 'B' and resid 331 through 337 Processing sheet with id= 12, first strand: chain 'B' and resid 40 through 43 removed outlier: 4.182A pdb=" N SER B 64 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR B 43 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN B 62 " --> pdb=" O THR B 43 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS B 86 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG B 307 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE B 213 " --> pdb=" O TYR B 222 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B 222 " --> pdb=" O ILE B 213 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'B' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY B 253 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'C' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 25 through 27 current: chain 'C' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 75 current: chain 'C' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER C 170 " --> pdb=" O ASN C 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA C 155 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR C 168 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL C 157 " --> pdb=" O ARG C 166 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ARG C 166 " --> pdb=" O VAL C 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 166 through 173 current: chain 'C' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 268 current: chain 'C' and resid 331 through 337 Processing sheet with id= 17, first strand: chain 'C' and resid 40 through 43 removed outlier: 4.183A pdb=" N SER C 64 " --> pdb=" O ASN C 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR C 43 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASN C 62 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'C' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS C 86 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'C' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG C 307 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE C 213 " --> pdb=" O TYR C 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR C 222 " --> pdb=" O ILE C 213 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'C' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY C 253 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'E' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 25 through 27 current: chain 'E' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 68 through 75 current: chain 'E' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER E 170 " --> pdb=" O ASN E 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA E 155 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR E 168 " --> pdb=" O ALA E 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL E 157 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG E 166 " --> pdb=" O VAL E 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 166 through 173 current: chain 'E' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 260 through 268 current: chain 'E' and resid 331 through 337 Processing sheet with id= 22, first strand: chain 'E' and resid 40 through 43 removed outlier: 4.183A pdb=" N SER E 64 " --> pdb=" O ASN E 41 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR E 43 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN E 62 " --> pdb=" O THR E 43 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'E' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS E 86 " --> pdb=" O ASP E 81 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'E' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG E 307 " --> pdb=" O LYS E 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE E 213 " --> pdb=" O TYR E 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR E 222 " --> pdb=" O ILE E 213 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'E' and resid 237 through 240 removed outlier: 4.037A pdb=" N GLY E 253 " --> pdb=" O LEU E 240 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'F' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 25 through 27 current: chain 'F' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 68 through 75 current: chain 'F' and resid 143 through 159 removed outlier: 6.801A pdb=" N SER F 170 " --> pdb=" O ASN F 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA F 155 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR F 168 " --> pdb=" O ALA F 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL F 157 " --> pdb=" O ARG F 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG F 166 " --> pdb=" O VAL F 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 166 through 173 current: chain 'F' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 260 through 268 current: chain 'F' and resid 331 through 337 Processing sheet with id= 27, first strand: chain 'F' and resid 40 through 43 removed outlier: 4.182A pdb=" N SER F 64 " --> pdb=" O ASN F 41 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR F 43 " --> pdb=" O ASN F 62 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASN F 62 " --> pdb=" O THR F 43 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'F' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS F 86 " --> pdb=" O ASP F 81 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'F' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG F 307 " --> pdb=" O LYS F 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE F 213 " --> pdb=" O TYR F 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR F 222 " --> pdb=" O ILE F 213 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'F' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY F 253 " --> pdb=" O LEU F 240 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'G' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 25 through 27 current: chain 'G' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 68 through 75 current: chain 'G' and resid 143 through 159 removed outlier: 6.801A pdb=" N SER G 170 " --> pdb=" O ASN G 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA G 155 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR G 168 " --> pdb=" O ALA G 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL G 157 " --> pdb=" O ARG G 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG G 166 " --> pdb=" O VAL G 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 166 through 173 current: chain 'G' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 260 through 268 current: chain 'G' and resid 331 through 337 Processing sheet with id= 32, first strand: chain 'G' and resid 40 through 43 removed outlier: 4.183A pdb=" N SER G 64 " --> pdb=" O ASN G 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR G 43 " --> pdb=" O ASN G 62 