Starting phenix.real_space_refine on Fri Apr 12 05:25:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmv_36427/04_2024/8jmv_36427.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmv_36427/04_2024/8jmv_36427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmv_36427/04_2024/8jmv_36427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmv_36427/04_2024/8jmv_36427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmv_36427/04_2024/8jmv_36427.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmv_36427/04_2024/8jmv_36427.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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 396 5.16 5 C 48081 2.51 5 N 14355 2.21 5 O 17193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 109": "OE1" <-> "OE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 208": "OD1" <-> "OD2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 208": "OD1" <-> "OD2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 208": "OD1" <-> "OD2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 208": "OD1" <-> "OD2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 208": "OD1" <-> "OD2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 208": "OD1" <-> "OD2" Residue "G GLU 109": "OE1" <-> "OE2" Residue "G TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 208": "OD1" <-> "OD2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "H TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 208": "OD1" <-> "OD2" Residue "I GLU 109": "OE1" <-> "OE2" Residue "I TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 208": "OD1" <-> "OD2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "J TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 208": "OD1" <-> "OD2" Residue "K GLU 109": "OE1" <-> "OE2" Residue "K TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 208": "OD1" <-> "OD2" Residue "L GLU 109": "OE1" <-> "OE2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 208": "OD1" <-> "OD2" Residue "M GLU 109": "OE1" <-> "OE2" Residue "M TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 208": "OD1" <-> "OD2" Residue "N GLU 109": "OE1" <-> "OE2" Residue "N TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 208": "OD1" <-> "OD2" Residue "O GLU 109": "OE1" <-> "OE2" Residue "O TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 208": "OD1" <-> "OD2" Residue "P GLU 109": "OE1" <-> "OE2" Residue "P TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 208": "OD1" <-> "OD2" Residue "Q GLU 109": "OE1" <-> "OE2" Residue "Q TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 208": "OD1" <-> "OD2" Residue "R GLU 109": "OE1" <-> "OE2" Residue "R TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 208": "OD1" <-> "OD2" Residue "S GLU 109": "OE1" <-> "OE2" Residue "S TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 208": "OD1" <-> "OD2" Residue "T GLU 109": "OE1" <-> "OE2" Residue "T TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 208": "OD1" <-> "OD2" Residue "V GLU 109": "OE1" <-> "OE2" Residue "V TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 208": "OD1" <-> "OD2" Residue "W GLU 109": "OE1" <-> "OE2" Residue "W TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 208": "OD1" <-> "OD2" Residue "X GLU 109": "OE1" <-> "OE2" Residue "X TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 208": "OD1" <-> "OD2" Residue "Y GLU 109": "OE1" <-> "OE2" Residue "Y TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 208": "OD1" <-> "OD2" Residue "Z GLU 109": "OE1" <-> "OE2" Residue "Z TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 208": "OD1" <-> "OD2" Residue "AA GLU 109": "OE1" <-> "OE2" Residue "AA TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA ASP 208": "OD1" <-> "OD2" Residue "BA GLU 109": "OE1" <-> "OE2" Residue "BA TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA ASP 208": "OD1" <-> "OD2" Residue "CA GLU 109": "OE1" <-> "OE2" Residue "CA TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA ASP 208": "OD1" <-> "OD2" Residue "DA GLU 109": "OE1" <-> "OE2" Residue "DA TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA ASP 208": "OD1" <-> "OD2" Residue "EA GLU 109": "OE1" <-> "OE2" Residue "EA TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EA ASP 208": "OD1" <-> "OD2" Residue "FA GLU 109": "OE1" <-> "OE2" Residue "FA TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FA ASP 208": "OD1" <-> "OD2" Residue "GA GLU 109": "OE1" <-> "OE2" Residue "GA TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GA ASP 208": "OD1" <-> "OD2" Residue "HA GLU 109": "OE1" <-> "OE2" Residue "HA TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HA ASP 208": "OD1" <-> "OD2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 80025 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "B" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "C" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "D" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "E" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "F" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "G" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "H" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "I" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "J" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "K" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "L" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "M" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "N" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "O" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "P" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "Q" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "R" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "S" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "T" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "V" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "W" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "X" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "Y" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "Z" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "AA" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "BA" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "CA" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "DA" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "EA" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "FA" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "GA" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Chain: "HA" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 2, 'TRANS': 321} Chain breaks: 1 Time building chain proxies: 32.60, per 1000 atoms: 0.41 Number of scatterers: 80025 At special positions: 0 Unit cell: (160.65, 160.65, 307.65, 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 396 16.00 O 17193 8.00 N 14355 7.00 C 48081 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: 24.97 Conformation dependent library (CDL) restraints added in 12.1 seconds 21120 Ramachandran restraints generated. 10560 Oldfield, 0 Emsley, 10560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 20196 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 132 sheets defined 62.0% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.72 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN A 21 " --> pdb=" O ASN A 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 96 removed outlier: 3.610A pdb=" N MET A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 92 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLU A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 288 removed outlier: 3.907A pdb=" N THR A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 318 removed outlier: 3.721A pdb=" N GLU A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEU A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG B 14 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ASN B 21 " --> pdb=" O ASN B 17 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 96 removed outlier: 3.610A pdb=" N MET B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS B 64 " --> pdb=" O ASP B 60 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER B 85 " --> pdb=" O ASN B 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU B 92 " --> pdb=" O GLN B 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA B 94 " --> pdb=" O MET B 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLU B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 288 removed outlier: 3.907A pdb=" N THR B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU B 254 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 318 removed outlier: 3.720A pdb=" N GLU B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN B 306 " --> pdb=" O ASN B 302 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEU B 325 " --> pdb=" O GLN B 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN C 21 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 96 removed outlier: 3.610A pdb=" N MET C 61 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C 76 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU C 82 " --> pdb=" O GLY C 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER C 85 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU C 92 " --> pdb=" O GLN C 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA C 94 " --> pdb=" O MET C 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLU C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU C 113 " --> pdb=" O GLU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 288 removed outlier: 3.907A pdb=" N THR C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU C 254 " --> pdb=" O THR C 250 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 318 removed outlier: 3.720A pdb=" N GLU C 297 " --> pdb=" O SER C 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN C 306 " --> pdb=" O ASN C 302 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEU C 325 " --> pdb=" O GLN C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG D 14 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN D 21 " --> pdb=" O ASN D 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 96 removed outlier: 3.610A pdb=" N MET D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS D 64 " --> pdb=" O ASP D 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER D 76 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU D 82 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER D 85 " --> pdb=" O ASN D 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA D 94 " --> pdb=" O MET D 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLU D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS D 112 " --> pdb=" O SER D 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU D 113 " --> pdb=" O GLU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 288 removed outlier: 3.907A pdb=" N THR D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR D 243 " --> pdb=" O SER D 239 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU D 254 " --> pdb=" O THR D 250 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 318 removed outlier: 3.721A pdb=" N GLU D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN D 306 " --> pdb=" O ASN D 302 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEU D 325 " --> pdb=" O GLN D 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ASN E 21 " --> pdb=" O ASN E 17 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 96 removed outlier: 3.610A pdb=" N MET E 61 " --> pdb=" O ARG E 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS E 64 " --> pdb=" O ASP E 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER E 76 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU E 82 " --> pdb=" O GLY E 78 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER E 85 " --> pdb=" O ASN E 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU E 92 " --> pdb=" O GLN E 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA E 94 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR E 95 " --> pdb=" O SER E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLU E 109 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS E 112 " --> pdb=" O SER E 108 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU E 113 " --> pdb=" O GLU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 288 removed outlier: 3.907A pdb=" N THR E 242 " --> pdb=" O SER E 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR E 243 " --> pdb=" O SER E 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU E 254 " --> pdb=" O THR E 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL E 261 " --> pdb=" O LYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 318 removed outlier: 3.720A pdb=" N GLU E 297 " --> pdb=" O SER E 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN E 306 " --> pdb=" O ASN E 302 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN E 314 " --> pdb=" O ALA E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEU E 325 " --> pdb=" O GLN E 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG F 14 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN F 21 " --> pdb=" O ASN F 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 96 removed outlier: 3.610A pdb=" N MET F 61 " --> pdb=" O ARG F 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS F 64 " --> pdb=" O ASP F 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER F 76 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU F 82 " --> pdb=" O GLY F 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER F 85 " --> pdb=" O ASN F 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU F 92 " --> pdb=" O GLN F 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA F 94 " --> pdb=" O MET F 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR F 95 " --> pdb=" O SER F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 128 removed outlier: 3.543A pdb=" N GLU F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS F 112 " --> pdb=" O SER F 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU F 113 " --> pdb=" O GLU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 288 removed outlier: 3.907A pdb=" N THR F 242 " --> pdb=" O SER F 238 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR F 243 " --> pdb=" O SER F 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU F 254 " --> pdb=" O THR F 250 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL F 261 " --> pdb=" O LYS F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 318 removed outlier: 3.721A pdb=" N GLU F 297 " --> pdb=" O SER F 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN F 306 " --> pdb=" O ASN F 302 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN F 314 " --> pdb=" O ALA F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEU F 325 " --> pdb=" O GLN F 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG G 14 " --> pdb=" O LEU G 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN G 21 " --> pdb=" O ASN G 17 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 96 removed outlier: 3.610A pdb=" N MET G 61 " --> pdb=" O ARG G 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS G 64 " --> pdb=" O ASP G 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER G 76 " --> pdb=" O LEU G 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU G 82 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER G 85 " --> pdb=" O ASN G 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU G 92 " --> pdb=" O GLN G 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA G 94 " --> pdb=" O MET G 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR G 95 " --> pdb=" O SER G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLU G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS G 112 " --> pdb=" O SER G 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU G 113 " --> pdb=" O GLU G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 288 removed outlier: 3.907A pdb=" N THR G 242 " --> pdb=" O SER G 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR G 243 " --> pdb=" O SER G 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU G 254 " --> pdb=" O THR G 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL G 261 " --> pdb=" O LYS G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 318 removed outlier: 3.720A pdb=" N GLU G 297 " --> pdb=" O SER G 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN G 306 " --> pdb=" O ASN G 302 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN G 314 " --> pdb=" O ALA G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEU G 325 " --> pdb=" O GLN G 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG H 14 " --> pdb=" O LEU H 10 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ASN H 21 " --> pdb=" O ASN H 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 96 removed outlier: 3.610A pdb=" N MET H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS H 64 " --> pdb=" O ASP H 60 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER H 76 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU H 82 " --> pdb=" O GLY H 78 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER H 85 " --> pdb=" O ASN H 81 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU H 92 " --> pdb=" O GLN H 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA H 94 " --> pdb=" O MET H 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR H 95 " --> pdb=" O SER H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLU H 109 " --> pdb=" O SER H 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS H 112 " --> pdb=" O SER H 108 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU H 113 " --> pdb=" O GLU H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 288 removed outlier: 3.907A pdb=" N THR H 242 " --> pdb=" O SER H 238 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR H 243 " --> pdb=" O SER H 239 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU H 254 " --> pdb=" O THR H 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL H 261 " --> pdb=" O LYS H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 318 removed outlier: 3.721A pdb=" N GLU H 297 " --> pdb=" O SER H 293 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN H 306 " --> pdb=" O ASN H 302 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN H 314 " --> pdb=" O ALA H 310 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEU H 325 " --> pdb=" O GLN H 321 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG I 14 " --> pdb=" O LEU I 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN I 21 " --> pdb=" O ASN I 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 96 removed outlier: 3.610A pdb=" N MET I 61 " --> pdb=" O ARG I 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS I 64 " --> pdb=" O ASP I 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER I 76 " --> pdb=" O LEU I 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU I 82 " --> pdb=" O GLY I 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER I 85 " --> pdb=" O ASN I 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU I 92 " --> pdb=" O GLN I 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA I 94 " --> pdb=" O MET I 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR I 95 " --> pdb=" O SER I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLU I 109 " --> pdb=" O SER I 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS I 112 " --> pdb=" O SER I 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU I 113 " --> pdb=" O GLU I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 233 through 288 removed outlier: 3.907A pdb=" N THR I 242 " --> pdb=" O SER I 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR I 243 " --> pdb=" O SER I 239 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU I 254 " --> pdb=" O THR I 250 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL I 261 " --> pdb=" O LYS I 257 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 318 removed outlier: 3.720A pdb=" N GLU I 297 " --> pdb=" O SER I 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN I 306 " --> pdb=" O ASN I 302 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN I 314 " --> pdb=" O ALA I 310 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEU I 325 " --> pdb=" O GLN I 321 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG J 14 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN J 21 " --> pdb=" O ASN J 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA J 22 " --> pdb=" O ALA J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 96 removed outlier: 3.610A pdb=" N MET J 61 " --> pdb=" O ARG J 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS J 64 " --> pdb=" O ASP J 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER J 76 " --> pdb=" O LEU J 72 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU J 82 " --> pdb=" O GLY J 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER J 85 " --> pdb=" O ASN J 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU J 92 " --> pdb=" O GLN J 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA J 94 " --> pdb=" O MET J 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR J 95 " --> pdb=" O SER J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 128 removed outlier: 3.543A pdb=" N GLU J 109 " --> pdb=" O SER J 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS J 112 " --> pdb=" O SER J 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU J 113 " --> pdb=" O GLU J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 288 removed outlier: 3.907A pdb=" N THR J 242 " --> pdb=" O SER J 238 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR J 243 " --> pdb=" O SER J 239 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU J 254 " --> pdb=" O THR J 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL J 261 " --> pdb=" O LYS J 257 " (cutoff:3.500A) Processing helix chain 'J' and resid 290 through 318 removed outlier: 3.721A pdb=" N GLU J 297 " --> pdb=" O SER J 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN J 306 " --> pdb=" O ASN J 302 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN J 314 " --> pdb=" O ALA J 310 " (cutoff:3.500A) Processing helix chain 'J' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEU J 325 " --> pdb=" O GLN J 321 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG K 14 " --> pdb=" O LEU K 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN K 21 " --> pdb=" O ASN K 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA K 22 " --> pdb=" O ALA K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 96 removed outlier: 3.610A pdb=" N MET K 61 " --> pdb=" O ARG K 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS K 64 " --> pdb=" O ASP K 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER K 76 " --> pdb=" O LEU K 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU K 82 " --> pdb=" O GLY K 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER K 85 " --> pdb=" O ASN K 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU K 92 " --> pdb=" O GLN K 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA K 94 " --> pdb=" O MET K 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR K 95 " --> pdb=" O SER K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLU K 109 " --> pdb=" O SER K 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS K 112 " --> pdb=" O SER K 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU K 113 " --> pdb=" O GLU K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 288 removed outlier: 3.907A pdb=" N THR K 242 " --> pdb=" O SER K 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR K 243 " --> pdb=" O SER K 239 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU K 254 " --> pdb=" O THR K 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL K 261 " --> pdb=" O LYS K 257 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 318 removed outlier: 3.721A pdb=" N GLU K 297 " --> pdb=" O SER K 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN K 306 " --> pdb=" O ASN K 302 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN K 314 " --> pdb=" O ALA K 310 " (cutoff:3.500A) Processing helix chain 'K' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEU K 325 " --> pdb=" O GLN K 321 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG L 14 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN L 21 " --> pdb=" O ASN L 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA L 22 " --> pdb=" O ALA L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 96 removed outlier: 3.610A pdb=" N MET L 61 " --> pdb=" O ARG L 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS L 64 " --> pdb=" O ASP L 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER L 76 " --> pdb=" O LEU L 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU L 82 " --> pdb=" O GLY L 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER L 85 " --> pdb=" O ASN L 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU L 92 " --> pdb=" O GLN L 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA L 94 " --> pdb=" O MET L 90 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR L 95 " --> pdb=" O SER L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLU L 109 " --> pdb=" O SER L 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS L 112 " --> pdb=" O SER L 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU L 113 " --> pdb=" O GLU L 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 288 removed outlier: 3.907A pdb=" N THR L 242 " --> pdb=" O SER L 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR L 243 " --> pdb=" O SER L 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU L 254 " --> pdb=" O THR L 250 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL