Starting phenix.real_space_refine on Sat Mar 23 20:15:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xl0_22231/03_2024/6xl0_22231.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xl0_22231/03_2024/6xl0_22231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xl0_22231/03_2024/6xl0_22231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xl0_22231/03_2024/6xl0_22231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xl0_22231/03_2024/6xl0_22231.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xl0_22231/03_2024/6xl0_22231.pdb" } resolution = 3.4 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= 0.004 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 80 5.16 5 C 23820 2.51 5 N 6720 2.21 5 O 8200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 88": "OD1" <-> "OD2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A ASP 140": "OD1" <-> "OD2" Residue "A ASP 212": "OD1" <-> "OD2" Residue "A ASP 234": "OD1" <-> "OD2" Residue "A ASP 236": "OD1" <-> "OD2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "B ASP 140": "OD1" <-> "OD2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B ASP 234": "OD1" <-> "OD2" Residue "B ASP 236": "OD1" <-> "OD2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C GLU 95": "OE1" <-> "OE2" Residue "C PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 116": "OD1" <-> "OD2" Residue "C ASP 140": "OD1" <-> "OD2" Residue "C ASP 212": "OD1" <-> "OD2" Residue "C ASP 234": "OD1" <-> "OD2" Residue "C ASP 236": "OD1" <-> "OD2" Residue "D ASP 88": "OD1" <-> "OD2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 116": "OD1" <-> "OD2" Residue "D ASP 140": "OD1" <-> "OD2" Residue "D ASP 212": "OD1" <-> "OD2" Residue "D ASP 234": "OD1" <-> "OD2" Residue "D ASP 236": "OD1" <-> "OD2" Residue "E ASP 88": "OD1" <-> "OD2" Residue "E GLU 95": "OE1" <-> "OE2" Residue "E PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 116": "OD1" <-> "OD2" Residue "E ASP 140": "OD1" <-> "OD2" Residue "E ASP 212": "OD1" <-> "OD2" Residue "E ASP 234": "OD1" <-> "OD2" Residue "E ASP 236": "OD1" <-> "OD2" Residue "F ASP 88": "OD1" <-> "OD2" Residue "F GLU 95": "OE1" <-> "OE2" Residue "F PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 116": "OD1" <-> "OD2" Residue "F ASP 140": "OD1" <-> "OD2" Residue "F ASP 212": "OD1" <-> "OD2" Residue "F ASP 234": "OD1" <-> "OD2" Residue "F ASP 236": "OD1" <-> "OD2" Residue "G ASP 88": "OD1" <-> "OD2" Residue "G GLU 95": "OE1" <-> "OE2" Residue "G PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 116": "OD1" <-> "OD2" Residue "G ASP 140": "OD1" <-> "OD2" Residue "G ASP 212": "OD1" <-> "OD2" Residue "G ASP 234": "OD1" <-> "OD2" Residue "G ASP 236": "OD1" <-> "OD2" Residue "H ASP 88": "OD1" <-> "OD2" Residue "H GLU 95": "OE1" <-> "OE2" Residue "H PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 116": "OD1" <-> "OD2" Residue "H ASP 140": "OD1" <-> "OD2" Residue "H ASP 212": "OD1" <-> "OD2" Residue "H ASP 234": "OD1" <-> "OD2" Residue "H ASP 236": "OD1" <-> "OD2" Residue "I ASP 88": "OD1" <-> "OD2" Residue "I GLU 95": "OE1" <-> "OE2" Residue "I PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 116": "OD1" <-> "OD2" Residue "I ASP 140": "OD1" <-> "OD2" Residue "I ASP 212": "OD1" <-> "OD2" Residue "I ASP 234": "OD1" <-> "OD2" Residue "I ASP 236": "OD1" <-> "OD2" Residue "J ASP 88": "OD1" <-> "OD2" Residue "J GLU 95": "OE1" <-> "OE2" Residue "J PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 116": "OD1" <-> "OD2" Residue "J ASP 140": "OD1" <-> "OD2" Residue "J ASP 212": "OD1" <-> "OD2" Residue "J ASP 234": "OD1" <-> "OD2" Residue "J ASP 236": "OD1" <-> "OD2" Residue "K ASP 88": "OD1" <-> "OD2" Residue "K GLU 95": "OE1" <-> "OE2" Residue "K PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 116": "OD1" <-> "OD2" Residue "K ASP 140": "OD1" <-> "OD2" Residue "K ASP 212": "OD1" <-> "OD2" Residue "K ASP 234": "OD1" <-> "OD2" Residue "K ASP 236": "OD1" <-> "OD2" Residue "L ASP 88": "OD1" <-> "OD2" Residue "L GLU 95": "OE1" <-> "OE2" Residue "L PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 116": "OD1" <-> "OD2" Residue "L ASP 140": "OD1" <-> "OD2" Residue "L ASP 212": "OD1" <-> "OD2" Residue "L ASP 234": "OD1" <-> "OD2" Residue "L ASP 236": "OD1" <-> "OD2" Residue "M ASP 88": "OD1" <-> "OD2" Residue "M GLU 95": "OE1" <-> "OE2" Residue "M PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 116": "OD1" <-> "OD2" Residue "M ASP 140": "OD1" <-> "OD2" Residue "M ASP 212": "OD1" <-> "OD2" Residue "M ASP 234": "OD1" <-> "OD2" Residue "M ASP 236": "OD1" <-> "OD2" Residue "N ASP 88": "OD1" <-> "OD2" Residue "N GLU 95": "OE1" <-> "OE2" Residue "N PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 116": "OD1" <-> "OD2" Residue "N ASP 140": "OD1" <-> "OD2" Residue "N ASP 212": "OD1" <-> "OD2" Residue "N ASP 234": "OD1" <-> "OD2" Residue "N ASP 236": "OD1" <-> "OD2" Residue "O ASP 88": "OD1" <-> "OD2" Residue "O GLU 95": "OE1" <-> "OE2" Residue "O PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 116": "OD1" <-> "OD2" Residue "O ASP 140": "OD1" <-> "OD2" Residue "O ASP 212": "OD1" <-> "OD2" Residue "O ASP 234": "OD1" <-> "OD2" Residue "O ASP 236": "OD1" <-> "OD2" Residue "P ASP 88": "OD1" <-> "OD2" Residue "P GLU 95": "OE1" <-> "OE2" Residue "P PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 116": "OD1" <-> "OD2" Residue "P ASP 140": "OD1" <-> "OD2" Residue "P ASP 212": "OD1" <-> "OD2" Residue "P ASP 234": "OD1" <-> "OD2" Residue "P ASP 236": "OD1" <-> "OD2" Residue "Q ASP 88": "OD1" <-> "OD2" Residue "Q GLU 95": "OE1" <-> "OE2" Residue "Q PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 116": "OD1" <-> "OD2" Residue "Q ASP 140": "OD1" <-> "OD2" Residue "Q ASP 212": "OD1" <-> "OD2" Residue "Q ASP 234": "OD1" <-> "OD2" Residue "Q ASP 236": "OD1" <-> "OD2" Residue "R ASP 88": "OD1" <-> "OD2" Residue "R GLU 95": "OE1" <-> "OE2" Residue "R PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 116": "OD1" <-> "OD2" Residue "R ASP 140": "OD1" <-> "OD2" Residue "R ASP 212": "OD1" <-> "OD2" Residue "R ASP 234": "OD1" <-> "OD2" Residue "R ASP 236": "OD1" <-> "OD2" Residue "S ASP 88": "OD1" <-> "OD2" Residue "S GLU 95": "OE1" <-> "OE2" Residue "S PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 116": "OD1" <-> "OD2" Residue "S ASP 140": "OD1" <-> "OD2" Residue "S ASP 212": "OD1" <-> "OD2" Residue "S ASP 234": "OD1" <-> "OD2" Residue "S ASP 236": "OD1" <-> "OD2" Residue "T ASP 88": "OD1" <-> "OD2" Residue "T GLU 95": "OE1" <-> "OE2" Residue "T PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 116": "OD1" <-> "OD2" Residue "T ASP 140": "OD1" <-> "OD2" Residue "T ASP 212": "OD1" <-> "OD2" Residue "T ASP 234": "OD1" <-> "OD2" Residue "T ASP 236": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 38820 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "B" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "C" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "D" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "E" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "F" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "G" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "H" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "I" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "J" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "K" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "L" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "M" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "N" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "O" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "P" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "Q" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "R" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "S" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "T" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Time building chain proxies: 21.21, per 1000 atoms: 0.55 Number of scatterers: 38820 At special positions: 0 Unit cell: (137.46, 137.46, 247.95, 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 80 16.00 O 8200 8.00 N 6720 7.00 C 23820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.95 Conformation dependent library (CDL) restraints added in 8.2 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 73.1% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'A' and resid 9 through 36 removed outlier: 3.825A pdb=" N MET A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR A 58 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA A 59 " --> pdb=" O GLN A 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP A 67 " --> pdb=" O ASN A 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 267 through 272' Processing helix chain 'B' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET B 13 " --> pdb=" O ASN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 101 removed outlier: 3.858A pdb=" N THR B 58 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP B 67 " --> pdb=" O ASN B 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE B 272 " --> pdb=" O ILE B 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 267 through 272' Processing helix chain 'C' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET C 13 " --> pdb=" O ASN C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR C 58 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C 59 " --> pdb=" O GLN C 55 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP C 67 " --> pdb=" O ASN C 63 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA C 112 " --> pdb=" O ALA C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 234 removed outlier: 3.868A pdb=" N THR C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 263 removed outlier: 3.727A pdb=" N GLU C 240 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN C 263 " --> pdb=" O SER C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE C 272 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 267 through 272' Processing helix chain 'D' and resid 9 through 36 removed outlier: 3.827A pdb=" N MET D 13 " --> pdb=" O ASN D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR D 58 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA D 59 " --> pdb=" O GLN D 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE D 110 " --> pdb=" O ASN D 106 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA D 112 " --> pdb=" O ALA D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 263 removed outlier: 3.727A pdb=" N GLU D 240 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU D 271 " --> pdb=" O SER D 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE D 272 " --> pdb=" O ILE D 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 267 through 272' Processing helix chain 'E' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET E 13 " --> pdb=" O ASN E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR E 58 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA E 59 " --> pdb=" O GLN E 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP E 67 " --> pdb=" O ASN E 63 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE E 110 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR E 185 " --> pdb=" O ALA E 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY E 188 " --> pdb=" O LYS E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU E 240 " --> pdb=" O ASP E 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA E 242 " --> pdb=" O ALA E 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN E 263 " --> pdb=" O SER E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU E 271 " --> pdb=" O SER E 267 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE E 272 " --> pdb=" O ILE E 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 267 through 272' Processing helix chain 'F' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR F 58 " --> pdb=" O ASN F 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA F 59 " --> pdb=" O GLN F 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP F 67 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 130 removed outlier: 3.697A pdb=" N PHE F 110 " --> pdb=" O ASN F 106 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN F 111 " --> pdb=" O THR F 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR F 185 " --> pdb=" O ALA F 181 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY F 188 " --> pdb=" O LYS F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU F 240 " --> pdb=" O ASP F 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA F 242 " --> pdb=" O ALA F 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN F 263 " --> pdb=" O SER F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU F 271 " --> pdb=" O SER F 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE F 272 " --> pdb=" O ILE F 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 267 through 272' Processing helix chain 'G' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET G 13 " --> pdb=" O ASN G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 101 removed outlier: 3.856A pdb=" N THR G 58 " --> pdb=" O ASN G 54 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA G 59 " --> pdb=" O GLN G 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP G 67 " --> pdb=" O ASN G 63 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE G 110 " --> pdb=" O ASN G 106 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN G 111 " --> pdb=" O THR G 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA G 112 " --> pdb=" O ALA G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR G 185 " --> pdb=" O ALA G 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY G 188 " --> pdb=" O LYS G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 263 removed outlier: 3.725A pdb=" N GLU G 240 " --> pdb=" O ASP G 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA G 242 " --> pdb=" O ALA G 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN G 263 " --> pdb=" O SER G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU G 271 " --> pdb=" O SER G 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE G 272 " --> pdb=" O ILE G 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 267 through 272' Processing helix chain 'H' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET H 13 " --> pdb=" O ASN H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 101 removed outlier: 3.856A pdb=" N THR H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA H 59 " --> pdb=" O GLN H 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE H 110 " --> pdb=" O ASN H 106 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN H 111 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA H 112 " --> pdb=" O ALA H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR H 185 " --> pdb=" O ALA H 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY H 188 " --> pdb=" O LYS H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU H 240 " --> pdb=" O ASP H 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN H 263 " --> pdb=" O SER H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 272 removed outlier: 3.921A pdb=" N LEU H 271 " --> pdb=" O SER H 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE H 272 " --> pdb=" O ILE H 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 267 through 272' Processing helix chain 'I' and resid 9 through 36 removed outlier: 3.827A pdb=" N MET I 13 " --> pdb=" O ASN I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 101 removed outlier: 3.856A pdb=" N THR I 58 " --> pdb=" O ASN I 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA I 59 " --> pdb=" O GLN I 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP I 67 " --> pdb=" O ASN I 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER I 68 " --> pdb=" O ALA I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE I 110 " --> pdb=" O ASN I 106 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN I 111 " --> pdb=" O THR I 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR I 185 " --> pdb=" O ALA I 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY I 188 " --> pdb=" O LYS I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU I 240 " --> pdb=" O ASP I 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA I 242 " --> pdb=" O ALA I 238 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN I 263 " --> pdb=" O SER I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU I 271 " --> pdb=" O SER I 267 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE I 272 " --> pdb=" O ILE I 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 267 through 272' Processing helix chain 'J' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET J 13 " --> pdb=" O ASN J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR J 58 " --> pdb=" O ASN J 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA J 59 " --> pdb=" O GLN J 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP J 67 " --> pdb=" O ASN J 63 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE J 110 " --> pdb=" O ASN J 106 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN J 111 " --> pdb=" O THR J 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA J 112 " --> pdb=" O ALA J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 234 removed outlier: 3.868A pdb=" N THR J 185 " --> pdb=" O ALA J 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY J 188 " --> pdb=" O LYS J 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU J 240 " --> pdb=" O ASP J 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA J 242 " --> pdb=" O ALA J 238 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN J 263 " --> pdb=" O SER J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 272 removed outlier: 3.921A pdb=" N LEU J 271 " --> pdb=" O SER J 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE J 272 " --> pdb=" O ILE J 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 267 through 272' Processing helix chain 'K' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET K 13 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR K 58 " --> pdb=" O ASN K 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA K 59 " --> pdb=" O GLN K 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP K 67 " --> pdb=" O ASN K 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER K 68 " --> pdb=" O ALA K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 130 removed outlier: 3.697A pdb=" N PHE K 110 " --> pdb=" O ASN K 106 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA K 112 " --> pdb=" O ALA K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR K 185 " --> pdb=" O ALA K 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY K 188 " --> pdb=" O LYS K 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU K 240 " --> pdb=" O ASP K 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA K 242 " --> pdb=" O ALA K 238 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN K 263 " --> pdb=" O SER K 259 " (cutoff:3.500A) Processing helix chain 'K' and resid 267 through 272 removed outlier: 3.921A pdb=" N LEU K 271 " --> pdb=" O SER K 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE K 272 " --> pdb=" O ILE K 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 267 through 272' Processing helix chain 'L' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET L 13 " --> pdb=" O ASN L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR L 58 " --> pdb=" O ASN L 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA L 59 " --> pdb=" O GLN L 55 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP L 67 " --> pdb=" O ASN L 