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN G 62 " --> pdb=" O THR G 43 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'G' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS G 86 " --> pdb=" O ASP G 81 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'G' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG G 307 " --> pdb=" O LYS G 356 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE G 213 " --> pdb=" O TYR G 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR G 222 " --> pdb=" O ILE G 213 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'G' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY G 253 " --> pdb=" O LEU G 240 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'H' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 25 through 27 current: chain 'H' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 68 through 75 current: chain 'H' and resid 143 through 159 removed outlier: 6.801A pdb=" N SER H 170 " --> pdb=" O ASN H 153 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA H 155 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR H 168 " --> pdb=" O ALA H 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL H 157 " --> pdb=" O ARG H 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG H 166 " --> pdb=" O VAL H 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 166 through 173 current: chain 'H' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 260 through 268 current: chain 'H' and resid 331 through 337 Processing sheet with id= 37, first strand: chain 'H' and resid 40 through 43 removed outlier: 4.182A pdb=" N SER H 64 " --> pdb=" O ASN H 41 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR H 43 " --> pdb=" O ASN H 62 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASN H 62 " --> pdb=" O THR H 43 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'H' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS H 86 " --> pdb=" O ASP H 81 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'H' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG H 307 " --> pdb=" O LYS H 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE H 213 " --> pdb=" O TYR H 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR H 222 " --> pdb=" O ILE H 213 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'H' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY H 253 " --> pdb=" O LEU H 240 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'I' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 25 through 27 current: chain 'I' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 68 through 75 current: chain 'I' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER I 170 " --> pdb=" O ASN I 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA I 155 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR I 168 " --> pdb=" O ALA I 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL I 157 " --> pdb=" O ARG I 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG I 166 " --> pdb=" O VAL I 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 166 through 173 current: chain 'I' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 260 through 268 current: chain 'I' and resid 331 through 337 Processing sheet with id= 42, first strand: chain 'I' and resid 40 through 43 removed outlier: 4.182A pdb=" N SER I 64 " --> pdb=" O ASN I 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR I 43 " --> pdb=" O ASN I 62 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASN I 62 " --> pdb=" O THR I 43 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'I' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS I 86 " --> pdb=" O ASP I 81 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'I' and resid 112 through 114 removed outlier: 4.301A pdb=" N ARG I 307 " --> pdb=" O LYS I 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE I 213 " --> pdb=" O TYR I 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR I 222 " --> pdb=" O ILE I 213 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'I' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY I 253 " --> pdb=" O LEU I 240 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'J' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 25 through 27 current: chain 'J' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 68 through 75 current: chain 'J' and resid 143 through 159 removed outlier: 6.801A pdb=" N SER J 170 " --> pdb=" O ASN J 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA J 155 " --> pdb=" O THR J 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR J 168 " --> pdb=" O ALA J 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL J 157 " --> pdb=" O ARG J 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG J 166 " --> pdb=" O VAL J 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 166 through 173 current: chain 'J' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 260 through 268 current: chain 'J' and resid 331 through 337 Processing sheet with id= 47, first strand: chain 'J' and resid 40 through 43 removed outlier: 4.182A pdb=" N SER J 64 " --> pdb=" O ASN J 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR J 43 " --> pdb=" O ASN J 62 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN J 62 " --> pdb=" O THR J 43 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'J' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS J 86 " --> pdb=" O ASP J 81 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'J' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG J 307 " --> pdb=" O LYS J 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE J 213 " --> pdb=" O TYR J 222 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR J 222 " --> pdb=" O ILE J 213 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'J' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY J 253 " --> pdb=" O LEU J 240 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'K' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 25 through 27 current: chain 'K' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 68 through 75 current: chain 'K' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER K 170 " --> pdb=" O ASN K 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA K 155 " --> pdb=" O THR K 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR K 168 " --> pdb=" O ALA K 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL K 157 " --> pdb=" O ARG K 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG K 166 " --> pdb=" O VAL K 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 166 through 173 current: chain 'K' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 260 through 268 current: chain 'K' and resid 331 through 337 Processing sheet with id= 52, first