L 261 " --> pdb=" O LYS L 257 " (cutoff:3.500A) Processing helix chain 'L' and resid 290 through 318 removed outlier: 3.720A pdb=" N GLU L 297 " --> pdb=" O SER L 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN L 306 " --> pdb=" O ASN L 302 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN L 314 " --> pdb=" O ALA L 310 " (cutoff:3.500A) Processing helix chain 'L' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEU L 325 " --> pdb=" O GLN L 321 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG M 14 " --> pdb=" O LEU M 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN M 21 " --> pdb=" O ASN M 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA M 22 " --> pdb=" O ALA M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 96 removed outlier: 3.610A pdb=" N MET M 61 " --> pdb=" O ARG M 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS M 64 " --> pdb=" O ASP M 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER M 76 " --> pdb=" O LEU M 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU M 82 " --> pdb=" O GLY M 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER M 85 " --> pdb=" O ASN M 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU M 92 " --> pdb=" O GLN M 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA M 94 " --> pdb=" O MET M 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR M 95 " --> pdb=" O SER M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLU M 109 " --> pdb=" O SER M 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS M 112 " --> pdb=" O SER M 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU M 113 " --> pdb=" O GLU M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 288 removed outlier: 3.907A pdb=" N THR M 242 " --> pdb=" O SER M 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR M 243 " --> pdb=" O SER M 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU M 254 " --> pdb=" O THR M 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL M 261 " --> pdb=" O LYS M 257 " (cutoff:3.500A) Processing helix chain 'M' and resid 290 through 318 removed outlier: 3.720A pdb=" N GLU M 297 " --> pdb=" O SER M 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN M 306 " --> pdb=" O ASN M 302 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN M 314 " --> pdb=" O ALA M 310 " (cutoff:3.500A) Processing helix chain 'M' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEU M 325 " --> pdb=" O GLN M 321 " (cutoff:3.500A) Processing helix chain 'N' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ASN N 21 " --> pdb=" O ASN N 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA N 22 " --> pdb=" O ALA N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 96 removed outlier: 3.610A pdb=" N MET N 61 " --> pdb=" O ARG N 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS N 64 " --> pdb=" O ASP N 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER N 76 " --> pdb=" O LEU N 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU N 82 " --> pdb=" O GLY N 78 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER N 85 " --> pdb=" O ASN N 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU N 92 " --> pdb=" O GLN N 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA N 94 " --> pdb=" O MET N 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR N 95 " --> pdb=" O SER N 91 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLU N 109 " --> pdb=" O SER N 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS N 112 " --> pdb=" O SER N 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU N 113 " --> pdb=" O GLU N 109 " (cutoff:3.500A) Processing helix chain 'N' and resid 233 through 288 removed outlier: 3.907A pdb=" N THR N 242 " --> pdb=" O SER N 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR N 243 " --> pdb=" O SER N 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU N 254 " --> pdb=" O THR N 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL N 261 " --> pdb=" O LYS N 257 " (cutoff:3.500A) Processing helix chain 'N' and resid 290 through 318 removed outlier: 3.720A pdb=" N GLU N 297 " --> pdb=" O SER N 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN N 306 " --> pdb=" O ASN N 302 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN N 314 " --> pdb=" O ALA N 310 " (cutoff:3.500A) Processing helix chain 'N' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEU N 325 " --> pdb=" O GLN N 321 " (cutoff:3.500A) Processing helix chain 'O' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG O 14 " --> pdb=" O LEU O 10 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ASN O 21 " --> pdb=" O ASN O 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA O 22 " --> pdb=" O ALA O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 96 removed outlier: 3.610A pdb=" N MET O 61 " --> pdb=" O ARG O 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS O 64 " --> pdb=" O ASP O 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER O 76 " --> pdb=" O LEU O 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU O 82 " --> pdb=" O GLY O 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER O 85 " --> pdb=" O ASN O 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU O 92 " --> pdb=" O GLN O 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA O 94 " --> pdb=" O MET O 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR O 95 " --> pdb=" O SER O 91 " (cutoff:3.500A) Processing helix chain 'O' and resid 103 through 128 removed outlier: 3.543A pdb=" N GLU O 109 " --> pdb=" O SER O 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS O 112 " --> pdb=" O SER O 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU O 113 " --> pdb=" O GLU O 109 " (cutoff:3.500A) Processing helix chain 'O' and resid 233 through 288 removed outlier: 3.906A pdb=" N THR O 242 " --> pdb=" O SER O 238 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR O 243 " --> pdb=" O SER O 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU O 254 " --> pdb=" O THR O 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL O 261 " --> pdb=" O LYS O 257 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 318 removed outlier: 3.720A pdb=" N GLU O 297 " --> pdb=" O SER O 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN O 306 " --> pdb=" O ASN O 302 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN O 314 " --> pdb=" O ALA O 310 " (cutoff:3.500A) Processing helix chain 'O' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEU O 325 " --> pdb=" O GLN O 321 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG P 14 " --> pdb=" O LEU P 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN P 21 " --> pdb=" O ASN P 17 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA P 22 " --> pdb=" O ALA P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 96 removed outlier: 3.611A pdb=" N MET P 61 " --> pdb=" O ARG P 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS P 64 " --> pdb=" O ASP P 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER P 76 " --> pdb=" O LEU P 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU P 82 " --> pdb=" O GLY P 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER P 85 " --> pdb=" O ASN P 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU P 92 " --> pdb=" O GLN P 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA P 94 " --> pdb=" O MET P 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR P 95 " --> pdb=" O SER P 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLU P 109 " --> pdb=" O SER P 105 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS P 112 " --> pdb=" O SER P 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU P 113 " --> pdb=" O GLU P 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 233 through 288 removed outlier: 3.907A pdb=" N THR P 242 " --> pdb=" O SER P 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR P 243 " --> pdb=" O SER P 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU P 254 " --> pdb=" O THR P 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL P 261 " --> pdb=" O LYS P 257 " (cutoff:3.500A) Processing helix chain 'P' and resid 290 through 318 removed outlier: 3.720A pdb=" N GLU P 297 " --> pdb=" O SER P 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN P 306 " --> pdb=" O ASN P 302 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN P 314 " --> pdb=" O ALA P 310 " (cutoff:3.500A) Processing helix chain 'P' and resid 321 through 327 removed outlier: 4.029A pdb=" N LEU P 325 " --> pdb=" O GLN P 321 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG Q 14 " --> pdb=" O LEU Q 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN Q 21 " --> pdb=" O ASN Q 17 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA Q 22 " --> pdb=" O ALA Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 96 removed outlier: 3.610A pdb=" N MET Q 61 " --> pdb=" O ARG Q 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS Q 64 " --> pdb=" O ASP Q 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER Q 76 " --> pdb=" O LEU Q 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU Q 82 " --> pdb=" O GLY Q 78 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER Q 85 " --> pdb=" O ASN Q 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU Q 92 " --> pdb=" O GLN Q 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA Q 94 " --> pdb=" O MET Q 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR Q 95 " --> pdb=" O SER Q 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLU Q 109 " --> pdb=" O SER Q 105 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS Q 112 " --> pdb=" O SER Q 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU Q 113 " --> pdb=" O GLU Q 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 233 through 288 removed outlier: 3.907A pdb=" N THR Q 242 " --> pdb=" O SER Q 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR Q 243 " --> pdb=" O SER Q 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU Q 254 " --> pdb=" O THR Q 250 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL Q 261 " --> pdb=" O LYS Q 257 " (cutoff:3.500A) Processing helix chain 'Q' and resid 290 through 318 removed outlier: 3.720A pdb=" N GLU Q 297 " --> pdb=" O SER Q 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN Q 306 " --> pdb=" O ASN Q 302 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN Q 314 " --> pdb=" O ALA Q 310 " (cutoff:3.500A) Processing helix chain 'Q' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEU Q 325 " --> pdb=" O GLN Q 321 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG R 14 " --> pdb=" O LEU R 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN R 21 " --> pdb=" O ASN R 17 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA R 22 " --> pdb=" O ALA R 18 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 96 removed outlier: 3.611A pdb=" N MET R 61 " --> pdb=" O ARG R 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS R 64 " --> pdb=" O ASP R 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER R 76 " --> pdb=" O LEU R 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU R 82 " --> pdb=" O GLY R 78 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER R 85 " --> pdb=" O ASN R 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU R 92 " --> pdb=" O GLN R 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA R 94 " --> pdb=" O MET R 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR R 95 " --> pdb=" O SER R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLU R 109 " --> pdb=" O SER R 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS R 112 " --> pdb=" O SER R 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU R 113 " --> pdb=" O GLU R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 233 through 288 removed outlier: 3.907A pdb=" N THR R 242 " --> pdb=" O SER R 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR R 243 " --> pdb=" O SER R 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU R 254 " --> pdb=" O THR R 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL R 261 " --> pdb=" O LYS R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 290 through 318 removed outlier: 3.721A pdb=" N GLU R 297 " --> pdb=" O SER R 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN R 306 " --> pdb=" O ASN R 302 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN R 314 " --> pdb=" O ALA R 310 " (cutoff:3.500A) Processing helix chain 'R' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEU R 325 " --> pdb=" O GLN R 321 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG S 14 " --> pdb=" O LEU S 10 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ASN S 21 " --> pdb=" O ASN S 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA S 22 " --> pdb=" O ALA S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 96 removed outlier: 3.610A pdb=" N MET S 61 " --> pdb=" O ARG S 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS S 64 " --> pdb=" O ASP S 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER S 76 " --> pdb=" O LEU S 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU S 82 " --> pdb=" O GLY S 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER S 85 " --> pdb=" O ASN S 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU S 92 " --> pdb=" O GLN S 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA S 94 " --> pdb=" O MET S 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR S 95 " --> pdb=" O SER S 91 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLU S 109 " --> pdb=" O SER S 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS S 112 " --> pdb=" O SER S 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU S 113 " --> pdb=" O GLU S 109 " (cutoff:3.500A) Processing helix chain 'S' and resid 233 through 288 removed outlier: 3.907A pdb=" N THR S 242 " --> pdb=" O SER S 238 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR S 243 " --> pdb=" O SER S 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU S 254 " --> pdb=" O THR S 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL S 261 " --> pdb=" O LYS S 257 " (cutoff:3.500A) Processing helix chain 'S' and resid 290 through 318 removed outlier: 3.721A pdb=" N GLU S 297 " --> pdb=" O SER S 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN S 306 " --> pdb=" O ASN S 302 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN S 314 " --> pdb=" O ALA S 310 " (cutoff:3.500A) Processing helix chain 'S' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEU S 325 " --> pdb=" O GLN S 321 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG T 14 " --> pdb=" O LEU T 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN T 21 " --> pdb=" O ASN T 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA T 22 " --> pdb=" O ALA T 18 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 96 removed outlier: 3.610A pdb=" N MET T 61 " --> pdb=" O ARG T 57 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS T 64 " --> pdb=" O ASP T 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER T 76 " --> pdb=" O LEU T 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU T 82 " --> pdb=" O GLY T 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER T 85 " --> pdb=" O ASN T 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU T 92 " --> pdb=" O GLN T 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA T 94 " --> pdb=" O MET T 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR T 95 " --> pdb=" O SER T 91 " (cutoff:3.500A) Processing helix chain 'T' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLU T 109 " --> pdb=" O SER T 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS T 112 " --> pdb=" O SER T 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU T 113 " --> pdb=" O GLU T 109 " (cutoff:3.500A) Processing helix chain 'T' and resid 233 through 288 removed outlier: 3.907A pdb=" N THR T 242 " --> pdb=" O SER T 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR T 243 " --> pdb=" O SER T 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU T 254 " --> pdb=" O THR T 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL T 261 " --> pdb=" O LYS T 257 " (cutoff:3.500A) Processing helix chain 'T' and resid 290 through 318 removed outlier: 3.721A pdb=" N GLU T 297 " --> pdb=" O SER T 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN T 306 " --> pdb=" O ASN T 302 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN T 314 " --> pdb=" O ALA T 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEU T 325 " --> pdb=" O GLN T 321 " (cutoff:3.500A) Processing helix chain 'V' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG V 14 " --> pdb=" O LEU V 10 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ASN V 21 " --> pdb=" O ASN V 17 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA V 22 " --> pdb=" O ALA V 18 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 96 removed outlier: 3.610A pdb=" N MET V 61 " --> pdb=" O ARG V 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS V 64 " --> pdb=" O ASP V 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER V 76 " --> pdb=" O LEU V 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU V 82 " --> pdb=" O GLY V 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER V 85 " --> pdb=" O ASN V 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU V 92 " --> pdb=" O GLN V 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA V 94 " --> pdb=" O MET V 90 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR V 95 " --> pdb=" O SER V 91 " (cutoff:3.500A) Processing helix chain 'V' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLU V 109 " --> pdb=" O SER V 105 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS V 112 " --> pdb=" O SER V 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU V 113 " --> pdb=" O GLU V 109 " (cutoff:3.500A) Processing helix chain 'V' and resid 233 through 288 removed outlier: 3.907A pdb=" N THR V 242 " --> pdb=" O SER V 238 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR V 243 " --> pdb=" O SER V 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU V 254 " --> pdb=" O THR V 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL V 261 " --> pdb=" O LYS V 257 " (cutoff:3.500A) Processing helix chain 'V' and resid 290 through 318 removed outlier: 3.720A pdb=" N GLU V 297 " --> pdb=" O SER V 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN V 306 " --> pdb=" O ASN V 302 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN V 314 " --> pdb=" O ALA V 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEU V 325 " --> pdb=" O GLN V 321 " (cutoff:3.500A) Processing helix chain 'W' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG W 14 " --> pdb=" O LEU W 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN W 21 " --> pdb=" O ASN W 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA W 22 " --> pdb=" O ALA W 18 " (cutoff:3.500A) Processing helix chain 'W' and resid 42 through 96 removed outlier: 3.611A pdb=" N MET W 61 " --> pdb=" O ARG W 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS W 64 " --> pdb=" O ASP W 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER W 76 " --> pdb=" O LEU W 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU W 82 " --> pdb=" O GLY W 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER W 85 " --> pdb=" O ASN W 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU W 92 " --> pdb=" O GLN W 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA W 94 " --> pdb=" O MET W 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR W 95 " --> pdb=" O SER W 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLU W 109 " --> pdb=" O SER W 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS W 112 " --> pdb=" O SER W 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU W 113 " --> pdb=" O GLU W 109 " (cutoff:3.500A) Processing helix chain 'W' and resid 233 through 288 removed outlier: 3.907A pdb=" N THR W 242 " --> pdb=" O SER W 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR W 243 " --> pdb=" O SER W 239 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU W 254 " --> pdb=" O THR W 250 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL W 261 " --> pdb=" O LYS W 257 " (cutoff:3.500A) Processing helix chain 'W' and resid 290 through 318 removed outlier: 3.721A pdb=" N GLU W 297 " --> pdb=" O SER W 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN W 306 " --> pdb=" O ASN W 302 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN W 314 " --> pdb=" O ALA W 310 " (cutoff:3.500A) Processing helix chain 'W' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEU W 325 " --> pdb=" O GLN W 321 " (cutoff:3.500A) Processing helix chain 'X' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG X 14 " --> pdb=" O LEU X 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN X 21 " --> pdb=" O ASN X 17 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA X 22 " --> pdb=" O ALA X 18 " (cutoff:3.500A) Processing helix chain 'X' and resid 42 through 96 removed outlier: 3.610A pdb=" N MET X 61 " --> pdb=" O ARG X 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS X 64 " --> pdb=" O ASP X 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER X 76 " --> pdb=" O LEU X 72 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU X 82 " --> pdb=" O GLY X 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER X 85 " --> pdb=" O ASN X 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU X 92 " --> pdb=" O GLN X 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA X 94 " --> pdb=" O MET X 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR X 95 " --> pdb=" O SER X 91 " (cutoff:3.500A) Processing helix chain 'X' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLU X 109 " --> pdb=" O SER X 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS X 112 " --> pdb=" O SER X 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU X 113 " --> pdb=" O GLU X 109 " (cutoff:3.500A) Processing helix chain 'X' and resid 233 through 288 removed outlier: 3.907A pdb=" N THR X 242 " --> pdb=" O SER X 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR X 243 " --> pdb=" O SER X 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU X 254 " --> pdb=" O THR X 250 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL X 261 " --> pdb=" O LYS X 257 " (cutoff:3.500A) Processing helix chain 'X' and resid 290 through 318 removed outlier: 3.720A pdb=" N GLU X 297 " --> pdb=" O SER X 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN X 306 " --> pdb=" O ASN X 302 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN X 314 " --> pdb=" O ALA X 310 " (cutoff:3.500A) Processing helix chain 'X' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEU X 325 " --> pdb=" O GLN X 321 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG Y 14 " --> pdb=" O LEU Y 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN Y 21 " --> pdb=" O ASN Y 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA Y 22 " --> pdb=" O ALA Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 96 removed outlier: 3.610A pdb=" N MET Y 61 " --> pdb=" O ARG Y 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS Y 64 " --> pdb=" O ASP Y 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER Y 76 " --> pdb=" O LEU Y 72 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU Y 82 " --> pdb=" O GLY Y 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER Y 85 " --> pdb=" O ASN Y 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU Y 92 " --> pdb=" O GLN Y 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA Y 94 " --> pdb=" O MET Y 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR Y 95 " --> pdb=" O SER Y 91 " (cutoff:3.500A) Processing helix chain 'Y' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLU Y 109 " --> pdb=" O SER Y 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS Y 112 " --> pdb=" O SER Y 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU Y 113 " --> pdb=" O GLU Y 109 " (cutoff:3.500A) Processing helix chain 'Y' and resid 233 through 288 removed outlier: 3.907A pdb=" N THR Y 242 " --> pdb=" O SER Y 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR Y 243 " --> pdb=" O SER Y 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU Y 254 " --> pdb=" O THR Y 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL Y 261 " --> pdb=" O LYS Y 257 " (cutoff:3.500A) Processing helix chain 'Y' and resid 290 through 318 removed outlier: 3.720A pdb=" N GLU Y 297 " --> pdb=" O SER Y 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN Y 306 " --> pdb=" O ASN Y 302 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN Y 314 " --> pdb=" O ALA Y 310 " (cutoff:3.500A) Processing helix chain 'Y' and resid 321 through 327 removed outlier: 4.029A pdb=" N LEU Y 325 " --> pdb=" O GLN Y 321 " (cutoff:3.500A) Processing helix chain 'Z' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARG Z 14 " --> pdb=" O LEU Z 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN Z 21 " --> pdb=" O ASN Z 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA Z 22 " --> pdb=" O ALA Z 18 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 96 removed outlier: 3.610A pdb=" N MET Z 61 " --> pdb=" O ARG Z 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS Z 64 " --> pdb=" O ASP Z 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER Z 76 " --> pdb=" O LEU Z 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU Z 82 " --> pdb=" O GLY Z 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER Z 85 " --> pdb=" O ASN Z 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU Z 92 " --> pdb=" O GLN Z 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA Z 94 " --> pdb=" O MET Z 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR Z 95 " --> pdb=" O