Starting phenix.real_space_refine on Tue Apr 16 09:19:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xky_22229/04_2024/6xky_22229.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xky_22229/04_2024/6xky_22229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xky_22229/04_2024/6xky_22229.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xky_22229/04_2024/6xky_22229.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xky_22229/04_2024/6xky_22229.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xky_22229/04_2024/6xky_22229.pdb" } resolution = 3.2 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= 0.005 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 100 5.16 5 C 23780 2.51 5 N 6700 2.21 5 O 8180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 95": "OE1" <-> "OE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 95": "OE1" <-> "OE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 95": "OE1" <-> "OE2" Residue "E PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 95": "OE1" <-> "OE2" Residue "F PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 95": "OE1" <-> "OE2" Residue "G PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 95": "OE1" <-> "OE2" Residue "H PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 95": "OE1" <-> "OE2" Residue "I PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 95": "OE1" <-> "OE2" Residue "J PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 95": "OE1" <-> "OE2" Residue "K PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 95": "OE1" <-> "OE2" Residue "L PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 95": "OE1" <-> "OE2" Residue "M PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 95": "OE1" <-> "OE2" Residue "N PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 95": "OE1" <-> "OE2" Residue "O PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 95": "OE1" <-> "OE2" Residue "P PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 95": "OE1" <-> "OE2" Residue "Q PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 95": "OE1" <-> "OE2" Residue "R PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 95": "OE1" <-> "OE2" Residue "S PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 95": "OE1" <-> "OE2" Residue "T PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 38760 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "B" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "C" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "D" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "E" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "F" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "G" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "H" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "I" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "J" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "K" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "L" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "M" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "N" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "O" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "P" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "Q" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "R" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "S" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "T" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Time building chain proxies: 19.45, per 1000 atoms: 0.50 Number of scatterers: 38760 At special positions: 0 Unit cell: (136.59, 138.33, 248.82, 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 100 16.00 O 8180 8.00 N 6700 7.00 C 23780 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.92 Conformation dependent library (CDL) restraints added in 7.4 seconds 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10040 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 20 sheets defined 73.8% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 9 through 36 removed outlier: 3.958A pdb=" N MET A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR A 58 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 59 " --> pdb=" O GLN A 55 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP A 67 " --> pdb=" O ASN A 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 130 removed outlier: 3.650A pdb=" N ASN A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 263 removed outlier: 3.741A pdb=" N ALA A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 272 removed outlier: 3.682A pdb=" N ILE A 268 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 269 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 270 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 36 removed outlier: 3.959A pdb=" N MET B 13 " --> pdb=" O ASN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR B 58 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP B 67 " --> pdb=" O ASN B 63 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 130 removed outlier: 3.649A pdb=" N ASN B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 234 removed outlier: 3.745A pdb=" N THR B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 263 removed outlier: 3.740A pdb=" N ALA B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 272 removed outlier: 3.683A pdb=" N ILE B 268 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU B 269 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 270 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 36 removed outlier: 3.959A pdb=" N MET C 13 " --> pdb=" O ASN C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR C 58 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA C 59 " --> pdb=" O GLN C 55 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP C 67 " --> pdb=" O ASN C 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 130 removed outlier: 3.650A pdb=" N ASN C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 130 " --> pdb=" O LYS C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 234 removed outlier: 3.743A pdb=" N THR C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 263 removed outlier: 3.740A pdb=" N ALA C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN C 263 " --> pdb=" O SER C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 272 removed outlier: 3.683A pdb=" N ILE C 268 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU C 269 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER C 270 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 36 removed outlier: 3.957A pdb=" N MET D 13 " --> pdb=" O ASN D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 101 removed outlier: 3.746A pdb=" N THR D 58 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA D 59 " --> pdb=" O GLN D 55 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 130 removed outlier: 3.650A pdb=" N ASN D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER D 130 " --> pdb=" O LYS D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 263 removed outlier: 3.741A pdb=" N ALA D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 272 removed outlier: 3.685A pdb=" N ILE D 268 " --> pdb=" O SER D 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU D 269 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER D 270 " --> pdb=" O SER D 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 36 removed outlier: 3.958A pdb=" N MET E 13 " --> pdb=" O ASN E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 101 removed outlier: 3.746A pdb=" N THR E 58 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA E 59 " --> pdb=" O GLN E 55 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP E 67 " --> pdb=" O ASN E 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 130 removed outlier: 3.650A pdb=" N ASN E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER E 130 " --> pdb=" O LYS E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR E 185 " --> pdb=" O ALA E 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY E 188 " --> pdb=" O LYS E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 263 removed outlier: 3.740A pdb=" N ALA E 242 " --> pdb=" O ALA E 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN E 263 " --> pdb=" O SER E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 272 removed outlier: 3.683A pdb=" N ILE E 268 " --> pdb=" O SER E 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU E 269 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER E 270 " --> pdb=" O SER E 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 36 removed outlier: 3.959A pdb=" N MET F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR F 58 " --> pdb=" O ASN F 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA F 59 " --> pdb=" O GLN F 55 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP F 67 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 130 removed outlier: 3.650A pdb=" N ASN F 111 " --> pdb=" O THR F 107 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR F 185 " --> pdb=" O ALA