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE L 110 " --> pdb=" O ASN L 106 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN L 111 " --> pdb=" O THR L 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA L 112 " --> pdb=" O ALA L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 234 removed outlier: 3.868A pdb=" N THR L 185 " --> pdb=" O ALA L 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 263 removed outlier: 3.727A pdb=" N GLU L 240 " --> pdb=" O ASP L 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA L 242 " --> pdb=" O ALA L 238 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN L 263 " --> pdb=" O SER L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU L 271 " --> pdb=" O SER L 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE L 272 " --> pdb=" O ILE L 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 267 through 272' Processing helix chain 'M' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET M 13 " --> pdb=" O ASN M 9 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR M 58 " --> pdb=" O ASN M 54 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA M 59 " --> pdb=" O GLN M 55 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP M 67 " --> pdb=" O ASN M 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER M 68 " --> pdb=" O ALA M 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE M 110 " --> pdb=" O ASN M 106 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN M 111 " --> pdb=" O THR M 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA M 112 " --> pdb=" O ALA M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR M 185 " --> pdb=" O ALA M 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY M 188 " --> pdb=" O LYS M 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU M 240 " --> pdb=" O ASP M 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA M 242 " --> pdb=" O ALA M 238 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN M 263 " --> pdb=" O SER M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 267 through 272 removed outlier: 3.921A pdb=" N LEU M 271 " --> pdb=" O SER M 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE M 272 " --> pdb=" O ILE M 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 267 through 272' Processing helix chain 'N' and resid 9 through 36 removed outlier: 3.825A pdb=" N MET N 13 " --> pdb=" O ASN N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 101 removed outlier: 3.858A pdb=" N THR N 58 " --> pdb=" O ASN N 54 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA N 59 " --> pdb=" O GLN N 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP N 67 " --> pdb=" O ASN N 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER N 68 " --> pdb=" O ALA N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE N 110 " --> pdb=" O ASN N 106 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN N 111 " --> pdb=" O THR N 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA N 112 " --> pdb=" O ALA N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR N 185 " --> pdb=" O ALA N 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY N 188 " --> pdb=" O LYS N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 236 through 263 removed outlier: 3.727A pdb=" N GLU N 240 " --> pdb=" O ASP N 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA N 242 " --> pdb=" O ALA N 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN N 263 " --> pdb=" O SER N 259 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU N 271 " --> pdb=" O SER N 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE N 272 " --> pdb=" O ILE N 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 267 through 272' Processing helix chain 'O' and resid 9 through 36 removed outlier: 3.825A pdb=" N MET O 13 " --> pdb=" O ASN O 9 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR O 58 " --> pdb=" O ASN O 54 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA O 59 " --> pdb=" O GLN O 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP O 67 " --> pdb=" O ASN O 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER O 68 " --> pdb=" O ALA O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 130 removed outlier: 3.695A pdb=" N PHE O 110 " --> pdb=" O ASN O 106 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN O 111 " --> pdb=" O THR O 107 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA O 112 " --> pdb=" O ALA O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 181 through 234 removed outlier: 3.868A pdb=" N THR O 185 " --> pdb=" O ALA O 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY O 188 " --> pdb=" O LYS O 184 " (cutoff:3.500A) Processing helix chain 'O' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU O 240 " --> pdb=" O ASP O 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA O 242 " --> pdb=" O ALA O 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN O 263 " --> pdb=" O SER O 259 " (cutoff:3.500A) Processing helix chain 'O' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU O 271 " --> pdb=" O SER O 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE O 272 " --> pdb=" O ILE O 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 267 through 272' Processing helix chain 'P' and resid 9 through 36 removed outlier: 3.827A pdb=" N MET P 13 " --> pdb=" O ASN P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 101 removed outlier: 3.856A pdb=" N THR P 58 " --> pdb=" O ASN P 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA P 59 " --> pdb=" O GLN P 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP P 67 " --> pdb=" O ASN P 63 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER P 68 " --> pdb=" O ALA P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE P 110 " --> pdb=" O ASN P 106 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN P 111 " --> pdb=" O THR P 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA P 112 " --> pdb=" O ALA P 108 " (cutoff:3.500A) Processing helix chain 'P' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR P 185 " --> pdb=" O ALA P 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY P 188 " --> pdb=" O LYS P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 263 removed outlier: 3.725A pdb=" N GLU P 240 " --> pdb=" O ASP P 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA P 242 " --> pdb=" O ALA P 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN P 263 " --> pdb=" O SER P 259 " (cutoff:3.500A) Processing helix chain 'P' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU P 271 " --> pdb=" O SER P 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE P 272 " --> pdb=" O ILE P 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 267 through 272' Processing helix chain 'Q' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET Q 13 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR Q 58 " --> pdb=" O ASN Q 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA Q 59 " --> pdb=" O GLN Q 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP Q 67 " --> pdb=" O ASN Q 63 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER Q 68 " --> pdb=" O ALA Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE Q 110 " --> pdb=" O ASN Q 106 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN Q 111 " --> pdb=" O THR Q 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA Q 112 " --> pdb=" O ALA Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR Q 185 " --> pdb=" O ALA Q 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY Q 188 " --> pdb=" O LYS Q 184 " (cutoff:3.500A) Processing helix chain 'Q' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU Q 240 " --> pdb=" O ASP Q 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA Q 242 " --> pdb=" O ALA Q 238 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN Q 263 " --> pdb=" O SER Q 259 " (cutoff:3.500A) Processing helix chain 'Q' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU Q 271 " --> pdb=" O SER Q 267 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE Q 272 " --> pdb=" O ILE Q 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 267 through 272' Processing helix chain 'R' and resid 9 through 36 removed outlier: 3.827A pdb=" N MET R 13 " --> pdb=" O ASN R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR R 58 " --> pdb=" O ASN R 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA R 59 " --> pdb=" O GLN R 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP R 67 " --> pdb=" O ASN R 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER R 68 " --> pdb=" O ALA R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE R 110 " --> pdb=" O ASN R 106 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN R 111 " --> pdb=" O THR R 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA R 112 " --> pdb=" O ALA R 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR R 185 " --> pdb=" O ALA R 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY R 188 " --> pdb=" O LYS R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU R 240 " --> pdb=" O ASP R 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA R 242 " --> pdb=" O ALA R 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN R 263 " --> pdb=" O SER R 259 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU R 271 " --> pdb=" O SER R 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE R 272 " --> pdb=" O ILE R 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 267 through 272' Processing helix chain 'S' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET S 13 " --> pdb=" O ASN S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA S 59 " --> pdb=" O GLN S 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP S 67 " --> pdb=" O ASN S 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER S 68 " --> pdb=" O ALA S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 