SER Z 91 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLU Z 109 " --> pdb=" O SER Z 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS Z 112 " --> pdb=" O SER Z 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU Z 113 " --> pdb=" O GLU Z 109 " (cutoff:3.500A) Processing helix chain 'Z' and resid 233 through 288 removed outlier: 3.907A pdb=" N THR Z 242 " --> pdb=" O SER Z 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR Z 243 " --> pdb=" O SER Z 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU Z 254 " --> pdb=" O THR Z 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL Z 261 " --> pdb=" O LYS Z 257 " (cutoff:3.500A) Processing helix chain 'Z' and resid 290 through 318 removed outlier: 3.720A pdb=" N GLU Z 297 " --> pdb=" O SER Z 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN Z 306 " --> pdb=" O ASN Z 302 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN Z 314 " --> pdb=" O ALA Z 310 " (cutoff:3.500A) Processing helix chain 'Z' and resid 321 through 327 removed outlier: 4.029A pdb=" N LEU Z 325 " --> pdb=" O GLN Z 321 " (cutoff:3.500A) Processing helix chain 'AA' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARGAA 14 " --> pdb=" O LEUAA 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASNAA 21 " --> pdb=" O ASNAA 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALAAA 22 " --> pdb=" O ALAAA 18 " (cutoff:3.500A) Processing helix chain 'AA' and resid 42 through 96 removed outlier: 3.610A pdb=" N METAA 61 " --> pdb=" O ARGAA 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYSAA 64 " --> pdb=" O ASPAA 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERAA 76 " --> pdb=" O LEUAA 72 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLUAA 82 " --> pdb=" O GLYAA 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SERAA 85 " --> pdb=" O ASNAA 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLUAA 92 " --> pdb=" O GLNAA 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALAAA 94 " --> pdb=" O METAA 90 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THRAA 95 " --> pdb=" O SERAA 91 " (cutoff:3.500A) Processing helix chain 'AA' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLUAA 109 " --> pdb=" O SERAA 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYSAA 112 " --> pdb=" O SERAA 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLUAA 113 " --> pdb=" O GLUAA 109 " (cutoff:3.500A) Processing helix chain 'AA' and resid 233 through 288 removed outlier: 3.907A pdb=" N THRAA 242 " --> pdb=" O SERAA 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THRAA 243 " --> pdb=" O SERAA 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLUAA 254 " --> pdb=" O THRAA 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VALAA 261 " --> pdb=" O LYSAA 257 " (cutoff:3.500A) Processing helix chain 'AA' and resid 290 through 318 removed outlier: 3.720A pdb=" N GLUAA 297 " --> pdb=" O SERAA 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLNAA 306 " --> pdb=" O ASNAA 302 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLNAA 314 " --> pdb=" O ALAAA 310 " (cutoff:3.500A) Processing helix chain 'AA' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEUAA 325 " --> pdb=" O GLNAA 321 " (cutoff:3.500A) Processing helix chain 'BA' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARGBA 14 " --> pdb=" O LEUBA 10 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ASNBA 21 " --> pdb=" O ASNBA 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALABA 22 " --> pdb=" O ALABA 18 " (cutoff:3.500A) Processing helix chain 'BA' and resid 42 through 96 removed outlier: 3.610A pdb=" N METBA 61 " --> pdb=" O ARGBA 57 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYSBA 64 " --> pdb=" O ASPBA 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERBA 76 " --> pdb=" O LEUBA 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLUBA 82 " --> pdb=" O GLYBA 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SERBA 85 " --> pdb=" O ASNBA 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLUBA 92 " --> pdb=" O GLNBA 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALABA 94 " --> pdb=" O METBA 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THRBA 95 " --> pdb=" O SERBA 91 " (cutoff:3.500A) Processing helix chain 'BA' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLUBA 109 " --> pdb=" O SERBA 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYSBA 112 " --> pdb=" O SERBA 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLUBA 113 " --> pdb=" O GLUBA 109 " (cutoff:3.500A) Processing helix chain 'BA' and resid 233 through 288 removed outlier: 3.907A pdb=" N THRBA 242 " --> pdb=" O SERBA 238 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THRBA 243 " --> pdb=" O SERBA 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLUBA 254 " --> pdb=" O THRBA 250 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VALBA 261 " --> pdb=" O LYSBA 257 " (cutoff:3.500A) Processing helix chain 'BA' and resid 290 through 318 removed outlier: 3.721A pdb=" N GLUBA 297 " --> pdb=" O SERBA 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLNBA 306 " --> pdb=" O ASNBA 302 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLNBA 314 " --> pdb=" O ALABA 310 " (cutoff:3.500A) Processing helix chain 'BA' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEUBA 325 " --> pdb=" O GLNBA 321 " (cutoff:3.500A) Processing helix chain 'CA' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARGCA 14 " --> pdb=" O LEUCA 10 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ASNCA 21 " --> pdb=" O ASNCA 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALACA 22 " --> pdb=" O ALACA 18 " (cutoff:3.500A) Processing helix chain 'CA' and resid 42 through 96 removed outlier: 3.610A pdb=" N METCA 61 " --> pdb=" O ARGCA 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYSCA 64 " --> pdb=" O ASPCA 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERCA 76 " --> pdb=" O LEUCA 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLUCA 82 " --> pdb=" O GLYCA 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SERCA 85 " --> pdb=" O ASNCA 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLUCA 92 " --> pdb=" O GLNCA 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALACA 94 " --> pdb=" O METCA 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THRCA 95 " --> pdb=" O SERCA 91 " (cutoff:3.500A) Processing helix chain 'CA' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLUCA 109 " --> pdb=" O SERCA 105 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYSCA 112 " --> pdb=" O SERCA 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLUCA 113 " --> pdb=" O GLUCA 109 " (cutoff:3.500A) Processing helix chain 'CA' and resid 233 through 288 removed outlier: 3.907A pdb=" N THRCA 242 " --> pdb=" O SERCA 238 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THRCA 243 " --> pdb=" O SERCA 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLUCA 254 " --> pdb=" O THRCA 250 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VALCA 261 " --> pdb=" O LYSCA 257 " (cutoff:3.500A) Processing helix chain 'CA' and resid 290 through 318 removed outlier: 3.721A pdb=" N GLUCA 297 " --> pdb=" O SERCA 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLNCA 306 " --> pdb=" O ASNCA 302 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLNCA 314 " --> pdb=" O ALACA 310 " (cutoff:3.500A) Processing helix chain 'CA' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEUCA 325 " --> pdb=" O GLNCA 321 " (cutoff:3.500A) Processing helix chain 'DA' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARGDA 14 " --> pdb=" O LEUDA 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASNDA 21 " --> pdb=" O ASNDA 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALADA 22 " --> pdb=" O ALADA 18 " (cutoff:3.500A) Processing helix chain 'DA' and resid 42 through 96 removed outlier: 3.610A pdb=" N METDA 61 " --> pdb=" O ARGDA 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYSDA 64 " --> pdb=" O ASPDA 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERDA 76 " --> pdb=" O LEUDA 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLUDA 82 " --> pdb=" O GLYDA 78 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SERDA 85 " --> pdb=" O ASNDA 81 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLUDA 92 " --> pdb=" O GLNDA 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALADA 94 " --> pdb=" O METDA 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THRDA 95 " --> pdb=" O SERDA 91 " (cutoff:3.500A) Processing helix chain 'DA' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLUDA 109 " --> pdb=" O SERDA 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYSDA 112 " --> pdb=" O SERDA 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLUDA 113 " --> pdb=" O GLUDA 109 " (cutoff:3.500A) Processing helix chain 'DA' and resid 233 through 288 removed outlier: 3.907A pdb=" N THRDA 242 " --> pdb=" O SERDA 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THRDA 243 " --> pdb=" O SERDA 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLUDA 254 " --> pdb=" O THRDA 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VALDA 261 " --> pdb=" O LYSDA 257 " (cutoff:3.500A) Processing helix chain 'DA' and resid 290 through 318 removed outlier: 3.721A pdb=" N GLUDA 297 " --> pdb=" O SERDA 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLNDA 306 " --> pdb=" O ASNDA 302 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLNDA 314 " --> pdb=" O ALADA 310 " (cutoff:3.500A) Processing helix chain 'DA' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEUDA 325 " --> pdb=" O GLNDA 321 " (cutoff:3.500A) Processing helix chain 'EA' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARGEA 14 " --> pdb=" O LEUEA 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASNEA 21 " --> pdb=" O ASNEA 17 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALAEA 22 " --> pdb=" O ALAEA 18 " (cutoff:3.500A) Processing helix chain 'EA' and resid 42 through 96 removed outlier: 3.610A pdb=" N METEA 61 " --> pdb=" O ARGEA 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYSEA 64 " --> pdb=" O ASPEA 60 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SEREA 76 " --> pdb=" O LEUEA 72 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLUEA 82 " --> pdb=" O GLYEA 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SEREA 85 " --> pdb=" O ASNEA 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLUEA 92 " --> pdb=" O GLNEA 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALAEA 94 " --> pdb=" O METEA 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THREA 95 " --> pdb=" O SEREA 91 " (cutoff:3.500A) Processing helix chain 'EA' and resid 103 through 128 removed outlier: 3.543A pdb=" N GLUEA 109 " --> pdb=" O SEREA 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYSEA 112 " --> pdb=" O SEREA 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLUEA 113 " --> pdb=" O GLUEA 109 " (cutoff:3.500A) Processing helix chain 'EA' and resid 233 through 288 removed outlier: 3.907A pdb=" N THREA 242 " --> pdb=" O SEREA 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THREA 243 " --> pdb=" O SEREA 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLUEA 254 " --> pdb=" O THREA 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VALEA 261 " --> pdb=" O LYSEA 257 " (cutoff:3.500A) Processing helix chain 'EA' and resid 290 through 318 removed outlier: 3.721A pdb=" N GLUEA 297 " --> pdb=" O SEREA 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLNEA 306 " --> pdb=" O ASNEA 302 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLNEA 314 " --> pdb=" O ALAEA 310 " (cutoff:3.500A) Processing helix chain 'EA' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEUEA 325 " --> pdb=" O GLNEA 321 " (cutoff:3.500A) Processing helix chain 'FA' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARGFA 14 " --> pdb=" O LEUFA 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASNFA 21 " --> pdb=" O ASNFA 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALAFA 22 " --> pdb=" O ALAFA 18 " (cutoff:3.500A) Processing helix chain 'FA' and resid 42 through 96 removed outlier: 3.610A pdb=" N METFA 61 " --> pdb=" O ARGFA 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYSFA 64 " --> pdb=" O ASPFA 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERFA 76 " --> pdb=" O LEUFA 72 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLUFA 82 " --> pdb=" O GLYFA 78 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SERFA 85 " --> pdb=" O ASNFA 81 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLUFA 92 " --> pdb=" O GLNFA 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALAFA 94 " --> pdb=" O METFA 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THRFA 95 " --> pdb=" O SERFA 91 " (cutoff:3.500A) Processing helix chain 'FA' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLUFA 109 " --> pdb=" O SERFA 105 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYSFA 112 " --> pdb=" O SERFA 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLUFA 113 " --> pdb=" O GLUFA 109 " (cutoff:3.500A) Processing helix chain 'FA' and resid 233 through 288 removed outlier: 3.907A pdb=" N THRFA 242 " --> pdb=" O SERFA 238 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THRFA 243 " --> pdb=" O SERFA 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLUFA 254 " --> pdb=" O THRFA 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VALFA 261 " --> pdb=" O LYSFA 257 " (cutoff:3.500A) Processing helix chain 'FA' and resid 290 through 318 removed outlier: 3.720A pdb=" N GLUFA 297 " --> pdb=" O SERFA 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLNFA 306 " --> pdb=" O ASNFA 302 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLNFA 314 " --> pdb=" O ALAFA 310 " (cutoff:3.500A) Processing helix chain 'FA' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEUFA 325 " --> pdb=" O GLNFA 321 " (cutoff:3.500A) Processing helix chain 'GA' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARGGA 14 " --> pdb=" O LEUGA 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASNGA 21 " --> pdb=" O ASNGA 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALAGA 22 " --> pdb=" O ALAGA 18 " (cutoff:3.500A) Processing helix chain 'GA' and resid 42 through 96 removed outlier: 3.610A pdb=" N METGA 61 " --> pdb=" O ARGGA 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYSGA 64 " --> pdb=" O ASPGA 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERGA 76 " --> pdb=" O LEUGA 72 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLUGA 82 " --> pdb=" O GLYGA 78 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SERGA 85 " --> pdb=" O ASNGA 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLUGA 92 " --> pdb=" O GLNGA 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALAGA 94 " --> pdb=" O METGA 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THRGA 95 " --> pdb=" O SERGA 91 " (cutoff:3.500A) Processing helix chain 'GA' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLUGA 109 " --> pdb=" O SERGA 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYSGA 112 " --> pdb=" O SERGA 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLUGA 113 " --> pdb=" O GLUGA 109 " (cutoff:3.500A) Processing helix chain 'GA' and resid 233 through 288 removed outlier: 3.907A pdb=" N THRGA 242 " --> pdb=" O SERGA 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THRGA 243 " --> pdb=" O SERGA 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLUGA 254 " --> pdb=" O THRGA 250 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VALGA 261 " --> pdb=" O LYSGA 257 " (cutoff:3.500A) Processing helix chain 'GA' and resid 290 through 318 removed outlier: 3.720A pdb=" N GLUGA 297 " --> pdb=" O SERGA 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLNGA 306 " --> pdb=" O ASNGA 302 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLNGA 314 " --> pdb=" O ALAGA 310 " (cutoff:3.500A) Processing helix chain 'GA' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEUGA 325 " --> pdb=" O GLNGA 321 " (cutoff:3.500A) Processing helix chain 'HA' and resid 6 through 33 removed outlier: 3.538A pdb=" N ARGHA 14 " --> pdb=" O LEUHA 10 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASNHA 21 " --> pdb=" O ASNHA 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALAHA 22 " --> pdb=" O ALAHA 18 " (cutoff:3.500A) Processing helix chain 'HA' and resid 42 through 96 removed outlier: 3.610A pdb=" N METHA 61 " --> pdb=" O ARGHA 57 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYSHA 64 " --> pdb=" O ASPHA 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERHA 76 " --> pdb=" O LEUHA 72 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLUHA 82 " --> pdb=" O GLYHA 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SERHA 85 " --> pdb=" O ASNHA 81 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLUHA 92 " --> pdb=" O GLNHA 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALAHA 94 " --> pdb=" O METHA 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THRHA 95 " --> pdb=" O SERHA 91 " (cutoff:3.500A) Processing helix chain 'HA' and resid 103 through 128 removed outlier: 3.544A pdb=" N GLUHA 109 " --> pdb=" O SERHA 105 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYSHA 112 " --> pdb=" O SERHA 108 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLUHA 113 " --> pdb=" O GLUHA 109 " (cutoff:3.500A) Processing helix chain 'HA' and resid 233 through 288 removed outlier: 3.907A pdb=" N THRHA 242 " --> pdb=" O SERHA 238 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THRHA 243 " --> pdb=" O SERHA 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLUHA 254 " --> pdb=" O THRHA 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VALHA 261 " --> pdb=" O LYSHA 257 " (cutoff:3.500A) Processing helix chain 'HA' and resid 290 through 318 removed outlier: 3.721A pdb=" N GLUHA 297 " --> pdb=" O SERHA 293 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLNHA 306 " --> pdb=" O ASNHA 302 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLNHA 314 " --> pdb=" O ALAHA 310 " (cutoff:3.500A) Processing helix chain 'HA' and resid 321 through 327 removed outlier: 4.028A pdb=" N LEUHA 325 " --> pdb=" O GLNHA 321 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 146 Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 191 Processing sheet with id=AA4, first strand: chain 'A' and resid 203 through 204 removed outlier: 6.571A pdb=" N TYR A 203 " --> pdb=" O VAL A 211 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 129 through 130 Processing sheet with id=AA6, first strand: chain 'B' and resid 145 through 146 Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 191 Processing sheet with id=AA8, first strand: chain 'B' and resid 203 through 204 removed outlier: 6.571A pdb=" N TYR B 203 " --> pdb=" O VAL B 211 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AB1, first strand: chain 'C' and resid 145 through 146 Processing sheet with id=AB2, first strand: chain 'C' and resid 189 through 191 Processing sheet with id=AB3, first strand: chain 'C' and resid 203 through 204 removed outlier: 6.571A pdb=" N TYR C 203 " --> pdb=" O VAL C 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 129 through 130 Processing sheet with id=AB5, first strand: chain 'D' and resid 145 through 146 Processing sheet with id=AB6, first strand: chain 'D' and resid 189 through 191 Processing sheet with id=AB7, first strand: chain 'D' and resid 203 through 204 removed outlier: 6.572A pdb=" N TYR D 203 " --> pdb=" O VAL D 211 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AB9, first strand: chain 'E' and resid 145 through 146 Processing sheet with id=AC1, first strand: chain 'E' and resid 189 through 191 Processing sheet with id=AC2, first strand: chain 'E' and resid 203 through 204 removed outlier: 6.571A pdb=" N TYR E 203 " --> pdb=" O VAL E 211 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 129 through 130 Processing sheet with id=AC4, first strand: chain 'F' and resid 145 through 146 Processing sheet with id=AC5, first strand: chain 'F' and resid 189 through 191 Processing sheet with id=AC6, first strand: chain 'F' and resid 203 through 204 removed outlier: 6.571A pdb=" N TYR F 203 " --> pdb=" O VAL F 211 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 129 through 130 Processing sheet with id=AC8, first strand: chain 'G' and resid 145 through 146 Processing sheet with id=AC9, first strand: chain 'G' and resid 189 through 191 Processing sheet with id=AD1, first strand: chain 'G' and resid 203 through 204 removed outlier: 6.571A pdb=" N TYR G 203 " --> pdb=" O VAL G 211 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 129 through 130 Processing sheet with id=AD3, first strand: chain 'H' and resid 145 through 146 Processing sheet with id=AD4, first strand: chain 'H' and resid 189 through 191 Processing sheet with id=AD5, first strand: chain 'H' and resid 203 through 204 removed outlier: 6.572A pdb=" N TYR H 203 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 129 through 130 Processing sheet with id=AD7, first strand: chain 'I' and resid 145 through 146 Processing sheet with id=AD8, first strand: chain 'I' and resid 189 through 191 Processing sheet with id=AD9, first strand: chain 'I' and resid 203 through 204 removed outlier: 6.572A pdb=" N TYR I 203 " --> pdb=" O VAL I 211 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 129 through 130 Processing sheet with id=AE2, first strand: chain 'J' and resid 145 through 146 Processing sheet with id=AE3, first strand: chain 'J' and resid 189 through 191 Processing sheet with id=AE4, first strand: chain 'J' and resid 203 through 204 removed outlier: 6.570A pdb=" N TYR J 203 " --> pdb=" O VAL J 211 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 129 through 130 Processing sheet with id=AE6, first strand: chain 'K' and resid 145 through 146 Processing sheet with id=AE7, first strand: chain 'K' and resid 189 through 191 Processing sheet with id=AE8, first strand: chain 'K' and resid 203 through 204 removed outlier: 6.572A pdb=" N TYR K 203 " --> pdb=" O VAL K 211 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 129 through 130 Processing sheet with id=AF1, first strand: chain 'L' and resid 145 through 146 Processing sheet with id=AF2, first strand: chain 'L' and resid 189 through 191 Processing sheet with id=AF3, first strand: chain 'L' and resid 203 through 204 removed outlier: 6.570A pdb=" N TYR L 203 " --> pdb=" O VAL L 211 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 129 through 130 Processing sheet with id=AF5, first strand: chain 'M' and resid 145 through 146 Processing sheet with id=AF6, first strand: chain 'M' and resid 189 through 191 Processing sheet with id=AF7, first strand: chain 'M' and resid 203 through 204 removed outlier: 6.570A pdb=" N TYR M 203 " --> pdb=" O VAL M 211 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 129 through 130 Processing sheet with id=AF9, first strand: chain 'N' and resid 145 through 146 Processing sheet with id=AG1, first strand: chain 'N' and resid 189 through 191 Processing sheet with id=AG2, first strand: chain 'N' and resid 203 through 204 removed outlier: 6.571A pdb=" N TYR N 203 " --> pdb=" O VAL N 211 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 129 through 130 Processing sheet with id=AG4, first strand: chain 'O' and resid 145 through 146 Processing sheet with id=AG5, first strand: chain 'O' and resid 189 through 191 Processing sheet with id=AG6, first strand: chain 'O' and resid 203 through 204 removed outlier: 6.571A pdb=" N TYR O 203 " --> pdb=" O VAL O 211 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 129 through 130 Processing sheet with id=AG8, first strand: chain 'P' and resid 145 through 146 Processing sheet with id=AG9, first strand: chain 'P' and resid 189 through 191 Processing sheet with id=AH1, first strand: chain 'P' and resid 203 through 204 removed outlier: 6.570A pdb=" N TYR P 203 " --> pdb=" O VAL P 211 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Q' and resid 129 through 130 Processing sheet with id=AH3, first strand: chain 'Q' and resid 145 through 146 Processing sheet with id=AH4, first strand: chain 'Q' and resid 189 through 191 Processing sheet with id=AH5, first strand: chain 'Q' and resid 203 through 204 removed outlier: 6.571A pdb=" N TYR Q 203 " --> pdb=" O VAL Q 211 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'R' and resid 129 through 130 Processing sheet with id=AH7, first strand: chain 'R' and resid 145 through 146 Processing sheet with id=AH8, first strand: chain 'R' and resid 189 through 191 Processing sheet with id=AH9, first strand: chain 'R' and resid 203 through 204 removed outlier: 6.571A pdb=" N TYR R 203 " --> pdb=" O VAL R 211 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'S' and resid 129 through 130 Processing sheet with id=AI2, first strand: chain 'S' and resid 145 through 146 Processing sheet with id=AI3, first strand: chain 'S' and resid 189 through 191 Processing sheet with id=AI4, first strand: chain 'S' and resid 203 through 204 removed outlier: 6.571A pdb=" N TYR S 203 " --> pdb=" O VAL S 211 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'T' and resid 129 through 130 Processing sheet with id=AI6, first strand: chain 'T' and resid 145 through 146 Processing sheet with id=AI7, first strand: chain 'T' and resid 189 through 191 Processing sheet with id=AI8, first strand: chain 'T' and resid 203 through 204 removed outlier: 6.570A pdb=" N TYR T 203 " --> pdb=" O VAL T 211 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'V' and resid 129 through 130 Processing sheet with id=AJ1, first