F 181 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY F 188 " --> pdb=" O LYS F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 263 removed outlier: 3.740A pdb=" N ALA F 242 " --> pdb=" O ALA F 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN F 263 " --> pdb=" O SER F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 272 removed outlier: 3.682A pdb=" N ILE F 268 " --> pdb=" O SER F 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU F 269 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER F 270 " --> pdb=" O SER F 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 36 removed outlier: 3.957A pdb=" N MET G 13 " --> pdb=" O ASN G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR G 58 " --> pdb=" O ASN G 54 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA G 59 " --> pdb=" O GLN G 55 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP G 67 " --> pdb=" O ASN G 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 130 removed outlier: 3.651A pdb=" N ASN G 111 " --> pdb=" O THR G 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER G 130 " --> pdb=" O LYS G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 234 removed outlier: 3.743A pdb=" N THR G 185 " --> pdb=" O ALA G 181 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY G 188 " --> pdb=" O LYS G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 263 removed outlier: 3.741A pdb=" N ALA G 242 " --> pdb=" O ALA G 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN G 263 " --> pdb=" O SER G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 272 removed outlier: 3.683A pdb=" N ILE G 268 " --> pdb=" O SER G 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU G 269 " --> pdb=" O SER G 266 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER G 270 " --> pdb=" O SER G 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 36 removed outlier: 3.958A pdb=" N MET H 13 " --> pdb=" O ASN H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA H 59 " --> pdb=" O GLN H 55 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 130 removed outlier: 3.651A pdb=" N ASN H 111 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER H 130 " --> pdb=" O LYS H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 234 removed outlier: 3.745A pdb=" N THR H 185 " --> pdb=" O ALA H 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY H 188 " --> pdb=" O LYS H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 263 removed outlier: 3.741A pdb=" N ALA H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN H 263 " --> pdb=" O SER H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 272 removed outlier: 3.684A pdb=" N ILE H 268 " --> pdb=" O SER H 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU H 269 " --> pdb=" O SER H 266 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER H 270 " --> pdb=" O SER H 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 36 removed outlier: 3.959A pdb=" N MET I 13 " --> pdb=" O ASN I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR I 58 " --> pdb=" O ASN I 54 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA I 59 " --> pdb=" O GLN I 55 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP I 67 " --> pdb=" O ASN I 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER I 68 " --> pdb=" O ALA I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 130 removed outlier: 3.650A pdb=" N ASN I 111 " --> pdb=" O THR I 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER I 130 " --> pdb=" O LYS I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR I 185 " --> pdb=" O ALA I 181 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY I 188 " --> pdb=" O LYS I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 263 removed outlier: 3.740A pdb=" N ALA I 242 " --> pdb=" O ALA I 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN I 263 " --> pdb=" O SER I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 272 removed outlier: 3.685A pdb=" N ILE I 268 " --> pdb=" O SER I 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU I 269 " --> pdb=" O SER I 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER I 270 " --> pdb=" O SER I 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 36 removed outlier: 3.959A pdb=" N MET J 13 " --> pdb=" O ASN J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 101 removed outlier: 3.744A pdb=" N THR J 58 " --> pdb=" O ASN J 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA J 59 " --> pdb=" O GLN J 55 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP J 67 " --> pdb=" O ASN J 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 130 removed outlier: 3.651A pdb=" N ASN J 111 " --> pdb=" O THR J 107 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER J 130 " --> pdb=" O LYS J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR J 185 " --> pdb=" O ALA J 181 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY J 188 " --> pdb=" O LYS J 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 263 removed outlier: 3.740A pdb=" N ALA J 242 " --> pdb=" O ALA J 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN J 263 " --> pdb=" O SER J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 272 removed outlier: 3.683A pdb=" N ILE J 268 " --> pdb=" O SER J 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU J 269 " --> pdb=" O SER J 266 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER J 270 " --> pdb=" O SER J 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 36 removed outlier: 3.957A pdb=" N MET K 13 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR K 58 " --> pdb=" O ASN K 54 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA K 59 " --> pdb=" O GLN K 55 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP K 67 " --> pdb=" O ASN K 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER K 68 " --> pdb=" O ALA K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 130 removed outlier: 3.650A pdb=" N ASN K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER K 130 " --> pdb=" O LYS K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 234 removed outlier: 3.745A pdb=" N THR K 185 " --> pdb=" O ALA K 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY K 188 " --> pdb=" O LYS K 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 263 removed outlier: 3.742A pdb=" N ALA K 242 " --> pdb=" O ALA K 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN K 263 " --> pdb=" O SER K 259 " (cutoff:3.500A) Processing helix chain 'K' and resid 265 through 272 removed outlier: 3.683A pdb=" N ILE K 268 " --> pdb=" O SER K 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU K 269 " --> pdb=" O SER K 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER K 270 " --> pdb=" O SER K 267 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 36 removed outlier: 3.958A pdb=" N MET L 13 " --> pdb=" O ASN L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 101 removed outlier: 3.746A pdb=" N THR L 58 " --> pdb=" O ASN L 54 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA L 59 " --> pdb=" O GLN L 55 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP L 67 " --> pdb=" O ASN L 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 130 removed outlier: 3.651A pdb=" N ASN L 111 " --> pdb=" O THR L 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER L 130 " --> pdb=" O LYS L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR L 185 " --> pdb=" O ALA L 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 263 removed outlier: 3.742A pdb=" N ALA L 242 " --> pdb=" O ALA L 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN L 263 " --> pdb=" O SER L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 265 through 272 removed outlier: 3.684A pdb=" N ILE L 268 " --> pdb=" O SER L 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU L 269 " --> pdb=" O SER L 266 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER L 270 " --> pdb=" O SER L 267 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 36 removed outlier: 3.959A pdb=" N MET M 13 " --> pdb=" O ASN M 9 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR M 58 " --> pdb=" O ASN M 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA M 59 " --> pdb=" O GLN M 55 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP M 67 " --> pdb=" O ASN M 63 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER M 68 " --> pdb=" O ALA M 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 130 removed outlier: 3.651A pdb=" N ASN M 111 " --> pdb=" O THR M 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER M 130 " --> pdb=" O LYS M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR M 185 " --> pdb=" O ALA M 181 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY M 188 " --> pdb=" O LYS M 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 236 through 263 removed outlier: 3.740A pdb=" N ALA M 242 " --> pdb=" O ALA M 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN M 263 " --> pdb=" O SER M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 265 