130 removed outlier: 3.697A pdb=" N PHE S 110 " --> pdb=" O ASN S 106 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN S 111 " --> pdb=" O THR S 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA S 112 " --> pdb=" O ALA S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR S 185 " --> pdb=" O ALA S 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY S 188 " --> pdb=" O LYS S 184 " (cutoff:3.500A) Processing helix chain 'S' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU S 240 " --> pdb=" O ASP S 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA S 242 " --> pdb=" O ALA S 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN S 263 " --> pdb=" O SER S 259 " (cutoff:3.500A) Processing helix chain 'S' and resid 267 through 272 removed outlier: 3.921A pdb=" N LEU S 271 " --> pdb=" O SER S 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE S 272 " --> pdb=" O ILE S 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 267 through 272' Processing helix chain 'T' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET T 13 " --> pdb=" O ASN T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR T 58 " --> pdb=" O ASN T 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA T 59 " --> pdb=" O GLN T 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP T 67 " --> pdb=" O ASN T 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER T 68 " --> pdb=" O ALA T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE T 110 " --> pdb=" O ASN T 106 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN T 111 " --> pdb=" O THR T 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA T 112 " --> pdb=" O ALA T 108 " (cutoff:3.500A) Processing helix chain 'T' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR T 185 " --> pdb=" O ALA T 181 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY T 188 " --> pdb=" O LYS T 184 " (cutoff:3.500A) Processing helix chain 'T' and resid 236 through 263 removed outlier: 3.727A pdb=" N GLU T 240 " --> pdb=" O ASP T 236 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN T 263 " --> pdb=" O SER T 259 " (cutoff:3.500A) Processing helix chain 'T' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU T 271 " --> pdb=" O SER T 267 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE T 272 " --> pdb=" O ILE T 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 267 through 272' 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 3260 hydrogen bonds defined for protein. 9780 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: 12.51 Time building geometry restraints manager: 19.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 11973 1.33 - 1.45: 4282 1.45 - 1.57: 22605 1.57 - 1.69: 0 1.69 - 1.81: 160 Bond restraints: 39020 Sorted by residual: bond pdb=" CB THR C 206 " pdb=" CG2 THR C 206 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.00e+00 bond pdb=" CB THR G 206 " pdb=" CG2 THR G 206 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 1.99e+00 bond pdb=" CB THR I 206 " pdb=" CG2 THR I 206 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 1.99e+00 bond pdb=" CB THR K 206 " pdb=" CG2 THR K 206 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.98e+00 bond pdb=" CB THR M 206 " pdb=" CG2 THR M 206 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.98e+00 ... (remaining 39015 not shown) Histogram of bond angle deviations from ideal: 99.15 - 106.12: 140 106.12 - 113.08: 23855 113.08 - 120.05: 13190 120.05 - 127.01: 15575 127.01 - 133.98: 60 Bond angle restraints: 52820 Sorted by residual: angle pdb=" CA LYS K 220 " pdb=" CB LYS K 220 " pdb=" CG LYS K 220 " ideal model delta sigma weight residual 114.10 122.75 -8.65 2.00e+00 2.50e-01 1.87e+01 angle pdb=" CA LYS T 220 " pdb=" CB LYS T 220 " pdb=" CG LYS T 220 " ideal model delta sigma weight residual 114.10 122.75 -8.65 2.00e+00 2.50e-01 1.87e+01 angle pdb=" CA LYS O 220 " pdb=" CB LYS O 220 " pdb=" CG LYS O 220 " ideal model delta sigma weight residual 114.10 122.75 -8.65 2.00e+00 2.50e-01 1.87e+01 angle pdb=" CA LYS Q 220 " pdb=" CB LYS Q 220 " pdb=" CG LYS Q 220 " ideal model delta sigma weight residual 114.10 122.73 -8.63 2.00e+00 2.50e-01 1.86e+01 angle pdb=" CA LYS H 220 " pdb=" CB LYS H 220 " pdb=" CG LYS H 220 " ideal model delta sigma weight residual 114.10 122.73 -8.63 2.00e+00 2.50e-01 1.86e+01 ... (remaining 52815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 21595 15.93 - 31.86: 1796 31.86 - 47.79: 329 47.79 - 63.73: 0 63.73 - 79.66: 60 Dihedral angle restraints: 23780 sinusoidal: 8340 harmonic: 15440 Sorted by residual: 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 -162.64 -17.36 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA LEU M 232 " pdb=" C LEU M 232 " pdb=" N VAL M 233 " pdb=" CA VAL M 233 " ideal model delta harmonic sigma weight residual -180.00 -162.64 -17.36 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA LEU R 232 " pdb=" C LEU R 232 " pdb=" N VAL R 233 " pdb=" CA VAL R 233 " ideal model delta harmonic sigma weight residual 180.00 -162.65 -17.35 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 23777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4987 0.045 - 0.091: 1422 0.091 - 0.136: 322 0.136 - 0.181: 49 0.181 - 0.226: 20 Chirality restraints: 6800 Sorted by residual: chirality pdb=" CB VAL J 233 " pdb=" CA VAL J 233 " pdb=" CG1 VAL J 233 " pdb=" CG2 VAL J 233 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB VAL K 233 " pdb=" CA VAL K 233 " pdb=" CG1 VAL K 233 " pdb=" CG2 VAL K 233 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB VAL T 233 " pdb=" CA VAL T 233 " pdb=" CG1 VAL T 233 " pdb=" CG2 VAL T 233 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 6797 not shown) Planarity restraints: 6760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP R 236 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.33e+00 pdb=" C ASP R 236 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP R 236 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU R 237 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP N 236 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C ASP N 236 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP N 236 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU N 237 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP P 236 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.26e+00 pdb=" C ASP P 236 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP P 236 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU P 237 " 0.013 2.00e-02 2.50e+03 ... (remaining 6757 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1335 2.69 - 3.24: 42520 3.24 - 3.79: 61092 3.79 - 4.35: 73802 4.35 - 4.90: 126436 Nonbonded interactions: 305185 Sorted by model distance: nonbonded pdb=" NZ LYS N 220 " pdb=" OE1 GLN T 17 " model vdw 2.137 2.520 nonbonded pdb=" NZ LYS K 220 " pdb=" OE1 GLN M 17 " model vdw 2.159 2.520 nonbonded pdb=" NZ LYS B 220 " pdb=" OE1 GLN H 17 " model vdw 2.166 2.520 nonbonded pdb=" NZ LYS O 220 " pdb=" OE1 GLN Q 17 " model vdw 2.189 2.520 nonbonded pdb=" OD1 ASP F 102 " pdb=" O THR L 147 " model vdw 2.207 3.040 ... (remaining 305180 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 9.260 Check model and map are aligned: 0.580 Set scattering table: 0.390 Process input model: 102.940 Find NCS groups from input model: 2.720 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 : 0.008 0.051 39020 Z= 0.516 Angle : 0.808 8.652 52820 Z= 0.447 Chirality : 0.047 0.226 6800 Planarity : 0.004 0.023 6760 Dihedral : 12.657 79.658 13740 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.11), residues: 5380 helix: 1.66 (0.07), residues: 3940 sheet: -1.88 (0.31), residues: 200 loop : -3.12 (0.13), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP G 49 HIS 0.001 0.000 HIS D 214 PHE 0.012 0.002 PHE B 117 ARG 0.003 0.001 ARG C 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 1105 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1105 time to evaluate : 4.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 THR cc_start: 0.8545 (m) cc_final: 0.8305 (m) REVERT: D 92 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8442 (mtmt) REVERT: E 32 ARG cc_start: 0.7445 (tpp80) cc_final: 0.7143 (ttm110) REVERT: E 140 ASP cc_start: 0.7835 (p0) cc_final: 0.7214 (t70) REVERT: F 88 ASP cc_start: 0.7495 (t0) cc_final: 0.7248 (t0) REVERT: G 92 LYS cc_start: 0.8548 (ttmt) cc_final: 0.8302 (mtpt) REVERT: G 123 GLN cc_start: 0.8020 (tp40) cc_final: 0.7608 (mt0) REVERT: G 231 ASN cc_start: 0.8132 (t0) cc_final: 0.7676 (m-40) REVERT: G 240 GLU cc_start: 0.6269 (mp0) cc_final: 0.6062 (mp0) REVERT: H 262 ASN cc_start: 0.7152 (m110) cc_final: 0.6663 (t0) REVERT: I 123 GLN cc_start: 0.7876 (tp40) cc_final: 0.7560 (mt0) REVERT: K 226 ASP cc_start: 0.7605 (m-30) cc_final: 0.7375 (m-30) REVERT: L 55 GLN cc_start: 0.7633 (tp40) cc_final: 0.6935 (tt0) REVERT: L 88 ASP cc_start: 0.8094 (t0) cc_final: 0.7690 (m-30) REVERT: O 231 ASN cc_start: 0.8059 (t0) cc_final: 0.7791 (m-40) REVERT: P 27 THR cc_start: 0.7976 (m) cc_final: 0.7723 (p) REVERT: P 125 GLU cc_start: 0.7657 (tp30) cc_final: 0.6963 (tp30) REVERT: P 184 LYS cc_start: 0.8031 (mmmt) cc_final: 0.7812 (ttpt) REVERT: P 186 MET cc_start: 0.7627 (tpp) cc_final: 0.7165 (tpp) REVERT: Q 110 PHE cc_start: 0.7901 (t80) cc_final: 0.7645 (t80) REVERT: R 43 LYS cc_start: 0.7330 (mtmt) cc_final: 0.7023 (mmtt) REVERT: R 102 ASP cc_start: 0.7737 (t0) cc_final: 0.7496 (t0) REVERT: S 239 LYS cc_start: 0.7947 (mttp) cc_final: 0.7602 (mtmm) REVERT: T 113 LEU cc_start: 0.8316 (mt) cc_final: 0.8114 (mt) REVERT: T 186 MET cc_start: 0.7621 (tpp) cc_final: 0.7000 (tpp) outliers start: 0 outliers final: 0 residues processed: 1105 average time/residue: 0.4850 time to fit residues: 885.9273 Evaluate side-chains 626 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 626 time to evaluate : 4.