strand: chain 'V' and resid 145 through 146 Processing sheet with id=AJ2, first strand: chain 'V' and resid 189 through 191 Processing sheet with id=AJ3, first strand: chain 'V' and resid 203 through 204 removed outlier: 6.571A pdb=" N TYR V 203 " --> pdb=" O VAL V 211 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'W' and resid 129 through 130 Processing sheet with id=AJ5, first strand: chain 'W' and resid 145 through 146 Processing sheet with id=AJ6, first strand: chain 'W' and resid 189 through 191 Processing sheet with id=AJ7, first strand: chain 'W' and resid 203 through 204 removed outlier: 6.571A pdb=" N TYR W 203 " --> pdb=" O VAL W 211 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'X' and resid 129 through 130 Processing sheet with id=AJ9, first strand: chain 'X' and resid 145 through 146 Processing sheet with id=AK1, first strand: chain 'X' and resid 189 through 191 Processing sheet with id=AK2, first strand: chain 'X' and resid 203 through 204 removed outlier: 6.572A pdb=" N TYR X 203 " --> pdb=" O VAL X 211 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'Y' and resid 129 through 130 Processing sheet with id=AK4, first strand: chain 'Y' and resid 145 through 146 Processing sheet with id=AK5, first strand: chain 'Y' and resid 189 through 191 Processing sheet with id=AK6, first strand: chain 'Y' and resid 203 through 204 removed outlier: 6.572A pdb=" N TYR Y 203 " --> pdb=" O VAL Y 211 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'Z' and resid 129 through 130 Processing sheet with id=AK8, first strand: chain 'Z' and resid 145 through 146 Processing sheet with id=AK9, first strand: chain 'Z' and resid 189 through 191 Processing sheet with id=AL1, first strand: chain 'Z' and resid 203 through 204 removed outlier: 6.571A pdb=" N TYR Z 203 " --> pdb=" O VAL Z 211 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'AA' and resid 129 through 130 Processing sheet with id=AL3, first strand: chain 'AA' and resid 145 through 146 Processing sheet with id=AL4, first strand: chain 'AA' and resid 189 through 191 Processing sheet with id=AL5, first strand: chain 'AA' and resid 203 through 204 removed outlier: 6.571A pdb=" N TYRAA 203 " --> pdb=" O VALAA 211 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'BA' and resid 129 through 130 Processing sheet with id=AL7, first strand: chain 'BA' and resid 145 through 146 Processing sheet with id=AL8, first strand: chain 'BA' and resid 189 through 191 Processing sheet with id=AL9, first strand: chain 'BA' and resid 203 through 204 removed outlier: 6.571A pdb=" N TYRBA 203 " --> pdb=" O VALBA 211 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'CA' and resid 129 through 130 Processing sheet with id=AM2, first strand: chain 'CA' and resid 145 through 146 Processing sheet with id=AM3, first strand: chain 'CA' and resid 189 through 191 Processing sheet with id=AM4, first strand: chain 'CA' and resid 203 through 204 removed outlier: 6.571A pdb=" N TYRCA 203 " --> pdb=" O VALCA 211 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'DA' and resid 129 through 130 Processing sheet with id=AM6, first strand: chain 'DA' and resid 145 through 146 Processing sheet with id=AM7, first strand: chain 'DA' and resid 189 through 191 Processing sheet with id=AM8, first strand: chain 'DA' and resid 203 through 204 removed outlier: 6.571A pdb=" N TYRDA 203 " --> pdb=" O VALDA 211 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'EA' and resid 129 through 130 Processing sheet with id=AN1, first strand: chain 'EA' and resid 145 through 146 Processing sheet with id=AN2, first strand: chain 'EA' and resid 189 through 191 Processing sheet with id=AN3, first strand: chain 'EA' and resid 203 through 204 removed outlier: 6.571A pdb=" N TYREA 203 " --> pdb=" O VALEA 211 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'FA' and resid 129 through 130 Processing sheet with id=AN5, first strand: chain 'FA' and resid 145 through 146 Processing sheet with id=AN6, first strand: chain 'FA' and resid 189 through 191 Processing sheet with id=AN7, first strand: chain 'FA' and resid 203 through 204 removed outlier: 6.572A pdb=" N TYRFA 203 " --> pdb=" O VALFA 211 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'GA' and resid 129 through 130 Processing sheet with id=AN9, first strand: chain 'GA' and resid 145 through 146 Processing sheet with id=AO1, first strand: chain 'GA' and resid 189 through 191 Processing sheet with id=AO2, first strand: chain 'GA' and resid 203 through 204 removed outlier: 6.570A pdb=" N TYRGA 203 " --> pdb=" O VALGA 211 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'HA' and resid 129 through 130 Processing sheet with id=AO4, first strand: chain 'HA' and resid 145 through 146 Processing sheet with id=AO5, first strand: chain 'HA' and resid 189 through 191 Processing sheet with id=AO6, first strand: chain 'HA' and resid 203 through 204 removed outlier: 6.572A pdb=" N TYRHA 203 " --> pdb=" O VALHA 211 " (cutoff:3.500A) 5544 hydrogen bonds defined for protein. 16434 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: 31.38 Time building geometry restraints manager: 27.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 28414 1.34 - 1.46: 14605 1.46 - 1.58: 36544 1.58 - 1.70: 0 1.70 - 1.82: 792 Bond restraints: 80355 Sorted by residual: bond pdb=" C SER P 85 " pdb=" N ILE P 86 " ideal model delta sigma weight residual 1.334 1.303 0.032 1.26e-02 6.30e+03 6.25e+00 bond pdb=" C SERHA 85 " pdb=" N ILEHA 86 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.26e-02 6.30e+03 6.19e+00 bond pdb=" C SER W 85 " pdb=" N ILE W 86 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.26e-02 6.30e+03 6.00e+00 bond pdb=" C SER F 85 " pdb=" N ILE F 86 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.26e-02 6.30e+03 6.00e+00 bond pdb=" C SER A 85 " pdb=" N ILE A 86 " ideal model delta sigma weight residual 1.334 1.304 0.031 1.26e-02 6.30e+03 5.90e+00 ... (remaining 80350 not shown) Histogram of bond angle deviations from ideal: 98.44 - 105.04: 631 105.04 - 111.64: 38939 111.64 - 118.24: 24682 118.24 - 124.83: 43625 124.83 - 131.43: 297 Bond angle restraints: 108174 Sorted by residual: angle pdb=" N THRAA 194 " pdb=" CA THRAA 194 " pdb=" CB THRAA 194 " ideal model delta sigma weight residual 111.50 104.84 6.66 1.70e+00 3.46e-01 1.53e+01 angle pdb=" N THR O 194 " pdb=" CA THR O 194 " pdb=" CB THR O 194 " ideal model delta sigma weight residual 111.50 104.84 6.66 1.70e+00 3.46e-01 1.53e+01 angle pdb=" N THR G 194 " pdb=" CA THR G 194 " pdb=" CB THR G 194 " ideal model delta sigma weight residual 111.50 104.85 6.65 1.70e+00 3.46e-01 1.53e+01 angle pdb=" N THRCA 194 " pdb=" CA THRCA 194 " pdb=" CB THRCA 194 " ideal model delta sigma weight residual 111.50 104.85 6.65 1.70e+00 3.46e-01 1.53e+01 angle pdb=" N THR K 194 " pdb=" CA THR K 194 " pdb=" CB THR K 194 " ideal model delta sigma weight residual 111.50 104.85 6.65 1.70e+00 3.46e-01 1.53e+01 ... (remaining 108169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 43427 17.80 - 35.60: 5676 35.60 - 53.40: 1222 53.40 - 71.21: 198 71.21 - 89.01: 99 Dihedral angle restraints: 50622 sinusoidal: 19635 harmonic: 30987 Sorted by residual: dihedral pdb=" N VAL J 193 " pdb=" C VAL J 193 " pdb=" CA VAL J 193 " pdb=" CB VAL J 193 " ideal model delta harmonic sigma weight residual 123.40 133.33 -9.93 0 2.50e+00 1.60e-01 1.58e+01 dihedral pdb=" N VALCA 193 " pdb=" C VALCA 193 " pdb=" CA VALCA 193 " pdb=" CB VALCA 193 " ideal model delta harmonic sigma weight residual 123.40 133.32 -9.92 0 2.50e+00 1.60e-01 1.58e+01 dihedral pdb=" CA LEUHA 93 " pdb=" C LEUHA 93 " pdb=" N ALAHA 94 " pdb=" CA ALAHA 94 " ideal model delta harmonic sigma weight residual 180.00 160.17 19.83 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 50619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 11880 0.067 - 0.134: 1089 0.134 - 0.201: 33 0.201 - 0.268: 0 0.268 - 0.335: 33 Chirality restraints: 13035 Sorted by residual: chirality pdb=" CA VALCA 193 " pdb=" N VALCA 193 " pdb=" C VALCA 193 " pdb=" CB VALCA 193 " both_signs ideal model delta sigma weight residual False 2.44 2.11 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CA VAL J 193 " pdb=" N VAL J 193 " pdb=" C VAL J 193 " pdb=" CB VAL J 193 " both_signs ideal model delta sigma weight residual False 2.44 2.11 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA VAL D 193 " pdb=" N VAL D 193 " pdb=" C VAL D 193 " pdb=" CB VAL D 193 " both_signs ideal model delta sigma weight residual False 2.44 2.11 0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 13032 not shown) Planarity restraints: 14289 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP X 208 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.67e+00 pdb=" CG ASP X 208 " -0.048 2.00e-02 2.50e+03 pdb=" OD1 ASP X 208 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP X 208 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP Q 208 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.64e+00 pdb=" CG ASP Q 208 " -0.048 2.00e-02 2.50e+03 pdb=" OD1 ASP Q 208 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP Q 208 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP T 208 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.63e+00 pdb=" CG ASP T 208 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASP T 208 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP T 208 " -0.017 2.00e-02 2.50e+03 ... (remaining 14286 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 2025 2.67 - 3.23: 80802 3.23 - 3.78: 124548 3.78 - 4.34: 183408 4.34 - 4.90: 301045 Nonbonded interactions: 691828 Sorted by model distance: nonbonded pdb=" O ASP E 100 " pdb=" OD1 ASP E 100 " model vdw 2.111 3.040 nonbonded pdb=" O ASP F 100 " pdb=" OD1 ASP F 100 " model vdw 2.111 3.040 nonbonded pdb=" O ASPAA 100 " pdb=" OD1 ASPAA 100 " model vdw 2.111 3.040 nonbonded pdb=" O ASP Q 100 " pdb=" OD1 ASP Q 100 " model vdw 2.111 3.040 nonbonded pdb=" O ASP T 100 " pdb=" OD1 ASP T 100 " model vdw 2.111 3.040 ... (remaining 691823 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 'AA' selection = chain 'B' selection = chain 'BA' selection = chain 'C' selection = chain 'CA' selection = chain 'D' selection = chain 'DA' selection = chain 'E' selection = chain 'EA' selection = chain 'F' selection = chain 'FA' selection = chain 'G' selection = chain 'GA' selection = chain 'H' selection = chain 'HA' 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 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.700 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: 0.110 Extract box with map and model: 10.030 Check model and map are aligned: 0.900 Set scattering table: 0.550 Process input model: 167.980 Find NCS groups from input model: 4.330 Set up NCS constraints: 0.730 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 196.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 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 : 0.007 0.045 80355 Z= 0.436 Angle : 0.694 9.444 108174 Z= 0.402 Chirality : 0.043 0.335 13035 Planarity : 0.004 0.028 14289 Dihedral : 16.754 89.008 30426 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 27.24 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.07), residues: 10560 helix: -1.16 (0.06), residues: 6600 sheet: -1.03 (0.18), residues: 726 loop : -2.18 (0.09), residues: 3234 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS I 84 PHE 0.003 0.001 PHE C 145 TYR 0.013 0.002 TYRGA 204 ARG 0.002 0.000 ARG L 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21120 Ramachandran restraints generated. 10560 Oldfield, 0 Emsley, 10560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21120 Ramachandran restraints generated. 10560 Oldfield, 0 Emsley, 10560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 8844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 891 time to evaluate : 7.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 311 MET cc_start: 0.8827 (mmm) cc_final: 0.8590 (mmp) REVERT: C 291 MET cc_start: 0.9047 (mmt) cc_final: 0.8476 (mmm) REVERT: C 295 MET cc_start: 0.8918 (tpt) cc_final: 0.8211 (tpt) REVERT: C 311 MET cc_start: 0.8737 (mmm) cc_final: 0.8518 (mpp) REVERT: D 61 MET cc_start: 0.8688 (tpp) cc_final: 0.8384 (tpt) REVERT: D 311 MET cc_start: 0.8667 (mmm) cc_final: 0.8379 (mmp) REVERT: F 291 MET cc_start: 0.9287 (mmt) cc_final: 0.9063 (mmm) REVERT: G 183 VAL cc_start: 0.8571 (t) cc_final: 0.8325 (p) REVERT: G 204 TYR cc_start: 0.8358 (m-80) cc_final: 0.7655 (m-80) REVERT: G 295 MET cc_start: 0.8685 (tpt) cc_final: 0.8417 (tpt) REVERT: H 61 MET cc_start: 0.8566 (tpp) cc_final: 0.8357 (tpp) REVERT: H 291 MET cc_start: 0.8930 (mmt) cc_final: 0.8692 (mmm) REVERT: H 296 MET cc_start: 0.8564 (ptm) cc_final: 0.8318 (ptm) REVERT: H 320 GLN cc_start: 0.8495 (tt0) cc_final: 0.7883 (mt0) REVERT: I 295 MET cc_start: 0.8938 (tpt) cc_final: 0.8644 (tpt) REVERT: I 320 GLN cc_start: 0.8319 (tt0) cc_final: 0.7936 (mt0) REVERT: J 291 MET cc_start: 0.8897 (mmt) cc_final: 0.8676 (mmm) REVERT: J 296 MET cc_start: 0.8494 (ptm) cc_final: 0.8209 (ptm) REVERT: J 311 MET cc_start: 0.8568 (mmm) cc_final: 0.8212 (mmp) REVERT: J 320 GLN cc_start: 0.8396 (tt0) cc_final: 0.8181 (tm-30) REVERT: K 52 MET cc_start: 0.8839 (tpp) cc_final: 0.8555 (mmp) REVERT: K 291 MET cc_start: 0.8995 (mmt) cc_final: 0.8191 (mmm) REVERT: K 320 GLN cc_start: 0.8517 (tt0) cc_final: 0.8077 (tm-30) REVERT: L 1 MET cc_start: 0.6746 (mmp) cc_final: 0.5519 (pp-130) REVERT: L 322 VAL cc_start: 0.9163 (m) cc_final: 0.8945 (t) REVERT: M 1 MET cc_start: 0.6571 (mmp) cc_final: 0.5991 (pp-130) REVERT: M 220 LYS cc_start: 0.8960 (tttt) cc_final: 0.8730 (tptm) REVERT: M 322 VAL cc_start: 0.9145 (m) cc_final: 0.8932 (t) REVERT: N 1 MET cc_start: 0.6438 (mmp) cc_final: 0.5465 (pp-130) REVERT: N 61 MET cc_start: 0.8931 (tpp) cc_final: 0.8706 (tpt) REVERT: N 291 MET cc_start: 0.9160 (mmt) cc_final: 0.8810 (mmp) REVERT: O 1 MET cc_start: 0.6304 (mmp) cc_final: 0.5730 (pp-130) REVERT: O 61 MET cc_start: 0.8880 (tpp) cc_final: 0.8363 (tpt) REVERT: P 61 MET cc_start: 0.8966 (tpp) cc_final: 0.8576 (tpt) REVERT: Q 1 MET cc_start: 0.6626 (mmp) cc_final: 0.5240 (pp-130) REVERT: R 1 MET cc_start: 0.6440 (mmp) cc_final: 0.5918 (pp-130) REVERT: S 1 MET cc_start: 0.6746 (mmp) cc_final: 0.5034 (pp-130) REVERT: S 61 MET cc_start: 0.8851 (tpp) cc_final: 0.8623 (tpp) REVERT: T 1 MET cc_start: 0.6356 (mmp) cc_final: 0.5343 (pp-130) REVERT: T 220 LYS cc_start: 0.8847 (tttt) cc_final: 0.8612 (tptp) REVERT: V 1 MET cc_start: 0.6875 (mmp) cc_final: 0.5361 (pp-130) REVERT: V 90 MET cc_start: 0.9232 (ttm) cc_final: 0.8863 (mtp) REVERT: W 1 MET cc_start: 0.6945 (mmp) cc_final: 0.4869 (pp-130) REVERT: X 291 MET cc_start: 0.8942 (mmt) cc_final: 0.8502 (mmm) REVERT: X 295 MET cc_start: 0.8845 (tpt) cc_final: 0.8534 (tpt) REVERT: Y 61 MET cc_start: 0.8765 (tpp) cc_final: 0.8504 (tpp) REVERT: Z 1 MET cc_start: 0.7258 (mmp) cc_final: 0.6920 (mmm) REVERT: Z 209 LYS cc_start: 0.8957 (mttt) cc_final: 0.8597 (mmmt) REVERT: Z 291 MET cc_start: 0.8890 (mmt) cc_final: 0.8448 (mmm) REVERT: Z 295 MET cc_start: 0.8862 (tpt) cc_final: 0.8637 (tpt) REVERT: AA 209 LYS cc_start: 0.8925 (mttt) cc_final: 0.8720 (mtpp) REVERT: BA 209 LYS cc_start: 0.8865 (mttt) cc_final: 0.8643 (mmmm) REVERT: BA 295 MET cc_start: 0.8856 (tpt) cc_final: 0.8543 (tpp) REVERT: BA 320 GLN cc_start: 0.8576 (tt0) cc_final: 0.8178 (tm-30) REVERT: CA 204 TYR cc_start: 0.8078 (m-80) cc_final: 0.7709 (m-80) REVERT: EA 203 TYR cc_start: 0.8383 (m-80) cc_final: 0.8124 (m-80) REVERT: EA 291 MET cc_start: 0.8987 (mmt) cc_final: 0.8716 (mmm) REVERT: EA 296 MET cc_start: 0.8759 (ptm) cc_final: 0.8511 (ptm) REVERT: FA 173 TYR cc_start: 0.8612 (m-80) cc_final: 0.8315 (m-80) REVERT: GA 173 TYR cc_start: 0.8656 (m-80) cc_final: 0.8380 (m-80) REVERT: GA 291 MET cc_start: 0.9004 (mmt) cc_final: 0.8750 (mmm) REVERT: GA 295 MET cc_start: 0.8623 (tpt) cc_final: 0.8265 (tpt) REVERT: GA 296 MET cc_start: 0.8654 (ptm) cc_final: 0.8368 (ttp) REVERT: HA 295 MET cc_start: 0.8776 (tpt) cc_final: 0.8066 (tpt) outliers start: 0 outliers final: 1 residues processed: 891 average time/residue: 1.7202 time to fit residues: 1988.3919 Evaluate side-chains 530 residues out of total 8844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 529 time to evaluate : 6.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 891 optimal weight: 0.9990 chunk 800 optimal weight: 2.9990 chunk 444 optimal weight: 6.9990 chunk 273 optimal weight: 10.0000 chunk 539 optimal weight: 0.9980 chunk 427 optimal weight: 3.9990 chunk 827 optimal weight: 1.9990 chunk 320 optimal weight: 9.9990 chunk 503 optimal weight: 5.9990 chunk 616 optimal weight: 0.8980 chunk 958 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 301 ASN A 309 GLN B 84 HIS B 271 ASN B 301 ASN B 309 GLN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 ASN C 301 ASN C 309 GLN D 84 HIS D 271 ASN D 301 ASN D 309 GLN D 318 GLN ** E 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 ASN E 301 ASN E 309 GLN F 17 ASN ** F 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 271 ASN F 301 ASN F 309 GLN ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 271 ASN G 301 ASN G 309 GLN H 17 ASN ** H 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 271 ASN H 301 ASN I 17 ASN I 84 HIS I 271 ASN I 301 ASN J 17 ASN ** J 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 271 ASN J 301 ASN ** K 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 271 ASN K 301 ASN L 17 ASN ** L 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 271 ASN L 301 ASN M 17 ASN M 84 HIS M 301 ASN N 17 ASN N 84 HIS N 301 ASN O 17 ASN O 84 HIS O 301 ASN O 309 GLN P 17 ASN P 84 HIS P 301 ASN Q 17 ASN Q 84 HIS Q 301 ASN R 17 ASN ** R 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 271 ASN R 301 ASN S 17 ASN S 271 ASN S 301 ASN T 17 ASN T 84 HIS T 271 ASN T 301 ASN T 309 GLN V 17 ASN V 271 ASN V 301 ASN V 309 GLN W 17 ASN ** W 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 271 ASN W 301 ASN W 309 GLN X 17 ASN X 84 HIS X 99 ASN X 271 ASN X 301 ASN Y 84 HIS Y 99 ASN Y 271 ASN Y 301 ASN Y 309 GLN Z 84 HIS Z 99 ASN Z 271 ASN Z 301 ASN AA 17 ASN AA 84 HIS AA 99 ASN AA 271 ASN AA 301 ASN BA 17 ASN BA 84 HIS BA 99 ASN BA 271 ASN BA 301 ASN CA 17 ASN CA 84 HIS CA 99 ASN CA 271 ASN CA 301 ASN DA 84 HIS DA 99 ASN DA 271 ASN DA 301 ASN EA 84 HIS EA 99 ASN EA 271 ASN EA 301 ASN FA 84 HIS FA 99 ASN FA 271 ASN FA 301 ASN GA 84 HIS GA 99 ASN GA 271 ASN GA 301 ASN HA 84 HIS HA 99 ASN HA 271 ASN HA 301 ASN Total number of N/Q/H flips: 125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 80355 Z= 0.168 Angle : 0.518 8.492 108174 Z= 0.289 Chirality : 0.034 0.151 13035 Planarity : 0.003 0.021 14289 Dihedral : 4.979 24.888 11222 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.71 % Allowed : 25.18 % Favored : 71.11 % 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: 0.02 (0.08), residues: 10560 helix: 0.90 (0.06), residues: 6633 sheet: 0.44 (0.24), residues: 396 loop : -1.74 (0.09), residues: 3531 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS I 84 PHE 0.004 0.001 PHEAA 130 TYR 0.014 0.001 TYR X 173 ARG 0.003 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21120 Ramachandran restraints generated. 10560 Oldfield, 0 Emsley, 10560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21120 Ramachandran restraints generated. 10560 Oldfield, 0 Emsley, 10560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 8844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 328 poor density : 641 time to evaluate : 8.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 309 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8475 (mt0) REVERT: B 311 MET cc_start: 0.8983 (mmm) cc_final: 0.8727 (mmp) REVERT: C 52 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8754 (mmp) REVERT: C 291 MET cc_start: 0.9019 (mmt) cc_final: 0.8440 (mmm) REVERT: C 295 MET cc_start: 0.8711 (tpt) cc_final: 0.8045 (tpt) REVERT: C 311 MET cc_start: 0.9033 (mmm) cc_final: 0.8698 (mmm) REVERT: E 291 MET cc_start: 0.9079 (mmt) cc_final: 0.8844 (tpt) REVERT: F 291 MET cc_start: 0.9259 (mmt) cc_final: 0.9010 (mmm) REVERT: G 52 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8801 (mtm) REVERT: G 177 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7787 (m-30) REVERT: H 88 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8002 (mp10) REVERT: H 296 MET cc_start: 0.8339 (ptm) cc_final: 0.8019 (ptm) REVERT: H 320 GLN cc_start: 0.8436 (tt0) cc_final: 0.7958 (mt0) REVERT: I 1 MET cc_start: 0.7390 (mmm) cc_final: 0.7133 (mmm) REVERT: I 320 GLN cc_start: 0.8297 (tt0) cc_final: 0.7983 (mt0) REVERT: J 1 MET cc_start: 0.7299 (mmm) cc_final: 0.6859 (mpm) REVERT: J 291 MET cc_start: 0.8988 (mmt) cc_final: 0.8729 (mmm) REVERT: J 295 MET cc_start: 0.8836 (tpt) cc_final: 0.8514 (tpt) REVERT: J 311 MET cc_start: 0.8510 (mmm) cc_final: 0.8231 (mmp) REVERT: K 52 MET cc_start: 0.8812 (tpp) cc_final: 0.8583 (mmp) REVERT: K 88 GLN cc_start: 0.9349 (OUTLIER) cc_final: 0.9129 (tp40) REVERT: K 291 MET cc_start: 0.9116 (mmt) cc_final: 0.8366 (mmm) REVERT: K 311 MET cc_start: 0.8639 (tpp) cc_final: 0.8393 (mmp) REVERT: K 320 GLN cc_start: 0.8476 (tt0) cc_final: 0.8136 (tm-30) REVERT: L 1 MET cc_start: 0.6756 (mmp) cc_final: 0.4684 (pp-130) REVERT: M 1 MET cc_start: 0.6692 (mmp) cc_final: 0.5998 (pp-130) REVERT: M 183 VAL cc_start: 0.9183 (t) cc_final: 0.8874 (m) REVERT: M 220 LYS cc_start: 0.9031 (tttt) cc_final: 0.8818 (tptm) REVERT: N 1 MET cc_start: 0.6464 (mmp) cc_final: 0.5359 (pp-130) REVERT: N 291 MET cc_start: 0.9069 (mmt) cc_final: 0.8692 (mmp) REVERT: N 296 MET cc_start: 0.8390 (ptm) cc_final: 0.7988 (ptm) REVERT: O 1 MET cc_start: 0.6433 (mmp) cc_final: 0.5903 (pp-130) REVERT: O 296 MET cc_start: 0.8415 (ptm) cc_final: 0.8208 (ptm) REVERT: P 61 MET cc_start: 0.8495 (tpp) cc_final: 0.8245 (tpt) REVERT: Q 1 MET cc_start: 0.6509 (mmp) cc_final: 0.5134 (pp-130) REVERT: R 1 MET cc_start: 0.6484 (mmp) cc_final: 0.5012 (pp-130) REVERT: R 50 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7751 (mt-10) REVERT: R 109 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8266 (tm-30) REVERT: R 162 MET cc_start: 0.9128 (mmp) cc_final: 0.8874 (mmp) REVERT: S 1 MET cc_start: 0.6702 (mmp) cc_final: 0.4261 (pp-130) REVERT: S 220 LYS cc_start: 0.8824 (tttp) cc_final: 0.8490 (tptm) REVERT: S 291 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8618 (mmp) REVERT: T 1 MET cc_start: 0.6429 (mmp) cc_final: 0.4642 (pp-130) REVERT: T 220 LYS cc_start: 0.8813 (tttt) cc_final: 0.8596 (tptt) REVERT: V 1 MET cc_start: 0.7059 (mmp) cc_final: 0.4339 (pp-130) REVERT: V 88 GLN cc_start: 0.9302 (OUTLIER) cc_final: 0.8019 (mp10) REVERT: V 90 MET cc_start: 0.9201 (ttm) cc_final: 0.8961 (mtp) REVERT: V 220 LYS cc_start: 0.9016 (tttt) cc_final: 0.8707 (tptt) REVERT: V 296 MET cc_start: 0.8623 (ptm) cc_final: 0.8397 (ptm) REVERT: W 1 MET cc_start: 0.6905 (mmp) cc_final: 0.4306 (pp-130) REVERT: W 220 LYS cc_start: 0.8994 (tttt) cc_final: 0.8758 (tptt) REVERT: X 1 MET cc_start: 0.7669 (mmm) cc_final: 0.7226 (mmm) REVERT: X 291 MET cc_start: 0.9044 (mmt) cc_final: 0.8689 (mmm) REVERT: X 295 MET cc_start: 0.8744 (tpt) cc_final: 0.8266 (tpt) REVERT: Y 61 MET cc_start: 0.8491 (tpp) cc_final: 0.8275 (tpp) REVERT: Z 1 MET cc_start: 0.7339 (mmp) cc_final: 0.6929 (mmm) REVERT: Z 162 MET cc_start: 0.9177 (mmp) cc_final: 0.8973 (mmp) REVERT: Z 291 MET cc_start: 0.8967 (mmt) cc_final: 0.8551 (mmm) REVERT: Z 295 MET cc_start: 0.8746 (tpt) cc_final: 0.8324 (tpt) REVERT: AA 1 MET cc_start: 0.7683 (mmm) cc_final: 0.7062 (mpm) REVERT: AA 296 MET cc_start: 0.8805 (ptm) cc_final: 0.8585 (ptm) REVERT: BA 67 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7976 (mt0) REVERT: BA 291 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8869 (tpt) REVERT: BA 320 GLN cc_start: 0.8573 (tt0) cc_final: 0.8266 (tm-30) REVERT: CA 1 MET cc_start: 0.7568 (mmm) cc_final: 0.7270 (mmm) REVERT: CA 88 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8827 (mm-40) REVERT: DA 1 MET cc_start: 0.7318 (mmm) cc_final: 0.7113 (mpm) REVERT: DA 67 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.8014 (mt0) REVERT: EA 1 MET cc_start: 0.7448 (mmm) cc_final: 0.7183 (mpm) REVERT: GA 1 MET cc_start: 0.7509 (mmm) cc_final: 0.7279 (mmm) REVERT: GA 208 ASP cc_start: 0.7032 (t0) cc_final: 0.6723 (t0) REVERT: GA 296 MET cc_start: 0.8660 (ptm) cc_final: 0.8459 (ptt) REVERT: HA 1 MET cc_start: 0.7280 (mmm) cc_final: 0.6851 (mmm) REVERT: HA 295 MET cc_start: 0.8773 (tpt) cc_final: 0.8113 (tpt) outliers start: 328 outliers final: 51 residues processed: 910 average time/residue: 1.5528 time to fit residues: 1880.4265 Evaluate side-chains 597 residues out of total 8844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 534 time to evaluate : 7.