through 272 removed outlier: 3.682A pdb=" N ILE M 268 " --> pdb=" O SER M 265 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU M 269 " --> pdb=" O SER M 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER M 270 " --> pdb=" O SER M 267 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 36 removed outlier: 3.959A pdb=" N MET N 13 " --> pdb=" O ASN N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR N 58 " --> pdb=" O ASN N 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA N 59 " --> pdb=" O GLN N 55 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP N 67 " --> pdb=" O ASN N 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER N 68 " --> pdb=" O ALA N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 130 removed outlier: 3.649A pdb=" N ASN N 111 " --> pdb=" O THR N 107 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER N 130 " --> pdb=" O LYS N 126 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR N 185 " --> pdb=" O ALA N 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY N 188 " --> pdb=" O LYS N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 236 through 263 removed outlier: 3.741A pdb=" N ALA N 242 " --> pdb=" O ALA N 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN N 263 " --> pdb=" O SER N 259 " (cutoff:3.500A) Processing helix chain 'N' and resid 265 through 272 removed outlier: 3.682A pdb=" N ILE N 268 " --> pdb=" O SER N 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU N 269 " --> pdb=" O SER N 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER N 270 " --> pdb=" O SER N 267 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 36 removed outlier: 3.958A pdb=" N MET O 13 " --> pdb=" O ASN O 9 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR O 58 " --> pdb=" O ASN O 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA O 59 " --> pdb=" O GLN O 55 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP O 67 " --> pdb=" O ASN O 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER O 68 " --> pdb=" O ALA O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 130 removed outlier: 3.652A pdb=" N ASN O 111 " --> pdb=" O THR O 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER O 130 " --> pdb=" O LYS O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 181 through 234 removed outlier: 3.743A pdb=" N THR O 185 " --> pdb=" O ALA O 181 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY O 188 " --> pdb=" O LYS O 184 " (cutoff:3.500A) Processing helix chain 'O' and resid 236 through 263 removed outlier: 3.741A pdb=" N ALA O 242 " --> pdb=" O ALA O 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN O 263 " --> pdb=" O SER O 259 " (cutoff:3.500A) Processing helix chain 'O' and resid 265 through 272 removed outlier: 3.682A pdb=" N ILE O 268 " --> pdb=" O SER O 265 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU O 269 " --> pdb=" O SER O 266 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER O 270 " --> pdb=" O SER O 267 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 36 removed outlier: 3.958A pdb=" N MET P 13 " --> pdb=" O ASN P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR P 58 " --> pdb=" O ASN P 54 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA P 59 " --> pdb=" O GLN P 55 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP P 67 " --> pdb=" O ASN P 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER P 68 " --> pdb=" O ALA P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 130 removed outlier: 3.649A pdb=" N ASN P 111 " --> pdb=" O THR P 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER P 130 " --> pdb=" O LYS P 126 " (cutoff:3.500A) Processing helix chain 'P' and resid 181 through 234 removed outlier: 3.745A pdb=" N THR P 185 " --> pdb=" O ALA P 181 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY P 188 " --> pdb=" O LYS P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 263 removed outlier: 3.741A pdb=" N ALA P 242 " --> pdb=" O ALA P 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN P 263 " --> pdb=" O SER P 259 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 272 removed outlier: 3.684A pdb=" N ILE P 268 " --> pdb=" O SER P 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU P 269 " --> pdb=" O SER P 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER P 270 " --> pdb=" O SER P 267 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 36 removed outlier: 3.958A pdb=" N MET Q 13 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 101 removed outlier: 3.744A pdb=" N THR Q 58 " --> pdb=" O ASN Q 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA Q 59 " --> pdb=" O GLN Q 55 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP Q 67 " --> pdb=" O ASN Q 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER Q 68 " --> pdb=" O ALA Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 130 removed outlier: 3.651A pdb=" N ASN Q 111 " --> pdb=" O THR Q 107 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER Q 130 " --> pdb=" O LYS Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR Q 185 " --> pdb=" O ALA Q 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY Q 188 " --> pdb=" O LYS Q 184 " (cutoff:3.500A) Processing helix chain 'Q' and resid 236 through 263 removed outlier: 3.740A pdb=" N ALA Q 242 " --> pdb=" O ALA Q 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN Q 263 " --> pdb=" O SER Q 259 " (cutoff:3.500A) Processing helix chain 'Q' and resid 265 through 272 removed outlier: 3.683A pdb=" N ILE Q 268 " --> pdb=" O SER Q 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU Q 269 " --> pdb=" O SER Q 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER Q 270 " --> pdb=" O SER Q 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 36 removed outlier: 3.959A pdb=" N MET R 13 " --> pdb=" O ASN R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR R 58 " --> pdb=" O ASN R 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA R 59 " --> pdb=" O GLN R 55 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP R 67 " --> pdb=" O ASN R 63 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER R 68 " --> pdb=" O ALA R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 130 removed outlier: 3.650A pdb=" N ASN R 111 " --> pdb=" O THR R 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER R 130 " --> pdb=" O LYS R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR R 185 " --> pdb=" O ALA R 181 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY R 188 " --> pdb=" O LYS R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 263 removed outlier: 3.740A pdb=" N ALA R 242 " --> pdb=" O ALA R 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN R 263 " --> pdb=" O SER R 259 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 272 removed outlier: 3.683A pdb=" N ILE R 268 " --> pdb=" O SER R 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU R 269 " --> pdb=" O SER R 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER R 270 " --> pdb=" O SER R 267 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 36 removed outlier: 3.958A pdb=" N MET S 13 " --> pdb=" O ASN S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 101 removed outlier: 3.744A pdb=" N THR S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA S 59 " --> pdb=" O GLN S 55 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP S 67 " --> pdb=" O ASN S 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER S 68 " --> pdb=" O ALA S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 130 removed outlier: 3.650A pdb=" N ASN S 111 " --> pdb=" O THR S 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER S 130 " --> pdb=" O LYS S 126 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR S 185 " --> pdb=" O ALA S 181 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY S 188 " --> pdb=" O LYS S 184 " (cutoff:3.500A) Processing helix chain 'S' and resid 236 through 263 removed outlier: 3.741A pdb=" N ALA S 242 " --> pdb=" O ALA S 238 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN S 263 " --> pdb=" O SER S 259 " (cutoff:3.500A) Processing helix chain 'S' and resid 265 through 272 removed outlier: 3.683A pdb=" N ILE S 268 " --> pdb=" O SER S 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU S 269 " --> pdb=" O SER S 266 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER S 270 " --> pdb=" O SER S 267 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 36 removed outlier: 3.958A pdb=" N MET T 13 " --> pdb=" O ASN T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR T 58 " --> pdb=" O ASN T 54 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA T 59 " --> pdb=" O GLN T 55 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP T 67 " --> pdb=" O ASN T 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER T 68 " --> pdb=" O ALA T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 130 removed outlier: 3.650A pdb=" N ASN T 111 " --> pdb=" O THR T 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER T 130 " --> pdb=" O LYS T 126 " (cutoff:3.500A) Processing helix chain 'T' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR T 185 " --> pdb=" O ALA T 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY T 188 " --> pdb=" O LYS T 184 " (cutoff:3.500A) Processing helix chain 'T' and resid 236 through 263 removed outlier: 3.740A pdb=" N ALA T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN T 263 " --> pdb=" O SER T 259 " (cutoff:3.500A) Processing helix chain 'T' and resid 265 through 272 removed outlier: 3.684A pdb=" N ILE T 268 " --> pdb=" O SER T 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU T 269 " --> pdb=" O SER T 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER T 270 " --> pdb=" O SER T 267 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 145 through 149 Processing sheet with id=AA2, first strand: chain 'B' and resid 145 through 149 Processing sheet with id=AA3, first strand: chain 'C' and resid 145 through 149 Processing sheet with id=AA4, first strand: chain 'D' and resid 145 through 149 Processing sheet with id=AA5, first strand: chain 'E' and resid 145 through 149 Processing sheet with id=AA6, first strand: chain 'F' and resid 145 through 149 Processing sheet with id=AA7, first strand: chain 'G' and resid 145 through 149 Processing sheet with id=AA8, first strand: chain 'H' and resid 145 through 149 Processing sheet with id=AA9, first strand: chain 'I' and resid 145 through 149 Processing sheet with id=AB1, first strand: chain 'J' and resid 145 through 149 Processing sheet with id=AB2, first strand: chain 'K' and resid 145 through 149 Processing sheet with id=AB3, first strand: chain 'L' and resid 145 through 149 Processing sheet with id=AB4, first strand: chain 'M' and resid 145 through 149 Processing sheet with id=AB5, first strand: chain 'N' and resid 145 through 149 Processing sheet with id=AB6, first strand: chain 'O' and resid 145 through 149 Processing sheet with id=AB7, first strand: chain 'P' and resid 145 through 149 Processing sheet with id=AB8, first strand: chain 'Q' and resid 145 through 149 Processing sheet with id=AB9, first strand: chain 'R' and resid 145 through 149 Processing sheet with id=AC1, first strand: chain 'S' and resid 145 through 149 Processing sheet with id=AC2, first strand: chain 'T' and resid 145 through 149 3340 hydrogen bonds defined for protein. 9900 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: 11.79 Time building geometry restraints manager: 17.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9398 1.33 - 1.45: 6425 1.45 - 1.57: 22957 1.57 - 1.69: 0 1.69 - 1.80: 180 Bond restraints: 38960 Sorted by residual: bond pdb=" CA SER H 101 " pdb=" C SER H 101 " ideal model delta sigma weight residual 1.523 1.495 0.027 1.41e-02 5.03e+03 3.78e+00 bond pdb=" CA SER B 101 " pdb=" C SER B 101 " ideal model delta sigma weight residual 1.523 1.495 0.027 1.41e-02 5.03e+03 3.73e+00 bond pdb=" CA SER N 101 " pdb=" C SER N 101 " ideal model delta sigma weight residual 1.523 1.495 0.027 1.41e-02 5.03e+03 3.71e+00 bond pdb=" CA SER P 101 " pdb=" C SER P 101 " ideal model delta sigma weight residual 1.523 1.496 0.027 1.41e-02 5.03e+03 3.69e+00 bond pdb=" CA SER Q 101 " pdb=" C SER Q 101 " ideal model delta sigma weight residual 1.523 1.496 0.027 1.41e-02 5.03e+03 3.66e+00 ... (remaining 38955 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.49: 124 106.49 - 113.39: 23997 113.39 - 120.29: 13830 120.29 - 127.19: 14709 127.19 - 134.09: 60 Bond angle restraints: 52720 Sorted by residual: angle pdb=" C LEU R 232 " pdb=" N VAL R 233 " pdb=" CA VAL R 233 " ideal model delta sigma weight residual 122.69 118.21 4.48 1.49e+00 4.50e-01 9.04e+00 angle pdb=" C THR K 172 " pdb=" N THR K 173 " pdb=" CA THR K 173 " ideal model delta sigma weight residual 121.31 125.78 -4.47 1.49e+00 4.50e-01 9.02e+00 angle pdb=" C LEU J 232 " pdb=" N VAL J 233 " pdb=" CA VAL J 233 " ideal model delta sigma weight residual 122.69 118.23 4.46 1.49e+00 4.50e-01 8.97e+00 angle pdb=" C THR T 172 " pdb=" N THR T 173 " pdb=" CA THR T 173 " ideal model delta sigma weight residual 121.31 125.77 -4.46 1.49e+00 4.50e-01 8.97e+00 angle pdb=" C LEU O 232 " pdb=" N VAL O 233 " pdb=" CA VAL O 233 " ideal model delta sigma weight residual 122.69 118.23 4.46 1.49e+00 4.50e-01 8.94e+00 ... (remaining 52715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.75: 21902 12.75 - 25.50: 1404 25.50 - 38.25: 294 38.25 - 51.00: 100 51.00 - 63.75: 60 Dihedral angle restraints: 23760 sinusoidal: 8320 harmonic: 15440 Sorted by residual: dihedral pdb=" CA LEU H 232 " pdb=" C LEU H 232 " pdb=" N VAL H 233 " pdb=" CA VAL H 233 " ideal model delta harmonic sigma weight residual -180.00 -163.29 -16.71 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA LEU L 232 " pdb=" C LEU L 232 " pdb=" N VAL L 233 " pdb=" CA VAL L 233 " ideal model delta harmonic sigma weight residual -180.00 -163.29 -16.71 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA LEU O 232 " pdb=" C LEU O 232 " pdb=" N VAL O 233 " pdb=" CA VAL O 233 " ideal model delta harmonic sigma weight residual -180.00 -163.29 -16.71 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 23757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 4003 0.027 - 0.053: 1918 0.053 - 0.080: 596 0.080 - 0.107: 243 0.107 - 0.133: 20 Chirality restraints: 6780 Sorted by residual: chirality pdb=" CA VAL N 159 " pdb=" N VAL N 159 " pdb=" C VAL N 159 " pdb=" CB VAL N 159 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA VAL A 159 " pdb=" N VAL A 159 " pdb=" C VAL A 159 " pdb=" CB VAL A 159 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA VAL J 159 " pdb=" N VAL J 159 " pdb=" C VAL J 159 " pdb=" CB VAL J 159 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 6777 not shown) Planarity restraints: 6740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR J 196 " 0.004 2.00e-02 2.50e+03 8.03e-03 6.45e-01 pdb=" C THR J 196 " -0.014 2.00e-02 2.50e+03 pdb=" O THR J 196 " 0.005 2.00e-02 2.50e+03 pdb=" N ALA J 197 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 196 " 0.004 2.00e-02 2.50e+03 7.87e-03 6.19e-01 pdb=" C THR R 196 " -0.014 2.00e-02 2.50e+03 pdb=" O THR R 196 " 0.005 2.00e-02 2.50e+03 pdb=" N ALA R 197 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR S 196 " -0.004 2.00e-02 2.50e+03 7.84e-03 6.14e-01 pdb=" C THR S 196 " 0.014 2.00e-02 2.50e+03 pdb=" O THR S 196 " -0.005 2.00e-02 2.50e+03 pdb=" N ALA S 197 " -0.005 2.00e-02 2.50e+03 ... (remaining 6737 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 9 2.25 - 2.91: 16607 2.91 - 3.58: 57126 3.58 - 4.24: 82288 4.24 - 4.90: 147466 Nonbonded interactions: 303496 Sorted by model distance: nonbonded pdb=" OD2 ASP K 234 " pdb=" OG SER N 5 " model vdw 1.588 2.440 nonbonded pdb=" OD2 ASP P 234 " pdb=" OG SER Q 5 " model vdw 1.647 2.440 nonbonded pdb=" OD2 ASP D 234 " pdb=" OG SER E 5 " model vdw 1.649 2.440 nonbonded pdb=" OD2 ASP L 234 " pdb=" OG SER M 5 " model vdw 1.650 2.440 nonbonded pdb=" OD2 ASP H 234 " pdb=" OG SER J 5 " model vdw 1.669 2.440 ... (remaining 303491 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 9.370 Check model and map are aligned: 0.560 Set scattering table: 0.420 Process input model: 94.220 Find NCS groups from input model: 2.940 Set up NCS constraints: 0.420 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: 0.020 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 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 : 0.006 0.030 38960 Z= 0.371 Angle : 0.546 5.184 52720 Z= 0.342 Chirality : 0.035 0.133 6780 Planarity : 0.002 0.008 6740 Dihedral : 10.036 63.748 13720 Min Nonbonded Distance : 1.588 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.48 % Allowed : 4.29 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.11), residues: 5380 helix: 3.04 (0.08), residues: 3980 sheet: -0.00 (0.35), residues: 200 loop : -2.67 (0.14), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 49 HIS 0.001 0.000 HIS O 214 PHE 0.007 0.001 PHE G 117 ARG 0.004 0.001 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 942 time to evaluate : 4.