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 455 optimal weight: 3.9990 chunk 409 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 276 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 423 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 257 optimal weight: 7.9990 chunk 315 optimal weight: 10.0000 chunk 490 optimal weight: 0.3980 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN B 55 GLN ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 GLN E 34 ASN E 45 ASN E 262 ASN F 31 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 GLN ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN H 123 GLN I 45 ASN I 73 GLN J 34 ASN J 123 GLN K 245 GLN L 18 ASN M 31 GLN M 262 ASN N 4 ASN N 31 GLN ** N 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 123 GLN Q 123 GLN Q 195 GLN Q 251 GLN R 34 ASN R 123 GLN R 134 ASN S 123 GLN S 245 GLN T 195 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39020 Z= 0.218 Angle : 0.492 7.089 52820 Z= 0.280 Chirality : 0.034 0.260 6800 Planarity : 0.002 0.033 6760 Dihedral : 3.656 17.986 5460 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.31 % Allowed : 11.21 % Favored : 86.48 % 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: 2.41 (0.12), residues: 5380 helix: 3.04 (0.08), residues: 3940 sheet: -2.07 (0.26), residues: 240 loop : -2.92 (0.15), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 49 HIS 0.002 0.001 HIS S 214 PHE 0.015 0.002 PHE E 217 ARG 0.003 0.000 ARG P 32 *********************** 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 836 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 739 time to evaluate : 4.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ASN cc_start: 0.6826 (m-40) cc_final: 0.6494 (m-40) REVERT: B 43 LYS cc_start: 0.5347 (mmtt) cc_final: 0.4796 (mmtt) REVERT: B 176 THR cc_start: 0.8256 (OUTLIER) cc_final: 0.7803 (p) REVERT: C 95 GLU cc_start: 0.6903 (tt0) cc_final: 0.6603 (tt0) REVERT: C 132 LYS cc_start: 0.7885 (mtmm) cc_final: 0.7684 (mtmm) REVERT: E 118 ASP cc_start: 0.7538 (m-30) cc_final: 0.7188 (m-30) REVERT: E 123 GLN cc_start: 0.7528 (tp40) cc_final: 0.7154 (mt0) REVERT: F 88 ASP cc_start: 0.7583 (t0) cc_final: 0.7378 (t0) REVERT: G 39 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8551 (mm) REVERT: H 231 ASN cc_start: 0.7810 (t0) cc_final: 0.7586 (m-40) REVERT: H 262 ASN cc_start: 0.7090 (m110) cc_final: 0.6659 (t0) REVERT: I 123 GLN cc_start: 0.7879 (tp40) cc_final: 0.7580 (mt0) REVERT: L 88 ASP cc_start: 0.8208 (t0) cc_final: 0.7549 (m-30) REVERT: L 102 ASP cc_start: 0.8182 (t0) cc_final: 0.7940 (t0) REVERT: M 271 LEU cc_start: 0.7685 (tp) cc_final: 0.7442 (mp) REVERT: O 43 LYS cc_start: 0.7354 (mtmt) cc_final: 0.7132 (tptt) REVERT: O 80 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8630 (mp) REVERT: O 262 ASN cc_start: 0.7705 (m110) cc_final: 0.7336 (m110) REVERT: P 27 THR cc_start: 0.7845 (m) cc_final: 0.7558 (p) REVERT: P 186 MET cc_start: 0.7411 (tpp) cc_final: 0.7038 (tpp) REVERT: Q 153 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7507 (m-30) REVERT: Q 186 MET cc_start: 0.7987 (tpp) cc_final: 0.7690 (tpt) REVERT: R 118 ASP cc_start: 0.6857 (m-30) cc_final: 0.6656 (p0) REVERT: S 239 LYS cc_start: 0.7976 (mttp) cc_final: 0.7715 (mtmm) outliers start: 97 outliers final: 63 residues processed: 798 average time/residue: 0.4260 time to fit residues: 585.8567 Evaluate side-chains 663 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 596 time to evaluate : 4.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 63 ASN Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 203 SER Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 63 ASN Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain J residue 7 ASN Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 264 SER Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 153 ASP Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 267 SER Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 153 ASP Chi-restraints excluded: chain Q residue 171 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain T residue 144 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 272 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 408 optimal weight: 0.0980 chunk 333 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 chunk 491 optimal weight: 1.9990 chunk 530 optimal weight: 4.9990 chunk 437 optimal weight: 2.9990 chunk 487 optimal weight: 9.9990 chunk 167 optimal weight: 4.9990 chunk 394 optimal weight: 3.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 262 ASN B 31 GLN D 7 ASN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN D 248 GLN E 45 ASN F 34 ASN F 262 ASN G 73 GLN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN H 73 GLN I 31 GLN J 4 ASN J 262 ASN K 31 GLN K 123 GLN K 151 ASN L 34 ASN O 34 ASN P 73 GLN Q 251 GLN R 248 GLN ** T 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 39020 Z= 0.235 Angle : 0.504 9.141 52820 Z= 0.282 Chirality : 0.035 0.260 6800 Planarity : 0.002 0.034 6760 Dihedral : 3.671 18.649 5460 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.17 % Allowed : 14.60 % Favored : 82.24 % 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: 2.74 (0.12), residues: 5380 helix: 3.25 (0.08), residues: 3940 sheet: -1.24 (0.29), residues: 200 loop : -2.82 (0.14), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 49 HIS 0.003 0.001 HIS E 214 PHE 0.014 0.002 PHE N 117 ARG 0.004 0.000 ARG Q 121 *********************** 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 811 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 678 time to evaluate : 4.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ASN cc_start: 0.7133 (m-40) cc_final: 0.6891 (m-40) REVERT: B 43 LYS cc_start: 0.5227 (mmtt) cc_final: 0.4826 (mmtt) REVERT: B 236 ASP cc_start: 0.6694 (t70) cc_final: 0.6125 (t70) REVERT: C 95 GLU cc_start: 0.6784 (tt0) cc_final: 0.6550 (tt0) REVERT: D 62 MET cc_start: 0.8530 (mmm) cc_final: 0.8309 (mpp) REVERT: E 123 GLN cc_start: 0.7699 (tp40) cc_final: 0.7449 (mt0) REVERT: E 136 VAL cc_start: 0.8630 (t) cc_final: 0.8276 (m) REVERT: F 88 ASP cc_start: 0.7647 (t0) cc_final: 0.7413 (t0) REVERT: G 39 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8423 (mm) REVERT: H 231 ASN cc_start: 0.7570 (t0) cc_final: 0.7198 (m-40) REVERT: H 262 ASN cc_start: 0.7320 (m110) cc_final: 0.6653 (t0) REVERT: I 123 GLN cc_start: 0.8031 (tp40) cc_final: 0.7621 (mt0) REVERT: K 239 LYS cc_start: 0.8072 (mttm) cc_final: 0.7769 (mtpp) REVERT: L 88 ASP cc_start: 0.8317 (t0) cc_final: 0.7645 (m-30) REVERT: L 102 ASP cc_start: 0.8260 (t0) cc_final: 0.7921 (t0) REVERT: M 101 SER cc_start: 0.8737 (t) cc_final: 0.8516 (p) REVERT: M 190 ILE cc_start: 0.8713 (mm) cc_final: 0.8512 (mm) REVERT: N 232 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8125 (tp) REVERT: O 80 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8804 (mp) REVERT: P 27 THR cc_start: 0.7826 (m) cc_final: 0.7578 (p) REVERT: P 121 ARG cc_start: 0.7337 (ttp80) cc_final: 0.7089 (ttp-170) REVERT: P 140 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8203 (p0) REVERT: Q 186 MET cc_start: 0.8108 (tpp) cc_final: 0.7860 (tpt) outliers start: 133 outliers final: 88 residues processed: 761 average time/residue: 0.4449 time to fit residues: 594.0981 Evaluate side-chains 662 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 570 time to evaluate : 4.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 203 SER Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 264 SER Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 232 LEU Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 259 SER Chi-restraints excluded: chain O residue 267 SER Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 155 SER Chi-restraints excluded: chain Q residue 171 LEU Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain S residue 76 ILE Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain T residue 24 SER Chi-restraints excluded: chain T residue 124 ILE Chi-restraints excluded: chain T residue 144 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 485 optimal weight: 10.0000 chunk 369 optimal weight: 10.0000 chunk 254 optimal weight: 2.9990 chunk 54 optimal weight: 220.0000 chunk 234 optimal weight: 6.9990 chunk 329 optimal weight: 2.9990 chunk 493 optimal weight: 0.9990 chunk 521 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 chunk 467 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN C 151 ASN E 45 ASN E 73 GLN E 262 ASN F 248 GLN H 31 GLN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN K 31 GLN L 151 ASN N 31 GLN O 73 GLN Q 251 GLN ** Q 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 39020 Z= 0.239 Angle : 0.499 8.130 52820 Z= 0.281 Chirality : 0.035 0.257 6800 Planarity : 0.002 0.033 6760 Dihedral : 3.693 19.157 5460 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.38 % Allowed : 15.79 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.12), residues: 5380 helix: 3.41 (0.08), residues: 3840 sheet: -1.07 (0.29), residues: 200 loop : -2.35 (0.14), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Q 49 HIS 0.002 0.001 HIS E 214 PHE 0.012 0.002 PHE N 117 ARG 0.002 0.000 ARG I 71 *********************** 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 778 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 636 time to evaluate : 4.