strand: chain 'K' and resid 40 through 43 removed outlier: 4.182A pdb=" N SER K 64 " --> pdb=" O ASN K 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR K 43 " --> pdb=" O ASN K 62 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN K 62 " --> pdb=" O THR K 43 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'K' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS K 86 " --> pdb=" O ASP K 81 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'K' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG K 307 " --> pdb=" O LYS K 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE K 213 " --> pdb=" O TYR K 222 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR K 222 " --> pdb=" O ILE K 213 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'K' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY K 253 " --> pdb=" O LEU K 240 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'L' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 25 through 27 current: chain 'L' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 68 through 75 current: chain 'L' and resid 143 through 159 removed outlier: 6.801A pdb=" N SER L 170 " --> pdb=" O ASN L 153 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA L 155 " --> pdb=" O THR L 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR L 168 " --> pdb=" O ALA L 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL L 157 " --> pdb=" O ARG L 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG L 166 " --> pdb=" O VAL L 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 166 through 173 current: chain 'L' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 260 through 268 current: chain 'L' and resid 331 through 337 Processing sheet with id= 57, first strand: chain 'L' and resid 40 through 43 removed outlier: 4.183A pdb=" N SER L 64 " --> pdb=" O ASN L 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR L 43 " --> pdb=" O ASN L 62 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ASN L 62 " --> pdb=" O THR L 43 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'L' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS L 86 " --> pdb=" O ASP L 81 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'L' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG L 307 " --> pdb=" O LYS L 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE L 213 " --> pdb=" O TYR L 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR L 222 " --> pdb=" O ILE L 213 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'L' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY L 253 " --> pdb=" O LEU L 240 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'M' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 25 through 27 current: chain 'M' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 68 through 75 current: chain 'M' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER M 170 " --> pdb=" O ASN M 153 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA M 155 " --> pdb=" O THR M 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR M 168 " --> pdb=" O ALA M 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL M 157 " --> pdb=" O ARG M 166 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ARG M 166 " --> pdb=" O VAL M 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 166 through 173 current: chain 'M' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 260 through 268 current: chain 'M' and resid 331 through 337 Processing sheet with id= 62, first strand: chain 'M' and resid 40 through 43 removed outlier: 4.182A pdb=" N SER M 64 " --> pdb=" O ASN M 41 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR M 43 " --> pdb=" O ASN M 62 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN M 62 " --> pdb=" O THR M 43 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'M' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS M 86 " --> pdb=" O ASP M 81 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'M' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG M 307 " --> pdb=" O LYS M 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE M 213 " --> pdb=" O TYR M 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR M 222 " --> pdb=" O ILE M 213 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'M' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY M 253 " --> pdb=" O LEU M 240 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'N' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 25 through 27 current: chain 'N' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 68 through 75 current: chain 'N' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER N 170 " --> pdb=" O ASN N 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA N 155 " --> pdb=" O THR N 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR N 168 " --> pdb=" O ALA N 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL N 157 " --> pdb=" O ARG N 166 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ARG N 166 " --> pdb=" O VAL N 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 166 through 173 current: chain 'N' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 260 through 268 current: chain 'N' and resid 331 through 337 Processing sheet with id= 67, first strand: chain 'N' and resid 40 through 43 removed outlier: 4.183A pdb=" N SER N 64 " --> pdb=" O ASN N 41 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR N 43 " --> pdb=" O ASN N 62 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ASN N 62 " --> pdb=" O THR N 43 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'N' and resid 79 through 81 removed outlier: 3.684A pdb=" N LYS N 86 " --> pdb=" O ASP N 81 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'N' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG N 307 " --> pdb=" O LYS N 356 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE N 213 " --> pdb=" O TYR N 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR N 222 " --> pdb=" O ILE N 213 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'N' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY N 253 " --> pdb=" O LEU N 240 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'O' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 25 through 27 current: chain 'O' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 68 through 75 current: chain 'O' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER O 170 " --> pdb=" O ASN O 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA O 155 " --> pdb=" O THR O 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR O 168 " --> pdb=" O ALA O 155 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL O 157 " --> pdb=" O ARG O 166 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ARG O 166 " --> pdb=" O