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.8086 (m-40) cc_final: 0.7857 (m-40) REVERT: A 132 LYS cc_start: 0.8416 (mtmm) cc_final: 0.8140 (mttt) REVERT: A 171 LEU cc_start: 0.8016 (mt) cc_final: 0.7770 (tp) REVERT: B 25 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7671 (mt-10) REVERT: B 134 ASN cc_start: 0.8575 (t0) cc_final: 0.8317 (t0) REVERT: B 226 ASP cc_start: 0.7646 (m-30) cc_final: 0.7333 (m-30) REVERT: C 125 GLU cc_start: 0.7886 (tp30) cc_final: 0.7573 (mm-30) REVERT: D 123 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7274 (mt0) REVERT: D 140 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.7022 (m-30) REVERT: E 30 GLN cc_start: 0.8201 (mt0) cc_final: 0.7786 (mt0) REVERT: E 34 ASN cc_start: 0.7415 (m-40) cc_final: 0.7129 (m-40) REVERT: E 63 ASN cc_start: 0.8213 (t0) cc_final: 0.8000 (t0) REVERT: E 123 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7736 (mt0) REVERT: F 213 THR cc_start: 0.8912 (m) cc_final: 0.8695 (p) REVERT: G 27 THR cc_start: 0.8814 (m) cc_final: 0.8478 (p) REVERT: G 31 GLN cc_start: 0.7749 (tp40) cc_final: 0.7539 (tt0) REVERT: H 236 ASP cc_start: 0.8223 (t0) cc_final: 0.8016 (t0) REVERT: I 119 SER cc_start: 0.8387 (t) cc_final: 0.8000 (m) REVERT: I 174 THR cc_start: 0.7594 (p) cc_final: 0.7361 (p) REVERT: J 41 SER cc_start: 0.8725 (t) cc_final: 0.8470 (m) REVERT: J 239 LYS cc_start: 0.7958 (ttpt) cc_final: 0.7602 (mmtt) REVERT: M 31 GLN cc_start: 0.8034 (tp40) cc_final: 0.7762 (tm-30) REVERT: M 32 ARG cc_start: 0.8481 (mtt90) cc_final: 0.8185 (mtt180) REVERT: M 119 SER cc_start: 0.8770 (t) cc_final: 0.8409 (p) REVERT: N 27 THR cc_start: 0.8673 (m) cc_final: 0.8399 (p) REVERT: N 151 ASN cc_start: 0.7918 (t0) cc_final: 0.7592 (t0) REVERT: O 116 ASP cc_start: 0.7431 (m-30) cc_final: 0.7112 (m-30) REVERT: R 151 ASN cc_start: 0.8055 (t0) cc_final: 0.7539 (t0) REVERT: S 77 ASP cc_start: 0.7229 (m-30) cc_final: 0.6935 (m-30) REVERT: S 132 LYS cc_start: 0.8052 (mtmm) cc_final: 0.7779 (ptpp) REVERT: S 179 THR cc_start: 0.9089 (p) cc_final: 0.8864 (t) REVERT: S 223 ASP cc_start: 0.7640 (m-30) cc_final: 0.7343 (m-30) outliers start: 20 outliers final: 13 residues processed: 945 average time/residue: 0.4723 time to fit residues: 745.7157 Evaluate side-chains 621 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 607 time to evaluate : 4.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain K residue 140 ASP Chi-restraints excluded: chain M residue 140 ASP Chi-restraints excluded: chain O residue 140 ASP Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain S residue 140 ASP Chi-restraints excluded: chain T residue 140 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 455 optimal weight: 2.9990 chunk 409 optimal weight: 7.9990 chunk 227 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 276 optimal weight: 1.9990 chunk 218 optimal weight: 9.9990 chunk 423 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 257 optimal weight: 0.6980 chunk 315 optimal weight: 0.6980 chunk 490 optimal weight: 8.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 123 GLN A 195 GLN A 222 GLN A 248 GLN B 195 GLN C 123 GLN C 222 GLN C 231 ASN C 252 GLN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN D 151 ASN D 222 GLN E 151 ASN E 222 GLN F 30 GLN F 111 ASN F 151 ASN F 222 GLN G 30 GLN G 222 GLN H 31 GLN H 55 GLN H 222 GLN H 248 GLN H 252 GLN I 151 ASN J 222 GLN K 31 GLN K 222 GLN L 30 GLN L 34 ASN L 55 GLN L 123 GLN L 252 GLN M 222 GLN M 256 GLN M 262 ASN N 222 GLN O 73 GLN O 106 ASN O 222 GLN O 256 GLN P 31 GLN P 34 ASN P 73 GLN P 222 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Q 222 GLN ** R 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 222 GLN ** S 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 123 GLN S 151 ASN S 252 GLN ** T 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 151 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 38960 Z= 0.182 Angle : 0.408 5.440 52720 Z= 0.241 Chirality : 0.031 0.180 6780 Planarity : 0.002 0.024 6740 Dihedral : 3.558 17.674 5488 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.71 % Allowed : 9.10 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.67 (0.12), residues: 5380 helix: 3.80 (0.08), residues: 3880 sheet: 0.15 (0.35), residues: 200 loop : -1.88 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 49 HIS 0.003 0.001 HIS P 214 PHE 0.011 0.001 PHE B 117 ARG 0.003 0.000 ARG E 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 665 time to evaluate : 4.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7625 (mt-10) REVERT: B 103 CYS cc_start: 0.7534 (m) cc_final: 0.7331 (m) REVERT: C 123 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7800 (mt0) REVERT: C 125 GLU cc_start: 0.7728 (tp30) cc_final: 0.7409 (mm-30) REVERT: D 123 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7618 (mt0) REVERT: D 250 LYS cc_start: 0.8873 (tttm) cc_final: 0.8587 (ttpt) REVERT: E 134 ASN cc_start: 0.8661 (t0) cc_final: 0.8416 (t0) REVERT: E 151 ASN cc_start: 0.7650 (t0) cc_final: 0.7197 (t0) REVERT: G 26 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8833 (tt) REVERT: G 134 ASN cc_start: 0.8462 (t0) cc_final: 0.8175 (t160) REVERT: H 31 GLN cc_start: 0.8297 (tp40) cc_final: 0.7944 (tp-100) REVERT: H 123 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7475 (mt0) REVERT: I 119 SER cc_start: 0.8440 (t) cc_final: 0.8104 (m) REVERT: J 26 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8481 (tt) REVERT: J 41 SER cc_start: 0.8847 (t) cc_final: 0.8626 (m) REVERT: J 151 ASN cc_start: 0.7909 (t0) cc_final: 0.7688 (t0) REVERT: M 31 GLN cc_start: 0.7969 (tp40) cc_final: 0.7760 (tm-30) REVERT: M 134 ASN cc_start: 0.8703 (t0) cc_final: 0.8232 (t0) REVERT: M 153 ASP cc_start: 0.6146 (m-30) cc_final: 0.5885 (m-30) REVERT: N 27 THR cc_start: 0.8549 (m) cc_final: 0.8274 (p) REVERT: P 41 SER cc_start: 0.8610 (m) cc_final: 0.8393 (p) REVERT: Q 26 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8724 (tt) REVERT: R 151 ASN cc_start: 0.8093 (t0) cc_final: 0.7827 (t0) REVERT: S 123 GLN cc_start: 0.8250 (mt0) cc_final: 0.8022 (mt0) REVERT: S 179 THR cc_start: 0.9135 (p) cc_final: 0.8891 (t) REVERT: T 151 ASN cc_start: 0.7318 (t0) cc_final: 0.7086 (t0) outliers start: 72 outliers final: 41 residues processed: 703 average time/residue: 0.4461 time to fit residues: 544.5889 Evaluate side-chains 600 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 555 time to evaluate : 4.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 267 SER Chi-restraints excluded: chain K residue 140 ASP Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 140 ASP Chi-restraints excluded: chain M residue 266 SER Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain O residue 140 ASP Chi-restraints excluded: chain P residue 106 ASN Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 245 GLN Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 176 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 272 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 408 optimal weight: 10.0000 chunk 333 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 491 optimal weight: 3.9990 chunk 530 optimal weight: 0.2980 chunk 437 optimal weight: 3.9990 chunk 487 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 394 optimal weight: 1.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 222 GLN B 134 ASN C 123 GLN C 151 ASN C 222 GLN C 231 ASN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 ASN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN F 222 GLN G 30 GLN ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 151 ASN H 252 GLN I 30 GLN I 151 ASN K 31 GLN N 34 ASN N 106 ASN N 151 ASN O 73 GLN P 17 GLN P 34 ASN P 55 GLN P 73 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN R 34 ASN ** R 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 151 ASN ** S 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 151 ASN S 222 GLN T 31 GLN ** T 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 38960 Z= 0.194 Angle : 0.399 5.105 52720 Z= 0.238 Chirality : 0.031 0.181 6780 Planarity : 0.002 0.019 6740 Dihedral : 3.469 17.078 5472 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.55 % Allowed : 10.26 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.12), residues: 5380 helix: 3.81 (0.08), residues: 3880 sheet: 0.18 (0.35), residues: 200 loop : -1.80 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 49 HIS 0.003 0.001 HIS P 214 PHE 0.009 0.001 PHE B 117 ARG 0.003 0.000 ARG E 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 587 time to evaluate : 4.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 125 GLU cc_start: 0.7959 (tp30) cc_final: 0.7680 (mm-30) REVERT: D 123 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7798 (mt0) REVERT: E 95 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7279 (tt0) REVERT: F 26 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8703 (tt) REVERT: G 26 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8853 (tt) REVERT: H 38 LYS cc_start: 0.8193 (mttp) cc_final: 0.7879 (mtpt) REVERT: H 123 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7694 (mt0) REVERT: I 119 SER cc_start: 0.8417 (t) cc_final: 0.8090 (m) REVERT: J 26 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8476 (tt) REVERT: J 41 SER cc_start: 0.8852 (t) cc_final: 0.8652 (m) REVERT: J 151 ASN cc_start: 0.8035 (t0) cc_final: 0.7707 (t0) REVERT: M 123 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7798 (mm-40) REVERT: M 134 ASN cc_start: 0.8772 (t0) cc_final: 0.8297 (t0) REVERT: M 140 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7141 (t0) REVERT: N 27 THR cc_start: 0.8502 (m) cc_final: 0.8149 (p) REVERT: N 62 MET cc_start: 0.8054 (mtt) cc_final: 0.7625 (mtt) REVERT: Q 26 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8759 (tt) REVERT: R 31 GLN cc_start: 0.7746 (tp40) cc_final: 0.7408 (tp40) REVERT: R 151 ASN cc_start: 0.8054 (t0) cc_final: 0.7816 (t0) REVERT: S 179 THR cc_start: 0.9151 (p) cc_final: 0.8924 (t) outliers start: 107 outliers final: 65 residues processed: 661 average time/residue: 0.4348 time to fit residues: 501.1524 Evaluate side-chains 617 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 547 time to evaluate : 4.