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.5248 (mmtt) cc_final: 0.4829 (mmtt) REVERT: C 95 GLU cc_start: 0.6789 (tt0) cc_final: 0.6524 (tt0) REVERT: E 77 ASP cc_start: 0.6320 (m-30) cc_final: 0.6069 (m-30) REVERT: E 123 GLN cc_start: 0.7749 (tp40) cc_final: 0.7489 (mt0) REVERT: E 136 VAL cc_start: 0.8698 (t) cc_final: 0.8357 (m) REVERT: F 88 ASP cc_start: 0.7612 (t0) cc_final: 0.7360 (t0) REVERT: F 151 ASN cc_start: 0.7632 (t0) cc_final: 0.7384 (t0) REVERT: G 39 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8372 (mm) REVERT: H 231 ASN cc_start: 0.7578 (t0) cc_final: 0.7220 (m-40) REVERT: H 262 ASN cc_start: 0.7331 (m110) cc_final: 0.6675 (t0) REVERT: K 239 LYS cc_start: 0.8031 (mttm) cc_final: 0.7679 (mtpp) REVERT: K 240 GLU cc_start: 0.6378 (mp0) cc_final: 0.6124 (mp0) REVERT: L 88 ASP cc_start: 0.8370 (t0) cc_final: 0.7579 (m-30) REVERT: L 102 ASP cc_start: 0.8191 (t0) cc_final: 0.7981 (t0) REVERT: M 101 SER cc_start: 0.8741 (t) cc_final: 0.8512 (p) REVERT: N 232 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8240 (tp) REVERT: O 80 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8839 (mp) REVERT: P 27 THR cc_start: 0.7852 (m) cc_final: 0.7609 (p) REVERT: P 111 ASN cc_start: 0.7736 (m-40) cc_final: 0.7327 (p0) REVERT: P 140 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8330 (p0) REVERT: R 271 LEU cc_start: 0.7227 (tp) cc_final: 0.6814 (mm) REVERT: T 13 MET cc_start: 0.8286 (mpp) cc_final: 0.7784 (mtt) REVERT: T 221 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8025 (tt) REVERT: T 262 ASN cc_start: 0.6820 (m-40) cc_final: 0.6339 (t0) outliers start: 142 outliers final: 115 residues processed: 726 average time/residue: 0.4013 time to fit residues: 512.1212 Evaluate side-chains 691 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 571 time to evaluate : 5.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 63 ASN Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 203 SER Chi-restraints excluded: chain H residue 264 SER Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain J residue 7 ASN Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 140 ASP Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 264 SER Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 186 MET Chi-restraints excluded: chain N residue 232 LEU Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 259 SER Chi-restraints excluded: chain O residue 267 SER Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 155 SER Chi-restraints excluded: chain Q residue 171 LEU Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain S residue 76 ILE Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain T residue 24 SER Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain T residue 144 THR Chi-restraints excluded: chain T residue 221 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 434 optimal weight: 6.9990 chunk 296 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 0.4980 chunk 445 optimal weight: 7.9990 chunk 360 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 266 optimal weight: 6.9990 chunk 468 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN B 34 ASN B 73 GLN C 151 ASN D 7 ASN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 GLN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 GLN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN I 55 GLN K 31 GLN K 55 GLN L 151 ASN N 31 GLN R 34 ASN ** T 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 39020 Z= 0.223 Angle : 0.489 9.306 52820 Z= 0.275 Chirality : 0.034 0.296 6800 Planarity : 0.002 0.034 6760 Dihedral : 3.646 18.947 5460 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.86 % Allowed : 16.81 % Favored : 79.33 % 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: 3.05 (0.12), residues: 5380 helix: 3.43 (0.08), residues: 3860 sheet: -0.95 (0.29), residues: 200 loop : -2.17 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Q 49 HIS 0.002 0.000 HIS E 214 PHE 0.011 0.002 PHE N 117 ARG 0.002 0.000 ARG T 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 756 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 594 time to evaluate : 3.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.9009 (ttmt) cc_final: 0.8790 (ttmm) REVERT: B 43 LYS cc_start: 0.5269 (mmtt) cc_final: 0.5020 (mmtt) REVERT: B 116 ASP cc_start: 0.6961 (m-30) cc_final: 0.6588 (m-30) REVERT: C 95 GLU cc_start: 0.6738 (tt0) cc_final: 0.6504 (tt0) REVERT: D 186 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7339 (mmt) REVERT: E 77 ASP cc_start: 0.6334 (m-30) cc_final: 0.6081 (m-30) REVERT: E 136 VAL cc_start: 0.8745 (t) cc_final: 0.8386 (m) REVERT: F 88 ASP cc_start: 0.7637 (t0) cc_final: 0.7389 (t0) REVERT: G 39 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8326 (mm) REVERT: G 220 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8493 (mptt) REVERT: H 84 ASP cc_start: 0.6815 (t0) cc_final: 0.6531 (t0) REVERT: H 231 ASN cc_start: 0.7488 (t0) cc_final: 0.7150 (m-40) REVERT: H 262 ASN cc_start: 0.7375 (m110) cc_final: 0.6695 (t0) REVERT: K 239 LYS cc_start: 0.7990 (mttm) cc_final: 0.7705 (mtpp) REVERT: K 240 GLU cc_start: 0.6519 (mp0) cc_final: 0.6171 (mp0) REVERT: L 88 ASP cc_start: 0.8376 (t0) cc_final: 0.7918 (m-30) REVERT: M 101 SER cc_start: 0.8739 (t) cc_final: 0.8486 (p) REVERT: M 271 LEU cc_start: 0.7395 (mp) cc_final: 0.7139 (mp) REVERT: N 232 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8170 (tp) REVERT: O 43 LYS cc_start: 0.5714 (tptt) cc_final: 0.5236 (mttm) REVERT: O 80 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8813 (mp) REVERT: P 27 THR cc_start: 0.7828 (m) cc_final: 0.7544 (p) REVERT: P 125 GLU cc_start: 0.7703 (tp30) cc_final: 0.6780 (tp30) REVERT: P 140 ASP cc_start: 0.8861 (p0) cc_final: 0.8391 (p0) REVERT: R 271 LEU cc_start: 0.7244 (tp) cc_final: 0.6804 (mm) REVERT: T 13 MET cc_start: 0.8296 (mpp) cc_final: 0.7806 (mtt) REVERT: T 221 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8022 (tt) outliers start: 162 outliers final: 130 residues processed: 697 average time/residue: 0.4009 time to fit residues: 491.3476 Evaluate side-chains 694 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 558 time to evaluate : 4.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 63 ASN Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 220 LYS Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 203 SER Chi-restraints excluded: chain H residue 264 SER Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 63 ASN Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain J residue 7 ASN Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 264 SER Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 232 LEU Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 259 SER Chi-restraints excluded: chain O residue 267 SER Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 155 SER Chi-restraints excluded: chain Q residue 163 THR Chi-restraints excluded: chain Q residue 171 LEU Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 76 ILE Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 163 THR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 234 ASP Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain T residue 24 SER Chi-restraints excluded: chain T residue 51 THR Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain T residue 144 THR Chi-restraints excluded: chain T residue 221 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 175 optimal weight: 0.9990 chunk 470 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 306 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 522 optimal weight: 8.9990 chunk 433 optimal weight: 5.9990 chunk 241 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 274 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN C 151 ASN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 ASN N 31 GLN N 34 ASN R 34 ASN S 263 GLN ** T 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 39020 Z= 0.309 Angle : 0.561 8.560 52820 Z= 0.311 Chirality : 0.036 0.250 6800 Planarity : 0.003 0.036 6760 Dihedral : 3.871 20.275 5460 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.19 % Allowed : 17.21 % Favored : 78.60 % 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: 2.70 (0.12), residues: 5380 helix: 3.20 (0.08), residues: 3840 sheet: -1.72 (0.27), residues: 240 loop : -2.20 (0.15), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 49 HIS 0.003 0.001 HIS E 214 PHE 0.016 0.002 PHE N 117 ARG 0.003 0.000 ARG T 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 745 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 569 time to evaluate : 4.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 116 ASP cc_start: 0.6855 (m-30) cc_final: 0.6481 (m-30) REVERT: B 176 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8527 (p) REVERT: C 95 GLU cc_start: 0.6832 (tt0) cc_final: 0.6559 (tt0) REVERT: E 77 ASP cc_start: 0.6420 (m-30) cc_final: 0.6170 (m-30) REVERT: E 136 VAL cc_start: 0.8776 (t) cc_final: 0.8426 (m) REVERT: F 43 LYS cc_start: 0.5720 (tptt) cc_final: 0.5328 (tptt) REVERT: G 39 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8190 (mm) REVERT: G 220 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8494 (mptt) REVERT: H 84 ASP cc_start: 0.6851 (t0) cc_final: 0.6441 (t0) REVERT: H 231 ASN cc_start: 0.7873 (t0) cc_final: 0.7528 (m-40) REVERT: K 239 LYS cc_start: 0.8050 (mttm) cc_final: 0.7764 (mtpp) REVERT: K 240 GLU cc_start: 0.6377 (mp0) cc_final: 0.5976 (mp0) REVERT: L 88 ASP cc_start: 0.8438 (t0) cc_final: 0.7933 (m-30) REVERT: M 101 SER cc_start: 0.8838 (t) cc_final: 0.8620 (p) REVERT: M 165 SER cc_start: 0.8220 (p) cc_final: 0.7836 (m) REVERT: M 231 ASN cc_start: 0.8036 (t0) cc_final: 0.7685 (m-40) REVERT: N 232 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8223 (tp) REVERT: O 43 LYS cc_start: 0.5932 (tptt) cc_final: 0.5357 (mttm) REVERT: P 27 THR cc_start: 0.7868 (m) cc_final: 0.7545 (p) REVERT: P 125 GLU cc_start: 0.7762 (tp30) cc_final: 0.6774 (tp30) REVERT: P 140 ASP cc_start: 0.8848 (p0) cc_final: 0.8475 (p0) REVERT: R 123 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7742 (mt0) REVERT: R 271 LEU cc_start: 0.7273 (tp) cc_final: 0.6888 (mm) REVERT: S 253 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7690 (tt) REVERT: T 13 MET cc_start: 0.8424 (mpp) cc_final: 0.7989 (mtt) REVERT: T 221 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8029 (tt) outliers start: 176 outliers final: 139 residues processed: 692 average time/residue: 0.4102 time to fit residues: 497.4451 Evaluate side-chains 681 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 535 time to evaluate : 4.