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain E residue 84 HIS Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain H residue 88 GLN Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain J residue 84 HIS Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain K residue 88 GLN Chi-restraints excluded: chain K residue 224 VAL Chi-restraints excluded: chain L residue 84 HIS Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain L residue 291 MET Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain N residue 178 ASP Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain O residue 52 MET Chi-restraints excluded: chain O residue 165 GLU Chi-restraints excluded: chain P residue 177 ASP Chi-restraints excluded: chain Q residue 291 MET Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 291 MET Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 291 MET Chi-restraints excluded: chain V residue 88 GLN Chi-restraints excluded: chain V residue 224 VAL Chi-restraints excluded: chain W residue 188 LYS Chi-restraints excluded: chain W residue 224 VAL Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain Y residue 84 HIS Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Y residue 224 VAL Chi-restraints excluded: chain Z residue 224 VAL Chi-restraints excluded: chain AA residue 84 HIS Chi-restraints excluded: chain AA residue 224 VAL Chi-restraints excluded: chain BA residue 67 GLN Chi-restraints excluded: chain BA residue 224 VAL Chi-restraints excluded: chain BA residue 291 MET Chi-restraints excluded: chain CA residue 67 GLN Chi-restraints excluded: chain CA residue 88 GLN Chi-restraints excluded: chain CA residue 224 VAL Chi-restraints excluded: chain DA residue 67 GLN Chi-restraints excluded: chain DA residue 132 THR Chi-restraints excluded: chain DA residue 208 ASP Chi-restraints excluded: chain DA residue 224 VAL Chi-restraints excluded: chain EA residue 132 THR Chi-restraints excluded: chain FA residue 90 MET Chi-restraints excluded: chain FA residue 186 ASP Chi-restraints excluded: chain FA residue 224 VAL Chi-restraints excluded: chain GA residue 224 VAL Chi-restraints excluded: chain HA residue 52 MET Chi-restraints excluded: chain HA residue 177 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 532 optimal weight: 5.9990 chunk 297 optimal weight: 9.9990 chunk 798 optimal weight: 0.9990 chunk 652 optimal weight: 8.9990 chunk 264 optimal weight: 8.9990 chunk 960 optimal weight: 10.0000 chunk 1037 optimal weight: 10.0000 chunk 855 optimal weight: 8.9990 chunk 952 optimal weight: 3.9990 chunk 327 optimal weight: 0.9980 chunk 770 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 88 GLN B 84 HIS B 88 GLN B 309 GLN B 318 GLN C 84 HIS D 84 HIS D 270 ASN E 84 HIS F 84 HIS F 318 GLN G 88 GLN H 84 HIS I 84 HIS I 88 GLN J 84 HIS J 88 GLN K 84 HIS K 99 ASN K 309 GLN L 84 HIS L 88 GLN ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 HIS M 88 GLN ** N 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 84 HIS P 84 HIS P 88 GLN Q 88 GLN R 88 GLN S 88 GLN S 131 ASN S 309 GLN T 88 GLN T 131 ASN ** V 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 84 HIS ** W 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 88 GLN X 309 GLN X 318 GLN Y 84 HIS Y 318 GLN Z 88 GLN Z 309 GLN Z 318 GLN AA 17 ASN AA 84 HIS AA 318 GLN BA 17 ASN CA 17 ASN CA 309 GLN DA 84 HIS DA 309 GLN DA 318 GLN EA 88 GLN FA 88 GLN FA 309 GLN GA 318 GLN ** HA 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 80355 Z= 0.246 Angle : 0.521 7.984 108174 Z= 0.291 Chirality : 0.036 0.157 13035 Planarity : 0.003 0.027 14289 Dihedral : 4.785 22.836 11220 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.41 % Allowed : 25.07 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.08), residues: 10560 helix: 1.83 (0.06), residues: 6600 sheet: 0.79 (0.24), residues: 396 loop : -1.54 (0.10), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.021 0.001 HIS Y 84 PHE 0.006 0.001 PHEAA 130 TYR 0.014 0.001 TYRFA 173 ARG 0.003 0.000 ARG E 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21120 Ramachandran restraints generated. 10560 Oldfield, 0 Emsley, 10560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21120 Ramachandran restraints generated. 10560 Oldfield, 0 Emsley, 10560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 8844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 557 time to evaluate : 7.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8784 (ttm) cc_final: 0.8478 (ptm) REVERT: B 311 MET cc_start: 0.9056 (mmm) cc_final: 0.8796 (mmp) REVERT: C 84 HIS cc_start: 0.9069 (OUTLIER) cc_final: 0.8281 (m90) REVERT: D 84 HIS cc_start: 0.8983 (OUTLIER) cc_final: 0.8257 (m-70) REVERT: D 88 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.7980 (mp10) REVERT: F 177 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8158 (m-30) REVERT: G 109 GLU cc_start: 0.5952 (OUTLIER) cc_final: 0.5603 (tm-30) REVERT: H 1 MET cc_start: 0.6913 (mmm) cc_final: 0.6483 (mmm) REVERT: H 84 HIS cc_start: 0.9112 (OUTLIER) cc_final: 0.8508 (m170) REVERT: H 320 GLN cc_start: 0.8480 (tt0) cc_final: 0.8001 (mt0) REVERT: I 320 GLN cc_start: 0.8409 (tt0) cc_final: 0.8085 (mt0) REVERT: J 1 MET cc_start: 0.7391 (mmm) cc_final: 0.6929 (mpm) REVERT: J 17 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7500 (m110) REVERT: J 109 GLU cc_start: 0.8287 (tp30) cc_final: 0.7904 (tm-30) REVERT: J 204 TYR cc_start: 0.8111 (m-80) cc_final: 0.7856 (m-80) REVERT: J 291 MET cc_start: 0.9024 (mmt) cc_final: 0.8805 (mmm) REVERT: J 320 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7760 (tm-30) REVERT: K 52 MET cc_start: 0.8920 (tpp) cc_final: 0.8713 (mmp) REVERT: K 90 MET cc_start: 0.9384 (OUTLIER) cc_final: 0.9082 (ttp) REVERT: K 291 MET cc_start: 0.9071 (mmt) cc_final: 0.8406 (mmm) REVERT: L 1 MET cc_start: 0.6408 (mmp) cc_final: 0.4698 (pp-130) REVERT: L 61 MET cc_start: 0.8474 (tpp) cc_final: 0.8059 (tpt) REVERT: M 1 MET cc_start: 0.6866 (mmp) cc_final: 0.6110 (pp-130) REVERT: M 52 MET cc_start: 0.8550 (mmp) cc_final: 0.8288 (mtp) REVERT: M 100 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8061 (m-30) REVERT: M 183 VAL cc_start: 0.9215 (t) cc_final: 0.8941 (m) REVERT: M 220 LYS cc_start: 0.9037 (tttt) cc_final: 0.8784 (tptm) REVERT: N 1 MET cc_start: 0.6685 (mmp) cc_final: 0.5529 (pp-130) REVERT: N 291 MET cc_start: 0.9091 (mmt) cc_final: 0.8714 (mmp) REVERT: O 1 MET cc_start: 0.6614 (mmp) cc_final: 0.5975 (pp-130) REVERT: O 88 GLN cc_start: 0.9283 (OUTLIER) cc_final: 0.8533 (mp10) REVERT: P 61 MET cc_start: 0.8583 (tpp) cc_final: 0.8271 (tpt) REVERT: Q 1 MET cc_start: 0.6681 (mmp) cc_final: 0.5357 (pp-130) REVERT: Q 67 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8590 (mm-40) REVERT: R 1 MET cc_start: 0.6547 (mmp) cc_final: 0.5164 (pp-130) REVERT: R 50 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7671 (mt-10) REVERT: R 52 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8736 (mtt) REVERT: R 100 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8154 (t0) REVERT: R 162 MET cc_start: 0.9305 (mmp) cc_final: 0.8967 (mmm) REVERT: S 1 MET cc_start: 0.6756 (mmp) cc_final: 0.4414 (pp-130) REVERT: S 220 LYS cc_start: 0.8874 (tttp) cc_final: 0.8541 (tptm) REVERT: T 1 MET cc_start: 0.6600 (mmp) cc_final: 0.4806 (pp-130) REVERT: T 88 GLN cc_start: 0.9332 (OUTLIER) cc_final: 0.9096 (tp40) REVERT: T 220 LYS cc_start: 0.8890 (tttt) cc_final: 0.8672 (tptm) REVERT: V 1 MET cc_start: 0.7074 (mmp) cc_final: 0.4335 (pp-130) REVERT: V 84 HIS cc_start: 0.8926 (OUTLIER) cc_final: 0.8404 (m-70) REVERT: V 88 GLN cc_start: 0.9320 (OUTLIER) cc_final: 0.7935 (mp10) REVERT: V 90 MET cc_start: 0.9239 (ttm) cc_final: 0.8987 (mtt) REVERT: V 220 LYS cc_start: 0.9050 (tttt) cc_final: 0.8699 (tptt) REVERT: W 1 MET cc_start: 0.6856 (mmp) cc_final: 0.3906 (pp-130) REVERT: W 114 MET cc_start: 0.9294 (tpt) cc_final: 0.9066 (tpp) REVERT: W 295 MET cc_start: 0.8832 (tpt) cc_final: 0.8547 (mmm) REVERT: X 84 HIS cc_start: 0.8988 (OUTLIER) cc_final: 0.8650 (m170) REVERT: X 291 MET cc_start: 0.9072 (mmt) cc_final: 0.8698 (mmm) REVERT: X 295 MET cc_start: 0.8558 (tpt) cc_final: 0.8235 (tpt) REVERT: Y 61 MET cc_start: 0.8679 (tpp) cc_final: 0.8403 (tpp) REVERT: Z 1 MET cc_start: 0.7500 (mmp) cc_final: 0.6840 (mmm) REVERT: Z 291 MET cc_start: 0.8988 (mmt) cc_final: 0.8648 (mmm) REVERT: Z 295 MET cc_start: 0.8574 (tpt) cc_final: 0.8316 (tpt) REVERT: AA 1 MET cc_start: 0.7861 (mmm) cc_final: 0.7387 (mmm) REVERT: AA 296 MET cc_start: 0.8792 (ptm) cc_final: 0.8572 (ptm) REVERT: BA 295 MET cc_start: 0.8798 (tpt) cc_final: 0.8415 (tpt) REVERT: CA 1 MET cc_start: 0.7516 (mmm) cc_final: 0.7247 (mmp) REVERT: CA 67 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8244 (tp40) REVERT: DA 151 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7630 (mt-10) REVERT: DA 193 VAL cc_start: 0.7563 (t) cc_final: 0.7353 (t) REVERT: EA 1 MET cc_start: 0.7544 (mmm) cc_final: 0.7260 (mpm) REVERT: EA 296 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8652 (ptm) REVERT: FA 295 MET cc_start: 0.8971 (tpt) cc_final: 0.8685 (tpt) REVERT: FA 296 MET cc_start: 0.8766 (ptm) cc_final: 0.8512 (ptt) REVERT: FA 311 MET cc_start: 0.8466 (tpp) cc_final: 0.8229 (mmm) REVERT: GA 1 MET cc_start: 0.7751 (mmm) cc_final: 0.7369 (mmm) REVERT: GA 67 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8130 (mt0) REVERT: GA 296 MET cc_start: 0.8704 (ptm) cc_final: 0.8455 (ptt) REVERT: HA 1 MET cc_start: 0.7347 (mmm) cc_final: 0.6898 (mmm) REVERT: HA 295 MET cc_start: 0.8660 (tpt) cc_final: 0.8092 (tpt) outliers start: 302 outliers final: 93 residues processed: 812 average time/residue: 1.5561 time to fit residues: 1680.3962 Evaluate side-chains 635 residues out of total 8844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 521 time to evaluate : 7.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain D residue 84 HIS Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain F residue 84 HIS Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 309 GLN Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain J residue 326 LEU Chi-restraints excluded: chain K residue 67 GLN Chi-restraints excluded: chain K residue 84 HIS Chi-restraints excluded: chain K residue 90 MET Chi-restraints excluded: chain K residue 224 VAL Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain M residue 177 ASP Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain N residue 84 HIS Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain O residue 84 HIS Chi-restraints excluded: chain O residue 88 GLN Chi-restraints excluded: chain O residue 181 LYS Chi-restraints excluded: chain P residue 177 ASP Chi-restraints excluded: chain P residue 325 LEU Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 67 GLN Chi-restraints excluded: chain Q residue 326 LEU Chi-restraints excluded: chain R residue 52 MET Chi-restraints excluded: chain R residue 84 HIS Chi-restraints excluded: chain R residue 100 ASP Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 84 HIS Chi-restraints excluded: chain T residue 88 GLN Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 291 MET Chi-restraints excluded: chain V residue 84 HIS Chi-restraints excluded: chain V residue 88 GLN Chi-restraints excluded: chain V residue 100 ASP Chi-restraints excluded: chain V residue 151 GLU Chi-restraints excluded: chain V residue 224 VAL Chi-restraints excluded: chain V residue 326 LEU Chi-restraints excluded: chain W residue 52 MET Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain W residue 188 LYS Chi-restraints excluded: chain W residue 224 VAL Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain X residue 84 HIS Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Y residue 224 VAL Chi-restraints excluded: chain Z residue 224 VAL Chi-restraints excluded: chain Z residue 309 GLN Chi-restraints excluded: chain AA residue 224 VAL Chi-restraints excluded: chain AA residue 309 GLN Chi-restraints excluded: chain BA residue 67 GLN Chi-restraints excluded: chain BA residue 224 VAL Chi-restraints excluded: chain CA residue 67 GLN Chi-restraints excluded: chain CA residue 84 HIS Chi-restraints excluded: chain CA residue 224 VAL Chi-restraints excluded: chain CA residue 326 LEU Chi-restraints excluded: chain DA residue 132 THR Chi-restraints excluded: chain DA residue 151 GLU Chi-restraints excluded: chain DA residue 177 ASP Chi-restraints excluded: chain DA residue 224 VAL Chi-restraints excluded: chain EA residue 132 THR Chi-restraints excluded: chain EA residue 296 MET Chi-restraints excluded: chain FA residue 84 HIS Chi-restraints excluded: chain FA residue 162 MET Chi-restraints excluded: chain FA residue 177 ASP Chi-restraints excluded: chain FA residue 224 VAL Chi-restraints excluded: chain GA residue 52 MET Chi-restraints excluded: chain GA residue 67 GLN Chi-restraints excluded: chain GA residue 84 HIS Chi-restraints excluded: chain GA residue 224 VAL Chi-restraints excluded: chain GA residue 326 LEU Chi-restraints excluded: chain HA residue 52 MET Chi-restraints excluded: chain HA residue 84 HIS Chi-restraints excluded: chain HA residue 177 ASP Chi-restraints excluded: chain HA residue 326 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 949 optimal weight: 30.0000 chunk 722 optimal weight: 7.9990 chunk 498 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 458 optimal weight: 2.9990 chunk 645 optimal weight: 8.9990 chunk 964 optimal weight: 20.0000 chunk 1020 optimal weight: 0.6980 chunk 503 optimal weight: 8.9990 chunk 913 optimal weight: 20.0000 chunk 275 optimal weight: 10.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 88 GLN A 318 GLN B 88 GLN B 309 GLN C 88 GLN E 84 HIS G 88 GLN H 17 ASN I 17 ASN I 84 HIS I 88 GLN J 84 HIS J 88 GLN L 84 HIS L 88 GLN M 84 HIS M 88 GLN P 84 HIS P 88 GLN Q 88 GLN Q 99 ASN Q 314 GLN R 88 GLN S 88 GLN T 88 GLN V 26 ASN W 84 HIS W 88 GLN X 17 ASN X 131 ASN Y 17 ASN Y 318 GLN Z 17 ASN Z 318 GLN AA 17 ASN CA 318 GLN DA 309 GLN DA 318 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 80355 Z= 0.239 Angle : 0.491 8.469 108174 Z= 0.273 Chirality : 0.036 0.154 13035 Planarity : 0.002 0.030 14289 Dihedral : 4.671 24.262 11220 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.51 % Allowed : 24.69 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.08), residues: 10560 helix: 2.25 (0.06), residues: 6600 sheet: 0.97 (0.24), residues: 396 loop : -1.48 (0.10), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.002 HIS H 84 PHE 0.005 0.001 PHE Z 130 TYR 0.014 0.001 TYRFA 173 ARG 0.005 0.000 ARG I 264 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21120 Ramachandran restraints generated. 10560 Oldfield, 0 Emsley, 10560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21120 Ramachandran restraints generated. 10560 Oldfield, 0 Emsley, 10560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 8844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 534 time to evaluate : 7.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8827 (ttm) cc_final: 0.8571 (ttm) REVERT: B 311 MET cc_start: 0.9069 (mmm) cc_final: 0.8840 (mmp) REVERT: D 88 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8012 (mp10) REVERT: D 100 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8410 (m-30) REVERT: F 61 MET cc_start: 0.8881 (tpt) cc_final: 0.8679 (tpp) REVERT: F 177 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8104 (m-30) REVERT: G 151 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7463 (mt-10) REVERT: H 35 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8396 (mtp85) REVERT: H 61 MET cc_start: 0.8555 (tpp) cc_final: 0.8300 (tpt) REVERT: H 188 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8563 (mmmm) REVERT: H 320 GLN cc_start: 0.8502 (tt0) cc_final: 0.8005 (mt0) REVERT: I 320 GLN cc_start: 0.8416 (tt0) cc_final: 0.8089 (mt0) REVERT: J 1 MET cc_start: 0.7298 (mmm) cc_final: 0.6853 (mpm) REVERT: J 52 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8597 (mtp) REVERT: J 109 GLU cc_start: 0.8292 (tp30) cc_final: 0.7977 (tm-30) REVERT: J 291 MET cc_start: 0.9005 (mmt) cc_final: 0.8792 (mmm) REVERT: J 320 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7651 (tm-30) REVERT: K 1 MET cc_start: 0.7186 (mmm) cc_final: 0.6697 (mpm) REVERT: K 52 MET cc_start: 0.8916 (tpp) cc_final: 0.8680 (mmp) REVERT: K 90 MET cc_start: 0.9380 (OUTLIER) cc_final: 0.9142 (ttp) REVERT: K 291 MET cc_start: 0.9051 (mmt) cc_final: 0.8362 (mmm) REVERT: K 309 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8523 (mt0) REVERT: L 1 MET cc_start: 0.6456 (mmp) cc_final: 0.4645 (pp-130) REVERT: L 61 MET cc_start: 0.8498 (tpp) cc_final: 0.8040 (tpt) REVERT: M 1 MET cc_start: 0.6917 (mmp) cc_final: 0.6127 (pp-130) REVERT: M 52 MET cc_start: 0.8537 (mmp) cc_final: 0.8310 (mtp) REVERT: M 100 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8084 (m-30) REVERT: M 183 VAL cc_start: 0.9211 (t) cc_final: 0.8837 (m) REVERT: M 189 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8353 (tp30) REVERT: M 220 LYS cc_start: 0.9022 (tttt) cc_final: 0.8758 (tptm) REVERT: N 1 MET cc_start: 0.6741 (mmp) cc_final: 0.5582 (pp-130) REVERT: N 291 MET cc_start: 0.9088 (mmt) cc_final: 0.8702 (mmp) REVERT: O 1 MET cc_start: 0.6747 (mmp) cc_final: 0.5826 (pp-130) REVERT: O 88 GLN cc_start: 0.9244 (OUTLIER) cc_final: 0.8971 (mm-40) REVERT: P 61 MET cc_start: 0.8575 (tpp) cc_final: 0.8215 (tpt) REVERT: Q 1 MET cc_start: 0.6854 (mmp) cc_final: 0.5304 (pp-130) REVERT: Q 35 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8689 (mtp85) REVERT: R 1 MET cc_start: 0.6671 (mmp) cc_final: 0.5137 (pp-130) REVERT: R 52 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8732 (mtt) REVERT: R 100 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8214 (t0) REVERT: R 162 MET cc_start: 0.9317 (mmp) cc_final: 0.8955 (mmm) REVERT: T 1 MET cc_start: 0.6552 (mmp) cc_final: 0.4753 (pp-130) REVERT: V 1 MET cc_start: 0.7145 (mmp) cc_final: 0.3957 (pp-130) REVERT: V 88 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.7913 (mp10) REVERT: V 90 MET cc_start: 0.9220 (ttm) cc_final: 0.8990 (mtt) REVERT: V 220 LYS cc_start: 0.9051 (tttt) cc_final: 0.8720 (tptt) REVERT: W 1 MET cc_start: 0.7011 (mmp) cc_final: 0.4039 (pp-130) REVERT: W 151 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6561 (tt0) REVERT: W 162 MET cc_start: 0.9248 (mmp) cc_final: 0.8994 (mmp) REVERT: X 61 MET cc_start: 0.8980 (tpp) cc_final: 0.8643 (tpt) REVERT: X 291 MET cc_start: 0.9036 (mmt) cc_final: 0.8669 (mmm) REVERT: Y 46 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8538 (tp) REVERT: Y 61 MET cc_start: 0.8700 (tpp) cc_final: 0.8454 (tpp) REVERT: Z 1 MET cc_start: 0.7532 (mmp) cc_final: 0.7143 (mmm) REVERT: Z 291 MET cc_start: 0.8982 (mmt) cc_final: 0.8616 (mmm) REVERT: Z 295 MET cc_start: 0.8541 (tpt) cc_final: 0.8294 (tpt) REVERT: AA 1 MET cc_start: 0.7952 (mmm) cc_final: 0.7463 (mmm) REVERT: AA 188 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8492 (mtmm) REVERT: AA 296 MET cc_start: 0.8772 (ptm) cc_final: 0.8519 (ptm) REVERT: BA 295 MET cc_start: 0.8787 (tpt) cc_final: 0.8380 (tpt) REVERT: CA 1 MET cc_start: 0.7513 (mmm) cc_final: 0.7277 (mmp) REVERT: CA 67 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8260 (tp40) REVERT: CA 88 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.7868 (mp10) REVERT: DA 1 MET cc_start: 0.7860 (mmm) cc_final: 0.7492 (mpm) REVERT: DA 61 MET cc_start: 0.8830 (tpt) cc_final: 0.8584 (mmm) REVERT: DA 67 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8388 (mm-40) REVERT: DA 177 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7726 (p0) REVERT: DA 193 VAL cc_start: 0.7489 (t) cc_final: 0.7278 (t) REVERT: EA 1 MET cc_start: 0.7638 (mmm) cc_final: 0.7430 (mpm) REVERT: EA 114 MET cc_start: 0.9115 (tpt) cc_final: 0.8887 (tpt) REVERT: FA 296 MET cc_start: 0.8714 (ptm) cc_final: 0.8483 (ptt) REVERT: FA 309 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8522 (mt0) REVERT: FA 311 MET cc_start: 0.8521 (tpp) cc_final: 0.8296 (mmm) REVERT: GA 1 MET cc_start: 0.7816 (mmm) cc_final: 0.7444 (mmm) REVERT: GA 67 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8166 (mt0) REVERT: GA 296 MET cc_start: 0.8710 (ptm) cc_final: 0.8468 (ptt) REVERT: HA 1 MET cc_start: 0.7380 (mmm) cc_final: 0.6979 (mmm) REVERT: HA 114 MET cc_start: 0.9293 (tpt) cc_final: 0.8958 (tpt) outliers start: 310 outliers final: 133 residues processed: 805 average time/residue: 1.5671 time to fit residues: 1676.8775 Evaluate side-chains 674 residues out of total 8844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 516 time to evaluate : 6.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain F residue 84 HIS Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain H residue 35 ARG Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain H residue 188 LYS Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 52 MET Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain K residue 90 MET Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 224 VAL Chi-restraints excluded: chain K residue 309 GLN Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain L residue 100 ASP Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain M residue 177 ASP Chi-restraints excluded: chain M residue 189 GLU Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 84 HIS Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 183 VAL Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain O residue 88 GLN Chi-restraints excluded: chain O residue 181 LYS Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 308 SER Chi-restraints excluded: chain O residue 326 LEU Chi-restraints excluded: chain P residue 177 ASP Chi-restraints excluded: chain P residue 178 ASP Chi-restraints excluded: chain P residue 183 VAL Chi-restraints excluded: chain P residue 325 LEU Chi-restraints excluded: chain Q residue 35 ARG Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 84 HIS Chi-restraints excluded: chain Q residue 183 VAL Chi-restraints excluded: chain Q residue 186 ASP Chi-restraints excluded: chain Q residue 326 LEU Chi-restraints excluded: chain R residue 52 MET Chi-restraints excluded: chain R residue 84 HIS Chi-restraints excluded: chain R residue 100 ASP Chi-restraints excluded: chain R residue 188 LYS Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 84 HIS Chi-restraints excluded: chain S residue 100 ASP Chi-restraints excluded: chain T residue 177 ASP Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 291 MET Chi-restraints excluded: chain V residue 88 GLN Chi-restraints excluded: chain V residue 100 ASP Chi-restraints excluded: chain V residue 177 ASP Chi-restraints excluded: chain V residue 224 VAL Chi-restraints excluded: chain V residue 293 SER Chi-restraints excluded: chain V residue 326 LEU Chi-restraints excluded: chain W residue 52 MET Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain W residue 151 GLU Chi-restraints excluded: chain W residue 188 LYS Chi-restraints excluded: chain W residue 224 VAL Chi-restraints excluded: chain X residue 52 MET Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 183 VAL Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 293 SER Chi-restraints excluded: chain Y residue 46 LEU Chi-restraints excluded: chain Y residue 52 MET Chi-restraints excluded: chain Y residue 84 HIS Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Y residue 224 VAL Chi-restraints excluded: chain Z residue 32 SER Chi-restraints excluded: chain Z residue 151 GLU Chi-restraints excluded: chain Z residue 224 VAL Chi-restraints excluded: chain AA residue 32 SER Chi-restraints excluded: chain AA residue 84 HIS Chi-restraints excluded: chain AA residue 188 LYS Chi-restraints excluded: chain AA residue 224 VAL Chi-restraints excluded: chain AA residue 320 GLN Chi-restraints excluded: chain AA residue 326 LEU Chi-restraints excluded: chain BA residue 224 VAL Chi-restraints excluded: chain BA residue 320 GLN Chi-restraints excluded: chain BA residue 326 LEU Chi-restraints excluded: chain CA residue 67 GLN Chi-restraints excluded: chain CA residue 84 HIS Chi-restraints excluded: chain CA residue 88 GLN Chi-restraints excluded: chain CA residue 224 VAL Chi-restraints excluded: chain CA residue 326 LEU Chi-restraints excluded: chain DA residue 67 GLN Chi-restraints excluded: chain DA residue 84 HIS Chi-restraints excluded: chain DA residue 177 ASP Chi-restraints excluded: chain DA residue 224 VAL Chi-restraints excluded: chain DA residue 289 VAL Chi-restraints excluded: chain DA residue 293 SER Chi-restraints excluded: chain EA residue 32 SER Chi-restraints excluded: chain EA residue 132 THR Chi-restraints excluded: chain EA residue 177 ASP Chi-restraints excluded: chain FA residue 32 SER Chi-restraints excluded: chain FA residue 84 HIS Chi-restraints excluded: chain FA residue 177 ASP Chi-restraints excluded: chain FA residue 224 VAL Chi-restraints excluded: chain FA residue 309 GLN Chi-restraints excluded: chain FA residue 326 LEU Chi-restraints excluded: chain GA residue 32 SER Chi-restraints excluded: chain GA residue 52 MET Chi-restraints excluded: chain GA residue 67 GLN Chi-restraints excluded: chain GA residue 84 HIS Chi-restraints excluded: chain GA residue 224 VAL Chi-restraints excluded: chain GA residue 293 SER Chi-restraints excluded: chain GA residue 326 LEU Chi-restraints excluded: chain HA residue 52 MET Chi-restraints excluded: chain HA residue 84 HIS Chi-restraints excluded: chain HA residue 151 GLU Chi-restraints excluded: chain HA residue 177 ASP Chi-restraints excluded: chain HA residue 293 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 850 optimal weight: 5.9990 chunk 579 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 760 optimal weight: 6.9990 chunk 421 optimal weight: 6.9990 chunk 871 optimal weight: 0.9990 chunk 705 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 521 optimal weight: 10.0000 chunk 916 optimal weight: 8.9990 chunk 257 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN B 84 HIS B 88 GLN ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 HIS G 88 GLN H 37 ASN I 84 HIS I 88 GLN I 318 GLN J 84 HIS J 88 GLN K 37 ASN K 84 HIS L 84 HIS L 88 GLN ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 HIS M 88 GLN N 88 GLN ** N 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 84 HIS P 84 HIS P 88 GLN Q 88 GLN R 88 GLN S 88 GLN T 88 GLN ** V 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 84 HIS W 88 GLN Y 318 GLN AA 17 ASN ** BA 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 318 GLN DA 309 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 80355 Z= 0.202 Angle : 0.471 9.383 108174 Z= 0.261 Chirality : 0.035 0.157 13035 Planarity : 0.002 0.027 14289 Dihedral : 4.519 24.040 11220 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.46 % Allowed : 24.88 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.08), residues: 10560 helix: 2.58 (0.06), residues: 6600 sheet: 1.08 (0.25), residues: 396 loop : -1.38 (0.10), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS V 84 PHE 0.004 0.001 PHE C 145 TYR 0.014 0.001 TYRFA 173 ARG 0.006 0.000 ARG N 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21120 Ramachandran restraints generated. 