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 267 SER Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 103 CYS Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 267 SER Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 140 ASP Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain O residue 44 ASP Chi-restraints excluded: chain O residue 140 ASP Chi-restraints excluded: chain P residue 106 ASN Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 103 CYS Chi-restraints excluded: chain Q residue 245 GLN Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 41 SER Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain T residue 103 CYS Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain T residue 176 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 485 optimal weight: 0.6980 chunk 369 optimal weight: 2.9990 chunk 254 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 234 optimal weight: 0.7980 chunk 329 optimal weight: 3.9990 chunk 493 optimal weight: 4.9990 chunk 521 optimal weight: 1.9990 chunk 257 optimal weight: 0.0270 chunk 467 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 123 GLN A 252 GLN C 151 ASN C 231 ASN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 ASN F 222 GLN G 30 GLN G 134 ASN H 252 GLN I 30 GLN I 151 ASN K 31 GLN N 106 ASN N 151 ASN O 73 GLN P 73 GLN P 248 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Q 252 GLN R 34 ASN ** R 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 151 ASN ** T 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 38960 Z= 0.153 Angle : 0.369 6.441 52720 Z= 0.221 Chirality : 0.030 0.177 6780 Planarity : 0.002 0.014 6740 Dihedral : 3.328 16.723 5466 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.50 % Allowed : 11.19 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.01 (0.12), residues: 5380 helix: 4.03 (0.08), residues: 3880 sheet: 0.25 (0.34), residues: 200 loop : -1.68 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP T 49 HIS 0.002 0.001 HIS P 214 PHE 0.009 0.001 PHE J 117 ARG 0.002 0.000 ARG N 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 599 time to evaluate : 4.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7270 (mp) REVERT: B 62 MET cc_start: 0.7714 (mtt) cc_final: 0.7489 (mtt) REVERT: B 95 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7251 (tm-30) REVERT: B 253 LEU cc_start: 0.9066 (tp) cc_final: 0.8848 (tp) REVERT: C 123 GLN cc_start: 0.8181 (mt0) cc_final: 0.7916 (mt0) REVERT: C 125 GLU cc_start: 0.7819 (tp30) cc_final: 0.7457 (mm-30) REVERT: D 107 THR cc_start: 0.7433 (OUTLIER) cc_final: 0.7229 (p) REVERT: D 123 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7759 (mt0) REVERT: D 151 ASN cc_start: 0.8423 (t0) cc_final: 0.8202 (t0) REVERT: E 62 MET cc_start: 0.8111 (mtp) cc_final: 0.7795 (mtt) REVERT: E 95 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7103 (tt0) REVERT: E 134 ASN cc_start: 0.8704 (t0) cc_final: 0.8383 (t0) REVERT: F 26 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8772 (tt) REVERT: F 30 GLN cc_start: 0.7891 (mt0) cc_final: 0.7564 (mt0) REVERT: G 26 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8895 (tt) REVERT: H 26 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8695 (tt) REVERT: H 31 GLN cc_start: 0.8121 (tp40) cc_final: 0.7822 (tt0) REVERT: H 38 LYS cc_start: 0.8233 (mttp) cc_final: 0.7920 (mtpt) REVERT: H 123 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7015 (tp-100) REVERT: I 119 SER cc_start: 0.8426 (t) cc_final: 0.8014 (m) REVERT: J 26 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8522 (tt) REVERT: J 151 ASN cc_start: 0.7857 (t0) cc_final: 0.7598 (t0) REVERT: M 123 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7772 (mm-40) REVERT: M 134 ASN cc_start: 0.8765 (t0) cc_final: 0.8295 (t0) REVERT: M 140 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.7149 (t0) REVERT: M 263 GLN cc_start: 0.7546 (pt0) cc_final: 0.7099 (mm-40) REVERT: N 24 SER cc_start: 0.8679 (m) cc_final: 0.8471 (t) REVERT: N 27 THR cc_start: 0.8395 (m) cc_final: 0.7966 (p) REVERT: N 62 MET cc_start: 0.7978 (mtt) cc_final: 0.7583 (mtt) REVERT: Q 26 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8718 (tt) REVERT: R 26 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8890 (tt) REVERT: R 151 ASN cc_start: 0.7881 (t0) cc_final: 0.7651 (t0) REVERT: S 179 THR cc_start: 0.9153 (p) cc_final: 0.8912 (t) outliers start: 105 outliers final: 68 residues processed: 670 average time/residue: 0.4378 time to fit residues: 510.0023 Evaluate side-chains 623 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 545 time to evaluate : 4.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 267 SER Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 103 CYS Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 268 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 123 GLN Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 267 SER Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 140 ASP Chi-restraints excluded: chain M residue 246 SER Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 44 ASP Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 140 ASP Chi-restraints excluded: chain P residue 106 ASN Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 245 GLN Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 103 CYS Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain T residue 103 CYS Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain T residue 176 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 434 optimal weight: 4.9990 chunk 296 optimal weight: 0.0980 chunk 7 optimal weight: 10.0000 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 0.0060 chunk 445 optimal weight: 9.9990 chunk 360 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 266 optimal weight: 5.9990 chunk 468 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 overall best weight: 2.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN B 134 ASN B 195 GLN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 GLN F 151 ASN F 222 GLN G 30 GLN G 222 GLN H 252 GLN I 73 GLN I 123 GLN I 151 ASN I 222 GLN J 222 GLN M 30 GLN N 151 ASN N 222 GLN ** P 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 73 GLN P 106 ASN P 123 GLN P 222 GLN P 245 GLN ** P 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 123 GLN Q 134 ASN Q 151 ASN R 34 ASN ** R 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 151 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 38960 Z= 0.236 Angle : 0.424 5.744 52720 Z= 0.249 Chirality : 0.032 0.176 6780 Planarity : 0.002 0.021 6740 Dihedral : 3.532 19.071 5466 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.81 % Allowed : 11.62 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.12), residues: 5380 helix: 3.78 (0.08), residues: 3880 sheet: 0.17 (0.34), residues: 200 loop : -1.69 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 49 HIS 0.003 0.001 HIS P 214 PHE 0.011 0.001 PHE P 177 ARG 0.003 0.000 ARG E 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 544 time to evaluate : 4.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7270 (mp) REVERT: B 125 GLU cc_start: 0.8001 (tp30) cc_final: 0.7645 (tp30) REVERT: B 226 ASP cc_start: 0.7700 (m-30) cc_final: 0.7380 (m-30) REVERT: C 123 GLN cc_start: 0.8153 (mt0) cc_final: 0.7827 (mt0) REVERT: D 123 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7917 (mt0) REVERT: D 151 ASN cc_start: 0.8350 (t0) cc_final: 0.8137 (t0) REVERT: E 107 THR cc_start: 0.7696 (OUTLIER) cc_final: 0.7469 (p) REVERT: F 30 GLN cc_start: 0.8026 (mt0) cc_final: 0.7637 (mt0) REVERT: F 213 THR cc_start: 0.8937 (m) cc_final: 0.8733 (p) REVERT: G 26 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8857 (tt) REVERT: H 31 GLN cc_start: 0.8117 (tp40) cc_final: 0.7843 (tt0) REVERT: H 38 LYS cc_start: 0.8233 (mttp) cc_final: 0.7908 (mtpt) REVERT: I 119 SER cc_start: 0.8432 (t) cc_final: 0.8018 (m) REVERT: J 26 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8484 (tt) REVERT: M 123 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7839 (mm-40) REVERT: M 134 ASN cc_start: 0.8833 (t0) cc_final: 0.8370 (t0) REVERT: M 140 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7053 (t0) REVERT: M 245 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7433 (mm110) REVERT: N 24 SER cc_start: 0.8709 (m) cc_final: 0.8473 (t) REVERT: N 27 THR cc_start: 0.8453 (m) cc_final: 0.8011 (p) REVERT: N 62 MET cc_start: 0.8144 (mtt) cc_final: 0.7712 (mtt) REVERT: O 252 GLN cc_start: 0.7840 (mt0) cc_final: 0.7399 (mt0) REVERT: Q 26 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8755 (tt) REVERT: R 151 ASN cc_start: 0.7868 (t0) cc_final: 0.7613 (t0) REVERT: S 179 THR cc_start: 0.9139 (p) cc_final: 0.8920 (t) outliers start: 118 outliers final: 89 residues processed: 626 average time/residue: 0.4224 time to fit residues: 463.0563 Evaluate side-chains 617 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 522 time to evaluate : 4.