VAL O 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 166 through 173 current: chain 'O' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 260 through 268 current: chain 'O' and resid 331 through 337 Processing sheet with id= 72, first strand: chain 'O' and resid 40 through 43 removed outlier: 4.183A pdb=" N SER O 64 " --> pdb=" O ASN O 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR O 43 " --> pdb=" O ASN O 62 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ASN O 62 " --> pdb=" O THR O 43 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'O' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS O 86 " --> pdb=" O ASP O 81 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'O' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG O 307 " --> pdb=" O LYS O 356 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE O 213 " --> pdb=" O TYR O 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR O 222 " --> pdb=" O ILE O 213 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'O' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY O 253 " --> pdb=" O LEU O 240 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'P' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 25 through 27 current: chain 'P' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 68 through 75 current: chain 'P' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER P 170 " --> pdb=" O ASN P 153 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA P 155 " --> pdb=" O THR P 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR P 168 " --> pdb=" O ALA P 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL P 157 " --> pdb=" O ARG P 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG P 166 " --> pdb=" O VAL P 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 166 through 173 current: chain 'P' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 260 through 268 current: chain 'P' and resid 331 through 337 Processing sheet with id= 77, first strand: chain 'P' and resid 40 through 43 removed outlier: 4.183A pdb=" N SER P 64 " --> pdb=" O ASN P 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR P 43 " --> pdb=" O ASN P 62 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASN P 62 " --> pdb=" O THR P 43 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'P' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS P 86 " --> pdb=" O ASP P 81 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'P' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG P 307 " --> pdb=" O LYS P 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE P 213 " --> pdb=" O TYR P 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR P 222 " --> pdb=" O ILE P 213 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'P' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY P 253 " --> pdb=" O LEU P 240 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'Q' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 25 through 27 current: chain 'Q' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 68 through 75 current: chain 'Q' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER Q 170 " --> pdb=" O ASN Q 153 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA Q 155 " --> pdb=" O THR Q 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR Q 168 " --> pdb=" O ALA Q 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL Q 157 " --> pdb=" O ARG Q 166 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ARG Q 166 " --> pdb=" O VAL Q 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 166 through 173 current: chain 'Q' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 260 through 268 current: chain 'Q' and resid 331 through 337 Processing sheet with id= 82, first strand: chain 'Q' and resid 40 through 43 removed outlier: 4.183A pdb=" N SER Q 64 " --> pdb=" O ASN Q 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR Q 43 " --> pdb=" O ASN Q 62 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ASN Q 62 " --> pdb=" O THR Q 43 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'Q' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS Q 86 " --> pdb=" O ASP Q 81 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'Q' and resid 112 through 114 removed outlier: 4.301A pdb=" N ARG Q 307 " --> pdb=" O LYS Q 356 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE Q 213 " --> pdb=" O TYR Q 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR Q 222 " --> pdb=" O ILE Q 213 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'Q' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY Q 253 " --> pdb=" O LEU Q 240 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'R' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 25 through 27 current: chain 'R' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 68 through 75 current: chain 'R' and resid 143 through 159 removed outlier: 6.801A pdb=" N SER R 170 " --> pdb=" O ASN R 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA R 155 " --> pdb=" O THR R 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR R 168 " --> pdb=" O ALA R 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL R 157 " --> pdb=" O ARG R 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG R 166 " --> pdb=" O VAL R 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 166 through 173 current: chain 'R' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 260 through 268 current: chain 'R' and resid 331 through 337 Processing sheet with id= 87, first strand: chain 'R' and resid 40 through 43 removed outlier: 4.182A pdb=" N SER R 64 " --> pdb=" O ASN R 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR R 43 " --> pdb=" O ASN R 62 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN R 62 " --> pdb=" O THR R 43 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'R' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS R 86 " --> pdb=" O ASP R 81 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'R' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG R 307 " --> pdb=" O LYS R 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE R 213 " --> pdb=" O TYR R 222 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR R 222 " --> pdb=" O ILE R 213 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'R' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY R 253 " --> pdb=" O LEU R 240 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'S' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 25 through 27 current: chain 'S' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 68 through 75 current: chain 'S' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER S 170 " --> pdb=" O ASN S 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA S 155 " --> pdb=" O