10560 Oldfield, 0 Emsley, 10560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21120 Ramachandran restraints generated. 10560 Oldfield, 0 Emsley, 10560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 8844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 535 time to evaluate : 7.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8863 (ttm) cc_final: 0.8626 (ttm) REVERT: B 311 MET cc_start: 0.9066 (mmm) cc_final: 0.8802 (mmp) REVERT: C 311 MET cc_start: 0.9166 (mmm) cc_final: 0.8921 (mmm) REVERT: D 35 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8412 (mtp85) REVERT: D 88 GLN cc_start: 0.9212 (OUTLIER) cc_final: 0.7957 (mp10) REVERT: D 100 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8344 (m-30) REVERT: H 1 MET cc_start: 0.6786 (mmm) cc_final: 0.6489 (mmm) REVERT: H 35 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8345 (mtp85) REVERT: H 188 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8525 (mmmm) REVERT: H 320 GLN cc_start: 0.8429 (tt0) cc_final: 0.7942 (mt0) REVERT: I 320 GLN cc_start: 0.8417 (tt0) cc_final: 0.8084 (mt0) REVERT: J 1 MET cc_start: 0.7473 (mmm) cc_final: 0.6850 (mpm) REVERT: J 27 MET cc_start: 0.9228 (ttm) cc_final: 0.8968 (ttm) REVERT: J 52 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8433 (mtp) REVERT: J 109 GLU cc_start: 0.8344 (tp30) cc_final: 0.8020 (tm-30) REVERT: J 291 MET cc_start: 0.9007 (mmt) cc_final: 0.8802 (mmm) REVERT: J 320 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7635 (tm-30) REVERT: K 1 MET cc_start: 0.7230 (mmm) cc_final: 0.6740 (mpm) REVERT: K 52 MET cc_start: 0.8901 (tpp) cc_final: 0.8644 (mmp) REVERT: K 67 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.8024 (mt0) REVERT: K 109 GLU cc_start: 0.5935 (OUTLIER) cc_final: 0.5198 (tm-30) REVERT: K 291 MET cc_start: 0.9024 (mmt) cc_final: 0.8331 (mmm) REVERT: K 309 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8467 (mt0) REVERT: L 1 MET cc_start: 0.6247 (mmp) cc_final: 0.4616 (pp-130) REVERT: L 61 MET cc_start: 0.8487 (tpp) cc_final: 0.8089 (tpt) REVERT: L 296 MET cc_start: 0.8476 (ptm) cc_final: 0.8083 (ttp) REVERT: M 1 MET cc_start: 0.7002 (mmp) cc_final: 0.6164 (pp-130) REVERT: M 52 MET cc_start: 0.8408 (mmp) cc_final: 0.8205 (mtp) REVERT: M 100 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8147 (m-30) REVERT: M 183 VAL cc_start: 0.9199 (t) cc_final: 0.8863 (m) REVERT: M 189 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8310 (tp30) REVERT: M 220 LYS cc_start: 0.9004 (tttt) cc_final: 0.8759 (tptm) REVERT: N 1 MET cc_start: 0.6778 (mmp) cc_final: 0.5664 (pp-130) REVERT: N 291 MET cc_start: 0.9088 (mmt) cc_final: 0.8717 (mmp) REVERT: O 1 MET cc_start: 0.6803 (mmp) cc_final: 0.6013 (pp-130) REVERT: O 84 HIS cc_start: 0.9043 (OUTLIER) cc_final: 0.8808 (m-70) REVERT: O 88 GLN cc_start: 0.9278 (OUTLIER) cc_final: 0.8521 (mp10) REVERT: O 184 THR cc_start: 0.7108 (t) cc_final: 0.6761 (t) REVERT: P 61 MET cc_start: 0.8545 (tpp) cc_final: 0.8261 (tpt) REVERT: P 114 MET cc_start: 0.9143 (tpt) cc_final: 0.8720 (tpt) REVERT: Q 1 MET cc_start: 0.7060 (mmp) cc_final: 0.5374 (pp-130) REVERT: Q 35 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8531 (mtp85) REVERT: Q 61 MET cc_start: 0.8578 (tpt) cc_final: 0.8223 (tpt) REVERT: Q 100 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7851 (m-30) REVERT: R 1 MET cc_start: 0.6590 (mmp) cc_final: 0.5025 (pp-130) REVERT: R 100 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.8165 (t0) REVERT: R 162 MET cc_start: 0.9317 (mmp) cc_final: 0.8948 (mmm) REVERT: R 320 GLN cc_start: 0.8851 (tt0) cc_final: 0.8480 (mt0) REVERT: V 1 MET cc_start: 0.7255 (mmp) cc_final: 0.4048 (pp-130) REVERT: V 88 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.7911 (mp10) REVERT: W 1 MET cc_start: 0.7056 (mmp) cc_final: 0.4065 (pp-130) REVERT: W 151 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.5815 (mt-10) REVERT: W 295 MET cc_start: 0.8852 (tpt) cc_final: 0.8632 (mmm) REVERT: X 291 MET cc_start: 0.8976 (mmt) cc_final: 0.8601 (mmm) REVERT: Y 35 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8591 (mtp85) REVERT: Y 46 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8613 (tp) REVERT: Y 61 MET cc_start: 0.8727 (tpp) cc_final: 0.8449 (tpp) REVERT: Y 291 MET cc_start: 0.8957 (mmt) cc_final: 0.8744 (mmp) REVERT: Z 1 MET cc_start: 0.7616 (mmp) cc_final: 0.7309 (mmm) REVERT: Z 291 MET cc_start: 0.8964 (mmt) cc_final: 0.8599 (mmm) REVERT: Z 295 MET cc_start: 0.8526 (tpt) cc_final: 0.8296 (tpt) REVERT: AA 1 MET cc_start: 0.7841 (mmm) cc_final: 0.7348 (mmm) REVERT: AA 296 MET cc_start: 0.8765 (ptm) cc_final: 0.8486 (ptm) REVERT: BA 295 MET cc_start: 0.8803 (tpt) cc_final: 0.8400 (tpt) REVERT: CA 1 MET cc_start: 0.7445 (mmm) cc_final: 0.7222 (mmp) REVERT: CA 35 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8707 (mtp85) REVERT: CA 67 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8231 (tp40) REVERT: CA 88 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.7853 (mp10) REVERT: DA 1 MET cc_start: 0.7884 (mmm) cc_final: 0.7528 (mpm) REVERT: DA 67 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8299 (mm-40) REVERT: DA 177 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7678 (p0) REVERT: DA 193 VAL cc_start: 0.7566 (t) cc_final: 0.7340 (t) REVERT: EA 114 MET cc_start: 0.9056 (tpt) cc_final: 0.8850 (tpt) REVERT: FA 296 MET cc_start: 0.8684 (ptm) cc_final: 0.8448 (ptt) REVERT: FA 309 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8549 (mt0) REVERT: GA 1 MET cc_start: 0.7802 (mmm) cc_final: 0.7417 (mmm) REVERT: GA 296 MET cc_start: 0.8696 (ptm) cc_final: 0.8452 (ptt) REVERT: HA 1 MET cc_start: 0.7342 (mmm) cc_final: 0.6923 (mmm) REVERT: HA 114 MET cc_start: 0.9329 (tpt) cc_final: 0.9050 (tpt) REVERT: HA 295 MET cc_start: 0.8669 (tpt) cc_final: 0.8020 (tpt) outliers start: 306 outliers final: 130 residues processed: 801 average time/residue: 1.5862 time to fit residues: 1683.1780 Evaluate side-chains 669 residues out of total 8844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 513 time to evaluate : 7.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain F residue 84 HIS Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 309 GLN Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain H residue 35 ARG Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 188 LYS Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 293 SER Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 52 MET Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain K residue 67 GLN Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 224 VAL Chi-restraints excluded: chain K residue 309 GLN Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain L residue 100 ASP Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain M residue 177 ASP Chi-restraints excluded: chain M residue 189 GLU Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 84 HIS Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain N residue 183 VAL Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain O residue 84 HIS Chi-restraints excluded: chain O residue 88 GLN Chi-restraints excluded: chain O residue 181 LYS Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 269 ILE Chi-restraints excluded: chain O residue 308 SER Chi-restraints excluded: chain O residue 326 LEU Chi-restraints excluded: chain P residue 178 ASP Chi-restraints excluded: chain P residue 183 VAL Chi-restraints excluded: chain P residue 325 LEU Chi-restraints excluded: chain Q residue 35 ARG Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 84 HIS Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain Q residue 183 VAL Chi-restraints excluded: chain Q residue 308 SER Chi-restraints excluded: chain Q residue 326 LEU Chi-restraints excluded: chain R residue 84 HIS Chi-restraints excluded: chain R residue 100 ASP Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 84 HIS Chi-restraints excluded: chain S residue 100 ASP Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 291 MET Chi-restraints excluded: chain V residue 84 HIS Chi-restraints excluded: chain V residue 88 GLN Chi-restraints excluded: chain V residue 151 GLU Chi-restraints excluded: chain V residue 177 ASP Chi-restraints excluded: chain V residue 224 VAL Chi-restraints excluded: chain V residue 293 SER Chi-restraints excluded: chain W residue 52 MET Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain W residue 151 GLU Chi-restraints excluded: chain W residue 188 LYS Chi-restraints excluded: chain W residue 224 VAL Chi-restraints excluded: chain X residue 52 MET Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 183 VAL Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 293 SER Chi-restraints excluded: chain Y residue 35 ARG Chi-restraints excluded: chain Y residue 46 LEU Chi-restraints excluded: chain Y residue 84 HIS Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Y residue 224 VAL Chi-restraints excluded: chain Y residue 326 LEU Chi-restraints excluded: chain Z residue 151 GLU Chi-restraints excluded: chain Z residue 224 VAL Chi-restraints excluded: chain AA residue 32 SER Chi-restraints excluded: chain AA residue 84 HIS Chi-restraints excluded: chain AA residue 224 VAL Chi-restraints excluded: chain AA residue 293 SER Chi-restraints excluded: chain AA residue 320 GLN Chi-restraints excluded: chain AA residue 326 LEU Chi-restraints excluded: chain BA residue 224 VAL Chi-restraints excluded: chain BA residue 326 LEU Chi-restraints excluded: chain CA residue 35 ARG Chi-restraints excluded: chain CA residue 67 GLN Chi-restraints excluded: chain CA residue 84 HIS Chi-restraints excluded: chain CA residue 88 GLN Chi-restraints excluded: chain CA residue 224 VAL Chi-restraints excluded: chain CA residue 326 LEU Chi-restraints excluded: chain DA residue 67 GLN Chi-restraints excluded: chain DA residue 84 HIS Chi-restraints excluded: chain DA residue 177 ASP Chi-restraints excluded: chain DA residue 224 VAL Chi-restraints excluded: chain DA residue 293 SER Chi-restraints excluded: chain EA residue 132 THR Chi-restraints excluded: chain EA residue 177 ASP Chi-restraints excluded: chain FA residue 32 SER Chi-restraints excluded: chain FA residue 84 HIS Chi-restraints excluded: chain FA residue 177 ASP Chi-restraints excluded: chain FA residue 224 VAL Chi-restraints excluded: chain FA residue 293 SER Chi-restraints excluded: chain FA residue 309 GLN Chi-restraints excluded: chain FA residue 326 LEU Chi-restraints excluded: chain GA residue 52 MET Chi-restraints excluded: chain GA residue 84 HIS Chi-restraints excluded: chain GA residue 186 ASP Chi-restraints excluded: chain GA residue 224 VAL Chi-restraints excluded: chain GA residue 326 LEU Chi-restraints excluded: chain HA residue 32 SER Chi-restraints excluded: chain HA residue 52 MET Chi-restraints excluded: chain HA residue 84 HIS Chi-restraints excluded: chain HA residue 151 GLU Chi-restraints excluded: chain HA residue 155 MET Chi-restraints excluded: chain HA residue 293 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 343 optimal weight: 7.9990 chunk 919 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 chunk 599 optimal weight: 20.0000 chunk 251 optimal weight: 0.8980 chunk 1021 optimal weight: 6.9990 chunk 848 optimal weight: 1.9990 chunk 473 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 337 optimal weight: 10.0000 chunk 536 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN B 88 GLN C 88 GLN D 84 HIS E 84 HIS G 88 GLN H 309 GLN I 84 HIS I 88 GLN J 84 HIS J 88 GLN K 84 HIS K 88 GLN L 84 HIS L 88 GLN ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 HIS M 88 GLN N 88 GLN ** N 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 HIS P 88 GLN Q 37 ASN Q 88 GLN R 88 GLN S 88 GLN T 88 GLN ** V 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 84 HIS W 88 GLN Y 318 GLN ** BA 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 318 GLN DA 309 GLN EA 318 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 80355 Z= 0.218 Angle : 0.474 8.501 108174 Z= 0.261 Chirality : 0.036 0.158 13035 Planarity : 0.002 0.032 14289 Dihedral : 4.478 24.364 11220 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.65 % Favored : 97.21 % Rotamer: Outliers : 3.38 % Allowed : 24.73 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.08), residues: 10560 helix: 2.68 (0.06), residues: 6600 sheet: 1.14 (0.25), residues: 396 loop : -1.32 (0.10), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.001 HIS B 84 PHE 0.004 0.001 PHEAA 130 TYR 0.015 0.001 TYRFA 173 ARG 0.006 0.000 ARG T 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21120 Ramachandran restraints generated. 10560 Oldfield, 0 Emsley, 10560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21120 Ramachandran restraints generated. 10560 Oldfield, 0 Emsley, 10560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 8844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 528 time to evaluate : 7.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8869 (ttm) cc_final: 0.8479 (ptm) REVERT: B 311 MET cc_start: 0.9076 (mmm) cc_final: 0.8807 (mmp) REVERT: D 35 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8422 (mtp85) REVERT: D 84 HIS cc_start: 0.8981 (OUTLIER) cc_final: 0.8328 (m-70) REVERT: D 88 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.7949 (mp10) REVERT: D 100 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8305 (m-30) REVERT: D 177 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.7906 (m-30) REVERT: F 61 MET cc_start: 0.8983 (tpp) cc_final: 0.8759 (tpt) REVERT: F 177 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8141 (m-30) REVERT: H 1 MET cc_start: 0.6834 (mmm) cc_final: 0.6539 (mmm) REVERT: H 35 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8329 (mtp85) REVERT: H 90 MET cc_start: 0.9290 (mtm) cc_final: 0.9084 (mtm) REVERT: H 188 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8476 (mmmm) REVERT: H 320 GLN cc_start: 0.8398 (tt0) cc_final: 0.7919 (mt0) REVERT: I 320 GLN cc_start: 0.8425 (tt0) cc_final: 0.8078 (mt0) REVERT: J 1 MET cc_start: 0.7557 (mmm) cc_final: 0.7127 (mpm) REVERT: J 27 MET cc_start: 0.9173 (ttm) cc_final: 0.8970 (ttm) REVERT: J 109 GLU cc_start: 0.8340 (tp30) cc_final: 0.8027 (tm-30) REVERT: J 291 MET cc_start: 0.9006 (mmt) cc_final: 0.8804 (mmm) REVERT: K 1 MET cc_start: 0.7243 (mmm) cc_final: 0.6800 (mpm) REVERT: K 52 MET cc_start: 0.8924 (tpp) cc_final: 0.8651 (mmp) REVERT: K 67 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8089 (mt0) REVERT: K 109 GLU cc_start: 0.5883 (OUTLIER) cc_final: 0.5028 (tm-30) REVERT: K 291 MET cc_start: 0.9018 (mmt) cc_final: 0.8348 (mmm) REVERT: L 1 MET cc_start: 0.6215 (mmp) cc_final: 0.4705 (pp-130) REVERT: L 61 MET cc_start: 0.8498 (tpp) cc_final: 0.8060 (tpt) REVERT: L 296 MET cc_start: 0.8536 (ptm) cc_final: 0.8113 (ttp) REVERT: M 1 MET cc_start: 0.7054 (mmp) cc_final: 0.6188 (pp-130) REVERT: M 100 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8107 (m-30) REVERT: M 183 VAL cc_start: 0.9205 (t) cc_final: 0.8877 (m) REVERT: M 189 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8305 (tp30) REVERT: M 220 LYS cc_start: 0.9032 (tttt) cc_final: 0.8741 (tptm) REVERT: N 1 MET cc_start: 0.6766 (mmp) cc_final: 0.5681 (pp-130) REVERT: N 61 MET cc_start: 0.8725 (tpp) cc_final: 0.8478 (tpt) REVERT: O 1 MET cc_start: 0.7002 (mmp) cc_final: 0.6001 (pp-130) REVERT: O 88 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.8483 (mp10) REVERT: P 61 MET cc_start: 0.8561 (tpp) cc_final: 0.8255 (tpt) REVERT: P 114 MET cc_start: 0.9238 (tpt) cc_final: 0.8693 (tpt) REVERT: Q 1 MET cc_start: 0.7170 (mmp) cc_final: 0.5375 (pp-130) REVERT: Q 35 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8702 (mtp85) REVERT: Q 61 MET cc_start: 0.8564 (tpt) cc_final: 0.8280 (tpt) REVERT: Q 100 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7952 (m-30) REVERT: R 1 MET cc_start: 0.6674 (mmp) cc_final: 0.4888 (pp-130) REVERT: R 100 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8215 (t0) REVERT: R 162 MET cc_start: 0.9314 (mmp) cc_final: 0.9050 (mmp) REVERT: R 320 GLN cc_start: 0.8855 (tt0) cc_final: 0.8473 (mt0) REVERT: S 90 MET cc_start: 0.9240 (ttm) cc_final: 0.9019 (mtm) REVERT: V 1 MET cc_start: 0.7175 (mmp) cc_final: 0.3865 (pp-130) REVERT: V 88 GLN cc_start: 0.9321 (OUTLIER) cc_final: 0.7929 (mp10) REVERT: W 1 MET cc_start: 0.7088 (mmp) cc_final: 0.3914 (pp-130) REVERT: W 109 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7834 (tp30) REVERT: W 151 GLU cc_start: 0.6318 (OUTLIER) cc_final: 0.5612 (mt-10) REVERT: X 291 MET cc_start: 0.9035 (mmt) cc_final: 0.8679 (mmm) REVERT: Y 35 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8605 (mtp85) REVERT: Y 46 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8631 (tp) REVERT: Y 61 MET cc_start: 0.8718 (tpp) cc_final: 0.8286 (tpp) REVERT: Z 1 MET cc_start: 0.7682 (mmp) cc_final: 0.7356 (mmm) REVERT: Z 46 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8629 (tp) REVERT: Z 291 MET cc_start: 0.8953 (mmt) cc_final: 0.8592 (mmm) REVERT: Z 295 MET cc_start: 0.8512 (tpt) cc_final: 0.8240 (tpt) REVERT: AA 1 MET cc_start: 0.7834 (mmm) cc_final: 0.7343 (mmm) REVERT: AA 296 MET cc_start: 0.8750 (ptm) cc_final: 0.8502 (ptm) REVERT: BA 295 MET cc_start: 0.8801 (tpt) cc_final: 0.8407 (tpt) REVERT: CA 1 MET cc_start: 0.7446 (mmm) cc_final: 0.7225 (mmp) REVERT: CA 35 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8711 (mtp85) REVERT: CA 67 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8257 (tp40) REVERT: CA 88 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.7844 (mp10) REVERT: DA 1 MET cc_start: 0.7888 (mmm) cc_final: 0.7537 (mpm) REVERT: DA 46 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8466 (tp) REVERT: DA 67 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8297 (mm-40) REVERT: DA 177 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7696 (p0) REVERT: DA 193 VAL cc_start: 0.7581 (t) cc_final: 0.7351 (t) REVERT: FA 296 MET cc_start: 0.8674 (ptm) cc_final: 0.8442 (ptt) REVERT: GA 1 MET cc_start: 0.7785 (mmm) cc_final: 0.7428 (mmm) REVERT: GA 295 MET cc_start: 0.8814 (tpt) cc_final: 0.8603 (tpt) REVERT: GA 296 MET cc_start: 0.8668 (ptm) cc_final: 0.8434 (ptt) REVERT: HA 1 MET cc_start: 0.7362 (mmm) cc_final: 0.6935 (mmm) REVERT: HA 114 MET cc_start: 0.9374 (tpt) cc_final: 0.9075 (tpt) outliers start: 299 outliers final: 151 residues processed: 793 average time/residue: 1.5434 time to fit residues: 1641.5591 Evaluate side-chains 688 residues out of total 8844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 509 time to evaluate : 7.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 84 HIS Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain F residue 84 HIS Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 309 GLN Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain H residue 35 ARG Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 188 LYS Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 293 SER Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain K residue 67 GLN Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 224 VAL Chi-restraints excluded: chain K residue 289 VAL Chi-restraints excluded: chain K residue 293 SER Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain L residue 100 ASP Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain M residue 177 ASP Chi-restraints excluded: chain M residue 189 GLU Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 284 SER Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 84 HIS Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 183 VAL Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain O residue 88 GLN Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 269 ILE Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 308 SER Chi-restraints excluded: chain O residue 326 LEU Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 183 VAL Chi-restraints excluded: chain P residue 325 LEU Chi-restraints excluded: chain Q residue 35 ARG Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 84 HIS Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain Q residue 183 VAL Chi-restraints excluded: chain Q residue 308 SER Chi-restraints excluded: chain R residue 84 HIS Chi-restraints excluded: chain R residue 100 ASP Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 188 LYS Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 84 HIS Chi-restraints excluded: chain S residue 100 ASP Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 284 SER Chi-restraints excluded: chain T residue 291 MET Chi-restraints excluded: chain V residue 88 GLN Chi-restraints excluded: chain V residue 151 GLU Chi-restraints excluded: chain V residue 177 ASP Chi-restraints excluded: chain V residue 224 VAL Chi-restraints excluded: chain V residue 293 SER Chi-restraints excluded: chain W residue 52 MET Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain W residue 151 GLU Chi-restraints excluded: chain W residue 188 LYS Chi-restraints excluded: chain W residue 224 VAL Chi-restraints excluded: chain X residue 52 MET Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 183 VAL Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain Y residue 35 ARG Chi-restraints excluded: chain Y residue 46 LEU Chi-restraints excluded: chain Y residue 52 MET Chi-restraints excluded: chain Y residue 84 HIS Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Y residue 224 VAL Chi-restraints excluded: chain Y residue 284 SER Chi-restraints excluded: chain Y residue 326 LEU Chi-restraints excluded: chain Z residue 32 SER Chi-restraints excluded: chain Z residue 46 LEU Chi-restraints excluded: chain Z residue 114 MET Chi-restraints excluded: chain Z residue 151 GLU Chi-restraints excluded: chain Z residue 224 VAL Chi-restraints excluded: chain Z residue 293 SER Chi-restraints excluded: chain AA residue 32 SER Chi-restraints excluded: chain AA residue 84 HIS Chi-restraints excluded: chain AA residue 224 VAL Chi-restraints excluded: chain AA residue 293 SER Chi-restraints excluded: chain AA residue 326 LEU Chi-restraints excluded: chain BA residue 224 VAL Chi-restraints excluded: chain BA residue 326 LEU Chi-restraints excluded: chain CA residue 35 ARG Chi-restraints excluded: chain CA residue 67 GLN Chi-restraints excluded: chain CA residue 84 HIS Chi-restraints excluded: chain CA residue 88 GLN Chi-restraints excluded: chain CA residue 224 VAL Chi-restraints excluded: chain CA residue 326 LEU Chi-restraints excluded: chain DA residue 46 LEU Chi-restraints excluded: chain DA residue 67 GLN Chi-restraints excluded: chain DA residue 84 HIS Chi-restraints excluded: chain DA residue 106 ASP Chi-restraints excluded: chain DA residue 177 ASP Chi-restraints excluded: chain DA residue 224 VAL Chi-restraints excluded: chain DA residue 289 VAL Chi-restraints excluded: chain DA residue 293 SER Chi-restraints excluded: chain EA residue 32 SER Chi-restraints excluded: chain EA residue 132 THR Chi-restraints excluded: chain EA residue 177 ASP Chi-restraints excluded: chain FA residue 32 SER Chi-restraints excluded: chain FA residue 84 HIS Chi-restraints excluded: chain FA residue 177 ASP Chi-restraints excluded: chain FA residue 293 SER Chi-restraints excluded: chain FA residue 326 LEU Chi-restraints excluded: chain GA residue 32 SER Chi-restraints excluded: chain GA residue 52 MET Chi-restraints excluded: chain GA residue 84 HIS Chi-restraints excluded: chain GA residue 177 ASP Chi-restraints excluded: chain GA residue 186 ASP Chi-restraints excluded: chain GA residue 224 VAL Chi-restraints excluded: chain GA residue 293 SER Chi-restraints excluded: chain GA residue 326 LEU Chi-restraints excluded: chain HA residue 32 SER Chi-restraints excluded: chain HA residue 52 MET Chi-restraints excluded: chain HA residue 84 HIS Chi-restraints excluded: chain HA residue 151 GLU Chi-restraints excluded: chain HA residue 155 MET Chi-restraints excluded: chain HA residue 177 ASP Chi-restraints excluded: chain HA residue 293 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 985 optimal weight: 1.9990 chunk 115 optimal weight: 30.0000 chunk 582 optimal weight: 6.9990 chunk 746 optimal weight: 9.9990 chunk 578 optimal weight: 6.9990 chunk 860 optimal weight: 8.9990 chunk 570 optimal weight: 3.9990 chunk 1017 optimal weight: 7.9990 chunk 636 optimal weight: 20.0000 chunk 620 optimal weight: 10.0000 chunk 469 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN B 84 HIS B 88 GLN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 HIS G 88 GLN I 84 HIS I 88 GLN J 17 ASN J 84 HIS J 88 GLN J 309 GLN J 318 GLN J 320 GLN K 84 HIS K 88 GLN L 84 HIS L 88 GLN ** L 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 ASN M 84 HIS M 88 GLN ** M 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 88 GLN O 84 HIS ** O 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 HIS P 88 GLN Q 88 GLN ** Q 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 88 GLN S 88 GLN T 88 GLN T 150 ASN T 309 GLN ** V 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 131 ASN V 150 ASN W 84 HIS W 88 GLN Y 318 GLN Z 309 GLN Z 318 GLN BA 84 HIS CA 37 ASN DA 318 GLN FA 318 GLN HA 318 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 80355 Z= 0.322 Angle : 0.527 9.902 108174 Z= 0.288 Chirality : 0.038 0.157 13035 Planarity : 0.003 0.028 14289 Dihedral : 4.614 24.180 11220 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.76 % Favored : 97.06 % Rotamer: Outliers : 3.69 % Allowed : 24.56 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.08), residues: 10560 helix: 2.50 (0.06), residues: 6600 sheet: -0.42 (0.19), residues: 726 loop : -1.26 (0.10), residues: 3234 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS D 84 PHE 0.006 0.001 PHE Z 130 TYR 0.015 0.001 TYRFA 173 ARG 0.006 0.000 ARG T 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21120 Ramachandran restraints generated. 