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 103 CYS Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 268 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 123 GLN Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 267 SER Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 140 ASP Chi-restraints excluded: chain M residue 246 SER Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 44 ASP Chi-restraints excluded: chain O residue 140 ASP Chi-restraints excluded: chain P residue 106 ASN Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 151 ASN Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 103 CYS Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain Q residue 245 GLN Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 140 ASP Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 233 VAL Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 103 CYS Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 255 VAL Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 103 CYS Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain T residue 176 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 175 optimal weight: 5.9990 chunk 470 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 306 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 522 optimal weight: 4.9990 chunk 433 optimal weight: 3.9990 chunk 241 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 274 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 231 ASN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN G 30 GLN H 252 GLN I 151 ASN K 7 ASN L 30 GLN O 34 ASN ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 134 ASN Q 151 ASN Q 252 GLN R 34 ASN ** R 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 151 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 38960 Z= 0.255 Angle : 0.433 5.887 52720 Z= 0.254 Chirality : 0.033 0.177 6780 Planarity : 0.002 0.023 6740 Dihedral : 3.620 18.779 5466 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.31 % Allowed : 11.48 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.55 (0.12), residues: 5380 helix: 3.62 (0.08), residues: 3900 sheet: 0.12 (0.34), residues: 200 loop : -1.70 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 49 HIS 0.003 0.001 HIS P 214 PHE 0.012 0.002 PHE P 177 ARG 0.003 0.000 ARG E 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 534 time to evaluate : 4.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7221 (mp) REVERT: B 125 GLU cc_start: 0.8056 (tp30) cc_final: 0.7713 (tp30) REVERT: B 226 ASP cc_start: 0.7739 (m-30) cc_final: 0.7425 (m-30) REVERT: C 123 GLN cc_start: 0.8171 (mt0) cc_final: 0.7839 (mt0) REVERT: D 123 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7911 (mt0) REVERT: D 151 ASN cc_start: 0.8402 (t0) cc_final: 0.8196 (t0) REVERT: G 16 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8348 (tt) REVERT: G 26 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8860 (tt) REVERT: H 31 GLN cc_start: 0.8119 (tp40) cc_final: 0.7826 (tt0) REVERT: H 38 LYS cc_start: 0.8281 (mttp) cc_final: 0.7939 (mtpt) REVERT: I 119 SER cc_start: 0.8437 (t) cc_final: 0.8024 (m) REVERT: J 26 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8476 (tt) REVERT: J 151 ASN cc_start: 0.7907 (t0) cc_final: 0.7629 (t0) REVERT: M 123 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7852 (mm-40) REVERT: M 134 ASN cc_start: 0.8852 (t0) cc_final: 0.8381 (t0) REVERT: M 245 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7496 (mm110) REVERT: M 263 GLN cc_start: 0.7574 (pt0) cc_final: 0.7155 (mm-40) REVERT: N 24 SER cc_start: 0.8717 (m) cc_final: 0.8493 (t) REVERT: N 27 THR cc_start: 0.8458 (m) cc_final: 0.8038 (p) REVERT: N 62 MET cc_start: 0.8157 (mtt) cc_final: 0.7719 (mtt) REVERT: O 252 GLN cc_start: 0.7836 (mt0) cc_final: 0.7390 (mt0) REVERT: Q 26 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8752 (tt) REVERT: R 151 ASN cc_start: 0.7922 (t0) cc_final: 0.7654 (t0) REVERT: S 123 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8362 (mt0) REVERT: S 179 THR cc_start: 0.9146 (p) cc_final: 0.8931 (t) outliers start: 139 outliers final: 105 residues processed: 635 average time/residue: 0.4207 time to fit residues: 476.1025 Evaluate side-chains 625 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 514 time to evaluate : 4.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 103 CYS Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 268 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 123 GLN Chi-restraints excluded: chain J residue 267 SER Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain M residue 140 ASP Chi-restraints excluded: chain M residue 246 SER Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 44 ASP Chi-restraints excluded: chain O residue 140 ASP Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 151 ASN Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 103 CYS Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain Q residue 245 GLN Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 138 ILE Chi-restraints excluded: chain R residue 140 ASP Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 233 VAL Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 41 SER Chi-restraints excluded: chain S residue 103 CYS Chi-restraints excluded: chain S residue 123 GLN Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 255 VAL Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 103 CYS Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 129 THR Chi-restraints excluded: chain T residue 140 ASP Chi-restraints excluded: chain T residue 176 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 503 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 297 optimal weight: 60.0000 chunk 381 optimal weight: 4.9990 chunk 295 optimal weight: 5.9990 chunk 439 optimal weight: 3.9990 chunk 291 optimal weight: 5.9990 chunk 520 optimal weight: 3.9990 chunk 325 optimal weight: 5.9990 chunk 317 optimal weight: 6.9990 chunk 240 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN C 231 ASN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 GLN I 151 ASN K 7 ASN L 30 GLN N 106 ASN ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN R 34 ASN ** R 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 222 GLN S 151 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 38960 Z= 0.346 Angle : 0.493 6.761 52720 Z= 0.284 Chirality : 0.035 0.179 6780 Planarity : 0.002 0.034 6740 Dihedral : 3.842 21.223 5466 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.12 % Allowed : 12.21 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.12), residues: 5380 helix: 3.35 (0.08), residues: 3900 sheet: 0.02 (0.34), residues: 200 loop : -1.79 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 49 HIS 0.004 0.001 HIS P 214 PHE 0.014 0.002 PHE P 177 ARG 0.004 0.001 ARG E 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 510 time to evaluate : 4.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7220 (mp) REVERT: B 125 GLU cc_start: 0.8062 (tp30) cc_final: 0.7769 (tp30) REVERT: B 226 ASP cc_start: 0.7801 (m-30) cc_final: 0.7502 (m-30) REVERT: D 123 GLN cc_start: 0.8360 (mm-40) cc_final: 0.7953 (mt0) REVERT: G 16 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8440 (tt) REVERT: G 26 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8846 (tt) REVERT: G 31 GLN cc_start: 0.7546 (tt0) cc_final: 0.7091 (pt0) REVERT: H 31 GLN cc_start: 0.8143 (tp40) cc_final: 0.7891 (tt0) REVERT: H 38 LYS cc_start: 0.8295 (mttp) cc_final: 0.7939 (mtpt) REVERT: I 119 SER cc_start: 0.8435 (t) cc_final: 0.8068 (m) REVERT: J 26 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8451 (tt) REVERT: J 151 ASN cc_start: 0.7817 (t0) cc_final: 0.7590 (t0) REVERT: M 134 ASN cc_start: 0.8896 (t0) cc_final: 0.8470 (t0) REVERT: N 24 SER cc_start: 0.8752 (m) cc_final: 0.8489 (t) REVERT: N 27 THR cc_start: 0.8552 (m) cc_final: 0.8121 (p) REVERT: N 62 MET cc_start: 0.8294 (mtt) cc_final: 0.7857 (mtt) REVERT: O 252 GLN cc_start: 0.7903 (mt0) cc_final: 0.7466 (mt0) REVERT: Q 26 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8732 (tt) REVERT: R 86 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8769 (mt) REVERT: R 151 ASN cc_start: 0.7952 (t0) cc_final: 0.7693 (t0) outliers start: 131 outliers final: 111 residues processed: 606 average time/residue: 0.4276 time to fit residues: 452.6446 Evaluate side-chains 607 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 490 time to evaluate : 4.