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 63 ASN Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 220 LYS Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 203 SER Chi-restraints excluded: chain H residue 264 SER Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 63 ASN Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain J residue 7 ASN Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 264 SER Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 186 MET Chi-restraints excluded: chain N residue 232 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 259 SER Chi-restraints excluded: chain O residue 267 SER Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 155 SER Chi-restraints excluded: chain Q residue 163 THR Chi-restraints excluded: chain Q residue 171 LEU Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 123 GLN Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain S residue 14 ILE Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 76 ILE Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 163 THR Chi-restraints excluded: chain S residue 234 ASP Chi-restraints excluded: chain S residue 253 LEU Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain T residue 51 THR Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain T residue 144 THR Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 221 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 503 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 297 optimal weight: 0.0070 chunk 381 optimal weight: 0.9980 chunk 295 optimal weight: 5.9990 chunk 439 optimal weight: 0.9990 chunk 291 optimal weight: 2.9990 chunk 520 optimal weight: 3.9990 chunk 325 optimal weight: 0.9980 chunk 317 optimal weight: 6.9990 chunk 240 optimal weight: 1.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN C 73 GLN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN K 123 GLN N 31 GLN N 73 GLN Q 134 ASN ** Q 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 34 ASN R 262 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 39020 Z= 0.155 Angle : 0.443 7.907 52820 Z= 0.253 Chirality : 0.033 0.286 6800 Planarity : 0.002 0.027 6760 Dihedral : 3.547 17.419 5460 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.81 % Allowed : 19.40 % Favored : 77.79 % 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: 3.39 (0.12), residues: 5380 helix: 3.64 (0.08), residues: 3860 sheet: -0.74 (0.29), residues: 200 loop : -1.89 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 49 HIS 0.001 0.000 HIS E 214 PHE 0.010 0.001 PHE C 110 ARG 0.002 0.000 ARG M 121 *********************** 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 790 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 672 time to evaluate : 4.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8821 (ttmt) cc_final: 0.8585 (ttmm) REVERT: A 231 ASN cc_start: 0.8053 (t0) cc_final: 0.7465 (m-40) REVERT: B 43 LYS cc_start: 0.5751 (mmtt) cc_final: 0.5487 (mmtt) REVERT: B 176 THR cc_start: 0.8475 (OUTLIER) cc_final: 0.8221 (p) REVERT: D 186 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.7231 (mmt) REVERT: E 136 VAL cc_start: 0.8819 (t) cc_final: 0.8455 (m) REVERT: E 231 ASN cc_start: 0.7032 (m-40) cc_final: 0.6798 (m-40) REVERT: E 247 LEU cc_start: 0.8187 (mt) cc_final: 0.7847 (mm) REVERT: G 39 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8049 (mm) REVERT: H 126 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7899 (ttpp) REVERT: K 239 LYS cc_start: 0.7839 (mttm) cc_final: 0.7582 (mtpp) REVERT: K 240 GLU cc_start: 0.6338 (mp0) cc_final: 0.5997 (mp0) REVERT: L 88 ASP cc_start: 0.8363 (t0) cc_final: 0.7850 (m-30) REVERT: M 101 SER cc_start: 0.8517 (t) cc_final: 0.8220 (p) REVERT: M 271 LEU cc_start: 0.7348 (mp) cc_final: 0.7047 (mp) REVERT: O 43 LYS cc_start: 0.5767 (tptt) cc_final: 0.5328 (mttm) REVERT: O 80 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8522 (mp) REVERT: P 27 THR cc_start: 0.7683 (m) cc_final: 0.7426 (p) REVERT: P 125 GLU cc_start: 0.7604 (tp30) cc_final: 0.7096 (tp30) REVERT: P 140 ASP cc_start: 0.8840 (p0) cc_final: 0.8417 (p0) REVERT: R 123 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7547 (tp-100) REVERT: R 271 LEU cc_start: 0.7245 (tp) cc_final: 0.6880 (mm) REVERT: T 13 MET cc_start: 0.8273 (mpp) cc_final: 0.7812 (mtt) REVERT: T 221 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8012 (tt) outliers start: 118 outliers final: 78 residues processed: 745 average time/residue: 0.4123 time to fit residues: 533.3962 Evaluate side-chains 673 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 588 time to evaluate : 4.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 63 ASN Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 126 LYS Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 203 SER Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 63 ASN Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain J residue 7 ASN Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 140 ASP Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 155 SER Chi-restraints excluded: chain Q residue 163 THR Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 123 GLN Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 163 THR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 234 ASP Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain T residue 51 THR Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 221 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 321 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 310 optimal weight: 10.0000 chunk 156 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 330 optimal weight: 1.9990 chunk 354 optimal weight: 1.9990 chunk 257 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 409 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 GLN ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN J 34 ASN J 262 ASN K 9 ASN K 34 ASN L 151 ASN N 31 GLN Q 134 ASN ** Q 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 34 ASN S 31 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39020 Z= 0.210 Angle : 0.491 7.992 52820 Z= 0.275 Chirality : 0.034 0.296 6800 Planarity : 0.002 0.027 6760 Dihedral : 3.530 18.846 5460 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.76 % Allowed : 20.45 % Favored : 76.79 % 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: 3.34 (0.12), residues: 5380 helix: 3.57 (0.08), residues: 3860 sheet: -0.71 (0.30), residues: 200 loop : -1.84 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 49 HIS 0.002 0.000 HIS E 214 PHE 0.011 0.001 PHE H 117 ARG 0.003 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 695 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 579 time to evaluate : 4.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8958 (ttmt) cc_final: 0.8731 (ttmm) REVERT: A 231 ASN cc_start: 0.8318 (t0) cc_final: 0.8091 (m-40) REVERT: B 43 LYS cc_start: 0.5411 (mmtt) cc_final: 0.5076 (mmtt) REVERT: B 176 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8329 (p) REVERT: C 95 GLU cc_start: 0.6526 (tt0) cc_final: 0.6310 (tt0) REVERT: D 186 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7334 (mmt) REVERT: D 251 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6194 (tm130) REVERT: E 136 VAL cc_start: 0.8816 (t) cc_final: 0.8471 (m) REVERT: E 231 ASN cc_start: 0.7285 (m-40) cc_final: 0.7052 (m-40) REVERT: G 39 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8123 (mm) REVERT: H 231 ASN cc_start: 0.7176 (t0) cc_final: 0.6970 (m-40) REVERT: H 247 LEU cc_start: 0.7601 (mm) cc_final: 0.7238 (mm) REVERT: K 239 LYS cc_start: 0.7946 (mttm) cc_final: 0.7656 (mtpp) REVERT: K 240 GLU cc_start: 0.6405 (mp0) cc_final: 0.5980 (mp0) REVERT: L 88 ASP cc_start: 0.8354 (t0) cc_final: 0.7845 (m-30) REVERT: M 101 SER cc_start: 0.8644 (t) cc_final: 0.8401 (p) REVERT: M 271 LEU cc_start: 0.7353 (mp) cc_final: 0.7068 (mp) REVERT: O 43 LYS cc_start: 0.5856 (tptt) cc_final: 0.5290 (mttm) REVERT: O 80 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8686 (mp) REVERT: P 27 THR cc_start: 0.7756 (m) cc_final: 0.7518 (p) REVERT: P 125 GLU cc_start: 0.7740 (tp30) cc_final: 0.6887 (tp30) REVERT: P 140 ASP cc_start: 0.8836 (p0) cc_final: 0.8478 (p0) REVERT: R 123 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7864 (mt0) REVERT: R 271 LEU cc_start: 0.7216 (tp) cc_final: 0.6845 (mm) REVERT: S 253 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7642 (tt) REVERT: T 13 MET cc_start: 0.8347 (mpp) cc_final: 0.7834 (mtt) REVERT: T 34 ASN cc_start: 0.6341 (m-40) cc_final: 0.5883 (m-40) outliers start: 116 outliers final: 89 residues processed: 654 average time/residue: 0.4080 time to fit residues: 466.7870 Evaluate side-chains 661 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 565 time to evaluate : 4.