10560 Oldfield, 0 Emsley, 10560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21120 Ramachandran restraints generated. 10560 Oldfield, 0 Emsley, 10560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 8844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 326 poor density : 525 time to evaluate : 7.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8873 (ttm) cc_final: 0.8633 (ttm) REVERT: B 311 MET cc_start: 0.9114 (mmm) cc_final: 0.8826 (mmp) REVERT: D 88 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.8011 (mp10) REVERT: D 177 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.7851 (m-30) REVERT: E 27 MET cc_start: 0.9273 (ttp) cc_final: 0.9067 (ttm) REVERT: F 61 MET cc_start: 0.9003 (tpp) cc_final: 0.8776 (tpt) REVERT: F 151 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7621 (mm-30) REVERT: F 177 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8141 (m-30) REVERT: H 35 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8569 (mtp85) REVERT: H 90 MET cc_start: 0.9327 (mtm) cc_final: 0.9117 (mtm) REVERT: H 188 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8488 (mmmm) REVERT: H 311 MET cc_start: 0.9106 (mmm) cc_final: 0.8843 (mmm) REVERT: H 320 GLN cc_start: 0.8473 (tt0) cc_final: 0.7970 (mt0) REVERT: I 320 GLN cc_start: 0.8498 (tt0) cc_final: 0.8126 (mt0) REVERT: J 1 MET cc_start: 0.7566 (mmm) cc_final: 0.6959 (mpm) REVERT: J 109 GLU cc_start: 0.8395 (tp30) cc_final: 0.7952 (tm-30) REVERT: K 1 MET cc_start: 0.7263 (mmm) cc_final: 0.6839 (mpm) REVERT: K 52 MET cc_start: 0.8994 (tpp) cc_final: 0.8599 (mmp) REVERT: K 67 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8015 (mt0) REVERT: K 90 MET cc_start: 0.9358 (OUTLIER) cc_final: 0.9123 (ttp) REVERT: K 109 GLU cc_start: 0.5876 (OUTLIER) cc_final: 0.5373 (tm-30) REVERT: K 291 MET cc_start: 0.9035 (mmt) cc_final: 0.8345 (mmm) REVERT: K 295 MET cc_start: 0.8849 (tpt) cc_final: 0.8629 (tpt) REVERT: L 1 MET cc_start: 0.6270 (mmp) cc_final: 0.5111 (pp-130) REVERT: L 61 MET cc_start: 0.8591 (tpp) cc_final: 0.8182 (tpt) REVERT: L 144 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.8932 (p) REVERT: L 296 MET cc_start: 0.8522 (ptm) cc_final: 0.8094 (ttp) REVERT: M 1 MET cc_start: 0.7045 (mmp) cc_final: 0.6241 (pp-130) REVERT: M 100 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8192 (m-30) REVERT: M 183 VAL cc_start: 0.9219 (t) cc_final: 0.8906 (m) REVERT: M 189 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8272 (tp30) REVERT: M 220 LYS cc_start: 0.9076 (tttt) cc_final: 0.8789 (tptm) REVERT: N 1 MET cc_start: 0.6931 (mmp) cc_final: 0.5727 (pp-130) REVERT: N 291 MET cc_start: 0.9106 (mmt) cc_final: 0.8779 (mmp) REVERT: O 1 MET cc_start: 0.7045 (mmp) cc_final: 0.6093 (pp-130) REVERT: O 84 HIS cc_start: 0.9082 (OUTLIER) cc_final: 0.8847 (m-70) REVERT: O 88 GLN cc_start: 0.9323 (OUTLIER) cc_final: 0.8571 (mp10) REVERT: P 61 MET cc_start: 0.8633 (tpp) cc_final: 0.8245 (tpt) REVERT: Q 1 MET cc_start: 0.7312 (mmp) cc_final: 0.5272 (pp-130) REVERT: Q 35 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8802 (mtp85) REVERT: Q 61 MET cc_start: 0.8634 (tpt) cc_final: 0.8288 (tpt) REVERT: Q 100 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.8089 (m-30) REVERT: R 1 MET cc_start: 0.6772 (mmp) cc_final: 0.5330 (pp-130) REVERT: R 162 MET cc_start: 0.9310 (mmp) cc_final: 0.9065 (mmp) REVERT: R 320 GLN cc_start: 0.8870 (tt0) cc_final: 0.8466 (mt0) REVERT: S 291 MET cc_start: 0.8970 (mmt) cc_final: 0.8696 (mmp) REVERT: V 1 MET cc_start: 0.7116 (mmp) cc_final: 0.4173 (pp-130) REVERT: V 88 GLN cc_start: 0.9345 (OUTLIER) cc_final: 0.7932 (mp10) REVERT: W 1 MET cc_start: 0.7102 (mmp) cc_final: 0.3927 (pp-130) REVERT: W 109 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7940 (tp30) REVERT: W 151 GLU cc_start: 0.5400 (OUTLIER) cc_final: 0.4762 (mt-10) REVERT: X 291 MET cc_start: 0.9054 (mmt) cc_final: 0.8739 (mmm) REVERT: Y 35 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8686 (mtp85) REVERT: Z 1 MET cc_start: 0.7769 (mmp) cc_final: 0.7466 (mmm) REVERT: Z 291 MET cc_start: 0.8967 (mmt) cc_final: 0.8633 (mmm) REVERT: Z 295 MET cc_start: 0.8522 (tpt) cc_final: 0.8275 (tpt) REVERT: AA 1 MET cc_start: 0.7820 (mmm) cc_final: 0.7351 (mmm) REVERT: AA 296 MET cc_start: 0.8815 (ptm) cc_final: 0.8580 (ptm) REVERT: BA 295 MET cc_start: 0.8817 (tpt) cc_final: 0.8398 (tpt) REVERT: CA 1 MET cc_start: 0.7602 (mmm) cc_final: 0.7387 (mmp) REVERT: CA 35 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8690 (mtp85) REVERT: CA 67 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8363 (tp40) REVERT: CA 88 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.7861 (mp10) REVERT: CA 212 TYR cc_start: 0.8962 (t80) cc_final: 0.8667 (t80) REVERT: DA 46 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8448 (tp) REVERT: DA 177 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7860 (p0) REVERT: DA 193 VAL cc_start: 0.7558 (t) cc_final: 0.7345 (t) REVERT: FA 296 MET cc_start: 0.8678 (ptm) cc_final: 0.8451 (ptt) REVERT: GA 296 MET cc_start: 0.8687 (ptm) cc_final: 0.8438 (ptt) REVERT: HA 1 MET cc_start: 0.7446 (mmm) cc_final: 0.6950 (mmm) REVERT: HA 114 MET cc_start: 0.9400 (tpt) cc_final: 0.9117 (tpt) outliers start: 326 outliers final: 176 residues processed: 817 average time/residue: 1.4955 time to fit residues: 1647.7865 Evaluate side-chains 705 residues out of total 8844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 504 time to evaluate : 7.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain F residue 84 HIS Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 309 GLN Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain H residue 35 ARG Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 188 LYS Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 293 SER Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 284 SER Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain K residue 67 GLN Chi-restraints excluded: chain K residue 90 MET Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 224 VAL Chi-restraints excluded: chain K residue 289 VAL Chi-restraints excluded: chain K residue 293 SER Chi-restraints excluded: chain L residue 100 ASP Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain M residue 189 GLU Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 284 SER Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 84 HIS Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 183 VAL Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain O residue 84 HIS Chi-restraints excluded: chain O residue 88 GLN Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 191 THR Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 308 SER Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 177 ASP Chi-restraints excluded: chain P residue 183 VAL Chi-restraints excluded: chain P residue 325 LEU Chi-restraints excluded: chain Q residue 35 ARG Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 84 HIS Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain Q residue 183 VAL Chi-restraints excluded: chain Q residue 186 ASP Chi-restraints excluded: chain Q residue 284 SER Chi-restraints excluded: chain Q residue 308 SER Chi-restraints excluded: chain R residue 84 HIS Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 188 LYS Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 293 SER Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 84 HIS Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 284 SER Chi-restraints excluded: chain T residue 291 MET Chi-restraints excluded: chain V residue 88 GLN Chi-restraints excluded: chain V residue 151 GLU Chi-restraints excluded: chain V residue 177 ASP Chi-restraints excluded: chain V residue 224 VAL Chi-restraints excluded: chain V residue 293 SER Chi-restraints excluded: chain W residue 52 MET Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain W residue 151 GLU Chi-restraints excluded: chain W residue 155 MET Chi-restraints excluded: chain W residue 188 LYS Chi-restraints excluded: chain W residue 224 VAL Chi-restraints excluded: chain W residue 284 SER Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain X residue 52 MET Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 183 VAL Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain X residue 293 SER Chi-restraints excluded: chain Y residue 35 ARG Chi-restraints excluded: chain Y residue 52 MET Chi-restraints excluded: chain Y residue 84 HIS Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Y residue 224 VAL Chi-restraints excluded: chain Y residue 284 SER Chi-restraints excluded: chain Y residue 326 LEU Chi-restraints excluded: chain Z residue 32 SER Chi-restraints excluded: chain Z residue 114 MET Chi-restraints excluded: chain Z residue 151 GLU Chi-restraints excluded: chain Z residue 224 VAL Chi-restraints excluded: chain Z residue 293 SER Chi-restraints excluded: chain AA residue 32 SER Chi-restraints excluded: chain AA residue 84 HIS Chi-restraints excluded: chain AA residue 186 ASP Chi-restraints excluded: chain AA residue 224 VAL Chi-restraints excluded: chain AA residue 293 SER Chi-restraints excluded: chain AA residue 326 LEU Chi-restraints excluded: chain BA residue 84 HIS Chi-restraints excluded: chain BA residue 177 ASP Chi-restraints excluded: chain BA residue 224 VAL Chi-restraints excluded: chain BA residue 326 LEU Chi-restraints excluded: chain CA residue 35 ARG Chi-restraints excluded: chain CA residue 67 GLN Chi-restraints excluded: chain CA residue 84 HIS Chi-restraints excluded: chain CA residue 88 GLN Chi-restraints excluded: chain CA residue 224 VAL Chi-restraints excluded: chain CA residue 284 SER Chi-restraints excluded: chain CA residue 326 LEU Chi-restraints excluded: chain DA residue 46 LEU Chi-restraints excluded: chain DA residue 84 HIS Chi-restraints excluded: chain DA residue 106 ASP Chi-restraints excluded: chain DA residue 177 ASP Chi-restraints excluded: chain DA residue 224 VAL Chi-restraints excluded: chain DA residue 284 SER Chi-restraints excluded: chain DA residue 289 VAL Chi-restraints excluded: chain DA residue 293 SER Chi-restraints excluded: chain EA residue 32 SER Chi-restraints excluded: chain EA residue 52 MET Chi-restraints excluded: chain EA residue 106 ASP Chi-restraints excluded: chain EA residue 132 THR Chi-restraints excluded: chain EA residue 177 ASP Chi-restraints excluded: chain FA residue 32 SER Chi-restraints excluded: chain FA residue 84 HIS Chi-restraints excluded: chain FA residue 177 ASP Chi-restraints excluded: chain FA residue 224 VAL Chi-restraints excluded: chain FA residue 293 SER Chi-restraints excluded: chain FA residue 326 LEU Chi-restraints excluded: chain GA residue 32 SER Chi-restraints excluded: chain GA residue 52 MET Chi-restraints excluded: chain GA residue 84 HIS Chi-restraints excluded: chain GA residue 155 MET Chi-restraints excluded: chain GA residue 177 ASP Chi-restraints excluded: chain GA residue 186 ASP Chi-restraints excluded: chain GA residue 224 VAL Chi-restraints excluded: chain GA residue 293 SER Chi-restraints excluded: chain HA residue 32 SER Chi-restraints excluded: chain HA residue 52 MET Chi-restraints excluded: chain HA residue 84 HIS Chi-restraints excluded: chain HA residue 106 ASP Chi-restraints excluded: chain HA residue 151 GLU Chi-restraints excluded: chain HA residue 155 MET Chi-restraints excluded: chain HA residue 177 ASP Chi-restraints excluded: chain HA residue 293 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 629 optimal weight: 40.0000 chunk 406 optimal weight: 8.9990 chunk 607 optimal weight: 4.9990 chunk 306 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 chunk 647 optimal weight: 2.9990 chunk 693 optimal weight: 3.9990 chunk 503 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 800 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 88 GLN B 37 ASN B 88 GLN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN D 84 HIS E 84 HIS E 213 GLN G 88 GLN I 84 HIS I 88 GLN J 84 HIS J 88 GLN J 309 GLN J 318 GLN K 84 HIS K 88 GLN L 84 HIS L 88 GLN ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 HIS M 88 GLN N 88 GLN ** N 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 ASN O 84 HIS ** O 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 HIS P 88 GLN Q 88 GLN R 37 ASN R 88 GLN S 88 GLN T 88 GLN T 309 GLN ** V 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 84 HIS W 88 GLN Y 318 GLN Z 318 GLN BA 84 HIS ** BA 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 318 GLN DA 309 GLN DA 318 GLN HA 318 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 80355 Z= 0.229 Angle : 0.489 9.334 108174 Z= 0.267 Chirality : 0.036 0.158 13035 Planarity : 0.002 0.033 14289 Dihedral : 4.526 24.514 11220 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.66 % Favored : 97.15 % Rotamer: Outliers : 3.20 % Allowed : 24.97 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.08), residues: 10560 helix: 2.68 (0.06), residues: 6600 sheet: -0.33 (0.19), residues: 726 loop : -1.17 (0.10), residues: 3234 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.023 0.001 HIS B 84 PHE 0.004 0.001 PHE C 145 TYR 0.015 0.001 TYRFA 173 ARG 0.005 0.000 ARG T 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21120 Ramachandran restraints generated. 10560 Oldfield, 0 Emsley, 10560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21120 Ramachandran restraints generated. 10560 Oldfield, 0 Emsley, 10560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 8844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 515 time to evaluate : 7.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8880 (ttm) cc_final: 0.8487 (ptm) REVERT: A 309 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8547 (mt0) REVERT: B 311 MET cc_start: 0.9099 (mmm) cc_final: 0.8869 (mmp) REVERT: C 109 GLU cc_start: 0.8181 (tp30) cc_final: 0.7914 (tp30) REVERT: D 84 HIS cc_start: 0.8980 (OUTLIER) cc_final: 0.8351 (m-70) REVERT: D 88 GLN cc_start: 0.9221 (OUTLIER) cc_final: 0.7936 (mp10) REVERT: D 90 MET cc_start: 0.9325 (OUTLIER) cc_final: 0.9111 (mtm) REVERT: D 109 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7813 (tp30) REVERT: D 177 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.7810 (m-30) REVERT: F 61 MET cc_start: 0.8963 (tpp) cc_final: 0.8745 (tpt) REVERT: F 133 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8320 (mtpp) REVERT: F 177 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8122 (m-30) REVERT: H 1 MET cc_start: 0.6742 (mmm) cc_final: 0.6417 (mmm) REVERT: H 188 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8474 (mmmm) REVERT: H 311 MET cc_start: 0.9127 (mmm) cc_final: 0.8898 (mmm) REVERT: H 320 GLN cc_start: 0.8463 (tt0) cc_final: 0.7972 (mt0) REVERT: I 320 GLN cc_start: 0.8486 (tt0) cc_final: 0.8116 (mt0) REVERT: J 1 MET cc_start: 0.7575 (mmm) cc_final: 0.7143 (mpm) REVERT: J 109 GLU cc_start: 0.8340 (tp30) cc_final: 0.7923 (tm-30) REVERT: K 1 MET cc_start: 0.7253 (mmm) cc_final: 0.6844 (mpm) REVERT: K 52 MET cc_start: 0.8954 (tpp) cc_final: 0.8652 (mmp) REVERT: K 67 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8099 (mt0) REVERT: K 90 MET cc_start: 0.9339 (OUTLIER) cc_final: 0.9117 (ttp) REVERT: K 291 MET cc_start: 0.9019 (mmt) cc_final: 0.8347 (mmm) REVERT: L 61 MET cc_start: 0.8551 (tpp) cc_final: 0.8122 (tpt) REVERT: L 144 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.8888 (p) REVERT: L 296 MET cc_start: 0.8589 (ptm) cc_final: 0.8142 (ttp) REVERT: M 1 MET cc_start: 0.7084 (mmp) cc_final: 0.5987 (pp-130) REVERT: M 100 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8160 (m-30) REVERT: M 183 VAL cc_start: 0.9202 (t) cc_final: 0.8909 (m) REVERT: M 189 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8331 (tp30) REVERT: M 220 LYS cc_start: 0.9057 (tttt) cc_final: 0.8766 (tptm) REVERT: N 1 MET cc_start: 0.6717 (mmp) cc_final: 0.5892 (pp-130) REVERT: N 291 MET cc_start: 0.9087 (mmt) cc_final: 0.8759 (mmp) REVERT: O 1 MET cc_start: 0.7061 (mmp) cc_final: 0.6100 (pp-130) REVERT: O 88 GLN cc_start: 0.9280 (OUTLIER) cc_final: 0.8524 (mp10) REVERT: P 27 MET cc_start: 0.9029 (ttp) cc_final: 0.8723 (tpp) REVERT: P 61 MET cc_start: 0.8605 (tpp) cc_final: 0.8201 (tpt) REVERT: Q 1 MET cc_start: 0.7309 (mmp) cc_final: 0.5336 (pp-130) REVERT: Q 35 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8689 (mtp85) REVERT: Q 61 MET cc_start: 0.8645 (tpt) cc_final: 0.8345 (tpt) REVERT: Q 100 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7929 (m-30) REVERT: R 1 MET cc_start: 0.6745 (mmp) cc_final: 0.5333 (pp-130) REVERT: R 162 MET cc_start: 0.9304 (mmp) cc_final: 0.9043 (mmp) REVERT: S 90 MET cc_start: 0.9263 (mtm) cc_final: 0.9029 (mtt) REVERT: S 291 MET cc_start: 0.8952 (mmt) cc_final: 0.8673 (mmp) REVERT: V 1 MET cc_start: 0.7051 (mmp) cc_final: 0.4114 (pp-130) REVERT: V 88 GLN cc_start: 0.9328 (OUTLIER) cc_final: 0.7918 (mp10) REVERT: W 1 MET cc_start: 0.6786 (mmp) cc_final: 0.3762 (pp-130) REVERT: W 109 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7921 (tp30) REVERT: W 151 GLU cc_start: 0.5251 (OUTLIER) cc_final: 0.4642 (mt-10) REVERT: X 291 MET cc_start: 0.9028 (mmt) cc_final: 0.8705 (mmm) REVERT: Y 35 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8660 (mtp85) REVERT: Y 61 MET cc_start: 0.8782 (tpt) cc_final: 0.8562 (mmm) REVERT: Y 155 MET cc_start: 0.8754 (ttp) cc_final: 0.8552 (ptm) REVERT: Z 1 MET cc_start: 0.7800 (mmp) cc_final: 0.7501 (mmm) REVERT: Z 291 MET cc_start: 0.8938 (mmt) cc_final: 0.8603 (mmm) REVERT: Z 295 MET cc_start: 0.8497 (tpt) cc_final: 0.8256 (tpt) REVERT: AA 1 MET cc_start: 0.7838 (mmm) cc_final: 0.7373 (mmm) REVERT: AA 296 MET cc_start: 0.8801 (ptm) cc_final: 0.8578 (ptm) REVERT: BA 151 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7537 (mt-10) REVERT: BA 295 MET cc_start: 0.8807 (tpt) cc_final: 0.8409 (tpt) REVERT: CA 35 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8684 (mtp85) REVERT: CA 67 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8314 (tp40) REVERT: CA 88 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.7852 (mp10) REVERT: CA 212 TYR cc_start: 0.8915 (t80) cc_final: 0.8620 (t80) REVERT: DA 46 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8458 (tp) REVERT: DA 177 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7862 (p0) REVERT: DA 193 VAL cc_start: 0.7520 (t) cc_final: 0.7302 (t) REVERT: GA 296 MET cc_start: 0.8669 (ptm) cc_final: 0.8417 (ptt) REVERT: HA 1 MET cc_start: 0.7455 (mmm) cc_final: 0.7043 (mmm) REVERT: HA 114 MET cc_start: 0.9342 (tpt) cc_final: 0.9119 (tpt) outliers start: 283 outliers final: 165 residues processed: 762 average time/residue: 1.4955 time to fit residues: 1531.7356 Evaluate side-chains 692 residues out of total 8844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 500 time to evaluate : 7.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain D residue 84 HIS Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain F residue 84 HIS Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 309 GLN Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 188 LYS Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 293 SER Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain K residue 67 GLN Chi-restraints excluded: chain K residue 90 MET Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 224 VAL Chi-restraints excluded: chain K residue 289 VAL Chi-restraints excluded: chain K residue 293 SER Chi-restraints excluded: chain L residue 100 ASP Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain M residue 189 GLU Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 284 SER Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 84 HIS Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 183 VAL Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain O residue 88 GLN Chi-restraints excluded: chain O residue 178 ASP Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 191 THR Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 308 SER Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 177 ASP Chi-restraints excluded: chain P residue 183 VAL Chi-restraints excluded: chain Q residue 32 SER Chi-restraints excluded: chain Q residue 35 ARG Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 84 HIS Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain Q residue 183 VAL Chi-restraints excluded: chain Q residue 186 ASP Chi-restraints excluded: chain Q residue 284 SER Chi-restraints excluded: chain R residue 84 HIS Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 188 LYS Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 284 SER Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 84 HIS Chi-restraints excluded: chain S residue 100 ASP Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 284 SER Chi-restraints excluded: chain T residue 291 MET Chi-restraints excluded: chain V residue 88 GLN Chi-restraints excluded: chain V residue 151 GLU Chi-restraints excluded: chain V residue 177 ASP Chi-restraints excluded: chain V residue 224 VAL Chi-restraints excluded: chain V residue 293 SER Chi-restraints excluded: chain W residue 52 MET Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain W residue 151 GLU Chi-restraints excluded: chain W residue 155 MET Chi-restraints excluded: chain W residue 177 ASP Chi-restraints excluded: chain W residue 188 LYS Chi-restraints excluded: chain W residue 224 VAL Chi-restraints excluded: chain X residue 52 MET Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 183 VAL Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain Y residue 35 ARG Chi-restraints excluded: chain Y residue 52 MET Chi-restraints excluded: chain Y residue 84 HIS Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Y residue 224 VAL Chi-restraints excluded: chain Y residue 284 SER Chi-restraints excluded: chain Z residue 32 SER Chi-restraints excluded: chain Z residue 151 GLU Chi-restraints excluded: chain Z residue 224 VAL Chi-restraints excluded: chain Z residue 293 SER Chi-restraints excluded: chain AA residue 32 SER Chi-restraints excluded: chain AA residue 84 HIS Chi-restraints excluded: chain AA residue 224 VAL Chi-restraints excluded: chain AA residue 284 SER Chi-restraints excluded: chain AA residue 293 SER Chi-restraints excluded: chain BA residue 32 SER Chi-restraints excluded: chain BA residue 84 HIS Chi-restraints excluded: chain BA residue 151 GLU Chi-restraints excluded: chain BA residue 224 VAL Chi-restraints excluded: chain CA residue 35 ARG Chi-restraints excluded: chain CA residue 67 GLN Chi-restraints excluded: chain CA residue 84 HIS Chi-restraints excluded: chain CA residue 88 GLN Chi-restraints excluded: chain CA residue 224 VAL Chi-restraints excluded: chain CA residue 284 SER Chi-restraints excluded: chain CA residue 326 LEU Chi-restraints excluded: chain DA residue 46 LEU Chi-restraints excluded: chain DA residue 84 HIS Chi-restraints excluded: chain DA residue 106 ASP Chi-restraints excluded: chain DA residue 177 ASP Chi-restraints excluded: chain DA residue 224 VAL Chi-restraints excluded: chain DA residue 289 VAL Chi-restraints excluded: chain DA residue 293 SER Chi-restraints excluded: chain EA residue 32 SER Chi-restraints excluded: chain EA residue 106 ASP Chi-restraints excluded: chain EA residue 132 THR Chi-restraints excluded: chain EA residue 177 ASP Chi-restraints excluded: chain FA residue 3 ILE Chi-restraints excluded: chain FA residue 32 SER Chi-restraints excluded: chain FA residue 84 HIS Chi-restraints excluded: chain FA residue 177 ASP Chi-restraints excluded: chain FA residue 224 VAL Chi-restraints excluded: chain FA residue 293 SER Chi-restraints excluded: chain FA residue 309 GLN Chi-restraints excluded: chain GA residue 32 SER Chi-restraints excluded: chain GA residue 52 MET Chi-restraints excluded: chain GA residue 84 HIS Chi-restraints excluded: chain GA residue 177 ASP Chi-restraints excluded: chain GA residue 186 ASP Chi-restraints excluded: chain GA residue 224 VAL Chi-restraints excluded: chain GA residue 293 SER Chi-restraints excluded: chain HA residue 32 SER Chi-restraints excluded: chain HA residue 52 MET Chi-restraints excluded: chain HA residue 84 HIS Chi-restraints excluded: chain HA residue 106 ASP Chi-restraints excluded: chain HA residue 151 GLU Chi-restraints excluded: chain HA residue 155 MET Chi-restraints excluded: chain HA residue 177 ASP Chi-restraints excluded: chain HA residue 293 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 925 optimal weight: 7.9990 chunk 975 optimal weight: 9.9990 chunk 889 optimal weight: 3.9990 chunk 948 optimal weight: 20.0000 chunk 974 optimal weight: 20.0000 chunk 570 optimal weight: 5.9990 chunk 413 optimal weight: 6.9990 chunk 744 optimal weight: 5.9990 chunk 291 optimal weight: 7.9990 chunk 857 optimal weight: 6.9990 chunk 897 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 88 GLN B 88 GLN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN D 84 HIS E 84 HIS G 88 GLN I 84 HIS I 88 GLN J 84 HIS J 88 GLN J 309 GLN J 318 GLN K 84 HIS K 88 GLN L 84 HIS L 88 GLN ** L 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 HIS M 88 GLN ** M 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 88 GLN O 84 HIS ** O 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 HIS P 88 GLN Q 88 GLN ** Q 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 88 GLN T 88 GLN T 309 GLN ** V 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 84 HIS W 88 GLN Y 318 GLN Z 318 GLN CA 318 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 80355 Z= 0.341 Angle : 0.547 9.470 108174 Z= 0.296 Chirality : 0.038 0.158 13035 Planarity : 0.003 0.032 14289 Dihedral : 4.638 24.311 11220 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.78 % Favored : 97.01 % Rotamer: Outliers : 3.18 % Allowed : 24.92 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.08), residues: 10560 helix: 2.49 (0.06), residues: 6600 sheet: -0.42 (0.19), residues: 726 loop : -1.17 (0.10), residues: 3234 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.002 HISBA 84 PHE 0.006 0.001 PHE Z 130 TYR 0.015 0.001 TYRFA 173 ARG 0.005 0.000 ARG T 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21120 Ramachandran restraints generated. 