THR S 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR S 168 " --> pdb=" O ALA S 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL S 157 " --> pdb=" O ARG S 166 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ARG S 166 " --> pdb=" O VAL S 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 166 through 173 current: chain 'S' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 260 through 268 current: chain 'S' and resid 331 through 337 Processing sheet with id= 92, first strand: chain 'S' and resid 40 through 43 removed outlier: 4.182A pdb=" N SER S 64 " --> pdb=" O ASN S 41 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR S 43 " --> pdb=" O ASN S 62 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN S 62 " --> pdb=" O THR S 43 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'S' and resid 79 through 81 removed outlier: 3.684A pdb=" N LYS S 86 " --> pdb=" O ASP S 81 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'S' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG S 307 " --> pdb=" O LYS S 356 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE S 213 " --> pdb=" O TYR S 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR S 222 " --> pdb=" O ILE S 213 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'S' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY S 253 " --> pdb=" O LEU S 240 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'T' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 25 through 27 current: chain 'T' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 68 through 75 current: chain 'T' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER T 170 " --> pdb=" O ASN T 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA T 155 " --> pdb=" O THR T 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR T 168 " --> pdb=" O ALA T 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL T 157 " --> pdb=" O ARG T 166 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ARG T 166 " --> pdb=" O VAL T 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 166 through 173 current: chain 'T' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 260 through 268 current: chain 'T' and resid 331 through 337 Processing sheet with id= 97, first strand: chain 'T' and resid 40 through 43 removed outlier: 4.183A pdb=" N SER T 64 " --> pdb=" O ASN T 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR T 43 " --> pdb=" O ASN T 62 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ASN T 62 " --> pdb=" O THR T 43 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'T' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS T 86 " --> pdb=" O ASP T 81 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'T' and resid 112 through 114 removed outlier: 4.300A pdb=" N ARG T 307 " --> pdb=" O LYS T 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE T 213 " --> pdb=" O TYR T 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR T 222 " --> pdb=" O ILE T 213 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'T' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY T 253 " --> pdb=" O LEU T 240 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'U' and resid 10 through 14 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 25 through 27 current: chain 'U' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 68 through 75 current: chain 'U' and resid 143 through 159 removed outlier: 6.800A pdb=" N SER U 170 " --> pdb=" O ASN U 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA U 155 " --> pdb=" O THR U 168 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR U 168 " --> pdb=" O ALA U 155 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL U 157 " --> pdb=" O ARG U 166 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG U 166 " --> pdb=" O VAL U 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 166 through 173 current: chain 'U' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 260 through 268 current: chain 'U' and resid 331 through 337 Processing sheet with id=102, first strand: chain 'U' and resid 40 through 43 removed outlier: 4.182A pdb=" N SER U 64 " --> pdb=" O ASN U 41 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR U 43 " --> pdb=" O ASN U 62 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN U 62 " --> pdb=" O THR U 43 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'U' and resid 79 through 81 removed outlier: 3.683A pdb=" N LYS U 86 " --> pdb=" O ASP U 81 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'U' and resid 112 through 114 removed outlier: 4.301A pdb=" N ARG U 307 " --> pdb=" O LYS U 356 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE U 213 " --> pdb=" O TYR U 222 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR U 222 " --> pdb=" O ILE U 213 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'U' and resid 237 through 240 removed outlier: 4.038A pdb=" N GLY U 253 " --> pdb=" O LEU U 240 " (cutoff:3.500A) 1344 hydrogen bonds defined for protein. 3654 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: 20.93 Time building geometry restraints manager: 19.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 20433 1.34 - 1.46: 14017 1.46 - 1.58: 27605 1.58 - 1.70: 0 1.70 - 1.81: 315 Bond restraints: 62370 Sorted by residual: bond pdb=" CA ILE G 250 " pdb=" C ILE G 250 " ideal model delta sigma weight residual 1.524 1.512 0.012 1.05e-02 9.07e+03 1.31e+00 bond pdb=" CA ILE I 250 " pdb=" C ILE I 250 " ideal model delta sigma weight residual 1.524 1.513 0.012 1.05e-02 9.07e+03 1.29e+00 bond pdb=" CA ILE S 250 " pdb=" C ILE S 250 " ideal model delta sigma weight residual 1.524 1.513 0.012 1.05e-02 9.07e+03 1.27e+00 bond pdb=" CA ILE J 250 " pdb=" C ILE J 250 " ideal model delta sigma weight residual 1.524 1.513 0.012 1.05e-02 9.07e+03 1.23e+00 bond pdb=" CA ILE A 250 " pdb=" C ILE A 250 " ideal model delta sigma weight residual 1.524 1.513 0.012 1.05e-02 9.07e+03 1.23e+00 ... (remaining 62365 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.18: 1916 107.18 - 113.89: 35728 113.89 - 120.59: 22126 120.59 - 127.30: 24692 127.30 - 134.01: 588 Bond angle restraints: 85050 Sorted by residual: angle pdb=" C LEU P 351 " pdb=" N GLY P 352 " pdb=" CA GLY P 352 " ideal model delta sigma weight residual 121.65 119.55 2.10 6.80e-01 2.16e+00 9.52e+00 angle pdb=" C LEU K 351 " pdb=" N GLY K 352 " pdb=" CA GLY K 352 " ideal model delta sigma weight residual 121.65 119.56 2.09 6.80e-01 2.16e+00 9.48e+00 angle pdb=" C LEU Q 351 " pdb=" N GLY Q 352 " pdb=" CA GLY Q 352 " ideal model delta sigma weight residual 121.65 119.56 2.09 6.80e-01 2.16e+00 9.40e+00 angle pdb=" C LEU F 351 " pdb=" N GLY F 352 " pdb=" CA GLY F 352 " ideal model delta sigma weight residual 121.65 119.57 2.08 6.80e-01 2.16e+00 9.38e+00 angle pdb=" C LEU I 351 " pdb=" N GLY I 352 " pdb=" CA GLY I 352 " ideal model delta sigma weight residual 121.65 119.57 2.08 6.80e-01 2.16e+00 9.36e+00 ... (remaining 85045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.16: 33027 14.16 - 28.31: 3034 28.31 - 42.47: 815 42.47 - 56.62: 215 56.62 - 70.78: 37 Dihedral angle restraints: 37128 sinusoidal: 14364 harmonic: 22764 Sorted by residual: dihedral pdb=" CA ARG N 56 " pdb=" C ARG N 56 " pdb=" N GLY N 57 " pdb=" CA GLY N 57 " ideal model delta harmonic sigma weight residual 180.00 -143.30 -36.70 0 5.00e+00 4.00e-02 5.39e+01 dihedral pdb=" CA ARG U 56 " pdb=" C ARG U 56 " pdb=" N GLY U 57 " pdb=" CA GLY U 57 " ideal model delta harmonic sigma weight residual -180.00 -143.30 -36.70 0 5.00e+00 4.00e-02 5.39e+01 dihedral pdb=" CA ARG B 56 " pdb=" C ARG B 56 " pdb=" N GLY B 57 " pdb=" CA GLY B 57 " ideal model delta harmonic sigma weight residual -180.00 -143.30 -36.70 0 5.00e+00 4.00e-02 5.39e+01 ... (remaining 37125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 7348 0.048 - 0.096: 2071 0.096 - 0.143: 430 0.143 - 0.191: 0 0.191 - 0.239: 21 Chirality restraints: 9870 Sorted by residual: chirality pdb=" CB ILE G 199 " pdb=" CA ILE G 199 " pdb=" CG1 ILE G 199 " pdb=" CG2 ILE G 199 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB ILE U 199 " pdb=" CA ILE U 199 " pdb=" CG1 ILE U 199 " pdb=" CG2 ILE U 199 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB ILE R 199 " pdb=" CA ILE R 199 " pdb=" CG1 ILE R 199 " pdb=" CG2 ILE R 199 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 9867 not shown) Planarity restraints: 11088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR J 92 " 0.013 2.00e-02 2.50e+03 1.18e-02 2.77e+00 pdb=" CG TYR J 92 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR J 92 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR J 92 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR J 92 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR J 92 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR J 92 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR J 92 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 92 " 0.013 2.00e-02 2.50e+03 1.17e-02 2.73e+00 pdb=" CG TYR Q 92 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 92 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 92 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 92 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 92 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR Q 92 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR Q 92 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 92 " -0.013 2.00e-02 2.50e+03 1.17e-02 2.72e+00 pdb=" CG TYR N 92 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR N 92 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR N 92 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR N 92 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR N 92 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR N 92 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR N 92 " 0.002 2.00e-02 2.50e+03 ... (remaining 11085 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 1736 2.68 - 3.24: 62418 3.24 - 3.79: 97068 3.79 - 4.35: 121805 4.35 - 4.90: 200027 Nonbonded interactions: 483054 Sorted by model distance: nonbonded pdb=" O ALA F 127 " pdb=" NH2 ARG M 53 " model vdw 2.127 2.520 nonbonded pdb=" O ALA G 127 " pdb=" NH2 ARG N 53 " model vdw 2.127 2.520 nonbonded pdb=" NH2 ARG F 53 " pdb=" O ALA T 127 " model vdw 2.127 2.520 nonbonded pdb=" O ALA K 127 " pdb=" NH2 ARG R 53 " model vdw 2.127 2.520 nonbonded pdb=" O ALA E 127 " pdb=" NH2 ARG L 53 " model vdw 2.127 2.520 ... (remaining 483049 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' } 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' } 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: 0.620 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: 0.050 Extract box with map and model: 5.420 Check model and map are aligned: 0.650 Set scattering table: 0.420 Process input model: 119.420 Find NCS groups from input model: 3.380 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.030 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 : 0.003 0.035 62370 Z= 0.215 Angle : 0.702 5.937 85050 Z= 0.415 Chirality : 0.045 0.239 9870 Planarity : 0.004 0.040 11088 Dihedral : 12.326 70.779 22512 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.99 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.09), residues: 7812 helix: 1.54 (0.17), residues: 861 sheet: 0.80 (0.11), residues: 2604 loop : -1.89 (0.08), residues: 4347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 70 HIS 0.002 0.001 HIS P 129 PHE 0.025 0.002 PHE S 353 TYR 0.027 0.002 TYR J 92 ARG 0.008 0.001 ARG N 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15624 Ramachandran restraints generated. 7812 Oldfield, 0 Emsley, 7812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15624 Ramachandran restraints generated. 7812 Oldfield, 0 Emsley, 7812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.249 Fit side-chains REVERT: A 216 MET cc_start: 0.8878 (mmm) cc_final: 0.8571 (mmm) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1609 time to fit residues: 5.0735 Evaluate side-chains 20 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 656 optimal weight: 5.9990 chunk 588 optimal weight: 5.9990 chunk 326 optimal weight: 6.9990 chunk 201 optimal weight: 0.1980 chunk 397 optimal weight: 7.9990 chunk 314 optimal weight: 0.8980 chunk 609 optimal weight: 9.9990 chunk 235 optimal weight: 4.9990 chunk 370 optimal weight: 9.9990 chunk 453 optimal weight: 1.9990 chunk 705 optimal weight: 8.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 87 GLN ** 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: 0.8393 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 62370 Z= 0.170 Angle : 0.538 7.432 85050 Z= 0.290 Chirality : 0.044 0.161 9870 Planarity : 0.004 0.037 11088 Dihedral : 5.347 20.550 8358 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.18 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.09), residues: 7812 helix: 1.84 (0.17), residues: 840 sheet: 0.94 (0.11), residues: 2394 loop : -1.73 (0.08), residues: 4578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 70 HIS 0.002 0.001 HIS K 318 PHE 0.010 0.001 PHE F 231 TYR 0.009 0.001 TYR K 268 ARG 0.011 0.001 ARG F 7 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14880 Ramachandran restraints generated. 7440 Oldfield, 0 Emsley, 7440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.263 Fit side-chains REVERT: I 197 MET cc_start: 0.9432 (tpp) cc_final: 0.9005 (tpp) REVERT: I 216 MET cc_start: 0.8385 (mmm) cc_final: 0.7763 (mmm) REVERT: I 294 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6766 (mt-10) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1138 time to fit residues: 3.1915 Evaluate side-chains 20 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 392 optimal weight: 0.0030 chunk 218 optimal weight: 0.0170 chunk 587 optimal weight: 9.9990 chunk 480 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 706 optimal weight: 0.5980 chunk 763 optimal weight: 3.9990 chunk 629 optimal weight: 9.9990 chunk 700 optimal weight: 0.0970 chunk 240 optimal weight: 1.9990 chunk 567 optimal weight: 0.0060 overall best weight: 0.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 182 GLN ** 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: 0.8322 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 62370 Z= 0.125 Angle : 0.494 4.408 85050 Z= 0.268 Chirality : 0.044 0.144 9870 Planarity : 0.004 0.036 11088 Dihedral : 4.964 17.058 8358 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.45 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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: -0.37 (0.10), residues: 7812 helix: 1.91 (0.18), residues: 840 sheet: 1.09 (0.11), residues: 2499 loop : -1.57 (0.09), residues: 4473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 144 HIS 0.002 0.001 HIS M 96 PHE 0.013 0.001 PHE G 259 TYR 0.012 0.001 TYR K 92 ARG 0.005 0.001 ARG H 7 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14136 Ramachandran restraints generated. 7068 Oldfield, 0 Emsley, 7068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14136 Ramachandran restraints generated. 7068 Oldfield, 0 Emsley, 7068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.264 Fit side-chains REVERT: J 197 MET cc_start: 0.9387 (tpp) cc_final: 0.9038 (tpp) REVERT: J 216 MET cc_start: 0.8635 (mmm) cc_final: 0.7234 (mmm) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1320 time to fit residues: 4.9427 Evaluate side-chains 21 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 698 optimal weight: 0.0030 chunk 531 optimal weight: 10.0000 chunk 366 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 337 optimal weight: 0.0010 chunk 474 optimal weight: 8.9990 chunk 709 optimal weight: 0.7980 chunk 751 optimal weight: 20.0000 chunk 370 optimal weight: 10.0000 chunk 672 optimal weight: 7.9990 chunk 202 optimal weight: 2.9990 overall best weight: 2.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 182 GLN ** 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: 0.8357 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 62370 Z= 0.149 Angle : 0.497 4.585 85050 Z= 0.267 Chirality : 0.043 0.141 9870 Planarity : 0.003 0.037 11088 Dihedral : 4.897 17.315 8358 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.45 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.10), residues: 7812 helix: 1.71 (0.17), residues: 882 sheet: 0.82 (0.11), residues: 2646 loop : -1.77 (0.09), residues: 4284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 144 HIS 0.002 0.001 HIS J 96 PHE 0.009 0.001 PHE S 231 TYR 0.013 0.001 TYR K 92 ARG 0.004 0.001 ARG N 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14136 Ramachandran restraints generated. 7068 Oldfield, 0 Emsley, 7068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14136 Ramachandran restraints generated. 7068 Oldfield, 0 Emsley, 7068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.254 Fit side-chains REVERT: J 5 LEU cc_start: 0.8961 (mt) cc_final: 0.8397 (tt) REVERT: J 6 LEU cc_start: 0.8620 (tp) cc_final: 0.7887 (mp) REVERT: J 197 MET cc_start: 0.9383 (tpp) cc_final: 0.9013 (tpp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1500 time to fit residues: 5.1505 Evaluate side-chains 21 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 625 optimal weight: 9.9990 chunk 426 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 559 optimal weight: 4.9990 chunk 309 optimal weight: 8.9990 chunk 640 optimal weight: 8.9990 chunk 519 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 383 optimal weight: 9.9990 chunk 674 optimal weight: 0.0170 chunk 189 optimal weight: 8.9990 overall best weight: 4.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 62370 Z= 0.219 Angle : 0.546 7.534 85050 Z= 0.290 Chirality : 0.043 0.144 9870 Planarity : 0.004 0.042 11088 Dihedral : 5.066 17.579 8358 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.53 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % 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: -0.51 (0.10), residues: 7812 helix: 2.00 (0.17), residues: 882 sheet: 1.11 (0.12), residues: 2394 loop : -1.76 (0.08), residues: 4536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 70 HIS 0.003 0.001 HIS Q 318 PHE 0.008 0.001 PHE G 259 TYR 0.014 0.001 TYR G 92 ARG 0.008 0.001 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.256 Fit side-chains REVERT: P 6 LEU cc_start: 0.8705 (tp) cc_final: 0.8151 (mp) REVERT: P 7 ARG cc_start: 0.6146 (ttt180) cc_final: 0.5804 (ttt180) REVERT: P 269 LEU cc_start: 0.8567 (tp) cc_final: 0.8292 (tp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1219 time to fit residues: 4.4999 Evaluate side-chains 19 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 252 optimal weight: 20.0000 chunk 676 optimal weight: 0.0000 chunk 148 optimal weight: 10.0000 chunk 440 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 chunk 751 optimal weight: 3.9990 chunk 624 optimal weight: 0.1980 chunk 348 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 248 optimal weight: 0.0070 chunk 394 optimal weight: 6.9990 overall best weight: 1.4406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 62370 Z= 0.132 Angle : 0.503 4.496 85050 Z= 0.267 Chirality : 0.043 0.142 9870 Planarity : 0.003 0.038 11088 Dihedral : 4.684 17.327 8358 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.65 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.10), residues: 7812 helix: 1.80 (0.17), residues: 882 sheet: 1.20 (0.12), residues: 2394 loop : -1.63 (0.08), residues: 4536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 70 HIS 0.002 0.001 HIS N 129 PHE 0.009 0.001 PHE G 259 TYR 0.024 0.001 TYR N 92 ARG 0.003 0.001 ARG G 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: I 5 LEU cc_start: 0.9090 (mt) cc_final: 0.8436 (tt) REVERT: I 6 LEU cc_start: 0.8607 (tp) cc_final: 0.8246 (mm) REVERT: I 197 MET cc_start: 0.9210 (tpp) cc_final: 0.8878 (tpp) REVERT: I 277 MET cc_start: 0.8547 (tpp) cc_final: 0.8287 (tpp) REVERT: I 364 ASN cc_start: 0.8970 (m-40) cc_final: 0.8286 (t0) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1162 time to fit residues: 4.8789 Evaluate side-chains 23 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 724 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 428 optimal weight: 0.0170 chunk 548 optimal weight: 9.9990 chunk 425 optimal weight: 2.9990 chunk 632 optimal weight: 0.9980 chunk 419 optimal weight: 9.9990 chunk 748 optimal weight: 6.9990 chunk 468 optimal weight: 0.0470 chunk 456 optimal weight: 8.9990 chunk 345 optimal weight: 10.0000 overall best weight: 1.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 62370 Z= 0.136 Angle : 0.491 5.588 85050 Z= 0.262 Chirality : 0.043 0.138 9870 Planarity : 0.004 0.038 11088 Dihedral : 4.766 23.988 8358 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.91 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.10), residues: 7812 helix: 1.83 (0.17), residues: 882 sheet: 1.11 (0.12), residues: 2394 loop : -1.62 (0.09), residues: 4536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 70 HIS 0.001 0.000 HIS J 96 PHE 0.014 0.001 PHE G 259 TYR 0.025 0.001 TYR G 92 ARG 0.005 0.001 ARG D 7 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.253 Fit side-chains REVERT: J 5 LEU cc_start: 0.9036 (mt) cc_final: 0.8460 (tt) REVERT: J 197 MET cc_start: 0.9121 (tpp) cc_final: 0.8816 (tpp) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1388 time to fit residues: 5.3700 Evaluate side-chains 22 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 463 optimal weight: 3.9990 chunk 299 optimal weight: 20.0000 chunk 447 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 476 optimal weight: 0.4980 chunk 510 optimal weight: 10.0000 chunk 370 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 588 optimal weight: 20.0000 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 62370 Z= 0.272 Angle : 0.591 5.437 85050 Z= 0.316 Chirality : 0.043 0.143 9870 Planarity : 0.005 0.077 11088 Dihedral : 5.163 16.649 8358 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.41 % Favored : 90.32 % 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: -0.56 (0.10), residues: 7812 helix: 2.04 (0.18), residues: 882 sheet: 0.68 (0.11), residues: 2646 loop : -1.68 (0.09), residues: 4284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 70 HIS 0.004 0.001 HIS B 318 PHE 0.009 0.001 PHE G 353 TYR 0.030 0.002 TYR G 92 ARG 0.015 0.001 ARG H 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.272 Fit side-chains REVERT: J 5 LEU cc_start: 0.8841 (mt) cc_final: 0.8276 (tt) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1296 time to fit residues: 4.2902 Evaluate side-chains 21 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 681 optimal weight: 5.9990 chunk 717 optimal weight: 2.9990 chunk 654 optimal weight: 6.9990 chunk 697 optimal weight: 10.0000 chunk 420 optimal weight: 10.0000 chunk 304 optimal weight: 0.1980 chunk 548 optimal weight: 0.9980 chunk 214 optimal weight: 0.0870 chunk 630 optimal weight: 6.9990 chunk 660 optimal weight: 0.0020 chunk 695 optimal weight: 0.3980 overall best weight: 0.3366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 62370 Z= 0.130 Angle : 0.533 6.471 85050 Z= 0.279 Chirality : 0.044 0.134 9870 Planarity : 0.003 0.037 11088 Dihedral : 4.850 23.028 8358 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.18 % Favored : 93.55 % 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: -0.43 (0.10), residues: 7812 helix: 1.83 (0.17), residues: 882 sheet: 1.01 (0.11), residues: 2541 loop : -1.63 (0.09), residues: 4389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 144 HIS 0.002 0.001 HIS F 113 PHE 0.010 0.001 PHE G 259 TYR 0.031 0.001 TYR R 92 ARG 0.011 0.001 ARG N 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.264 Fit side-chains REVERT: J 197 MET cc_start: 0.9348 (tpp) cc_final: 0.9111 (tpp) REVERT: J 245 MET cc_start: 0.5943 (pmm) cc_final: 0.5655 (pmm) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0904 time to fit residues: 3.3498 Evaluate side-chains 25 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 458 optimal weight: 5.9990 chunk 737 optimal weight: 0.4980 chunk 450 optimal weight: 0.5980 chunk 350 optimal weight: 9.9990 chunk 513 optimal weight: 0.0980 chunk 774 optimal weight: 0.6980 chunk 712 optimal weight: 4.9990 chunk 616 optimal weight: 10.0000 chunk 64 optimal weight: 0.5980 chunk 476 optimal weight: 3.9990 chunk 377 optimal weight: 0.0000 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 62370 Z= 0.116 Angle : 0.505 6.575 85050 Z= 0.261 Chirality : 0.044 0.151 9870 Planarity : 0.003 0.037 11088 Dihedral : 4.645 21.985 8358 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.18 % Favored : 93.55 % 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: -0.43 (0.10), residues: 7812 helix: 1.69 (0.17), residues: 882 sheet: 1.03 (0.11), residues: 2541 loop : -1.63 (0.09), residues: 4389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 95 HIS 0.002 0.001 HIS J 96 PHE 0.008 0.001 PHE O 231 TYR 0.031 0.001 TYR F 92 ARG 0.007 0.001 ARG G 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13392 Ramachandran restraints generated. 6696 Oldfield, 0 Emsley, 6696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.258 Fit side-chains REVERT: J 197 MET cc_start: 0.9337 (tpp) cc_final: 0.9099 (tpp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1158 time to fit residues: 4.4682 Evaluate side-chains 24 residues out of total 325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 777 random chunks: chunk 489 optimal weight: 0.0050 chunk 656 optimal weight: 3.9990 chunk 188 optimal weight: 10.0000 chunk 568 optimal weight: 9.9990 chunk 91 optimal weight: 0.0870 chunk 171 optimal weight: 8.9990 chunk 617 optimal weight: 10.0000 chunk 258 optimal weight: 8.9990 chunk 633 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 113 optimal weight: 0.4980 overall best weight: 2.7176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.055142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.045231 restraints weight = 15616.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.046794 restraints weight = 9999.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.047945 restraints weight = 7182.899| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 62370 Z= 0.162 Angle : 0.535 9.699 85050 Z= 0.279 Chirality : 0.043 0.135 9870 Planarity : 0.003 0.037 11088 Dihedral : 4.762 19.652 8358 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.99 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.10), residues: 7812 helix: 2.09 (0.17), residues: 882 sheet: 0.84 (0.11), residues: 2730 loop : -1.68 (0.09), residues: 4200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Q 70 HIS 0.002 0.001 HIS M 318 PHE 0.006 0.001 PHE M 231 TYR 0.028 0.001 TYR F 92 ARG 0.005 0.001 ARG B 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4439.12 seconds wall clock time: 83 minutes 21.28 seconds (5001.28 seconds total)