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 251 GLN Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 63 ASN Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 203 SER Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 140 ASP Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 186 MET Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 111 ASN Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 155 SER Chi-restraints excluded: chain Q residue 163 THR Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 123 GLN Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain R residue 259 SER Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 163 THR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 234 ASP Chi-restraints excluded: chain S residue 253 LEU Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain T residue 51 THR Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain T residue 163 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 473 optimal weight: 9.9990 chunk 498 optimal weight: 2.9990 chunk 454 optimal weight: 0.9990 chunk 485 optimal weight: 8.9990 chunk 291 optimal weight: 0.9990 chunk 211 optimal weight: 4.9990 chunk 380 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 438 optimal weight: 0.9980 chunk 458 optimal weight: 0.1980 chunk 483 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN F 34 ASN ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 GLN Q 134 ASN ** Q 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 34 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 39020 Z= 0.161 Angle : 0.459 8.981 52820 Z= 0.259 Chirality : 0.033 0.293 6800 Planarity : 0.002 0.025 6760 Dihedral : 3.474 19.719 5460 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.33 % Allowed : 21.00 % Favored : 76.67 % 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: 3.50 (0.12), residues: 5380 helix: 3.68 (0.08), residues: 3860 sheet: -0.56 (0.30), residues: 200 loop : -1.73 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 49 HIS 0.001 0.000 HIS E 214 PHE 0.010 0.001 PHE S 117 ARG 0.003 0.000 ARG P 32 *********************** 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 710 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 612 time to evaluate : 4.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8879 (ttmt) cc_final: 0.8618 (ttmm) REVERT: A 231 ASN cc_start: 0.8007 (t0) cc_final: 0.7805 (m-40) REVERT: B 43 LYS cc_start: 0.5411 (mmtt) cc_final: 0.4831 (mttm) REVERT: B 176 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8177 (p) REVERT: D 186 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7266 (mmt) REVERT: E 136 VAL cc_start: 0.8804 (t) cc_final: 0.8450 (m) REVERT: E 231 ASN cc_start: 0.6978 (m-40) cc_final: 0.6735 (m-40) REVERT: E 247 LEU cc_start: 0.8217 (mt) cc_final: 0.7931 (mm) REVERT: G 39 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8089 (mm) REVERT: K 239 LYS cc_start: 0.7940 (mttm) cc_final: 0.7657 (mtpp) REVERT: K 240 GLU cc_start: 0.6346 (mp0) cc_final: 0.5932 (mp0) REVERT: L 88 ASP cc_start: 0.8344 (t0) cc_final: 0.7805 (m-30) REVERT: M 62 MET cc_start: 0.8152 (mmt) cc_final: 0.7939 (mmt) REVERT: M 101 SER cc_start: 0.8517 (t) cc_final: 0.8248 (p) REVERT: M 271 LEU cc_start: 0.7220 (mp) cc_final: 0.6921 (mp) REVERT: O 43 LYS cc_start: 0.5845 (tptt) cc_final: 0.5329 (mttm) REVERT: O 80 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8532 (mp) REVERT: O 236 ASP cc_start: 0.6322 (t70) cc_final: 0.6005 (t0) REVERT: P 27 THR cc_start: 0.7585 (m) cc_final: 0.7357 (p) REVERT: P 84 ASP cc_start: 0.7237 (t0) cc_final: 0.6974 (t0) REVERT: P 88 ASP cc_start: 0.7524 (m-30) cc_final: 0.7167 (m-30) REVERT: P 125 GLU cc_start: 0.7675 (tp30) cc_final: 0.6968 (tp30) REVERT: P 140 ASP cc_start: 0.8829 (p0) cc_final: 0.8446 (p0) REVERT: R 247 LEU cc_start: 0.7838 (mm) cc_final: 0.7562 (mm) REVERT: R 271 LEU cc_start: 0.7214 (tp) cc_final: 0.6849 (mm) REVERT: S 253 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7620 (tt) outliers start: 98 outliers final: 85 residues processed: 670 average time/residue: 0.4007 time to fit residues: 471.3511 Evaluate side-chains 668 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 578 time to evaluate : 4.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 63 ASN Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 203 SER Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain J residue 7 ASN Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 155 SER Chi-restraints excluded: chain Q residue 163 THR Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 163 THR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 234 ASP Chi-restraints excluded: chain S residue 253 LEU Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain T residue 51 THR Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain T residue 163 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 318 optimal weight: 6.9990 chunk 512 optimal weight: 0.9980 chunk 313 optimal weight: 3.9990 chunk 243 optimal weight: 6.9990 chunk 356 optimal weight: 2.9990 chunk 537 optimal weight: 0.9990 chunk 495 optimal weight: 2.9990 chunk 428 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 330 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 GLN B 263 GLN ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 ASN N 31 GLN Q 134 ASN ** Q 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 34 ASN S 31 GLN ** T 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 39020 Z= 0.214 Angle : 0.509 9.465 52820 Z= 0.282 Chirality : 0.034 0.330 6800 Planarity : 0.002 0.030 6760 Dihedral : 3.525 17.671 5460 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.57 % Allowed : 20.88 % Favored : 76.55 % 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: 3.28 (0.12), residues: 5380 helix: 3.46 (0.08), residues: 3940 sheet: -0.58 (0.30), residues: 200 loop : -2.01 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 49 HIS 0.002 0.000 HIS E 214 PHE 0.011 0.001 PHE O 217 ARG 0.003 0.000 ARG P 121 ********************** REFINEMENT MACRO_CYCLE 10 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 669 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 561 time to evaluate : 4.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASN cc_start: 0.8331 (t0) cc_final: 0.8114 (m-40) REVERT: B 43 LYS cc_start: 0.5371 (mmtt) cc_final: 0.4764 (mttm) REVERT: B 176 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8369 (p) REVERT: C 95 GLU cc_start: 0.6512 (tt0) cc_final: 0.6297 (tt0) REVERT: D 186 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7362 (mmt) REVERT: D 251 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6222 (tm130) REVERT: E 136 VAL cc_start: 0.8806 (t) cc_final: 0.8433 (m) REVERT: E 231 ASN cc_start: 0.7190 (m-40) cc_final: 0.6989 (m-40) REVERT: G 39 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8112 (mm) REVERT: H 231 ASN cc_start: 0.7223 (t0) cc_final: 0.6974 (m-40) REVERT: H 247 LEU cc_start: 0.7591 (mm) cc_final: 0.7114 (mm) REVERT: K 239 LYS cc_start: 0.7980 (mttm) cc_final: 0.7732 (mtpp) REVERT: L 88 ASP cc_start: 0.8355 (t0) cc_final: 0.7840 (m-30) REVERT: M 101 SER cc_start: 0.8637 (t) cc_final: 0.8396 (p) REVERT: M 271 LEU cc_start: 0.7286 (mp) cc_final: 0.7028 (mp) REVERT: O 43 LYS cc_start: 0.5864 (tptt) cc_final: 0.5379 (mttm) REVERT: O 80 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8686 (mp) REVERT: P 27 THR cc_start: 0.7708 (m) cc_final: 0.7442 (p) REVERT: P 125 GLU cc_start: 0.7692 (tp30) cc_final: 0.6873 (tp30) REVERT: P 129 THR cc_start: 0.8336 (t) cc_final: 0.7942 (t) REVERT: P 140 ASP cc_start: 0.8832 (p0) cc_final: 0.8479 (p0) REVERT: R 271 LEU cc_start: 0.7218 (tp) cc_final: 0.6850 (mm) REVERT: S 253 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7635 (tt) outliers start: 108 outliers final: 97 residues processed: 628 average time/residue: 0.4165 time to fit residues: 461.0411 Evaluate side-chains 658 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 555 time to evaluate : 4.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 251 GLN Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 63 ASN Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 203 SER Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 192 THR Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 176 THR Chi-restraints excluded: chain N residue 186 MET Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 111 ASN Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 155 SER Chi-restraints excluded: chain Q residue 163 THR Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 163 THR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 234 ASP Chi-restraints excluded: chain S residue 253 LEU Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain T residue 51 THR Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain T residue 163 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 340 optimal weight: 20.0000 chunk 456 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 395 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 429 optimal weight: 0.8980 chunk 179 optimal weight: 0.0010 chunk 440 optimal weight: 0.9990 chunk 54 optimal weight: 120.0000 chunk 79 optimal weight: 6.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 ASN N 31 GLN N 73 GLN ** Q 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 34 ASN ** T 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.146092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.132102 restraints weight = 63411.198| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.90 r_work: 0.3470 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 39020 Z= 0.178 Angle : 0.480 9.702 52820 Z= 0.269 Chirality : 0.033 0.319 6800 Planarity : 0.002 0.031 6760 Dihedral : 3.497 17.383 5460 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.55 % Allowed : 20.83 % Favored : 76.62 % 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: 3.37 (0.12), residues: 5380 helix: 3.52 (0.08), residues: 3940 sheet: -0.49 (0.30), residues: 200 loop : -1.94 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 49 HIS 0.001 0.000 HIS E 214 PHE 0.009 0.001 PHE R 157 ARG 0.003 0.000 ARG P 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9896.99 seconds wall clock time: 181 minutes 12.31 seconds (10872.31 seconds total)