10560 Oldfield, 0 Emsley, 10560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21120 Ramachandran restraints generated. 10560 Oldfield, 0 Emsley, 10560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 8844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 515 time to evaluate : 7.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8849 (ttm) cc_final: 0.8610 (ttm) REVERT: B 311 MET cc_start: 0.9118 (mmm) cc_final: 0.8870 (mmp) REVERT: D 84 HIS cc_start: 0.9004 (OUTLIER) cc_final: 0.8376 (m-70) REVERT: D 88 GLN cc_start: 0.9221 (OUTLIER) cc_final: 0.7915 (mp10) REVERT: D 109 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7943 (tp30) REVERT: D 177 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.7800 (m-30) REVERT: F 61 MET cc_start: 0.9003 (tpp) cc_final: 0.8771 (tpt) REVERT: F 133 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8318 (mtpp) REVERT: F 177 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8191 (m-30) REVERT: H 1 MET cc_start: 0.6784 (mmm) cc_final: 0.6458 (mmm) REVERT: H 188 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8484 (mmmm) REVERT: H 311 MET cc_start: 0.9143 (mmm) cc_final: 0.8938 (mmm) REVERT: H 320 GLN cc_start: 0.8480 (tt0) cc_final: 0.8003 (mt0) REVERT: I 320 GLN cc_start: 0.8566 (tt0) cc_final: 0.8125 (mt0) REVERT: J 1 MET cc_start: 0.7622 (mmm) cc_final: 0.7099 (mpm) REVERT: J 109 GLU cc_start: 0.8326 (tp30) cc_final: 0.7858 (tm-30) REVERT: K 1 MET cc_start: 0.7268 (mmm) cc_final: 0.6854 (mpm) REVERT: K 52 MET cc_start: 0.8997 (tpp) cc_final: 0.8635 (mmp) REVERT: K 67 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8021 (mt0) REVERT: K 90 MET cc_start: 0.9353 (OUTLIER) cc_final: 0.9121 (ttp) REVERT: K 291 MET cc_start: 0.9030 (mmt) cc_final: 0.8347 (mmm) REVERT: L 61 MET cc_start: 0.8603 (tpp) cc_final: 0.8189 (tpt) REVERT: L 144 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8923 (p) REVERT: L 296 MET cc_start: 0.8638 (ptm) cc_final: 0.8189 (ttp) REVERT: M 1 MET cc_start: 0.7167 (mmp) cc_final: 0.6040 (pp-130) REVERT: M 61 MET cc_start: 0.8742 (tpt) cc_final: 0.8511 (tpt) REVERT: M 100 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8192 (m-30) REVERT: M 183 VAL cc_start: 0.9148 (t) cc_final: 0.8908 (m) REVERT: M 189 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8270 (tp30) REVERT: M 220 LYS cc_start: 0.9075 (tttt) cc_final: 0.8799 (tptm) REVERT: N 1 MET cc_start: 0.6935 (mmp) cc_final: 0.5910 (pp-130) REVERT: O 1 MET cc_start: 0.7137 (mmp) cc_final: 0.6080 (pp-130) REVERT: O 84 HIS cc_start: 0.9055 (OUTLIER) cc_final: 0.8820 (m-70) REVERT: O 88 GLN cc_start: 0.9326 (OUTLIER) cc_final: 0.8566 (mp10) REVERT: P 61 MET cc_start: 0.8655 (tpp) cc_final: 0.8254 (tpt) REVERT: Q 1 MET cc_start: 0.7435 (mmp) cc_final: 0.5367 (pp-130) REVERT: Q 35 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8804 (mtp85) REVERT: Q 61 MET cc_start: 0.8648 (tpt) cc_final: 0.8307 (tpt) REVERT: Q 100 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8117 (m-30) REVERT: R 1 MET cc_start: 0.6783 (mmp) cc_final: 0.5381 (pp-130) REVERT: R 162 MET cc_start: 0.9306 (mmp) cc_final: 0.9047 (mmp) REVERT: S 90 MET cc_start: 0.9311 (mtm) cc_final: 0.9103 (mtt) REVERT: S 291 MET cc_start: 0.8973 (mmt) cc_final: 0.8703 (mmp) REVERT: V 1 MET cc_start: 0.6984 (mmp) cc_final: 0.6769 (mmm) REVERT: V 88 GLN cc_start: 0.9346 (OUTLIER) cc_final: 0.7924 (mp10) REVERT: W 109 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7972 (tp30) REVERT: X 291 MET cc_start: 0.9038 (mmt) cc_final: 0.8724 (mmm) REVERT: Y 35 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8686 (mtp85) REVERT: Y 61 MET cc_start: 0.8858 (tpt) cc_final: 0.8518 (tpt) REVERT: Z 1 MET cc_start: 0.7865 (mmp) cc_final: 0.7588 (mmm) REVERT: Z 291 MET cc_start: 0.8949 (mmt) cc_final: 0.8625 (mmm) REVERT: AA 1 MET cc_start: 0.7819 (mmm) cc_final: 0.7358 (mmm) REVERT: AA 296 MET cc_start: 0.8804 (ptm) cc_final: 0.8568 (ptm) REVERT: BA 151 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: BA 177 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7567 (m-30) REVERT: BA 295 MET cc_start: 0.8811 (tpt) cc_final: 0.8394 (tpt) REVERT: CA 35 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8676 (mtp85) REVERT: CA 67 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8374 (tp40) REVERT: CA 88 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.7865 (mp10) REVERT: CA 212 TYR cc_start: 0.8987 (t80) cc_final: 0.8672 (t80) REVERT: DA 46 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8447 (tp) REVERT: DA 177 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7898 (p0) REVERT: DA 193 VAL cc_start: 0.7317 (t) cc_final: 0.7110 (t) REVERT: GA 296 MET cc_start: 0.8687 (ptm) cc_final: 0.8433 (ptt) REVERT: HA 1 MET cc_start: 0.7418 (mmm) cc_final: 0.7021 (mmm) REVERT: HA 114 MET cc_start: 0.9362 (tpt) cc_final: 0.9147 (tpt) REVERT: HA 326 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7956 (mp) outliers start: 281 outliers final: 178 residues processed: 763 average time/residue: 1.5235 time to fit residues: 1563.2763 Evaluate side-chains 707 residues out of total 8844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 502 time to evaluate : 7.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain D residue 84 HIS Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain F residue 84 HIS Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 309 GLN Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 188 LYS Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 293 SER Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain I residue 284 SER Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain K residue 67 GLN Chi-restraints excluded: chain K residue 90 MET Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 224 VAL Chi-restraints excluded: chain K residue 289 VAL Chi-restraints excluded: chain K residue 293 SER Chi-restraints excluded: chain L residue 100 ASP Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 144 THR Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain M residue 178 ASP Chi-restraints excluded: chain M residue 189 GLU Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 284 SER Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain N residue 32 SER Chi-restraints excluded: chain N residue 84 HIS Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 183 VAL Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain O residue 84 HIS Chi-restraints excluded: chain O residue 88 GLN Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 191 THR Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 289 VAL Chi-restraints excluded: chain O residue 308 SER Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 177 ASP Chi-restraints excluded: chain P residue 183 VAL Chi-restraints excluded: chain Q residue 32 SER Chi-restraints excluded: chain Q residue 35 ARG Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 84 HIS Chi-restraints excluded: chain Q residue 100 ASP Chi-restraints excluded: chain Q residue 183 VAL Chi-restraints excluded: chain Q residue 186 ASP Chi-restraints excluded: chain Q residue 284 SER Chi-restraints excluded: chain Q residue 308 SER Chi-restraints excluded: chain R residue 84 HIS Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 188 LYS Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 284 SER Chi-restraints excluded: chain R residue 293 SER Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 84 HIS Chi-restraints excluded: chain S residue 177 ASP Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 284 SER Chi-restraints excluded: chain T residue 291 MET Chi-restraints excluded: chain V residue 88 GLN Chi-restraints excluded: chain V residue 151 GLU Chi-restraints excluded: chain V residue 177 ASP Chi-restraints excluded: chain V residue 224 VAL Chi-restraints excluded: chain V residue 293 SER Chi-restraints excluded: chain W residue 52 MET Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain W residue 144 THR Chi-restraints excluded: chain W residue 155 MET Chi-restraints excluded: chain W residue 177 ASP Chi-restraints excluded: chain W residue 188 LYS Chi-restraints excluded: chain W residue 224 VAL Chi-restraints excluded: chain W residue 284 SER Chi-restraints excluded: chain W residue 326 LEU Chi-restraints excluded: chain X residue 52 MET Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 183 VAL Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain Y residue 35 ARG Chi-restraints excluded: chain Y residue 52 MET Chi-restraints excluded: chain Y residue 84 HIS Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Y residue 224 VAL Chi-restraints excluded: chain Z residue 32 SER Chi-restraints excluded: chain Z residue 114 MET Chi-restraints excluded: chain Z residue 151 GLU Chi-restraints excluded: chain Z residue 224 VAL Chi-restraints excluded: chain Z residue 289 VAL Chi-restraints excluded: chain Z residue 293 SER Chi-restraints excluded: chain AA residue 32 SER Chi-restraints excluded: chain AA residue 84 HIS Chi-restraints excluded: chain AA residue 186 ASP Chi-restraints excluded: chain AA residue 224 VAL Chi-restraints excluded: chain AA residue 284 SER Chi-restraints excluded: chain AA residue 293 SER Chi-restraints excluded: chain AA residue 326 LEU Chi-restraints excluded: chain BA residue 32 SER Chi-restraints excluded: chain BA residue 151 GLU Chi-restraints excluded: chain BA residue 177 ASP Chi-restraints excluded: chain BA residue 224 VAL Chi-restraints excluded: chain CA residue 35 ARG Chi-restraints excluded: chain CA residue 67 GLN Chi-restraints excluded: chain CA residue 84 HIS Chi-restraints excluded: chain CA residue 88 GLN Chi-restraints excluded: chain CA residue 114 MET Chi-restraints excluded: chain CA residue 224 VAL Chi-restraints excluded: chain CA residue 284 SER Chi-restraints excluded: chain CA residue 326 LEU Chi-restraints excluded: chain DA residue 46 LEU Chi-restraints excluded: chain DA residue 84 HIS Chi-restraints excluded: chain DA residue 106 ASP Chi-restraints excluded: chain DA residue 177 ASP Chi-restraints excluded: chain DA residue 224 VAL Chi-restraints excluded: chain DA residue 289 VAL Chi-restraints excluded: chain DA residue 293 SER Chi-restraints excluded: chain EA residue 32 SER Chi-restraints excluded: chain EA residue 106 ASP Chi-restraints excluded: chain EA residue 177 ASP Chi-restraints excluded: chain FA residue 3 ILE Chi-restraints excluded: chain FA residue 32 SER Chi-restraints excluded: chain FA residue 84 HIS Chi-restraints excluded: chain FA residue 177 ASP Chi-restraints excluded: chain FA residue 224 VAL Chi-restraints excluded: chain FA residue 293 SER Chi-restraints excluded: chain FA residue 309 GLN Chi-restraints excluded: chain GA residue 32 SER Chi-restraints excluded: chain GA residue 52 MET Chi-restraints excluded: chain GA residue 84 HIS Chi-restraints excluded: chain GA residue 155 MET Chi-restraints excluded: chain GA residue 186 ASP Chi-restraints excluded: chain GA residue 224 VAL Chi-restraints excluded: chain GA residue 293 SER Chi-restraints excluded: chain HA residue 3 ILE Chi-restraints excluded: chain HA residue 32 SER Chi-restraints excluded: chain HA residue 52 MET Chi-restraints excluded: chain HA residue 84 HIS Chi-restraints excluded: chain HA residue 106 ASP Chi-restraints excluded: chain HA residue 151 GLU Chi-restraints excluded: chain HA residue 155 MET Chi-restraints excluded: chain HA residue 177 ASP Chi-restraints excluded: chain HA residue 293 SER Chi-restraints excluded: chain HA residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 945 optimal weight: 20.0000 chunk 622 optimal weight: 1.9990 chunk 1002 optimal weight: 10.0000 chunk 612 optimal weight: 2.9990 chunk 475 optimal weight: 0.9980 chunk 697 optimal weight: 0.9990 chunk 1052 optimal weight: 9.9990 chunk 968 optimal weight: 2.9990 chunk 837 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 647 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN A 99 ASN B 88 GLN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS E 84 HIS G 88 GLN ** H 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 HIS I 88 GLN J 84 HIS J 88 GLN J 309 GLN J 318 GLN K 84 HIS K 88 GLN L 84 HIS L 88 GLN ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 HIS M 88 GLN ** N 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 84 HIS P 84 HIS P 88 GLN P 99 ASN Q 88 GLN R 84 HIS R 88 GLN T 88 GLN ** V 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 84 HIS W 88 GLN Z 318 GLN ** BA 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 318 GLN DA 309 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 80355 Z= 0.163 Angle : 0.474 9.716 108174 Z= 0.258 Chirality : 0.035 0.160 13035 Planarity : 0.002 0.032 14289 Dihedral : 4.441 25.698 11220 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.53 % Favored : 97.26 % Rotamer: Outliers : 2.17 % Allowed : 26.07 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.08), residues: 10560 helix: 2.90 (0.06), residues: 6600 sheet: -0.26 (0.18), residues: 726 loop : -1.06 (0.10), residues: 3234 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.001 HIS O 84 PHE 0.004 0.001 PHE C 145 TYR 0.015 0.001 TYRFA 173 ARG 0.004 0.000 ARG T 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21120 Ramachandran restraints generated. 10560 Oldfield, 0 Emsley, 10560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21120 Ramachandran restraints generated. 10560 Oldfield, 0 Emsley, 10560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 8844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 534 time to evaluate : 7.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8886 (ttm) cc_final: 0.8504 (ptm) REVERT: A 309 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8560 (mt0) REVERT: B 311 MET cc_start: 0.9081 (mmm) cc_final: 0.8857 (mmp) REVERT: C 109 GLU cc_start: 0.8271 (tp30) cc_final: 0.8069 (tp30) REVERT: C 311 MET cc_start: 0.9151 (mmm) cc_final: 0.8918 (mmm) REVERT: D 88 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.7905 (mp10) REVERT: D 90 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8990 (mtp) REVERT: D 177 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.7968 (m-30) REVERT: F 61 MET cc_start: 0.8937 (tpp) cc_final: 0.8724 (tpt) REVERT: H 1 MET cc_start: 0.6830 (mmm) cc_final: 0.6528 (mmm) REVERT: H 113 GLU cc_start: 0.8185 (tt0) cc_final: 0.7974 (tt0) REVERT: H 188 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8437 (mmmm) REVERT: H 320 GLN cc_start: 0.8381 (tt0) cc_final: 0.7901 (mt0) REVERT: I 320 GLN cc_start: 0.8473 (tt0) cc_final: 0.8109 (mt0) REVERT: J 1 MET cc_start: 0.7623 (mmm) cc_final: 0.7195 (mpm) REVERT: J 109 GLU cc_start: 0.8222 (tp30) cc_final: 0.7884 (tm-30) REVERT: K 1 MET cc_start: 0.7247 (mmm) cc_final: 0.6875 (mpm) REVERT: K 52 MET cc_start: 0.8920 (tpp) cc_final: 0.8636 (mmp) REVERT: K 67 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.8005 (mt0) REVERT: K 90 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.9087 (ttp) REVERT: K 291 MET cc_start: 0.8995 (mmt) cc_final: 0.8277 (mmm) REVERT: L 1 MET cc_start: 0.6380 (mmm) cc_final: 0.5248 (pp-130) REVERT: L 61 MET cc_start: 0.8505 (tpp) cc_final: 0.8048 (tpt) REVERT: L 109 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8084 (mm-30) REVERT: L 296 MET cc_start: 0.8579 (ptm) cc_final: 0.8133 (ttp) REVERT: M 1 MET cc_start: 0.7134 (mmp) cc_final: 0.5887 (pp-130) REVERT: M 61 MET cc_start: 0.8671 (tpt) cc_final: 0.8356 (tpt) REVERT: M 183 VAL cc_start: 0.9182 (t) cc_final: 0.8925 (m) REVERT: M 189 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8302 (tp30) REVERT: M 220 LYS cc_start: 0.9044 (tttt) cc_final: 0.8785 (tptm) REVERT: N 1 MET cc_start: 0.6923 (mmp) cc_final: 0.5957 (pp-130) REVERT: N 291 MET cc_start: 0.9076 (mmt) cc_final: 0.8735 (mmp) REVERT: O 1 MET cc_start: 0.7082 (mmp) cc_final: 0.6117 (pp-130) REVERT: O 184 THR cc_start: 0.7099 (t) cc_final: 0.6779 (t) REVERT: P 27 MET cc_start: 0.8989 (ttp) cc_final: 0.8724 (tpp) REVERT: P 61 MET cc_start: 0.8555 (tpp) cc_final: 0.8214 (tpt) REVERT: Q 1 MET cc_start: 0.7419 (mmp) cc_final: 0.5378 (pp-130) REVERT: Q 35 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8709 (mtp85) REVERT: Q 61 MET cc_start: 0.8642 (tpt) cc_final: 0.8415 (tpt) REVERT: Q 184 THR cc_start: 0.7449 (t) cc_final: 0.7105 (t) REVERT: R 1 MET cc_start: 0.6793 (mmp) cc_final: 0.5332 (pp-130) REVERT: R 61 MET cc_start: 0.8556 (tpp) cc_final: 0.8268 (mmm) REVERT: R 162 MET cc_start: 0.9258 (mmp) cc_final: 0.8981 (mmp) REVERT: R 320 GLN cc_start: 0.8856 (tt0) cc_final: 0.8456 (mt0) REVERT: S 90 MET cc_start: 0.9222 (mtm) cc_final: 0.8995 (mtt) REVERT: T 311 MET cc_start: 0.9105 (mmm) cc_final: 0.8832 (mmm) REVERT: V 88 GLN cc_start: 0.9313 (OUTLIER) cc_final: 0.7930 (mp10) REVERT: V 151 GLU cc_start: 0.5248 (OUTLIER) cc_final: 0.5021 (mt-10) REVERT: W 1 MET cc_start: 0.6766 (mmp) cc_final: 0.4023 (pp-130) REVERT: W 109 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7888 (tp30) REVERT: W 296 MET cc_start: 0.8385 (ptm) cc_final: 0.8113 (ptp) REVERT: X 291 MET cc_start: 0.9004 (mmt) cc_final: 0.8675 (mmm) REVERT: Y 35 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8598 (mtp85) REVERT: Z 291 MET cc_start: 0.8916 (mmt) cc_final: 0.8581 (mmm) REVERT: AA 1 MET cc_start: 0.7839 (mmm) cc_final: 0.7375 (mmm) REVERT: AA 296 MET cc_start: 0.8772 (ptm) cc_final: 0.8549 (ptm) REVERT: BA 295 MET cc_start: 0.8820 (tpt) cc_final: 0.8301 (tpt) REVERT: CA 67 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8238 (tp40) REVERT: CA 88 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.7807 (mp10) REVERT: CA 212 TYR cc_start: 0.8897 (t80) cc_final: 0.8607 (t80) REVERT: DA 46 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8455 (tp) REVERT: DA 177 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7960 (p0) REVERT: DA 193 VAL cc_start: 0.7257 (t) cc_final: 0.7048 (t) REVERT: FA 296 MET cc_start: 0.8676 (ptm) cc_final: 0.8444 (ptt) REVERT: GA 296 MET cc_start: 0.8634 (ptm) cc_final: 0.8394 (ptt) REVERT: HA 1 MET cc_start: 0.7372 (mmm) cc_final: 0.6948 (mmm) REVERT: HA 295 MET cc_start: 0.8651 (tpt) cc_final: 0.8029 (tpt) outliers start: 192 outliers final: 114 residues processed: 706 average time/residue: 1.5480 time to fit residues: 1458.7136 Evaluate side-chains 644 residues out of total 8844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 512 time to evaluate : 6.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 84 HIS Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain D residue 84 HIS Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain F residue 84 HIS Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 188 LYS Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 224 VAL Chi-restraints excluded: chain K residue 67 GLN Chi-restraints excluded: chain K residue 90 MET Chi-restraints excluded: chain K residue 224 VAL Chi-restraints excluded: chain K residue 289 VAL Chi-restraints excluded: chain L residue 100 ASP Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 189 GLU Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 284 SER Chi-restraints excluded: chain M residue 308 SER Chi-restraints excluded: chain N residue 84 HIS Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 183 VAL Chi-restraints excluded: chain N residue 224 VAL Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 177 ASP Chi-restraints excluded: chain P residue 183 VAL Chi-restraints excluded: chain Q residue 32 SER Chi-restraints excluded: chain Q residue 35 ARG Chi-restraints excluded: chain Q residue 84 HIS Chi-restraints excluded: chain Q residue 183 VAL Chi-restraints excluded: chain R residue 84 HIS Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 188 LYS Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 84 HIS Chi-restraints excluded: chain S residue 100 ASP Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 291 MET Chi-restraints excluded: chain V residue 88 GLN Chi-restraints excluded: chain V residue 151 GLU Chi-restraints excluded: chain V residue 224 VAL Chi-restraints excluded: chain V residue 293 SER Chi-restraints excluded: chain W residue 52 MET Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 125 SER Chi-restraints excluded: chain W residue 224 VAL Chi-restraints excluded: chain W residue 284 SER Chi-restraints excluded: chain X residue 52 MET Chi-restraints excluded: chain X residue 132 THR Chi-restraints excluded: chain X residue 183 VAL Chi-restraints excluded: chain X residue 224 VAL Chi-restraints excluded: chain Y residue 35 ARG Chi-restraints excluded: chain Y residue 84 HIS Chi-restraints excluded: chain Y residue 224 VAL Chi-restraints excluded: chain Z residue 32 SER Chi-restraints excluded: chain Z residue 114 MET Chi-restraints excluded: chain Z residue 151 GLU Chi-restraints excluded: chain Z residue 224 VAL Chi-restraints excluded: chain AA residue 84 HIS Chi-restraints excluded: chain AA residue 224 VAL Chi-restraints excluded: chain AA residue 284 SER Chi-restraints excluded: chain AA residue 320 GLN Chi-restraints excluded: chain BA residue 32 SER Chi-restraints excluded: chain BA residue 224 VAL Chi-restraints excluded: chain CA residue 67 GLN Chi-restraints excluded: chain CA residue 84 HIS Chi-restraints excluded: chain CA residue 88 GLN Chi-restraints excluded: chain CA residue 224 VAL Chi-restraints excluded: chain CA residue 284 SER Chi-restraints excluded: chain CA residue 326 LEU Chi-restraints excluded: chain DA residue 32 SER Chi-restraints excluded: chain DA residue 46 LEU Chi-restraints excluded: chain DA residue 84 HIS Chi-restraints excluded: chain DA residue 106 ASP Chi-restraints excluded: chain DA residue 177 ASP Chi-restraints excluded: chain DA residue 224 VAL Chi-restraints excluded: chain DA residue 289 VAL Chi-restraints excluded: chain EA residue 177 ASP Chi-restraints excluded: chain FA residue 84 HIS Chi-restraints excluded: chain FA residue 309 GLN Chi-restraints excluded: chain GA residue 52 MET Chi-restraints excluded: chain GA residue 84 HIS Chi-restraints excluded: chain GA residue 186 ASP Chi-restraints excluded: chain GA residue 224 VAL Chi-restraints excluded: chain HA residue 52 MET Chi-restraints excluded: chain HA residue 84 HIS Chi-restraints excluded: chain HA residue 151 GLU Chi-restraints excluded: chain HA residue 177 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 513 optimal weight: 10.0000 chunk 665 optimal weight: 3.9990 chunk 892 optimal weight: 9.9990 chunk 256 optimal weight: 20.0000 chunk 772 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 232 optimal weight: 0.9980 chunk 839 optimal weight: 3.9990 chunk 351 optimal weight: 10.0000 chunk 861 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 88 GLN A 99 ASN A 318 GLN B 88 GLN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN D 84 HIS E 84 HIS G 88 GLN I 84 HIS I 88 GLN J 84 HIS J 88 GLN J 318 GLN K 84 HIS K 88 GLN L 84 HIS L 88 GLN ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 HIS M 88 GLN N 88 GLN ** N 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 84 HIS ** O 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 HIS P 88 GLN Q 88 GLN R 88 GLN ** V 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 84 HIS Z 318 GLN CA 318 GLN ** HA 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.085026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.069262 restraints weight = 172539.887| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.85 r_work: 0.3206 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 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 : 0.005 0.042 80355 Z= 0.303 Angle : 0.535 10.023 108174 Z= 0.288 Chirality : 0.038 0.160 13035 Planarity : 0.003 0.031 14289 Dihedral : 4.531 23.731 11220 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.59 % Favored : 97.21 % Rotamer: Outliers : 2.50 % Allowed : 25.75 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.08), residues: 10560 helix: 2.70 (0.06), residues: 6600 sheet: -0.31 (0.18), residues: 726 loop : -1.09 (0.10), residues: 3234 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.002 HIS R 84 PHE 0.006 0.001 PHE K 130 TYR 0.015 0.001 TYRFA 173 ARG 0.006 0.000 ARG H 264 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24439.61 seconds wall clock time: 430 minutes 41.22 seconds (25841.22 seconds total)