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 103 CYS Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 191 ASP Chi-restraints excluded: chain I residue 268 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 123 GLN Chi-restraints excluded: chain J residue 267 SER Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain M residue 140 ASP Chi-restraints excluded: chain M residue 246 SER Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain O residue 44 ASP Chi-restraints excluded: chain O residue 140 ASP Chi-restraints excluded: chain O residue 151 ASN Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 151 ASN Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain P residue 253 LEU Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 103 CYS Chi-restraints excluded: chain Q residue 136 VAL Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain Q residue 232 LEU Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 138 ILE Chi-restraints excluded: chain R residue 140 ASP Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 233 VAL Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 103 CYS Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 255 VAL Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 103 CYS Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 129 THR Chi-restraints excluded: chain T residue 140 ASP Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 232 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 321 optimal weight: 0.6980 chunk 207 optimal weight: 3.9990 chunk 310 optimal weight: 0.0670 chunk 156 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 330 optimal weight: 3.9990 chunk 354 optimal weight: 0.9990 chunk 257 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 409 optimal weight: 10.0000 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN C 106 ASN C 231 ASN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 ASN D 222 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 GLN F 134 ASN G 30 GLN G 222 GLN I 151 ASN ** I 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 222 GLN K 7 ASN L 30 GLN N 106 ASN ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 GLN P 73 GLN P 123 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Q 252 GLN R 34 ASN ** R 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 222 GLN R 231 ASN ** S 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 151 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 38960 Z= 0.146 Angle : 0.374 5.897 52720 Z= 0.224 Chirality : 0.030 0.175 6780 Planarity : 0.002 0.013 6740 Dihedral : 3.374 17.766 5466 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.00 % Allowed : 13.64 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.03 (0.12), residues: 5380 helix: 3.99 (0.08), residues: 3900 sheet: 0.23 (0.34), residues: 200 loop : -1.59 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 49 HIS 0.002 0.000 HIS P 214 PHE 0.009 0.001 PHE B 117 ARG 0.002 0.000 ARG P 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 580 time to evaluate : 4.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7149 (mp) REVERT: B 226 ASP cc_start: 0.7431 (m-30) cc_final: 0.7089 (m-30) REVERT: C 123 GLN cc_start: 0.8119 (mt0) cc_final: 0.7889 (mt0) REVERT: D 123 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7765 (mt0) REVERT: E 62 MET cc_start: 0.8071 (mtp) cc_final: 0.7779 (mtt) REVERT: G 26 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8929 (tt) REVERT: H 31 GLN cc_start: 0.8067 (tp40) cc_final: 0.7742 (tt0) REVERT: H 38 LYS cc_start: 0.8293 (mttp) cc_final: 0.7939 (mtpt) REVERT: I 119 SER cc_start: 0.8439 (t) cc_final: 0.7974 (m) REVERT: J 93 MET cc_start: 0.8683 (mtp) cc_final: 0.8465 (mtm) REVERT: J 151 ASN cc_start: 0.7844 (t0) cc_final: 0.7619 (t0) REVERT: M 123 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7768 (mm-40) REVERT: M 134 ASN cc_start: 0.8778 (t0) cc_final: 0.8385 (t0) REVERT: M 140 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7170 (t0) REVERT: M 263 GLN cc_start: 0.7428 (pt0) cc_final: 0.7129 (mm-40) REVERT: N 27 THR cc_start: 0.8335 (m) cc_final: 0.7873 (p) REVERT: N 62 MET cc_start: 0.7947 (mtt) cc_final: 0.7575 (mtt) REVERT: O 92 LYS cc_start: 0.7971 (mtmm) cc_final: 0.7768 (mtmm) REVERT: O 123 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7687 (mt0) REVERT: R 151 ASN cc_start: 0.7914 (t0) cc_final: 0.7673 (t0) REVERT: S 123 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8145 (mt0) REVERT: T 209 VAL cc_start: 0.8976 (t) cc_final: 0.8627 (m) outliers start: 84 outliers final: 56 residues processed: 635 average time/residue: 0.4289 time to fit residues: 476.9393 Evaluate side-chains 588 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 528 time to evaluate : 4.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 103 CYS Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 123 GLN Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 140 ASP Chi-restraints excluded: chain M residue 246 SER Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 245 GLN Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 103 CYS Chi-restraints excluded: chain S residue 123 GLN Chi-restraints excluded: chain T residue 103 CYS Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 140 ASP Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 232 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 473 optimal weight: 7.9990 chunk 498 optimal weight: 4.9990 chunk 454 optimal weight: 1.9990 chunk 485 optimal weight: 0.9990 chunk 291 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 380 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 438 optimal weight: 1.9990 chunk 458 optimal weight: 10.0000 chunk 483 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 ASN D 222 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN E 123 GLN E 222 GLN G 30 GLN I 151 ASN I 222 GLN J 222 GLN K 7 ASN N 106 ASN ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 73 GLN P 245 GLN ** P 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 123 GLN Q 151 ASN R 34 ASN ** R 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 151 ASN ** S 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 38960 Z= 0.184 Angle : 0.393 7.350 52720 Z= 0.233 Chirality : 0.031 0.203 6780 Planarity : 0.002 0.020 6740 Dihedral : 3.373 17.479 5462 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.83 % Allowed : 14.05 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.99 (0.12), residues: 5380 helix: 3.96 (0.08), residues: 3900 sheet: 0.24 (0.34), residues: 200 loop : -1.55 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 49 HIS 0.002 0.001 HIS P 214 PHE 0.010 0.001 PHE D 177 ARG 0.002 0.000 ARG E 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 551 time to evaluate : 4.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7127 (mp) REVERT: C 34 ASN cc_start: 0.7390 (m-40) cc_final: 0.7126 (m-40) REVERT: C 123 GLN cc_start: 0.8117 (mt0) cc_final: 0.7832 (mt0) REVERT: D 123 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7870 (mt0) REVERT: G 26 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8908 (tt) REVERT: H 31 GLN cc_start: 0.8078 (tp40) cc_final: 0.7773 (tt0) REVERT: H 38 LYS cc_start: 0.8340 (mttp) cc_final: 0.7965 (mtpt) REVERT: I 119 SER cc_start: 0.8405 (t) cc_final: 0.7982 (m) REVERT: J 151 ASN cc_start: 0.7845 (t0) cc_final: 0.7597 (t0) REVERT: M 123 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7856 (mm-40) REVERT: M 134 ASN cc_start: 0.8837 (t0) cc_final: 0.8464 (t0) REVERT: M 140 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.7142 (t0) REVERT: M 263 GLN cc_start: 0.7479 (pt0) cc_final: 0.7135 (mm-40) REVERT: N 27 THR cc_start: 0.8379 (m) cc_final: 0.7968 (p) REVERT: N 62 MET cc_start: 0.8090 (mtt) cc_final: 0.7676 (mtt) REVERT: O 123 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7770 (mt0) REVERT: R 151 ASN cc_start: 0.7880 (t0) cc_final: 0.7601 (t0) REVERT: S 123 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8298 (mt0) outliers start: 77 outliers final: 62 residues processed: 602 average time/residue: 0.4046 time to fit residues: 426.1815 Evaluate side-chains 600 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 534 time to evaluate : 4.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 103 CYS Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain I residue 67 ASP Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 123 GLN Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 140 ASP Chi-restraints excluded: chain M residue 246 SER Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 44 ASP Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 253 LEU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 62 MET Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 140 ASP Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 103 CYS Chi-restraints excluded: chain S residue 123 GLN Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 140 ASP Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 318 optimal weight: 7.9990 chunk 512 optimal weight: 4.9990 chunk 313 optimal weight: 0.0270 chunk 243 optimal weight: 8.9990 chunk 356 optimal weight: 1.9990 chunk 537 optimal weight: 0.9990 chunk 495 optimal weight: 1.9990 chunk 428 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 330 optimal weight: 5.9990 chunk 262 optimal weight: 2.9990 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: